Starting phenix.real_space_refine on Wed Feb 4 13:04:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hvy_52445/02_2026/9hvy_52445.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hvy_52445/02_2026/9hvy_52445.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9hvy_52445/02_2026/9hvy_52445.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hvy_52445/02_2026/9hvy_52445.map" model { file = "/net/cci-nas-00/data/ceres_data/9hvy_52445/02_2026/9hvy_52445.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hvy_52445/02_2026/9hvy_52445.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.017 sd= 0.319 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 49 5.16 5 C 6632 2.51 5 N 1835 2.21 5 O 1939 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10456 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 10455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1396, 10455 Classifications: {'peptide': 1396} Incomplete info: {'truncation_to_alanine': 121} Link IDs: {'PCIS': 1, 'PTRANS': 65, 'TRANS': 1329} Chain breaks: 7 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 460 Unresolved non-hydrogen angles: 593 Unresolved non-hydrogen dihedrals: 390 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'ARG:plan': 6, 'TYR:plan': 10, 'GLU:plan': 6, 'GLN:plan1': 12, 'PHE:plan': 9, 'ASP:plan': 8, 'HIS:plan': 3, 'TRP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 277 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5278 SG CYS A1146 31.627 76.971 93.185 1.00 30.00 S ATOM 5292 SG CYS A1148 34.914 75.049 93.667 1.00 30.00 S ATOM 5312 SG CYS A1151 31.646 73.765 95.234 1.00 30.00 S Time building chain proxies: 2.18, per 1000 atoms: 0.21 Number of scatterers: 10456 At special positions: 0 Unit cell: (85.8792, 87.831, 170.783, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 49 16.00 O 1939 8.00 N 1835 7.00 C 6632 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 484 " - pdb=" SG CYS A 506 " distance=2.05 Simple disulfide: pdb=" SG CYS A 637 " - pdb=" SG CYS A 687 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.78 Conformation dependent library (CDL) restraints added in 365.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2201 " pdb="ZN ZN A2201 " - pdb=" ND1 HIS A1142 " pdb="ZN ZN A2201 " - pdb=" SG CYS A1146 " pdb="ZN ZN A2201 " - pdb=" SG CYS A1151 " pdb="ZN ZN A2201 " - pdb=" SG CYS A1148 " Number of angles added : 3 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2640 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 2 sheets defined 74.1% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 331 through 352 Processing helix chain 'A' and resid 356 through 380 Processing helix chain 'A' and resid 389 through 415 Processing helix chain 'A' and resid 419 through 442 Processing helix chain 'A' and resid 451 through 470 Processing helix chain 'A' and resid 473 through 489 Proline residue: A 482 - end of helix Processing helix chain 'A' and resid 499 through 518 removed outlier: 3.622A pdb=" N PHE A 507 " --> pdb=" O LEU A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 534 Processing helix chain 'A' and resid 538 through 560 removed outlier: 4.424A pdb=" N GLU A 544 " --> pdb=" O GLU A 540 " (cutoff:3.500A) Proline residue: A 545 - end of helix Processing helix chain 'A' and resid 561 through 567 removed outlier: 3.769A pdb=" N GLN A 565 " --> pdb=" O ASP A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 574 removed outlier: 3.768A pdb=" N SER A 572 " --> pdb=" O THR A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 595 Processing helix chain 'A' and resid 599 through 614 removed outlier: 3.683A pdb=" N ARG A 603 " --> pdb=" O THR A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 639 removed outlier: 4.266A pdb=" N TYR A 638 " --> pdb=" O GLN A 634 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N HIS A 639 " --> pdb=" O VAL A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 645 removed outlier: 3.529A pdb=" N THR A 645 " --> pdb=" O THR A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 663 Processing helix chain 'A' and resid 669 through 703 removed outlier: 4.714A pdb=" N ASP A 675 " --> pdb=" O ASP A 671 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ALA A 678 " --> pdb=" O LEU A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 725 Processing helix chain 'A' and resid 728 through 734 Processing helix chain 'A' and resid 735 through 737 No H-bonds generated for 'chain 'A' and resid 735 through 737' Processing helix chain 'A' and resid 738 through 760 removed outlier: 4.112A pdb=" N ALA A 742 " --> pdb=" O ALA A 738 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU A 747 " --> pdb=" O GLN A 743 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N LYS A 760 " --> pdb=" O GLU A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 786 removed outlier: 3.630A pdb=" N THR A 772 " --> pdb=" O CYS A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 807 removed outlier: 3.607A pdb=" N ALA A 792 " --> pdb=" O LYS A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 827 Processing helix chain 'A' and resid 828 through 844 removed outlier: 3.989A pdb=" N ALA A 832 " --> pdb=" O CYS A 828 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN A 833 " --> pdb=" O PRO A 829 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LEU A 834 " --> pdb=" O SER A 830 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N HIS A 835 " --> pdb=" O TYR A 831 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS A 844 " --> pdb=" O ALA A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 871 removed outlier: 3.621A pdb=" N LEU A 854 " --> pdb=" O THR A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 886 Processing helix chain 'A' and resid 894 through 912 removed outlier: 3.509A pdb=" N LEU A 899 " --> pdb=" O LYS A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 929 Processing helix chain 'A' and resid 934 through 954 Processing helix chain 'A' and resid 955 through 959 removed outlier: 4.053A pdb=" N ILE A 958 " --> pdb=" O GLY A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 1002 Processing helix chain 'A' and resid 1003 through 1022 Processing helix chain 'A' and resid 1023 through 1041 Processing helix chain 'A' and resid 1043 through 1062 Processing helix chain 'A' and resid 1138 through 1142 Processing helix chain 'A' and resid 1148 through 1153 Processing helix chain 'A' and resid 1153 through 1175 Processing helix chain 'A' and resid 1179 through 1207 Proline residue: A1192 - end of helix Processing helix chain 'A' and resid 1219 through 1237 removed outlier: 3.679A pdb=" N ASN A1236 " --> pdb=" O LEU A1232 " (cutoff:3.500A) Processing helix chain 'A' and resid 1241 through 1257 removed outlier: 3.569A pdb=" N GLN A1248 " --> pdb=" O GLN A1244 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG A1257 " --> pdb=" O PHE A1253 " (cutoff:3.500A) Processing helix chain 'A' and resid 1261 through 1278 Processing helix chain 'A' and resid 1288 through 1292 Processing helix chain 'A' and resid 1573 through 1586 Processing helix chain 'A' and resid 1593 through 1609 removed outlier: 3.583A pdb=" N ALA A1598 " --> pdb=" O SER A1594 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS A1599 " --> pdb=" O GLY A1595 " (cutoff:3.500A) Processing helix chain 'A' and resid 1612 through 1622 Processing helix chain 'A' and resid 1625 through 1644 removed outlier: 3.659A pdb=" N ARG A1629 " --> pdb=" O SER A1625 " (cutoff:3.500A) Processing helix chain 'A' and resid 1668 through 1678 Processing helix chain 'A' and resid 1688 through 1701 removed outlier: 3.804A pdb=" N LEU A1701 " --> pdb=" O GLU A1697 " (cutoff:3.500A) Processing helix chain 'A' and resid 1749 