Starting phenix.real_space_refine on Wed Jun 3 21:21:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9z3k_73787/06_2026/9z3k_73787_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9z3k_73787/06_2026/9z3k_73787.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9z3k_73787/06_2026/9z3k_73787.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9z3k_73787/06_2026/9z3k_73787.map" model { file = "/net/cci-nas-00/data/ceres_data/9z3k_73787/06_2026/9z3k_73787_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9z3k_73787/06_2026/9z3k_73787_neut.cif" } resolution = 3.3 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= 0.000 sd= 0.016 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 27 5.16 5 C 5385 2.51 5 N 1506 2.21 5 O 1530 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8448 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 2732 Classifications: {'peptide': 404} Incomplete info: {'truncation_to_alanine': 158} Link IDs: {'PTRANS': 11, 'TRANS': 392} Chain breaks: 4 Unresolved non-hydrogen bonds: 436 Unresolved non-hydrogen angles: 554 Unresolved non-hydrogen dihedrals: 329 Unresolved non-hydrogen chiralities: 56 Planarities with less than four sites: {'GLN:plan1': 13, 'ASN:plan1': 9, 'ARG:plan': 1, 'GLU:plan': 17, 'HIS:plan': 3, 'ASP:plan': 11, 'PHE:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 213 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Restraints were copied for chains: B, C Time building chain proxies: 1.86, per 1000 atoms: 0.22 Number of scatterers: 8448 At special positions: 0 Unit cell: (71.294, 70.465, 285.176, 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 27 16.00 O 1530 8.00 N 1506 7.00 C 5385 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1738 " - pdb=" SG CYS A1760 " distance=2.03 Simple disulfide: pdb=" SG CYS A1743 " - pdb=" SG CYS A1749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1738 " - pdb=" SG CYS B1760 " distance=2.03 Simple disulfide: pdb=" SG CYS C1738 " - pdb=" SG CYS C1760 " distance=2.03 Simple disulfide: pdb=" SG CYS B1743 " - pdb=" SG CYS B1749 " distance=2.04 Simple disulfide: pdb=" SG CYS C1743 " - pdb=" SG CYS C1749 " distance=2.04 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 Links applied NAG-ASN " NAG A1401 " - " ASN A1846 " " NAG A1402 " - " ASN A1709 " " NAG A1403 " - " ASN A1074 " " NAG A1404 " - " ASN A1717 " " NAG A1405 " - " ASN A1098 " " NAG A1406 " - " ASN A1801 " " NAG B1401 " - " ASN B1846 " " NAG B1402 " - " ASN B1709 " " NAG B1403 " - " ASN B1074 " " NAG B1404 " - " ASN B1717 " " NAG B1405 " - " ASN B1098 " " NAG B1406 " - " ASN B1801 " " NAG C1401 " - " ASN C1846 " " NAG C1402 " - " ASN C1709 " " NAG C1403 " - " ASN C1074 " " NAG C1404 " - " ASN C1717 " " NAG C1405 " - " ASN C1098 " " NAG C1406 " - " ASN C1801 " Time building additional restraints: 0.98 Conformation dependent library (CDL) restraints added in 456.4 milliseconds 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2310 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 9 sheets defined 58.0% alpha, 22.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 866 through 1033 Processing helix chain 'A' and resid 1704 through 1708 Processing helix chain 'A' and resid 1737 through 1743 Processing helix chain 'A' and resid 1746 through 1754 removed outlier: 3.516A pdb=" N LEU A1754 " --> pdb=" O SER A1750 " (cutoff:3.500A) Processing helix chain 'A' and resid 1755 through 1757 No H-bonds generated for 'chain 'A' and resid 1755 through 1757' Processing helix chain 'A' and resid 1758 through 1768 removed outlier: 3.599A pdb=" N GLN A1762 " --> pdb=" O SER A1758 " (cutoff:3.500A) Processing helix chain 'A' and resid 1834 through 1865 Processing helix chain 'B' and resid 867 through 1033 Processing helix chain 'B' and resid 1704 through 1708 Processing helix chain 'B' and resid 1737 through 1743 Processing helix chain 'B' and resid 1746 through 1754 removed outlier: 3.517A pdb=" N LEU B1754 " --> pdb=" O SER B1750 " (cutoff:3.500A) Processing helix chain 'B' and resid 1755 through 1757 No H-bonds generated for 'chain 'B' and resid 1755 through 1757' Processing helix chain 'B' and resid 1758 through 1768 removed outlier: 3.599A pdb=" N GLN B1762 " --> pdb=" O SER B1758 " (cutoff:3.500A) Processing helix chain 'B' and resid 1834 through 1865 Processing helix chain 'C' and resid 867 through 1033 Processing helix chain 'C' and resid 1704 through 1708 Processing helix chain 