Starting phenix.real_space_refine on Wed Aug 5 19:33:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/11hw_75705/08_2026/11hw_75705_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/11hw_75705/08_2026/11hw_75705.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/11hw_75705/08_2026/11hw_75705.map" default_real_map = "/net/cci-nas-00/data/ceres_data/11hw_75705/08_2026/11hw_75705.map" model { file = "/net/cci-nas-00/data/ceres_data/11hw_75705/08_2026/11hw_75705_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/11hw_75705/08_2026/11hw_75705_neut.cif" } resolution = 2.8 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= 0.070 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 33 5.16 5 C 7095 2.51 5 N 1926 2.21 5 O 2082 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 69 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11136 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1389 Classifications: {'peptide': 184} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 3, 'TRANS': 180} Chain breaks: 1 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 8, 'GLN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 48 Chain: "C" Number of atoms: 1272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1272 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 170} Chain breaks: 3 Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 3, 'ASP:plan': 3, 'PHE:plan': 1, 'ASN:plan1': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 56 Chain: "D" Number of atoms: 992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 992 Classifications: {'peptide': 149} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 138} Chain breaks: 2 Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 180 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'ASP:plan': 7, 'ARG:plan': 2, 'GLU:plan': 3, 'GLN:plan1': 2, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 57 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "C" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "E" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "H" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "I" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Restraints were copied for chains: B, G, E, H, F, I Time building chain proxies: 2.25, per 1000 atoms: 0.20 Number of scatterers: 11136 At special positions: 0 Unit cell: (140.101, 137.614, 166.629, 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 33 16.00 O 2082 8.00 N 1926 7.00 C 7095 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 149 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.13 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 149 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS H 149 " - pdb=" SG CYS H 205 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.13 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.13 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 A1801 " " NAG A1402 " - " ASN A 121 " " NAG B1401 " - " ASN B1801 " " NAG B1402 " - " ASN B 121 " " NAG G1401 " - " ASN G1801 " " NAG G1402 " - " ASN G 121 " Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 547.0 milliseconds 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2898 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 27 sheets defined 32.7% alpha, 27.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 108 through 970 Processing helix chain 'A' and resid 1816 through 1823 Processing helix chain 'A' and resid 1836 through 1873 Processing helix chain 'C' and resid 28 through 32 Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'C' and resid 211 through 213 No H-bonds generated for 'chain 'C' and resid 211 through 213' Processing helix chain 'D' and resid 79 through 83 removed outlier: 4.200A pdb=" N PHE D 83 " --> pdb=" O ALA D 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 970 Processing helix chain 'B' and resid 1816 through 1823 Processing helix chain 'B' and resid 1836 through 1873 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 211 through 213 No H-bonds generated for 'chain 'E' and resid 211 through 213' Processing helix chain 'F' and resid 79 through 83 removed outlier: 4.201A pdb=" N PHE F 83 " --> pdb=" O ALA F 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 970 Processing helix chain 'G' and resid 1816 through 1823 Processing helix chain 'G' and resid 1836 through 1873 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 211 through 213 No H-bonds generated for 'chain 'H' and resid 211 through 213' Processing helix chain 'I' and resid 79 through 83 removed outlier: 4.201A pdb=" N PHE I 83 " --> pdb=" O ALA I 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'C' and resid 11 through 12 removed outlier: 6.535A pdb=" N MET C 34 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N VAL C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 129 through 131 removed outlier: 5.937A pdb=" N TYR C 185 " --> pdb=" O ASP C 153 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 129 through 131 removed outlier: 5.937A pdb=" N TYR C 185 " --> pdb=" O ASP C 153 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 159 through 162 Processing sheet with id=AA6, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.660A pdb=" N ASP D 70 " --> pdb=" O SER D 67 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.401A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 10 through 13 removed outlier: 3.609A pdb=" N THR D 97 " --> pdb=" O GLN D 90 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 114 through 117 removed outlier: 3.548A pdb=" N SER D 114 " --> pdb=" O ASN D 137 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N TYR D 173 " --> pdb=" O ASN D 138 