through 1769 removed outlier: 3.834A pdb=" N SER A1769 " --> pdb=" O LYS A1765 " (cutoff:3.500A) Processing helix chain 'A' and resid 1772 through 1797 removed outlier: 3.570A pdb=" N GLU A1795 " --> pdb=" O ILE A1791 " (cutoff:3.500A) Processing helix chain 'A' and resid 1799 through 1801 No H-bonds generated for 'chain 'A' and resid 1799 through 1801' Processing helix chain 'A' and resid 1802 through 1807 removed outlier: 4.275A pdb=" N LEU A1806 " --> pdb=" O TRP A1802 " (cutoff:3.500A) Processing helix chain 'A' and resid 1813 through 1828 removed outlier: 3.565A pdb=" N ARG A1821 " --> pdb=" O GLN A1817 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU A1824 " --> pdb=" O SER A1820 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASP A1828 " --> pdb=" O GLU A1824 " (cutoff:3.500A) Processing helix chain 'A' and resid 1835 through 1845 removed outlier: 3.723A pdb=" N LEU A1839 " --> pdb=" O ASP A1835 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLY A1845 " --> pdb=" O ILE A1841 " (cutoff:3.500A) Processing helix chain 'A' and resid 1850 through 1862 Processing helix chain 'A' and resid 1865 through 1881 Processing helix chain 'A' and resid 1903 through 1911 removed outlier: 3.656A pdb=" N SER A1906 " --> pdb=" O PRO A1903 " (cutoff:3.500A) Proline residue: A1908 - end of helix removed outlier: 3.626A pdb=" N GLN A1911 " --> pdb=" O PRO A1908 " (cutoff:3.500A) Processing helix chain 'A' and resid 1921 through 1933 removed outlier: 3.931A pdb=" N LEU A1925 " --> pdb=" O PHE A1921 " (cutoff:3.500A) Processing helix chain 'A' and resid 1936 through 1941 Processing helix chain 'A' and resid 1959 through 1965 Processing helix chain 'A' and resid 1966 through 1971 Processing helix chain 'A' and resid 1984 through 1994 Processing helix chain 'A' and resid 2011 through 2018 Processing helix chain 'A' and resid 2044 through 2052 removed outlier: 3.673A pdb=" N LYS A2048 " --> pdb=" O GLY A2044 " (cutoff:3.500A) Processing helix chain 'A' and resid 2067 through 2084 removed outlier: 4.400A pdb=" N GLY A2084 " --> pdb=" O TRP A2080 " (cutoff:3.500A) Processing helix chain 'A' and resid 2088 through 2097 removed outlier: 3.803A pdb=" N TYR A2092 " --> pdb=" O PRO A2088 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1737 through 1742 removed outlier: 3.759A pdb=" N VAL A1737 " --> pdb=" O ARG A1729 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG A1729 " --> pdb=" O VAL A1737 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1975 through 1979 removed outlier: 3.565A pdb=" N TYR A1950 " --> pdb=" O ARG A1976 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N TYR A1998 " --> pdb=" O LEU A2025 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA A2024 " --> pdb=" O LEU A2058 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N ASN A2060 " --> pdb=" O ALA A2024 " (cutoff:3.500A) removed outlier: 9.484A pdb=" N LEU A2026 " --> pdb=" O ASN A2060 " (cutoff:3.500A) 745 hydrogen bonds defined for protein. 2214 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.73 Time building geometry restraints manager: 1.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 3502 1.35 - 1.47: 2265 1.47 - 1.59: 4822 1.59 - 1.72: 0 1.72 - 1.84: 60 Bond restraints: 10649 Sorted by residual: bond pdb=" N ILE A 528 " pdb=" CA ILE A 528 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.17e-02 7.31e+03 8.43e+00 bond pdb=" N VAL A 498 " pdb=" CA VAL A 498 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.23e-02 6.61e+03 7.59e+00 bond pdb=" N VAL A 527 " pdb=" CA VAL A 527 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.26e-02 6.30e+03 7.31e+00 bond pdb=" N ILE A 958 " pdb=" CA ILE A 958 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.26e-02 6.30e+03 7.23e+00 bond pdb=" N LEU A1202 " pdb=" CA LEU A1202 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.21e-02 