'C' and resid 1737 through 1743 Processing helix chain 'C' and resid 1746 through 1754 removed outlier: 3.516A pdb=" N LEU C1754 " --> pdb=" O SER C1750 " (cutoff:3.500A) Processing helix chain 'C' and resid 1755 through 1757 No H-bonds generated for 'chain 'C' and resid 1755 through 1757' Processing helix chain 'C' and resid 1758 through 1768 removed outlier: 3.599A pdb=" N GLN C1762 " --> pdb=" O SER C1758 " (cutoff:3.500A) Processing helix chain 'C' and resid 1834 through 1865 Processing sheet with id=AA1, first strand: chain 'A' and resid 1047 through 1056 removed outlier: 5.578A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1047 through 1056 removed outlier: 5.578A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ASN A1717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N GLU A1072 " --> pdb=" O PRO A1715 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ASN A1074 " --> pdb=" O ALA A1713 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ALA A1713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N THR A1076 " --> pdb=" O SER A1711 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N SER A1711 " --> pdb=" O THR A1076 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1088 through 1090 Processing sheet with id=AA4, first strand: chain 'B' and resid 1047 through 1056 removed outlier: 5.577A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 1047 through 1056 removed outlier: 5.577A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ASN B1717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N GLU B1072 " --> pdb=" O PRO B1715 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ASN B1074 " --> pdb=" O ALA B1713 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ALA B1713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N THR B1076 " --> pdb=" O SER B1711 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N SER B1711 " --> pdb=" O THR B1076 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1088 through 1090 Processing sheet with id=AA7, first strand: chain 'C' and resid 1047 through 1056 removed outlier: 5.578A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLN C1106 " --> pdb=" O GLU C1111 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N GLU C1111 " --> pdb=" O GLN C1106 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 1047 through 1056 removed outlier: 5.578A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ASN C1717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N GLU C1072 " --> pdb=" O PRO C1715 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ASN C1074 " --> pdb=" O ALA C1713 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ALA C1713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N THR C1076 " --> pdb=" O SER C1711 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N SER C1711 " --> pdb=" O THR C1076 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 1088 through 1090 733 hydrogen bonds defined for protein. 2154 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: 1.46 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1413 1.30 - 1.43: 2189 1.43 - 1.56: 4936 1.56 - 1.69: 12 1.69 - 1.82: 36 Bond restraints: 8586 Sorted by residual: bond pdb=" C ASN C1709 " pdb=" O ASN C1709 " ideal model delta sigma weight residual 1.234 1.167 0.067 1.23e-02 6.61e+03 2.97e+01 bond pdb=" C ASN A1709 " pdb=" O ASN A1709 " ideal model delta sigma weight residual 1.234 1.168 0.066 1.23e-02 6.61e+03 2.91e+01 bond pdb=" C ASN B1709 " pdb=" O ASN B1709 " ideal model delta sigma weight residual 1.234 1.168 0.066 1.23e-02 6.61e+03 2.88e+01 bond pdb=" CA ASN C1074 " pdb=" CB ASN C1074 " ideal model delta sigma weight residual 1.526 1.460 0.066 1.26e-02 6.30e+03 2.75e+01 bond pdb=" CA ASN A1074 " pdb=" CB ASN A1074 " ideal model delta sigma weight residual 1.526 1.460 0.066 1.26e-02 6.30e+03 2.74e+01 ... (remaining 8581 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 10231 1.52 - 3.04: 1270 3.04 - 4.56: 160 4.56 - 6.08: 58 6.08 - 7.60: 32 Bond angle restraints: 11751 Sorted by residual: angle pdb=" C LEU C1828 " pdb=" N PRO C1829 " pdb=" CA PRO C1829 " ideal model delta sigma weight residual 119.85 126.86 -7.01 1.01e+00 9.80e-01 4.81e+01 angle pdb=" C LEU B1828 " pdb=" N PRO B1829 " pdb=" CA PRO B1829 " ideal model delta sigma weight residual 119.85 126.84 -6.99 1.01e+00 9.80e-01 4.79e+01 angle pdb=" C LEU A1828 " pdb=" N PRO A1829 " pdb=" CA PRO A1829 " ideal model delta