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.535A pdb=" N MET E 34 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N VAL E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 129 through 131 removed outlier: 5.938A pdb=" N TYR E 185 " --> pdb=" O ASP E 153 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 129 through 131 removed outlier: 5.938A pdb=" N TYR E 185 " --> pdb=" O ASP E 153 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 159 through 162 Processing sheet with id=AB6, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.659A pdb=" N ASP F 70 " --> pdb=" O SER F 67 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.401A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 10 through 13 removed outlier: 3.609A pdb=" N THR F 97 " --> pdb=" O GLN F 90 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 114 through 117 removed outlier: 3.548A pdb=" N SER F 114 " --> pdb=" O ASN F 137 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N TYR F 173 " --> pdb=" O ASN F 138 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AC2, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.535A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 129 through 131 removed outlier: 5.936A pdb=" N TYR H 185 " --> pdb=" O ASP H 153 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 129 through 131 removed outlier: 5.936A pdb=" N TYR H 185 " --> pdb=" O ASP H 153 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 159 through 162 Processing sheet with id=AC6, first strand: chain 'I' and resid 4 through 7 removed outlier: 3.660A pdb=" N ASP I 70 " --> pdb=" O SER I 67 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 10 through 13 removed outlier: 6.401A pdb=" N LEU I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N TYR I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 10 through 13 removed outlier: 3.609A pdb=" N THR I 97 " --> pdb=" O GLN I 90 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 114 through 117 removed outlier: 3.548A pdb=" N SER I 114 " --> pdb=" O ASN I 137 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N TYR I 173 " --> pdb=" O ASN I 138 " (cutoff:3.500A) 739 hydrogen bonds defined for protein. 1992 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: 1.96 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1937 1.32 - 1.45: 3012 1.45 - 1.57: 6274 1.57 - 1.70: 3 1.70 - 1.83: 48 Bond restraints: 11274 Sorted by residual: bond pdb=" C ASN B 121 " pdb=" O ASN B 121 " ideal model delta sigma weight residual 1.237 1.187 0.050 1.19e-02 7.06e+03 1.77e+01 bond pdb=" C ASN A 121 " pdb=" O ASN A 121 " ideal model delta sigma weight residual 1.237 1.187 0.050 1.19e-02 7.06e+03 1.75e+01 bond pdb=" C ASN G 121 " pdb=" O ASN G 121 " ideal model delta sigma weight residual 1.237 1.187 0.050 1.19e-02 7.06e+03 1.73e+01 bond pdb=" NE ARG G1862 " pdb=" CZ ARG G1862 " ideal model delta sigma weight residual 1.326 1.363 -0.037 1.10e-02 8.26e+03 1.12e+01 bond pdb=" NE ARG A1862 " pdb=" CZ ARG A1862 " ideal model delta sigma weight residual 1.326 1.363 -0.037 1.10e-02 8.26e+03 1.10e+01 ... (remaining 11269 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 13606 1.65 - 3.30: 1521 3.30 - 4.94: 140 4.94 - 6.59: 82 6.59 - 8.24: 35 Bond angle restraints: 15384 Sorted by residual: angle pdb=" C ASP B1808 " pdb=" N PRO B1809 " pdb=" CA PRO B1809 " ideal model delta sigma weight residual 119.56 127.80 -8.24 1.02e+00 9.61e-01 6.52e+01 angle pdb=" C ASP A1808 " pdb=" N PRO A1809 " pdb=" CA PRO A1809 " ideal model delta sigma weight residual 119.56 127.79 -8.23 1.02e+00 9.61e-01 6.50e+01 angle pdb=" C ASP G1808 " pdb=" N PRO G1809 " pdb=" CA PRO G1809 " ideal model delta sigma weight residual 119.56 127.77 -8.21 1.02e+00 9.61e-01 6.48e+01 angle pdb=" C PHE F 118 " pdb=" N PRO F 119 " pdb=" CA PRO F 119 " ideal model delta sigma weight residual 119.66 125.42 -5.76 7.20e-01 1.93e+00 6.40e+01 angle pdb=" C PHE D 118 " pdb=" N PRO D 119 " pdb=" CA PRO D 119 " ideal model delta sigma weight residual 119.66 125.41 -5.75 7.20e-01 1.93e+00 6.39e+01 ... (remaining 15379 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.97: 6333 14.97 - 29.95: 246 29.95 - 44.92: 81 44.92 - 59.89: 30 59.89 - 74.87: 12 Dihedral angle restraints: 6702 sinusoidal: 2241 harmonic: 4461 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 49.67 43.33 1 1.00e+01 1.00e-02 2.62e+01 dihedral pdb=" CB CYS C 22 " pdb=" SG CYS C 22 " pdb=" SG CYS C 96 " pdb=" CB CYS C 96 " ideal model delta sinusoidal sigma weight residual 93.00 49.68 43.32 1 1.00e+01 1.00e-02 2.62e+01 dihedral pdb=" CB CYS E 22 " pdb=" SG CYS E 22 " pdb=" SG CYS E 96 " pdb=" CB CYS E 96 " ideal model delta sinusoidal sigma weight residual 93.00 49.69 43.31 1 1.00e+01 1.00e-02 2.61e+01 ... (remaining 6699 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1242 0.058 - 0.116: 389 0.116 - 0.173: 117 0.173 - 0.231: 19 0.231 - 0.289: 12 Chirality restraints: 1779 Sorted by residual: chirality pdb=" C2 NAG B1402 " pdb=" C1 NAG B1402 " pdb=" C3 NAG B1402 " pdb=" N2 NAG B1402 " both_signs ideal model delta sigma weight residual False -2.49 -2.78 0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CG LEU B1858 " pdb=" CB LEU B1858 " pdb=" CD1 LEU B1858 " pdb=" CD2 LEU B1858 " both_signs ideal model delta sigma weight residual False -2.59 -2.88 0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" CG LEU G1858 " pdb=" CB LEU G1858 " pdb=" CD1 LEU G1858 " pdb=" CD2 LEU G1858 " both_signs ideal model delta sigma weight residual False -2.59 -2.88 0.29 2.00e-01 2.50e+01 2.08e+00 ... (remaining 1776 not shown) Planarity restraints: 2022 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP H 47 " 