6.83e+03 6.56e+00 ... (remaining 10644 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 14176 2.19 - 4.38: 277 4.38 - 6.57: 29 6.57 - 8.76: 13 8.76 - 10.95: 2 Bond angle restraints: 14497 Sorted by residual: angle pdb=" N PRO A 331 " pdb=" CA PRO A 331 " pdb=" CB PRO A 331 " ideal model delta sigma weight residual 103.00 110.42 -7.42 1.10e+00 8.26e-01 4.54e+01 angle pdb=" N PRO A 332 " pdb=" CA PRO A 332 " pdb=" CB PRO A 332 " ideal model delta sigma weight residual 103.33 110.14 -6.81 1.10e+00 8.26e-01 3.84e+01 angle pdb=" CB ARG A 558 " pdb=" CG ARG A 558 " pdb=" CD ARG A 558 " ideal model delta sigma weight residual 111.30 120.17 -8.87 2.30e+00 1.89e-01 1.49e+01 angle pdb=" CA GLU A 481 " pdb=" CB GLU A 481 " pdb=" CG GLU A 481 " ideal model delta sigma weight residual 114.10 121.62 -7.52 2.00e+00 2.50e-01 1.41e+01 angle pdb=" N LEU A1219 " pdb=" CA LEU A1219 " pdb=" C LEU A1219 " ideal model delta sigma weight residual 113.30 108.37 4.93 1.34e+00 5.57e-01 1.36e+01 ... (remaining 14492 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 5880 17.85 - 35.71: 422 35.71 - 53.56: 107 53.56 - 71.41: 47 71.41 - 89.27: 9 Dihedral angle restraints: 6465 sinusoidal: 2408 harmonic: 4057 Sorted by residual: dihedral pdb=" CB CYS A 637 " pdb=" SG CYS A 637 " pdb=" SG CYS A 687 " pdb=" CB CYS A 687 " ideal model delta sinusoidal sigma weight residual -86.00 -165.06 79.06 1 1.00e+01 1.00e-02 7.78e+01 dihedral pdb=" CA LEU A 673 " pdb=" C LEU A 673 " pdb=" N LEU A 674 " pdb=" CA LEU A 674 " ideal model delta harmonic sigma weight residual 180.00 162.11 17.89 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA ASP A 675 " pdb=" C ASP A 675 " pdb=" N ASP A 676 " pdb=" CA ASP A 676 " ideal model delta harmonic sigma weight residual 180.00 162.46 17.54 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 6462 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1390 0.046 - 0.092: 246 0.092 - 0.138: 61 0.138 - 0.183: 10 0.183 - 0.229: 6 Chirality restraints: 1713 Sorted by residual: chirality pdb=" CA PRO A 331 " pdb=" N PRO A 331 " pdb=" C PRO A 331 " pdb=" CB PRO A 331 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA PRO A 332 " pdb=" N PRO A 332 " pdb=" C PRO A 332 " pdb=" CB PRO A 332 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA TYR A 495 " pdb=" N TYR A 495 " pdb=" C TYR A 495 " pdb=" CB TYR A 495 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.81e-01 ... (remaining 1710 not shown) Planarity restraints: 1864 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 675 " 0.018 2.00e-02 2.50e+03 3.65e-02 1.33e+01 pdb=" C ASP A 675 " -0.063 2.00e-02 2.50e+03 pdb=" O ASP A 675 " 0.023 2.00e-02 2.50e+03 pdb=" N ASP A 676 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A1953 " 0.057 5.00e-02 4.00e+02 8.53e-02 1.16e+01 pdb=" N PRO A1954 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO A1954 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO A1954 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A1687 " 0.030 5.00e-02 4.00e+02 4.56e-02 3.33e+00 pdb=" N PRO A1688 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO A1688 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A1688 " 0.023 5.00e-02 4.00e+02 ... (remaining 1861 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 88 2.64 - 3.20: 9750 3.20 - 3.77: 16518 3.77 - 4.33: 20620 4.33 - 4.90: 33988 Nonbonded interactions: 80964 Sorted by model distance: nonbonded pdb=" O ARG A1879 " pdb=" NH1 ARG A1879 " model vdw 2.073 3.120 nonbonded pdb=" N GLN A1852 " pdb=" OE1 GLN A1852 " model vdw 2.213 3.120 nonbonded pdb=" N GLU A 563 " pdb=" OE1 GLU A 563 " model vdw 2.234 3.120 nonbonded pdb=" ND2 ASN A1953 " pdb=" OE1 GLU A1962 " model vdw 2.235 3.120 nonbonded pdb=" NH1 ARG A1729 " pdb=" O LEU A1805 " model vdw 2.305 3.120 ... (remaining 80959 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.870 