sigma weight residual 119.85 126.82 -6.97 1.01e+00 9.80e-01 4.77e+01 angle pdb=" C GLU C1111 " pdb=" N PRO C1112 " pdb=" CA PRO C1112 " ideal model delta sigma weight residual 119.83 127.23 -7.40 1.08e+00 8.57e-01 4.70e+01 angle pdb=" C GLU A1111 " pdb=" N PRO A1112 " pdb=" CA PRO A1112 " ideal model delta sigma weight residual 119.83 127.21 -7.38 1.08e+00 8.57e-01 4.68e+01 ... (remaining 11746 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.97: 5095 15.97 - 31.93: 143 31.93 - 47.90: 18 47.90 - 63.87: 18 63.87 - 79.83: 15 Dihedral angle restraints: 5289 sinusoidal: 1755 harmonic: 3534 Sorted by residual: dihedral pdb=" CB CYS A1743 " pdb=" SG CYS A1743 " pdb=" SG CYS A1749 " pdb=" CB CYS A1749 " ideal model delta sinusoidal sigma weight residual -86.00 -63.95 -22.05 1 1.00e+01 1.00e-02 7.02e+00 dihedral pdb=" CB CYS B1743 " pdb=" SG CYS B1743 " pdb=" SG CYS B1749 " pdb=" CB CYS B1749 " ideal model delta sinusoidal sigma weight residual -86.00 -63.97 -22.03 1 1.00e+01 1.00e-02 7.01e+00 dihedral pdb=" CB CYS C1743 " pdb=" SG CYS C1743 " pdb=" SG CYS C1749 " pdb=" CB CYS C1749 " ideal model delta sinusoidal sigma weight residual -86.00 -63.98 -22.02 1 1.00e+01 1.00e-02 7.00e+00 ... (remaining 5286 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 906 0.053 - 0.106: 398 0.106 - 0.158: 92 0.158 - 0.211: 41 0.211 - 0.264: 21 Chirality restraints: 1458 Sorted by residual: chirality pdb=" CA ASN A1709 " pdb=" N ASN A1709 " pdb=" C ASN A1709 " pdb=" CB ASN A1709 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CA ASN B1709 " pdb=" N ASN B1709 " pdb=" C ASN B1709 " pdb=" CB ASN B1709 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" C2 NAG C1403 " pdb=" C1 NAG C1403 " pdb=" C3 NAG C1403 " pdb=" N2 NAG C1403 " both_signs ideal model delta sigma weight residual False -2.49 -2.75 0.26 2.00e-01 2.50e+01 1.73e+00 ... (remaining 1455 not shown) Planarity restraints: 1554 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C1707 " -0.059 2.00e-02 2.50e+03 3.80e-02 2.89e+01 pdb=" CG TYR C1707 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR C1707 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TYR C1707 " 0.062 2.00e-02 2.50e+03 pdb=" CE1 TYR C1707 " 0.026 2.00e-02 2.50e+03 pdb=" CE2 TYR C1707 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR C1707 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR C1707 " -0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A1707 " 0.059 2.00e-02 2.50e+03 3.79e-02 2.87e+01 pdb=" CG TYR A1707 " 0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR A1707 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 TYR A1707 " -0.062 2.00e-02 2.50e+03 pdb=" CE1 TYR A1707 " -0.026 2.00e-02 2.50e+03 pdb=" CE2 TYR A1707 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A1707 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A1707 " 0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B1707 " 0.059 2.00e-02 2.50e+03 3.77e-02 2.85e+01 pdb=" CG TYR B1707 " 0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR B1707 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 TYR B1707 " -0.062 2.00e-02 2.50e+03 pdb=" CE1 TYR B1707 " -0.026 2.00e-02 2.50e+03 pdb=" CE2 TYR B1707 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR B1707 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR B1707 " 0.048 2.00e-02 2.50e+03 ... (remaining 1551 not shown) Histogram of nonbonded interaction distances: 2.59 - 3.05: 5505 3.05 - 3.51: 9170 3.51 - 3.97: 13286 3.97 - 4.44: 15969 4.44 - 4.90: 23085 Nonbonded interactions: 67015 Sorted by model distance: nonbonded pdb=" NH2 ARG C1091 " pdb=" O THR C1117 " model vdw 2.587 3.120 nonbonded pdb=" NH2 ARG A1091 " pdb=" O THR A1117 " model vdw 2.587 3.120 nonbonded pdb=" NH2 ARG B1091 " pdb=" O THR B1117 " model vdw 2.588 3.120 nonbonded pdb=" N VAL C1729 " pdb=" N SER C1730 " model vdw 2.613 2.560 nonbonded pdb=" N VAL B1729 " pdb=" N SER B1730 " model vdw 2.613 2.560 ... (remaining 67010 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 18.790 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: 0.200 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 9.390 Find NCS groups from input model: 0.070 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 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 : 0.012 0.075 8613 Z= 0.756 Angle : 1.155 7.604 11823 Z= 0.786 Chirality : 0.069 0.264 1458 Planarity : 0.006 0.039 1536 Dihedral : 10.215 79.833 2952 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 0.