0.059 2.00e-02 2.50e+03 2.86e-02 2.04e+01 pdb=" CG TRP H 47 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 TRP H 47 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP H 47 " -0.029 2.00e-02 2.50e+03 pdb=" NE1 TRP H 47 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TRP H 47 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP H 47 " -0.033 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 47 " 0.033 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 47 " -0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP H 47 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 47 " -0.058 2.00e-02 2.50e+03 2.85e-02 2.03e+01 pdb=" CG TRP C 47 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TRP C 47 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP C 47 " 0.029 2.00e-02 2.50e+03 pdb=" NE1 TRP C 47 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP C 47 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP C 47 " 0.033 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 47 " -0.032 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 47 " 0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP C 47 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 47 " -0.058 2.00e-02 2.50e+03 2.84e-02 2.02e+01 pdb=" CG TRP E 47 " 0.017 2.00e-02 2.50e+03 pdb=" CD1 TRP E 47 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP E 47 " 0.029 2.00e-02 2.50e+03 pdb=" NE1 TRP E 47 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP E 47 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP E 47 " 0.033 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 47 " -0.033 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 47 " 0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP E 47 " -0.030 2.00e-02 2.50e+03 ... (remaining 2019 not shown) Histogram of nonbonded interaction distances: 2.44 - 2.93: 4688 2.93 - 3.42: 10639 3.42 - 3.91: 19134 3.91 - 4.41: 21840 4.41 - 4.90: 36473 Nonbonded interactions: 92774 Sorted by model distance: nonbonded pdb=" O PRO E 108 " pdb=" O HOH E 301 " model vdw 2.437 3.040 nonbonded pdb=" O PRO H 108 " pdb=" O HOH H 301 " model vdw 2.437 3.040 nonbonded pdb=" O PRO C 108 " pdb=" O HOH C 301 " model vdw 2.437 3.040 nonbonded pdb=" O ALA E 33 " pdb=" N GLY E 99 " model vdw 2.520 3.120 nonbonded pdb=" O ALA H 33 " pdb=" N GLY H 99 " model vdw 2.520 3.120 ... (remaining 92769 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'G' } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'I' } 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: 23.720 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: 0.020 Extract box with map and model: 0.310 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.800 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 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 : 0.011 0.095 11289 Z= 0.626 Angle : 1.190 8.239 15420 Z= 0.812 Chirality : 0.066 0.289 1779 Planarity : 0.007 0.087 2016 Dihedral : 10.732 74.866 3777 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 0.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Rotamer: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.74 % 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: 2.18 (0.20), residues: 1488 helix: 3.29 (0.18), residues: 441 sheet: 0.40 (0.23), residues: 441 loop : 1.02 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.002 ARG E 87 TYR 0.058 0.007 TYR D 140 PHE 0.029 0.005 PHE B1872 TRP 0.059 0.007 TRP H 47 HIS 0.004 0.001 HIS G 115 Details of bonding type rmsd/Z covalent geometry : bond 0.01096 / 0.62 (11274) covalent geometry : angle 1.18272 / 0.81 (15384) SS BOND : bond 0.05519 / 4.11 ( 9) SS BOND : angle 3.48682 / 2.50 ( 18) hydrogen bonds : bond 0.15065 / 10.38 ( 703) hydrogen bonds : angle 6.49601 / 4.84 ( 1992) link_NAG-ASN : bond 0.04487 / 2.75 ( 6) link_NAG-ASN : angle 2.27930 / 1.71 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.399 Fit side-chains REVERT: A 133 LYS cc_start: 0.8042 (tttt) cc_final: 0.7760 (tttm) REVERT: C 88 VAL cc_start: 0.8051 (t) cc_final: 0.7688 (p) REVERT: D 82 ASP cc_start: 0.7575 (m-30) cc_final: 0.7092 (m-30) REVERT: B 1857 THR cc_start: 0.8032 (m) cc_final: 0.7742 (t) REVERT: B 1864 THR cc_start: 0.7506 (m) cc_final: 0.7039 (p) REVERT: E 84 ASN cc_start: 0.8135 (m-40) cc_final: 0.7932 (m110) REVERT: E 88 VAL cc_start: 0.8018 (t) cc_final: 0.7713 (p) REVERT: F 32 LYS cc_start: 0.8189 (mmtt) cc_final: 0.7797 (mmtp) REVERT: G 133 LYS cc_start: 0.8008 (tttt) cc_final: 0.7530 (tttm) REVERT: G 1864 THR cc_start: 0.7552 (m) cc_final: 0.7121 (p) REVERT: I 27 GLN cc_start: 0.7415 (mt0) cc_final: 0.7117 (mt0) REVERT: I 32 LYS cc_start: 0.8258 (mmtt) cc_final: 0.8051 (mmtt) REVERT: I 45 LYS cc_start: 0.7967 (ttpt) cc_final: 0.7055 (mptt) REVERT: I 82 ASP cc_start: 0.7621 (m-30) cc_final: 0.7329 (m-30) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.7362 time to fit residues: 167.8994 Evaluate side-chains 148 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 10.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 954 GLN D 27 GLN D 61 GLN B 954 GLN F 6 GLN F 27 GLN G 949 GLN G 957 GLN I 6 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.172252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.117000 restraints weight = 12505.718| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.03 r_work: 0.3098 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 11289 Z= 0.168 Angle : 0.526 5.878 15420 Z= 0.279 Chirality : 0.042 0.168 1779 Planarity : 0.004 0.028 2016 Dihedral : 4.368 29.554 1737 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 2.20 % Allowed : 7.15 % Favored : 90.