Starting phenix.real_space_refine on Sat Jul 4 17:12:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cg9_45578/07_2026/9cg9_45578.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cg9_45578/07_2026/9cg9_45578.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9cg9_45578/07_2026/9cg9_45578.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cg9_45578/07_2026/9cg9_45578.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cg9_45578/07_2026/9cg9_45578.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cg9_45578/07_2026/9cg9_45578.map" } resolution = 2.94 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= 0.009 sd= 0.043 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 379 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians P 308 5.49 5 S 14 5.16 5 C 7021 2.51 5 N 2376 2.21 5 O 2987 1.98 5 H 10013 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 81 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22719 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 1629 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 1307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 1307 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 1720 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 1504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 1504 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 1621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 1621 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "F" Number of atoms: 1307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 1307 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "G" Number of atoms: 1707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 1707 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 1504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 1504 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "I" Number of atoms: 4901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 4901 Classifications: {'DNA': 154} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 153} Chain: "J" Number of atoms: 4871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 4871 Classifications: {'DNA': 154} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 153} Chain: "K" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 648 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 1, 'TRANS': 60} Chain breaks: 1 Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 162 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 6, 'HIS:plan': 2, 'ASN:plan1': 1, 'PHE:plan': 1, 'ASP:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 76 Time building chain proxies: 2.92, per 1000 atoms: 0.13 Number of scatterers: 22719 At special positions: 0 Unit cell: (85.902, 140.112, 131.772, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 14 16.00 P 308 15.00 O 2987 8.00 N 2376 7.00 C 7021 6.00 H 10013 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.46 Conformation dependent library (CDL) restraints added in 310.6 milliseconds 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1552 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 10 sheets defined 73.9% alpha, 2.7% beta 106 base pairs and 278 stacking pairs defined. Time for finding SS restraints: 4.04 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.686A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N MET A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.558A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.608A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.548A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.450A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.623A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 125 removed outlier: 3.671A pdb=" N HIS D 109 " --> pdb=" O GLU D 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 removed outlier: 4.059A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.616A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N MET E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP E 106 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA E 114 " --> pdb=" O ALA E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.633A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.542A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.547A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 removed outlier: 3.536A pdb=" N ARG G 20 " --> pdb=" O THR G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.394A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.546A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 123 removed outlier: 3.636A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER H 123 " --> pdb=" O THR H 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 13 through 28 Processing helix chain 'K' and resid 36 through 49 removed outlier: 4.194A pdb=" N PHE K 40 " --> pdb=" O ASN K 36 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N LYS K 42 " --> pdb=" O SER K 38 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LYS K 43 " --> pdb=" O GLU K 39 " (cutoff:3.500A) Processing helix chain 'K' and resid 52 through 74 removed outlier: 3.680A pdb=" N ARG K 72 " --> pdb=" O ALA K 68 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.754A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.496A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.020A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.485A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.783A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.000A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 433 hydrogen bonds defined for protein. 