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.42 (0.21), residues: 1182 helix: 2.70 (0.16), residues: 678 sheet: 0.67 (0.32), residues: 153 loop : -0.17 (0.30), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 905 TYR 0.062 0.008 TYR C1707 PHE 0.026 0.005 PHE C1121 TRP 0.030 0.005 TRP A1840 HIS 0.002 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.01203 / 0.74 ( 8586) covalent geometry : angle 1.14161 / 0.78 (11751) SS BOND : bond 0.01136 / 0.73 ( 9) SS BOND : angle 2.77947 / 1.96 ( 18) hydrogen bonds : bond 0.15798 / 11.47 ( 709) hydrogen bonds : angle 6.71094 / 4.88 ( 2154) link_NAG-ASN : bond 0.06035 / 4.06 ( 18) link_NAG-ASN : angle 2.43081 / 2.00 ( 54) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.323 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.1323 time to fit residues: 14.8091 Evaluate side-chains 36 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 117 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1088 HIS A1849 HIS B1088 HIS B1849 HIS C1088 HIS C1849 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.051068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.040374 restraints weight = 43650.237| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 3.93 r_work: 0.2968 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 8613 Z= 0.174 Angle : 0.487 5.719 11823 Z= 0.267 Chirality : 0.039 0.123 1458 Planarity : 0.003 0.027 1536 Dihedral : 3.686 23.271 1632 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.69 % Allowed : 4.74 % Favored : 93.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.62 (0.23), residues: 1182 helix: 5.00 (0.16), residues: 666 sheet: 0.82 (0.31), residues: 174 loop : 0.05 (0.31), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1107 TYR 0.011 0.001 TYR C1067 PHE 0.013 0.002 PHE B1823 TRP 0.005 0.001 TRP B1840 HIS 0.005 0.002 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 ( 8586) covalent geometry : angle 0.47505 / 0.26 (11751) SS BOND : bond 0.00190 / 0.12 ( 9) SS BOND : angle 1.16569 / 0.77 ( 18) hydrogen bonds : bond 0.05616 / 3.99 ( 709) hydrogen bonds : angle 4.11081 / 2.99 ( 2154) link_NAG-ASN : bond 0.00120 / 0.08 ( 18) link_NAG-ASN : angle 1.50617 / 1.22 ( 54) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.352 Fit side-chains REVERT: A 1014 ARG cc_start: 0.9116 (ttm-80) cc_final: 0.8789 (tpp-160) REVERT: C 1014 ARG cc_start: 0.9172 (ttm-80) cc_final: 0.8807 (tpp-160) REVERT: C 1045 LYS cc_start: 0.8862 (OUTLIER) cc_final: 0.8492 (ttmm) outliers start: 10 outliers final: 3 residues processed: 47 average time/residue: 0.1281 time to fit residues: 7.9948 Evaluate side-chains 44 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1849 HIS Chi-restraints excluded: chain B residue 1849 HIS Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1849 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 83 optimal weight: 0.6980 chunk 66 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 114 optimal weight: 5.9990 chunk 70 optimal weight: 0.9980 chunk 27 optimal weight: 0.0070 chunk 105 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 17 optimal weight: 0.4980 chunk 78 optimal weight: 0.9980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1113 GLN B1113 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.050721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.039974 restraints weight = 43433.286| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 3.91 r_work: 0.2960 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 8613 Z= 0.142 Angle : 0.421 5.137 11823 Z= 0.229 Chirality : 0.038 0.117 1458 Planarity : 0.003 0.022 1536 Dihedral : 3.611 22.301 1632 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 0.51 % Allowed : 5.08 % Favored : 94.