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.74 % 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: 3.30 (0.22), residues: 1488 helix: 5.00 (0.17), residues: 444 sheet: 0.82 (0.24), residues: 423 loop : 1.15 (0.27), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A1862 TYR 0.012 0.002 TYR D 91 PHE 0.012 0.002 PHE A1802 TRP 0.017 0.002 TRP C 47 HIS 0.003 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 (11274) covalent geometry : angle 0.51671 / 0.28 (15384) SS BOND : bond 0.00677 / 0.50 ( 9) SS BOND : angle 1.52835 / 1.09 ( 18) hydrogen bonds : bond 0.05281 / 3.63 ( 703) hydrogen bonds : angle 4.30758 / 3.13 ( 1992) link_NAG-ASN : bond 0.00253 / 0.15 ( 6) link_NAG-ASN : angle 2.49132 / 2.03 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 0.266 Fit side-chains REVERT: C 76 ARG cc_start: 0.7587 (mtp85) cc_final: 0.7293 (mtp-110) REVERT: B 131 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8037 (mt) REVERT: B 947 LYS cc_start: 0.8842 (mmtp) cc_final: 0.8518 (mmtt) REVERT: B 954 GLN cc_start: 0.8360 (tt0) cc_final: 0.7935 (tm-30) REVERT: B 1864 THR cc_start: 0.7535 (m) cc_final: 0.7021 (p) REVERT: E 58 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8584 (mp0) REVERT: E 76 ARG cc_start: 0.7699 (OUTLIER) cc_final: 0.7218 (mtm-85) REVERT: F 32 LYS cc_start: 0.8611 (mmtt) cc_final: 0.8259 (mmtp) REVERT: G 1844 ARG cc_start: 0.8375 (tpp80) cc_final: 0.8143 (mmt180) REVERT: G 1845 LYS cc_start: 0.8449 (ttmt) cc_final: 0.8153 (ttpp) REVERT: G 1864 THR cc_start: 0.7638 (m) cc_final: 0.7142 (p) REVERT: I 32 LYS cc_start: 0.8653 (mmtt) cc_final: 0.8383 (mmmt) REVERT: I 82 ASP cc_start: 0.7982 (m-30) cc_final: 0.7562 (m-30) outliers start: 20 outliers final: 4 residues processed: 151 average time/residue: 0.6458 time to fit residues: 104.1284 Evaluate side-chains 141 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 134 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1803 SER Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 58 GLU Chi-restraints excluded: chain E residue 76 ARG Chi-restraints excluded: chain H residue 12 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 42 optimal weight: 0.6980 chunk 68 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 chunk 82 optimal weight: 0.0770 chunk 74 optimal weight: 0.1980 chunk 80 optimal weight: 0.0060 chunk 145 optimal weight: 0.8980 chunk 140 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 overall best weight: 0.3354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1849 ASN D 27 GLN B1849 ASN F 27 GLN G1849 ASN I 27 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.174185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.119355 restraints weight = 12570.510| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.02 r_work: 0.3101 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 11289 Z= 0.108 Angle : 0.440 4.744 15420 Z= 0.235 Chirality : 0.040 0.180 1779 Planarity : 0.004 0.031 2016 Dihedral : 4.035 30.229 1737 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 2.20 % Allowed : 8.58 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.74 % 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: 3.64 (0.22), residues: 1488 helix: 5.28 (0.17), residues: 444 sheet: 1.16 (0.25), residues: 423 loop : 1.23 (0.27), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 108 TYR 0.012 0.001 TYR D 49 PHE 0.008 0.001 PHE C 29 TRP 0.012 0.001 TRP H 47 HIS 0.002 0.001 HIS C 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.11 (11274) covalent geometry : angle 0.43460 / 0.23 (15384) SS BOND : bond 0.00417 / 0.31 ( 9) SS BOND : angle 0.86878 / 0.62 ( 18) hydrogen bonds : bond 0.04315 / 2.98 ( 703) hydrogen bonds : angle 3.82517 / 2.78 ( 1992) link_NAG-ASN : bond 0.00291 / 0.19 ( 6) link_NAG-ASN : angle 2.00398 / 1.65 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 146 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 954 GLN cc_start: 0.8388 (tt0) cc_final: 0.8063 (tm-30) REVERT: C 76 ARG cc_start: 0.7559 (mtp85) cc_final: 0.7229 (mtm-85) REVERT: B 131 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.7953 (mt) REVERT: B 947 LYS cc_start: 0.8806 (mmtp) cc_final: 0.8501 (mmtt) REVERT: B 1864 THR cc_start: 0.7444 (m) cc_final: 0.6885 (p) REVERT: E 76 ARG cc_start: 0.7724 (OUTLIER) cc_final: 0.6944 (mtp-110) REVERT: E 82 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8098 (tt0) REVERT: F 32 LYS cc_start: 0.8568 (mmtt) cc_final: 0.8246 (mmtp) REVERT: G 1844 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.8070 (mmt180) REVERT: G 1864 THR cc_start: 0.7509 (m) cc_final: 0.6967 (p) REVERT: H 51 MET cc_start: 0.9164 (OUTLIER) cc_final: 0.8963 (tpt) REVERT: H 76 ARG cc_start: 0.7667 (OUTLIER) cc_final: 0.7327 (mtm-85) REVERT: I 32 LYS cc_start: 0.8598 (mmtt) cc_final: 0.8356 (mmmt) REVERT: I 82 ASP cc_start: 0.7955 (m-30) cc_final: 0.7606 (m-30) outliers start: 20 outliers final: 8 residues processed: 148 average time/residue: 0.6593 time to fit residues: 104.7267 Evaluate side-chains 145 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain D residue 108 ARG Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1803 SER Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 76 ARG Chi-restraints excluded: chain E residue 82 GLU Chi-restraints excluded: chain G residue 963 VAL Chi-restraints excluded: chain G residue 1844 ARG Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 76 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 133 optimal weight: 0.0060 chunk 71 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 139 optimal weight: 0.8980 chunk 116 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 89 optimal weight: 0.6980 chunk 66 optimal weight: 0.5980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1849 