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.560 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 10655 Z= 0.253 Angle : 0.702 10.947 14504 Z= 0.418 Chirality : 0.040 0.229 1713 Planarity : 0.005 0.085 1864 Dihedral : 14.603 89.266 3819 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.37 % Allowed : 13.67 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.23), residues: 1380 helix: 2.29 (0.16), residues: 953 sheet: 1.33 (0.81), residues: 48 loop : -1.45 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 558 TYR 0.031 0.001 TYR A 973 PHE 0.018 0.002 PHE A 735 TRP 0.017 0.001 TRP A1776 HIS 0.012 0.001 HIS A 541 Details of bonding type rmsd covalent geometry : bond 0.00421 (10649) covalent geometry : angle 0.70129 (14497) SS BOND : bond 0.01090 ( 2) SS BOND : angle 2.09896 ( 4) hydrogen bonds : bond 0.15696 ( 745) hydrogen bonds : angle 4.91365 ( 2214) metal coordination : bond 0.01258 ( 4) metal coordination : angle 0.80095 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 130 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 954 MET cc_start: 0.8273 (mtm) cc_final: 0.8031 (mtm) REVERT: A 1218 LEU cc_start: 0.7638 (tp) cc_final: 0.7377 (tp) outliers start: 4 outliers final: 1 residues processed: 132 average time/residue: 0.1457 time to fit residues: 24.7125 Evaluate side-chains 111 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 110 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 959 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 522 GLN A 535 GLN A 601 GLN A 605 ASN A 933 GLN A1048 GLN A1295 GLN A1599 HIS A1941 GLN A1964 GLN A2060 ASN A2098 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.057273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.047461 restraints weight = 38987.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.048731 restraints weight = 19954.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.049563 restraints weight = 12649.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.050118 restraints weight = 9240.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.050461 restraints weight = 7407.722| |-----------------------------------------------------------------------------| r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10655 Z= 0.161 Angle : 0.601 8.956 14504 Z= 0.307 Chirality : 0.037 0.174 1713 Planarity : 0.005 0.054 1864 Dihedral : 4.093 41.849 1482 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.97 % Allowed : 13.11 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.97 (0.23), residues: 1380 helix: 2.22 (0.16), residues: 970 sheet: 1.57 (0.78), residues: 48 loop : -1.35 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 508 TYR 0.017 0.001 TYR A2104 PHE 0.019 0.002 PHE A 728 TRP 0.015 0.001 TRP A1776 HIS 0.006 0.001 HIS A 504 Details of bonding type rmsd covalent geometry : bond 0.00355 (10649) covalent geometry : angle 0.59961 (14497) SS BOND : bond 0.00504 ( 2) SS BOND : angle 2.14845 ( 4) hydrogen bonds : bond 0.06167 ( 745) hydrogen bonds : angle 4.24142 ( 2214) metal coordination : bond 0.02154 ( 4) metal coordination : angle 2.11025 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 526 MET cc_start: 0.8134 (mtm) cc_final: 0.7493 (mtp) REVERT: A 1199 THR cc_start: 0.8513 (OUTLIER) cc_final: 0.8292 (m) outliers start: 21 outliers final: 8 residues processed: 132 average time/residue: 0.1287 time to fit residues: 22.6355 Evaluate side-chains 120 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 111 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1199 THR Chi-restraints excluded: chain A residue 1288 PHE Chi-restraints excluded: chain A residue 1686 HIS Chi-restraints excluded: chain A residue 1873 LEU Chi-restraints excluded: chain A residue 1979 VAL Chi-restraints excluded: chain A residue 2046 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 111 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 5 optimal weight: 9.9990 chunk 53 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 137 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1208 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.056421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.046513 restraints weight = 39012.