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.80 (0.23), residues: 1182 helix: 5.17 (0.16), residues: 669 sheet: 0.81 (0.33), residues: 165 loop : 0.10 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1014 TYR 0.028 0.001 TYR A1110 PHE 0.010 0.001 PHE B1823 TRP 0.005 0.001 TRP B1840 HIS 0.010 0.002 HIS A1849 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 ( 8586) covalent geometry : angle 0.41164 / 0.23 (11751) SS BOND : bond 0.00112 / 0.07 ( 9) SS BOND : angle 0.90084 / 0.59 ( 18) hydrogen bonds : bond 0.05243 / 3.72 ( 709) hydrogen bonds : angle 3.75798 / 2.74 ( 2154) link_NAG-ASN : bond 0.00170 / 0.13 ( 18) link_NAG-ASN : angle 1.29567 / 1.04 ( 54) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 0.380 Fit side-chains REVERT: A 1014 ARG cc_start: 0.9101 (ttm-80) cc_final: 0.8803 (tpp-160) REVERT: C 888 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.8956 (mp) REVERT: C 1014 ARG cc_start: 0.9190 (ttm-80) cc_final: 0.8773 (tpp-160) REVERT: C 1045 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8534 (ttmm) outliers start: 3 outliers final: 0 residues processed: 44 average time/residue: 0.1402 time to fit residues: 7.9823 Evaluate side-chains 44 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 42 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 888 LEU Chi-restraints excluded: chain C residue 1045 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 114 optimal weight: 0.1980 chunk 15 optimal weight: 0.9990 chunk 106 optimal weight: 5.9990 chunk 115 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 87 optimal weight: 9.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1048 HIS B1048 HIS C1048 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.049494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.038893 restraints weight = 45304.939| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 3.97 r_work: 0.2924 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8613 Z= 0.151 Angle : 0.411 4.649 11823 Z= 0.225 Chirality : 0.038 0.137 1458 Planarity : 0.003 0.024 1536 Dihedral : 3.266 17.456 1632 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 0.85 % Allowed : 4.40 % Favored : 94.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.94 (0.23), residues: 1182 helix: 5.33 (0.15), residues: 666 sheet: 0.93 (0.38), residues: 135 loop : 0.15 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 905 TYR 0.011 0.001 TYR C1067 PHE 0.009 0.001 PHE C 970 TRP 0.003 0.001 TRP B1102 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 ( 8586) covalent geometry : angle 0.40232 / 0.22 (11751) SS BOND : bond 0.00118 / 0.08 ( 9) SS BOND : angle 0.79350 / 0.52 ( 18) hydrogen bonds : bond 0.05068 / 3.59 ( 709) hydrogen bonds : angle 3.59807 / 2.63 ( 2154) link_NAG-ASN : bond 0.00152 / 0.10 ( 18) link_NAG-ASN : angle 1.22283 / 1.01 ( 54) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.366 Fit side-chains REVERT: A 1014 ARG cc_start: 0.9115 (ttm-80) cc_final: 0.8832 (tpp-160) REVERT: B 1110 TYR cc_start: 0.9327 (t80) cc_final: 0.8981 (t80) REVERT: C 888 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.8965 (mp) REVERT: C 1014 ARG cc_start: 0.9229 (ttm-80) cc_final: 0.8825 (tpp-160) outliers start: 5 outliers final: 3 residues processed: 42 average time/residue: 0.1427 time to fit residues: 8.0009 Evaluate side-chains 44 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1849 HIS Chi-restraints excluded: chain B residue 1849 HIS Chi-restraints excluded: chain C residue 888 LEU Chi-restraints excluded: chain C residue 1849 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 0.0020 chunk 88 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 chunk 114 optimal weight: 0.0470 chunk 44 optimal weight: 0.5980 chunk 26 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 56 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 overall best weight: 0.3686 ------------------------------------------------------------------------------- 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 = 0.3482 r_free = 0.3482 target = 0.050091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.039596 restraints weight = 44613.657| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 3.93 r_work: 0.2957 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8613 Z= 0.109 Angle : 0.372 4.677 11823 Z= 0.204 Chirality : 0.037 0.119 1458 Planarity : 0.003 0.029 1536 Dihedral : 3.053 18.005 1632 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 0.85 % Allowed : 4.57 % Favored : 94.