ASN D 27 GLN B1849 ASN F 27 GLN I 27 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.172439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.116827 restraints weight = 12499.884| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.03 r_work: 0.3092 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 11289 Z= 0.139 Angle : 0.458 5.118 15420 Z= 0.242 Chirality : 0.040 0.150 1779 Planarity : 0.004 0.033 2016 Dihedral : 4.097 30.992 1737 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.86 % Allowed : 9.79 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.74 % 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: 3.65 (0.22), residues: 1488 helix: 5.28 (0.17), residues: 444 sheet: 1.15 (0.24), residues: 441 loop : 1.26 (0.28), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G1815 TYR 0.012 0.001 TYR D 49 PHE 0.011 0.001 PHE F 87 TRP 0.016 0.002 TRP E 47 HIS 0.003 0.001 HIS C 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (11274) covalent geometry : angle 0.45148 / 0.24 (15384) SS BOND : bond 0.00583 / 0.43 ( 9) SS BOND : angle 1.12276 / 0.79 ( 18) hydrogen bonds : bond 0.04297 / 2.98 ( 703) hydrogen bonds : angle 3.75005 / 2.72 ( 1992) link_NAG-ASN : bond 0.00424 / 0.27 ( 6) link_NAG-ASN : angle 2.07228 / 1.69 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 140 time to evaluate : 0.449 Fit side-chains revert: symmetry clash REVERT: A 954 GLN cc_start: 0.8393 (tt0) cc_final: 0.7976 (tm-30) REVERT: B 947 LYS cc_start: 0.8844 (mmtp) cc_final: 0.8540 (mmtt) REVERT: B 1864 THR cc_start: 0.7552 (m) cc_final: 0.7001 (p) REVERT: E 76 ARG cc_start: 0.7719 (OUTLIER) cc_final: 0.6959 (mtp-110) REVERT: E 82 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8187 (tt0) REVERT: F 32 LYS cc_start: 0.8622 (mmtt) cc_final: 0.8406 (mmtp) REVERT: G 1844 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.8044 (mmt180) REVERT: G 1856 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.7018 (mt-10) REVERT: H 76 ARG cc_start: 0.7679 (OUTLIER) cc_final: 0.7320 (mtm-85) REVERT: I 32 LYS cc_start: 0.8670 (mmtt) cc_final: 0.8437 (mmmt) outliers start: 26 outliers final: 10 residues processed: 148 average time/residue: 0.6820 time to fit residues: 108.1322 Evaluate side-chains 140 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1803 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain D residue 108 ARG Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1803 SER Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 76 ARG Chi-restraints excluded: chain E residue 82 GLU Chi-restraints excluded: chain G residue 963 VAL Chi-restraints excluded: chain G residue 1844 ARG Chi-restraints excluded: chain G residue 1856 GLU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 76 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 110 optimal weight: 0.0370 chunk 67 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 24 optimal weight: 0.0470 chunk 116 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 overall best weight: 0.4956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1849 ASN A1867 GLN D 27 GLN B1849 ASN F 27 GLN I 27 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.171143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.114729 restraints weight = 12469.452| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.08 r_work: 0.3073 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 11289 Z= 0.120 Angle : 0.437 5.302 15420 Z= 0.231 Chirality : 0.040 0.208 1779 Planarity : 0.003 0.033 2016 Dihedral : 3.995 32.247 1737 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.86 % Allowed : 10.01 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.74 % 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: 3.69 (0.22), residues: 1488 helix: 5.32 (0.17), residues: 444 sheet: 1.12 (0.24), residues: 447 loop : 1.32 (0.28), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 108 TYR 0.012 0.001 TYR D 49 PHE 0.011 0.001 PHE G1800 TRP 0.014 0.002 TRP E 47 HIS 0.002 0.001 HIS C 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (11274) covalent geometry : angle 0.43190 / 0.23 (15384) SS BOND : bond 0.00478 / 0.35 ( 9) SS BOND : angle 0.91127 / 0.64 ( 18) hydrogen bonds : bond 0.04071 / 2.82 ( 703) hydrogen bonds : angle 3.65129 / 2.65 ( 1992) link_NAG-ASN : bond 0.00248 / 0.19 ( 6) link_NAG-ASN : angle 1.80481 / 1.50 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 130 time to evaluate : 0.390 Fit side-chains revert: symmetry clash REVERT: A 954 GLN cc_start: 0.8396 (tt0) cc_final: 0.7958 (tm-30) REVERT: B 947 LYS cc_start: 0.8835 (mmtp) cc_final: 0.8523 (mmtt) REVERT: B 1845 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.7639 (ttmt) REVERT: B 1864 THR cc_start: 0.7552 (m) cc_final: 0.6985 (p) REVERT: E 76 ARG cc_start: 0.7750 (OUTLIER) cc_final: 0.6935 (mtp-110) REVERT: E 82 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8167 (tt0) REVERT: F 32 LYS cc_start: 0.8629 (mmtt) cc_final: 0.8423 (mmtp) REVERT: G 1844 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.8031 (mmt180) REVERT: G 1864 THR cc_start: 0.7376 (m) cc_final: 0.6873 (p) REVERT: H 76 ARG cc_start: 0.7639 (OUTLIER) cc_final: 0.7292 (mtm-85) REVERT: I 32 LYS cc_start: 0.8674 (mmtt) cc_final: 0.8443 (mmmt) outliers start: 26 outliers final: 9 residues processed: 142 average time/residue: 0.6225 time to fit residues: 94.7517 Evaluate side-chains 135 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1803 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain D residue 108 ARG Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1803 SER Chi-restraints excluded: chain B residue 1845 LYS Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 