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.047794 restraints weight = 19973.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.048630 restraints weight = 12696.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.049174 restraints weight = 9259.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.049550 restraints weight = 7445.394| |-----------------------------------------------------------------------------| r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 10655 Z= 0.160 Angle : 0.582 8.102 14504 Z= 0.298 Chirality : 0.037 0.166 1713 Planarity : 0.005 0.046 1864 Dihedral : 4.114 40.803 1482 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.43 % Allowed : 12.73 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.23), residues: 1380 helix: 2.18 (0.16), residues: 984 sheet: 1.61 (0.76), residues: 48 loop : -1.47 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 702 TYR 0.015 0.001 TYR A2104 PHE 0.015 0.002 PHE A 728 TRP 0.015 0.001 TRP A1776 HIS 0.010 0.001 HIS A 541 Details of bonding type rmsd covalent geometry : bond 0.00362 (10649) covalent geometry : angle 0.57911 (14497) SS BOND : bond 0.00571 ( 2) SS BOND : angle 2.70257 ( 4) hydrogen bonds : bond 0.05761 ( 745) hydrogen bonds : angle 4.08641 ( 2214) metal coordination : bond 0.02599 ( 4) metal coordination : angle 2.35369 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 113 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 505 ARG cc_start: 0.7738 (ttt-90) cc_final: 0.7518 (ttt-90) REVERT: A 567 LYS cc_start: 0.8569 (ptpp) cc_final: 0.7832 (ptpp) REVERT: A 1842 MET cc_start: 0.8956 (mmm) cc_final: 0.8600 (mpp) outliers start: 26 outliers final: 18 residues processed: 130 average time/residue: 0.1008 time to fit residues: 17.5123 Evaluate side-chains 130 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 504 HIS Chi-restraints excluded: chain A residue 535 GLN Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 728 PHE Chi-restraints excluded: chain A residue 735 PHE Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1288 PHE Chi-restraints excluded: chain A residue 1581 LEU Chi-restraints excluded: chain A residue 1686 HIS Chi-restraints excluded: chain A residue 1707 THR Chi-restraints excluded: chain A residue 1873 LEU Chi-restraints excluded: chain A residue 1979 VAL Chi-restraints excluded: chain A residue 2046 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 81 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 2 optimal weight: 0.2980 chunk 58 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 106 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 541 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 835 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.056536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.046705 restraints weight = 39118.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.047997 restraints weight = 19942.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.048833 restraints weight = 12602.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.049384 restraints weight = 9161.