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 5.19 (0.23), residues: 1182 helix: 5.52 (0.15), residues: 666 sheet: 1.46 (0.41), residues: 123 loop : 0.14 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 995 TYR 0.011 0.001 TYR C1067 PHE 0.008 0.001 PHE C 970 TRP 0.004 0.001 TRP A1840 HIS 0.002 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.11 ( 8586) covalent geometry : angle 0.36481 / 0.20 (11751) SS BOND : bond 0.00038 / 0.02 ( 9) SS BOND : angle 0.78747 / 0.51 ( 18) hydrogen bonds : bond 0.04774 / 3.37 ( 709) hydrogen bonds : angle 3.33459 / 2.44 ( 2154) link_NAG-ASN : bond 0.00079 / 0.05 ( 18) link_NAG-ASN : angle 1.08959 / 0.90 ( 54) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.341 Fit side-chains REVERT: A 1014 ARG cc_start: 0.9113 (ttm-80) cc_final: 0.8769 (tpp-160) REVERT: C 888 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.8953 (mp) REVERT: C 1014 ARG cc_start: 0.9217 (ttm-80) cc_final: 0.8843 (tpp-160) outliers start: 5 outliers final: 4 residues processed: 40 average time/residue: 0.1397 time to fit residues: 7.3637 Evaluate side-chains 44 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1849 HIS Chi-restraints excluded: chain B residue 1849 HIS Chi-restraints excluded: chain C residue 888 LEU Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1849 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 7 optimal weight: 0.7980 chunk 64 optimal weight: 0.7980 chunk 17 optimal weight: 0.3980 chunk 14 optimal weight: 0.3980 chunk 90 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3455 r_free = 0.3455 target = 0.049229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.038639 restraints weight = 44434.197| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 3.94 r_work: 0.2930 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8613 Z= 0.141 Angle : 0.391 4.146 11823 Z= 0.214 Chirality : 0.037 0.117 1458 Planarity : 0.003 0.030 1536 Dihedral : 3.054 17.490 1632 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 0.85 % Allowed : 5.41 % Favored : 93.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 5.17 (0.23), residues: 1182 helix: 5.49 (0.15), residues: 666 sheet: 1.13 (0.39), residues: 135 loop : 0.25 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 905 TYR 0.011 0.001 TYR A1067 PHE 0.009 0.001 PHE C 970 TRP 0.004 0.001 TRP C1837 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 ( 8586) covalent geometry : angle 0.38438 / 0.21 (11751) SS BOND : bond 0.00132 / 0.08 ( 9) SS BOND : angle 0.79042 / 0.52 ( 18) hydrogen bonds : bond 0.04866 / 3.43 ( 709) hydrogen bonds : angle 3.41163 / 2.50 ( 2154) link_NAG-ASN : bond 0.00080 / 0.05 ( 18) link_NAG-ASN : angle 1.09150 / 0.90 ( 54) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.360 Fit side-chains REVERT: A 1014 ARG cc_start: 0.9095 (ttm-80) cc_final: 0.8758 (tpp-160) REVERT: B 1014 ARG cc_start: 0.9103 (ttm-80) cc_final: 0.8804 (tpp-160) REVERT: C 888 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.8965 (mp) REVERT: C 1014 ARG cc_start: 0.9215 (ttm-80) cc_final: 0.8814 (tpp-160) outliers start: 5 outliers final: 4 residues processed: 42 average time/residue: 0.1497 time to fit residues: 8.1024 Evaluate side-chains 44 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1849 HIS Chi-restraints excluded: chain B residue 1849 HIS Chi-restraints excluded: chain C residue 888 LEU Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1849 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 101 optimal weight: 0.4980 chunk 29 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 110 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1849 HIS B1849 HIS C1849 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.049233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.038564 restraints weight = 45271.747| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 3.98 r_work: 0.2930 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8613 Z= 0.142 Angle : 0.398 4.798 11823 Z= 0.218 Chirality : 0.037 0.114 1458 Planarity : 0.003 0.030 1536 Dihedral : 3.100 18.753 1632 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 0.85 % Allowed : 6.26 % Favored : 92.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 5.16 (0.23), residues: 1182 helix: 5.48 (0.15), residues: 666 sheet: 1.20 (0.39), residues: 135 loop : 0.22 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 905 TYR 0.012 0.001 TYR C1067 PHE 0.008 0.001 PHE B1823 TRP 0.004 0.001 TRP C1837 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 ( 8586) covalent geometry : angle 0.39083 / 0.22 (11751) SS BOND : bond 0.00122 / 0.08 ( 9) SS BOND : angle 0.77261 / 0.50 ( 18) hydrogen bonds : bond 0.04887 / 3.46 ( 709) hydrogen bonds : angle 3.40841 / 2.49 ( 2154) link_NAG-ASN : bond 0.00090 / 0.06 ( 18) link_NAG-ASN : angle 1.13151 / 0.93 ( 54) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.327 Fit side-chains REVERT: A 1014 ARG cc_start: 0.9119 (ttm-80) cc_final: 0.8843 (tpp-160) REVERT: B 1014 ARG cc_start: 0.9124 (ttm-80) cc_final: 