76 ARG Chi-restraints excluded: chain E residue 82 GLU Chi-restraints excluded: chain G residue 963 VAL Chi-restraints excluded: chain G residue 1844 ARG Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 76 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 148 optimal weight: 7.9990 chunk 1 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 48 optimal weight: 7.9990 chunk 143 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 106 optimal weight: 0.8980 chunk 19 optimal weight: 0.2980 chunk 107 optimal weight: 0.5980 chunk 76 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1849 ASN D 27 GLN B1849 ASN F 27 GLN I 27 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.169904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.113256 restraints weight = 12670.871| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.09 r_work: 0.3058 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 11289 Z= 0.138 Angle : 0.451 5.379 15420 Z= 0.238 Chirality : 0.040 0.199 1779 Planarity : 0.003 0.032 2016 Dihedral : 4.052 32.570 1737 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 3.19 % Allowed : 9.90 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.74 % 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: 3.64 (0.22), residues: 1488 helix: 5.27 (0.17), residues: 444 sheet: 1.09 (0.24), residues: 447 loop : 1.31 (0.29), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 108 TYR 0.013 0.001 TYR I 49 PHE 0.014 0.001 PHE G1800 TRP 0.015 0.002 TRP E 47 HIS 0.003 0.001 HIS C 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (11274) covalent geometry : angle 0.44664 / 0.24 (15384) SS BOND : bond 0.00549 / 0.41 ( 9) SS BOND : angle 1.01725 / 0.71 ( 18) hydrogen bonds : bond 0.04155 / 2.87 ( 703) hydrogen bonds : angle 3.66758 / 2.66 ( 1992) link_NAG-ASN : bond 0.00129 / 0.08 ( 6) link_NAG-ASN : angle 1.67287 / 1.37 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 127 time to evaluate : 0.437 Fit side-chains revert: symmetry clash REVERT: A 954 GLN cc_start: 0.8412 (tt0) cc_final: 0.7926 (tm-30) REVERT: C 82 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8323 (tt0) REVERT: C 87 ARG cc_start: 0.7385 (OUTLIER) cc_final: 0.7137 (mtm180) REVERT: B 947 LYS cc_start: 0.8863 (mmtp) cc_final: 0.8557 (mmtt) REVERT: B 1845 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.7575 (ttmt) REVERT: B 1864 THR cc_start: 0.7433 (m) cc_final: 0.6860 (p) REVERT: E 76 ARG cc_start: 0.7773 (OUTLIER) cc_final: 0.6950 (mtp-110) REVERT: E 82 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8175 (tt0) REVERT: G 1844 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.8045 (mmt180) REVERT: G 1864 THR cc_start: 0.7351 (m) cc_final: 0.6812 (p) REVERT: H 76 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.7425 (mtm-85) REVERT: I 32 LYS cc_start: 0.8696 (mmtt) cc_final: 0.8469 (mmmt) outliers start: 29 outliers final: 12 residues processed: 143 average time/residue: 0.6712 time to fit residues: 102.9108 Evaluate side-chains 140 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1803 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain D residue 108 ARG Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1803 SER Chi-restraints excluded: chain B residue 1845 LYS Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 76 ARG Chi-restraints excluded: chain E residue 82 GLU Chi-restraints excluded: chain G residue 963 VAL Chi-restraints excluded: chain G residue 1844 ARG Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 19 ARG Chi-restraints excluded: chain H residue 76 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 145 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 63 optimal weight: 0.6980 chunk 108 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 134 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1849 ASN D 27 GLN B1849 ASN F 27 GLN I 27 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.168684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.112365 restraints weight = 12507.793| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.03 r_work: 0.3032 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 11289 Z= 0.199 Angle : 0.521 6.280 15420 Z= 0.271 Chirality : 0.042 0.221 1779 Planarity : 0.004 0.039 2016 Dihedral : 4.453 31.700 1737 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 3.52 % Allowed : 10.12 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.74 % 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: 3.32 (0.22), residues: 1488 helix: 4.60 (0.19), residues: 462 sheet: 1.16 (0.23), residues: 432 loop : 1.13 (0.28), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 108 TYR 0.017 0.002 TYR D 49 PHE 0.015 0.002 PHE G1800 TRP 0.020 0.002 TRP E 47 HIS 0.003 0.001 HIS C 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.20 (11274) covalent geometry : angle 0.51084 / 0.27 (15384) SS BOND : bond 0.00747 / 0.55 ( 9) SS BOND : angle 1.50119 / 1.07 ( 18) hydrogen bonds : bond 0.04563 / 3.15 ( 703) hydrogen bonds : angle 3.87099 / 2.80 ( 1992) link_NAG-ASN : bond 0.00384 / 0.23 ( 6) link_NAG-ASN : angle 2.75722 / 2.19 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 126 time to evaluate : 0.449 Fit side-chains revert: symmetry clash REVERT: C 82 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8360 (tt0) REVERT: C 87 ARG cc_start: 0.7400 (OUTLIER) cc_final: 0.7121 (mtm180) REVERT: B 1845 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.7629 (ttmt) REVERT: B 1864 THR cc_start: 0.7503 (m) cc_final: 0.6928 (p) REVERT: E 76 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.7447 (mtm-85) REVERT: E 87 ARG cc_start: 0.7457 (OUTLIER) cc_final: 0.7234 (mtm180) REVERT: G 