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.049732 restraints weight = 7342.789| |-----------------------------------------------------------------------------| r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10655 Z= 0.144 Angle : 0.578 11.518 14504 Z= 0.294 Chirality : 0.036 0.135 1713 Planarity : 0.005 0.046 1864 Dihedral : 4.071 40.222 1482 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.15 % Allowed : 14.61 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.08 (0.23), residues: 1380 helix: 2.27 (0.16), residues: 984 sheet: 1.66 (0.75), residues: 48 loop : -1.40 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A2017 TYR 0.012 0.001 TYR A2092 PHE 0.013 0.001 PHE A 728 TRP 0.016 0.001 TRP A1776 HIS 0.008 0.001 HIS A 541 Details of bonding type rmsd covalent geometry : bond 0.00317 (10649) covalent geometry : angle 0.57581 (14497) SS BOND : bond 0.00426 ( 2) SS BOND : angle 2.49683 ( 4) hydrogen bonds : bond 0.05295 ( 745) hydrogen bonds : angle 3.97624 ( 2214) metal coordination : bond 0.02286 ( 4) metal coordination : angle 2.32437 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 112 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1966 ARG cc_start: 0.7103 (ttm-80) cc_final: 0.6879 (ttm-80) outliers start: 23 outliers final: 18 residues processed: 127 average time/residue: 0.1379 time to fit residues: 23.0562 Evaluate side-chains 126 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 535 GLN Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 735 PHE Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 783 TYR Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1012 LEU Chi-restraints excluded: chain A residue 1288 PHE Chi-restraints excluded: chain A residue 1581 LEU Chi-restraints excluded: chain A residue 1686 HIS Chi-restraints excluded: chain A residue 1707 THR Chi-restraints excluded: chain A residue 1721 VAL Chi-restraints excluded: chain A residue 1825 LEU Chi-restraints excluded: chain A residue 1979 VAL Chi-restraints excluded: chain A residue 2046 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 68.6298 > 50: distance: 22 - 41: 35.005 distance: 29 - 49: 24.583 distance: 36 - 41: 34.266 distance: 41 - 42: 56.922 distance: 42 - 43: 56.459 distance: 43 - 44: 57.918 distance: 43 - 49: 57.292 distance: 45 - 46: 20.309 distance: 46 - 47: 25.046 distance: 46 - 48: 45.852 distance: 49 - 50: 13.831 distance: 50 - 51: 3.184 distance: 50 - 53: 7.606 distance: 51 - 52: 21.421 distance: 51 - 55: 9.963 distance: 53 - 54: 57.376 distance: 54 - 157: 32.243 distance: 55 - 56: 40.313 distance: 57 - 67: 24.079 distance: 60 - 61: 29.217 distance: 60 - 62: 40.350 distance: 61 - 63: 19.102 distance: 62 - 64: 13.151 distance: 63 - 65: 15.122 distance: 64 - 65: 28.717 distance: 65 - 66: 39.433 distance: 67 - 68: 29.772 distance: 68 - 69: 39.535 distance: 68 - 71: 14.840 distance: 69 - 70: 29.325 distance: 69 - 77: 10.104 distance: 71 - 72: 40.940 distance: 72 - 73: 36.669 distance: 72 - 74: 39.353 distance: 73 - 75: 38.947 distance: 75 - 76: 40.325 distance: 77 - 78: 9.027 distance: 78 - 79: 31.384 distance: 78 - 81: 50.894 distance: 79 - 80: 4.763 distance: 81 - 82: 51.635 distance: 82 - 83: 6.747 distance: 82 - 84: 27.782 distance: 85 - 86: 47.420 distance: 86 - 87: 14.896 distance: 86 - 89: 38.037 distance: 87 - 88: 56.404 distance: 88 - 112: 37.591 distance: 89 - 90: 29.565 distance: 90 - 91: 45.282 distance: 90 - 92: 40.878 distance: 91 - 93: 37.053 distance: 92 - 94: 39.391 distance: 93 - 95: 24.446 distance: 94 - 95: 41.298 distance: 96 - 97: 40.095 distance: 97 - 98: 31.884 distance: 97 - 100: 38.565 distance: 98 - 99: 7.187 distance: 98 - 103: 22.171 distance: 100 - 101: 6.678 distance: 100 - 102: 29.127 distance: 103 - 104: 8.521 distance: 104 - 105: 8.507 distance: 104 - 107: 31.661 distance: 108 - 109: 34.166 distance: 109 - 110: 6.610 distance: 109 - 111: 49.354 distance: 113 - 114: 51.423 distance: 113 - 116: 13.025 distance: 114 - 115: 19.947 distance: 114 - 121: 15.309 distance: 116 - 117: 41.291 distance: 117 - 118: 14.845 distance: 118 - 119: 44.532 distance: 118 - 120: 54.183 distance: 121 - 122: 10.532 distance: 122 - 125: 6.772 distance: 123 - 128: 34.380 distance: 125 - 126: 23.643 distance: 125 - 127: 35.307