0.8822 (tpp-160) REVERT: C 888 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.8976 (mp) REVERT: C 1014 ARG cc_start: 0.9213 (ttm-80) cc_final: 0.8804 (tpp-160) outliers start: 5 outliers final: 4 residues processed: 42 average time/residue: 0.1466 time to fit residues: 7.9729 Evaluate side-chains 45 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1849 HIS Chi-restraints excluded: chain B residue 1849 HIS Chi-restraints excluded: chain C residue 888 LEU Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1849 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 85 optimal weight: 0.0770 chunk 93 optimal weight: 0.8980 chunk 113 optimal weight: 5.9990 chunk 96 optimal weight: 0.5980 chunk 53 optimal weight: 0.5980 chunk 95 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 110 optimal weight: 0.5980 overall best weight: 0.4938 ------------------------------------------------------------------------------- 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 = 0.3459 r_free = 0.3459 target = 0.049315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.038725 restraints weight = 44868.779| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 3.97 r_work: 0.2942 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8613 Z= 0.120 Angle : 0.386 5.232 11823 Z= 0.211 Chirality : 0.037 0.115 1458 Planarity : 0.003 0.031 1536 Dihedral : 3.113 19.833 1632 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 0.34 % Allowed : 6.94 % Favored : 92.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 5.19 (0.23), residues: 1182 helix: 5.51 (0.15), residues: 666 sheet: 1.19 (0.39), residues: 135 loop : 0.24 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 905 TYR 0.012 0.001 TYR B1067 PHE 0.007 0.001 PHE C 970 TRP 0.005 0.001 TRP A1840 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.12 ( 8586) covalent geometry : angle 0.37959 / 0.21 (11751) SS BOND : bond 0.00078 / 0.05 ( 9) SS BOND : angle 0.78040 / 0.51 ( 18) hydrogen bonds : bond 0.04818 / 3.39 ( 709) hydrogen bonds : angle 3.32699 / 2.44 ( 2154) link_NAG-ASN : bond 0.00152 / 0.12 ( 18) link_NAG-ASN : angle 1.02584 / 0.86 ( 54) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 40 time to evaluate : 0.312 Fit side-chains REVERT: A 1014 ARG cc_start: 0.9085 (ttm-80) cc_final: 0.8810 (tpp-160) REVERT: B 1014 ARG cc_start: 0.9092 (ttm-80) cc_final: 0.8797 (tpp-160) REVERT: C 888 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.8966 (mp) REVERT: C 1014 ARG cc_start: 0.9203 (ttm-80) cc_final: 0.8805 (tpp-160) outliers start: 2 outliers final: 0 residues processed: 41 average time/residue: 0.1504 time to fit residues: 7.9373 Evaluate side-chains 40 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 39 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 888 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 88 optimal weight: 0.9980 chunk 84 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 80 optimal weight: 0.3980 chunk 37 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 97 optimal weight: 0.3980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3463 r_free = 0.3463 target = 0.049270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.038747 restraints weight = 45027.644| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 3.95 r_work: 0.2932 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8613 Z= 0.132 Angle : 0.392 4.885 11823 Z= 0.214 Chirality : 0.037 0.117 1458 Planarity : 0.003 0.030 1536 Dihedral : 2.968 14.424 1632 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 0.17 % Allowed : 6.94 % Favored : 92.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 5.19 (0.23), residues: 1182 helix: 5.51 (0.15), residues: 666 sheet: 1.17 (0.39), residues: 135 loop : 0.25 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 905 TYR 0.012 0.001 TYR C1067 PHE 0.008 0.001 PHE C 970 TRP 0.004 0.001 TRP A1840 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 ( 8586) covalent geometry : angle 0.38498 / 0.21 (11751) SS BOND : bond 0.00107 / 0.07 ( 9) SS BOND : angle 0.77226 / 0.50 ( 18) hydrogen bonds : bond 0.04819 / 3.41 ( 709) hydrogen bonds : angle 3.33154 / 2.44 ( 2154) link_NAG-ASN : bond 0.00079 / 0.06 ( 18) link_NAG-ASN : angle 1.07378 / 0.89 ( 54) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 40 time to evaluate : 0.334 Fit side-chains REVERT: A 1014 ARG cc_start: 0.9114 (ttm-80) cc_final: 0.8782 (tpp-160) REVERT: B 1014 ARG cc_start: 