1844 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.8123 (mmt180) REVERT: G 1864 THR cc_start: 0.7251 (m) cc_final: 0.6750 (p) REVERT: H 76 ARG cc_start: 0.7725 (OUTLIER) cc_final: 0.7389 (mtm-85) REVERT: H 87 ARG cc_start: 0.7483 (OUTLIER) cc_final: 0.7160 (mtm180) REVERT: I 32 LYS cc_start: 0.8739 (mmtt) cc_final: 0.8520 (mmmt) outliers start: 32 outliers final: 13 residues processed: 143 average time/residue: 0.6609 time to fit residues: 101.6001 Evaluate side-chains 141 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1803 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain D residue 108 ARG Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1803 SER Chi-restraints excluded: chain B residue 1845 LYS Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 76 ARG Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain G residue 963 VAL Chi-restraints excluded: chain G residue 1844 ARG Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 19 ARG Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain H residue 87 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 39 optimal weight: 0.4980 chunk 17 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 89 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 120 optimal weight: 2.9990 chunk 145 optimal weight: 0.5980 chunk 107 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1849 ASN A1867 GLN D 27 GLN B1849 ASN F 27 GLN G1849 ASN I 27 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.170150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.113911 restraints weight = 12458.405| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.05 r_work: 0.3057 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11289 Z= 0.138 Angle : 0.496 7.514 15420 Z= 0.254 Chirality : 0.044 0.646 1779 Planarity : 0.003 0.032 2016 Dihedral : 4.735 42.899 1737 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 2.64 % Allowed : 11.55 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.74 % 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: 3.46 (0.22), residues: 1488 helix: 4.72 (0.19), residues: 462 sheet: 1.33 (0.23), residues: 423 loop : 1.13 (0.28), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 108 TYR 0.015 0.001 TYR D 49 PHE 0.024 0.001 PHE B1800 TRP 0.016 0.002 TRP E 47 HIS 0.003 0.001 HIS C 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (11274) covalent geometry : angle 0.47283 / 0.25 (15384) SS BOND : bond 0.00492 / 0.37 ( 9) SS BOND : angle 0.93125 / 0.67 ( 18) hydrogen bonds : bond 0.04168 / 2.88 ( 703) hydrogen bonds : angle 3.71219 / 2.70 ( 1992) link_NAG-ASN : bond 0.01143 / 0.58 ( 6) link_NAG-ASN : angle 4.32522 / 3.60 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 0.479 Fit side-chains revert: symmetry clash REVERT: C 87 ARG cc_start: 0.7363 (OUTLIER) cc_final: 0.7075 (mtm180) REVERT: B 1864 THR cc_start: 0.7459 (m) cc_final: 0.6869 (p) REVERT: E 76 ARG cc_start: 0.7763 (OUTLIER) cc_final: 0.6957 (mtp-110) REVERT: E 87 ARG cc_start: 0.7439 (OUTLIER) cc_final: 0.7092 (mtm180) REVERT: G 1844 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.8076 (mmt180) REVERT: H 76 ARG cc_start: 0.7700 (OUTLIER) cc_final: 0.7347 (mtm-85) REVERT: H 87 ARG cc_start: 0.7464 (OUTLIER) cc_final: 0.7098 (mtm180) REVERT: I 32 LYS cc_start: 0.8721 (mmtt) cc_final: 0.8469 (mmmt) outliers start: 24 outliers final: 11 residues processed: 136 average time/residue: 0.6711 time to fit residues: 97.8746 Evaluate side-chains 136 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1803 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain D residue 108 ARG Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1803 SER Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 76 ARG Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain G residue 963 VAL Chi-restraints excluded: chain G residue 1844 ARG Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain H residue 87 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 22 optimal weight: 0.7980 chunk 127 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 35 optimal weight: 20.0000 chunk 139 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 72 optimal weight: 0.2980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1849 ASN D 27 GLN B1849 ASN F 27 GLN I 27 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.169464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.113048 restraints weight = 12415.709| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.05 r_work: 0.3044 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11289 Z= 0.151 Angle : 0.502 6.875 15420 Z= 0.259 Chirality : 0.046 0.614 1779 Planarity : 0.004 0.033 2016 Dihedral : 5.266 51.450 1737 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.53 % Allowed : 11.66 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.74 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 3.43 (0.22), residues: 1488 helix: 4.69 (0.19), residues: 462 sheet: 1.33 (0.23), residues: 423 loop : 1.10 (0.28), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 108 TYR 0.015 0.002 TYR D 49 PHE 0.022 0.001 PHE A1800 TRP 0.017 0.002 TRP E 47 HIS 0.003 0.001 HIS C 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (11274) covalent geometry : angle 0.48565 / 0.26 (15384) SS BOND : bond 0.00560 / 0.41 ( 9) SS BOND : angle 1.15868 / 0.85 ( 18) hydrogen bonds : bond 0.04200 / 2.90 ( 703) hydrogen bonds : angle 3.71143 / 2.70 ( 1992) link_NAG-ASN : bond 0.01729 / 1.06 ( 6) link_NAG-ASN : angle 3.56489 / 3.07 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 0.443 Fit side-chains revert: symmetry clash REVERT: C 87 ARG cc_start: 0.7379 (OUTLIER) cc_final: 0.7093 (mtm180) REVERT: B 1864 THR cc_start: 0.7442 (m) cc_final: 0.6854 (p) REVERT: E 76 ARG cc_start: 0.7755 (OUTLIER) cc_final: 0.6959 (mtp-110) REVERT: E 87 ARG cc_start: 0.7426 (OUTLIER) cc_final: 0.7074 (mtm180) REVERT: G 1844 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.8081 (mmt180) REVERT: H 76 ARG cc_start: 0.7692 (OUTLIER) cc_final: 0.7340 (mtm-85) REVERT: H 87 ARG cc_start: 0.7440 (OUTLIER) cc_final: 0.7114 (mtm180) REVERT: I 32 LYS cc_start: 0.8720 (mmtt) cc_final: 0.8474 (mmmt) outliers start: 23 outliers final: 11 residues processed: 134 average time/residue: 0.6821 time to fit residues: 98.0957 Evaluate side-chains 133 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1803 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain D residue 108 ARG Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 76 ARG Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain G residue 963 VAL Chi-restraints excluded: chain G residue 1844 ARG Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain H residue 87 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 74 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 144 optimal weight: 0.8980 chunk 101 optimal weight: 0.5980 chunk 50 optimal weight: 0.8980 chunk 78 optimal weight: 0.8980 chunk 106 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 23 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1849 ASN D 27 GLN B1849 ASN F 27 GLN I 27 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.169692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.113698 restraints weight = 12508.300| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.03 r_work: 0.3057 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 11289 Z= 0.149 Angle : 0.482 7.029 15420 Z= 0.249 Chirality : 0.043 0.478 1779 Planarity : 0.003 0.031 2016 Dihedral : 4.815 46.738 1737 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.87 % Allowed : 12.43 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.74 % 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: 3.50 (0.22), residues: 1488 helix: 5.08 (0.17), residues: 444 sheet: 1.14 (0.23), residues: 432 loop : 1.18 (0.28), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 108 TYR 0.016 0.002 TYR D 49 PHE 0.011 0.001 PHE G1800 TRP 0.017 0.002 TRP E 47 HIS 0.003 0.001 HIS C 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (11274) covalent geometry : angle 0.47504 / 0.25 (15384) SS BOND : bond 0.00560 / 0.41 ( 9) SS BOND : angle 1.19021 / 0.89 ( 18) hydrogen bonds : bond 0.04206 / 2.91 ( 703) hydrogen bonds : angle 3.69859 / 2.69 ( 1992) link_NAG-ASN : bond 0.00170 / 0.10 ( 6) link_NAG-ASN : angle 2.23388 / 1.94 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 0.484 Fit side-chains revert: symmetry clash REVERT: C 87 ARG cc_start: 0.7405 (OUTLIER) cc_final: 0.7118 (mtm180) REVERT: B 1864 THR cc_start: 0.7464 (m) cc_final: 0.6872 (p) REVERT: E 76 ARG cc_start: 0.7785 (OUTLIER) cc_final: 0.7018 (mtp-110) REVERT: E 87 ARG cc_start: 0.7442 (OUTLIER) cc_final: 0.7084 (mtm180) REVERT: G 1844 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.8088 (mmt180) REVERT: H 76 ARG cc_start: 0.7752 (OUTLIER) cc_final: 0.7395 (mtm-85) REVERT: H 87 ARG cc_start: 0.7480 (OUTLIER) cc_final: 0.7151 (mtm180) REVERT: I 32 LYS cc_start: 0.8736 (mmtt) cc_final: 0.8490 (mmmt) outliers start: 17 outliers final: 10 residues processed: 133 average time/residue: 0.6506 time to fit residues: 92.6925 Evaluate side-chains 132 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 938 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1803 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain D residue 108 ARG Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 76 ARG Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain G residue 963 VAL Chi-restraints excluded: chain G residue 1844 ARG Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain H residue 87 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 106 optimal weight: 0.9980 chunk 121 optimal weight: 0.5980 chunk 53 optimal weight: 0.5980 chunk 118 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 89 optimal weight: 0.6980 chunk 35 optimal weight: 0.4980 chunk 73 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 129 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 HIS A1849 ASN D 27 GLN B1849 ASN F 27 GLN I 27 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.169909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.113642 restraints weight = 12590.597| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.07 r_work: 0.3059 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 11289 Z= 0.133 Angle : 0.458 5.359 15420 Z= 0.239 Chirality : 0.040 0.241 1779 Planarity : 0.003 0.031 2016 Dihedral : 4.650 45.714 1737 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.87 % Allowed : 12.43 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.74 % 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: 3.45 (0.22), residues: 1488 helix: 4.74 (0.19), residues: 462 sheet: 1.28 (0.23), residues: 432 loop : 1.13 (0.29), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 108 TYR 0.016 0.001 TYR D 49 PHE 0.011 0.001 PHE G1802 TRP 0.016 0.002 TRP E 47 HIS 0.003 0.001 HIS C 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (11274) covalent geometry : angle 0.45374 / 0.24 (15384) SS BOND : bond 0.00506 / 0.37 ( 9) SS BOND : angle 1.05603 / 0.78 ( 18) hydrogen bonds : bond 0.04052 / 2.80 ( 703) hydrogen bonds : angle 3.62887 / 2.64 ( 1992) link_NAG-ASN : bond 0.00148 / 0.09 ( 6) link_NAG-ASN : angle 1.49628 / 1.24 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5915.43 seconds wall clock time: 101 minutes 10.41 seconds (6070.41 seconds total)