0.9105 (ttm-80) cc_final: 0.8808 (tpp-160) REVERT: C 888 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.8976 (mp) REVERT: C 1014 ARG cc_start: 0.9185 (ttm-80) cc_final: 0.8782 (tpp-160) outliers start: 1 outliers final: 0 residues processed: 41 average time/residue: 0.1345 time to fit residues: 7.1510 Evaluate side-chains 41 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 40 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 888 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 51 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 96 optimal weight: 0.5980 chunk 39 optimal weight: 9.9990 chunk 68 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 86 optimal weight: 2.9990 chunk 119 optimal weight: 10.0000 chunk 95 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1849 HIS C1849 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.048709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.038132 restraints weight = 45746.737| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 4.00 r_work: 0.2911 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.3879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8613 Z= 0.165 Angle : 0.419 5.072 11823 Z= 0.228 Chirality : 0.037 0.120 1458 Planarity : 0.003 0.029 1536 Dihedral : 3.125 17.790 1632 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 0.68 % Allowed : 6.43 % Favored : 92.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 5.17 (0.23), residues: 1182 helix: 5.49 (0.15), residues: 663 sheet: 1.11 (0.40), residues: 135 loop : 0.31 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A1107 TYR 0.012 0.001 TYR B1067 PHE 0.009 0.001 PHE C 970 TRP 0.004 0.001 TRP C1837 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.17 ( 8586) covalent geometry : angle 0.41193 / 0.23 (11751) SS BOND : bond 0.00167 / 0.10 ( 9) SS BOND : angle 0.79834 / 0.52 ( 18) hydrogen bonds : bond 0.04956 / 3.50 ( 709) hydrogen bonds : angle 3.45276 / 2.53 ( 2154) link_NAG-ASN : bond 0.00125 / 0.09 ( 18) link_NAG-ASN : angle 1.15305 / 0.96 ( 54) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2364 Ramachandran restraints generated. 1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.337 Fit side-chains REVERT: A 1014 ARG cc_start: 0.9113 (ttm-80) cc_final: 0.8834 (tpp-160) REVERT: B 1014 ARG cc_start: 0.9120 (ttm-80) cc_final: 0.8806 (tpp-160) REVERT: C 888 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.8996 (mp) REVERT: C 1014 ARG cc_start: 0.9189 (ttm-80) cc_final: 0.8761 (tpp-160) outliers start: 4 outliers final: 3 residues processed: 42 average time/residue: 0.1477 time to fit residues: 7.9333 Evaluate side-chains 43 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1849 HIS Chi-restraints excluded: chain B residue 1849 HIS Chi-restraints excluded: chain C residue 888 LEU Chi-restraints excluded: chain C residue 1849 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 106 optimal weight: 4.9990 chunk 13 optimal weight: 0.5980 chunk 107 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 0.0040 chunk 108 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- 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 = 0.3452 r_free = 0.3452 target = 0.048884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.038452 restraints weight = 45471.289| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 3.97 r_work: 0.2917 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8613 Z= 0.133 Angle : 0.402 6.175 11823 Z= 0.219 Chirality : 0.037 0.119 1458 Planarity : 0.003 0.030 1536 Dihedral : 3.090 17.836 1632 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 0.34 % Allowed : 6.77 % Favored : 92.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 5.16 (0.23), residues: 1182 helix: 5.51 (0.15), residues: 663 sheet: 1.08 (0.40), residues: 135 loop : 0.26 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 905 TYR 0.012 0.001 TYR B1067 PHE 0.008 0.001 PHE C 970 TRP 0.004 0.001 TRP A1840 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 ( 8586) covalent geometry : angle 0.39556 / 0.22 (11751) SS BOND : bond 0.00109 / 0.07 ( 9) SS BOND : angle 0.77344 / 0.50 ( 18) hydrogen bonds : bond 0.04882 / 3.46 ( 709) hydrogen bonds : angle 3.38232 / 2.47 ( 2154) link_NAG-ASN : bond 0.00113 / 0.08 ( 18) link_NAG-ASN : angle 1.07677 / 0.90 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2281.52 seconds wall clock time: 39 minutes 44.32 seconds (2384.32 seconds total)