1272 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 263 hydrogen bonds 526 hydrogen bond angles 0 basepair planarities 106 basepair parallelities 278 stacking parallelities Total time for adding SS restraints: 4.82 Time building geometry restraints manager: 2.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 10011 1.13 - 1.30: 1411 1.30 - 1.48: 6695 1.48 - 1.65: 5430 1.65 - 1.82: 26 Bond restraints: 23573 Sorted by residual: bond pdb=" N SER E 57 " pdb=" H SER E 57 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N4 DC I 64 " pdb=" H42 DC I 64 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" CD2 HIS E 39 " pdb=" HD2 HIS E 39 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N ARG A 131 " pdb=" H ARG A 131 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N ALA G 47 " pdb=" H ALA G 47 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 ... (remaining 23568 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.99: 42095 5.99 - 11.99: 565 11.99 - 17.98: 14 17.98 - 23.97: 3 23.97 - 29.97: 3 Bond angle restraints: 42680 Sorted by residual: angle pdb=" C6 DA I 46 " pdb=" N6 DA I 46 " pdb=" H61 DA I 46 " ideal model delta sigma weight residual 120.00 90.03 29.97 3.00e+00 1.11e-01 9.98e+01 angle pdb=" C6 DA I 83 " pdb=" N6 DA I 83 " pdb=" H61 DA I 83 " ideal model delta sigma weight residual 120.00 92.87 27.13 3.00e+00 1.11e-01 8.18e+01 angle pdb=" C6 DA I 13 " pdb=" N6 DA I 13 " pdb=" H61 DA I 13 " ideal model delta sigma weight residual 120.00 93.27 26.73 3.00e+00 1.11e-01 7.94e+01 angle pdb=" C6 DA I 11 " pdb=" N6 DA I 11 " pdb=" H61 DA I 11 " ideal model delta sigma weight residual 120.00 97.26 22.74 3.00e+00 1.11e-01 5.75e+01 angle pdb=" O3' DT J 31 " pdb=" C3' DT J 31 " pdb=" C2' DT J 31 " ideal model delta sigma weight residual 109.40 127.95 -18.55 2.50e+00 1.60e-01 5.50e+01 ... (remaining 42675 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.11: 7910 32.11 - 64.22: 1842 64.22 - 96.32: 75 96.32 - 128.43: 2 128.43 - 160.54: 2 Dihedral angle restraints: 9831 sinusoidal: 7146 harmonic: 2685 Sorted by residual: dihedral pdb=" CA LEU C 116 " pdb=" C LEU C 116 " pdb=" N PRO C 117 " pdb=" CA PRO C 117 " ideal model delta harmonic sigma weight residual -180.00 -153.24 -26.76 0 5.00e+00 4.00e-02 2.86e+01 dihedral pdb=" CA ARG E 40 " pdb=" C ARG E 40 " pdb=" N TYR E 41 " pdb=" CA TYR E 41 " ideal model delta harmonic sigma weight residual 180.00 157.53 22.47 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA ARG A 40 " pdb=" C ARG A 40 " pdb=" N TYR A 41 " pdb=" CA TYR A 41 " ideal model delta harmonic sigma weight residual 180.00 157.97 22.03 0 5.00e+00 4.00e-02 1.94e+01 ... (remaining 9828 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.285: 2238 0.285 - 0.569: 5 0.569 - 0.854: 0 0.854 - 1.138: 0 1.138 - 1.423: 1 Chirality restraints: 2244 Sorted by residual: chirality pdb=" C3' DT J 31 " pdb=" C4' DT J 31 " pdb=" O3' DT J 31 " pdb=" C2' DT J 31 " both_signs ideal model delta sigma weight residual False -2.73 -1.31 -1.42 2.00e-01 2.50e+01 5.06e+01 chirality pdb=" C3' DC I 95 " pdb=" C4' DC I 95 " pdb=" O3' DC I 95 " pdb=" C2' DC I 95 " both_signs ideal model delta sigma weight residual False -2.73 -2.32 -0.41 2.00e-01 2.50e+01 4.19e+00 chirality pdb=" CA ARG G 99 " pdb=" N ARG G 99 " pdb=" C ARG G 99 " pdb=" CB ARG G 99 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.89e+00 ... (remaining 2241 not shown) Planarity restraints: 2453 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 57 " -0.126 2.00e-02 2.50e+03 5.13e-02 7.91e+01 pdb=" CG TYR C 57 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR C 57 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 TYR C 57 " 0.022 2.00e-02 2.50e+03 pdb=" CE1 TYR C 57 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR C 57 " 0.016 2.00e-02 2.50e+03 pdb=" CZ TYR C 57 " -0.017 2.00e-02 2.50e+03 pdb=" OH TYR C 57 " -0.088 2.00e-02 2.50e+03 pdb=" HD1 TYR C 57 " 0.058 2.00e-02 2.50e+03 pdb=" HD2 TYR C 57 " 0.031 2.00e-02 2.50e+03 pdb=" HE1 TYR C 57 " 0.010 2.00e-02 2.50e+03 pdb=" HE2 TYR C 57 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP K 48 " 0.120 2.00e-02 2.50e+03 4.17e-02 6.94e+01 pdb=" CG TRP K 48 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TRP K 48 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP K 48 " -0.041 2.00e-02 2.50e+03 pdb=" NE1 TRP K 48 " -0.026 2.00e-02 2.50e+03 pdb=" CE2 TRP K 48 " -0.027 2.00e-02 2.50e+03 pdb=" CE3 TRP K 48 " -0.031 2.00e-02 2.50e+03 pdb=" CZ2 TRP K 48 " 0.015 2.00e-02 2.50e+03 pdb=" CZ3 TRP K 48 " -0.013 2.00e-02 2.50e+03 pdb=" CH2 TRP K 48 " 0.023 2.00e-02 2.50e+03 pdb=" HD1 TRP K 48 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 TRP K 48 " -0.037 2.00e-02 2.50e+03 pdb=" HE3 TRP K 48 " -0.036 2.00e-02 2.50e+03 pdb=" HZ2 TRP K 48 " 0.041 2.00e-02 2.50e+03 pdb=" HZ3 TRP K 48 " -0.027 2.00e-02 2.50e+03 pdb=" HH2 TRP K 48 " 0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 121 " -0.118 2.00e-02 2.50e+03 4.68e-02 6.58e+01 pdb=" CG TYR D 121 " 0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR D 121 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR D 121 " 0.023 2.00e-02 2.50e+03 pdb=" CE1 TYR D 121 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR D 121 " 0.012 2.00e-02 2.50e+03 pdb=" CZ TYR D 121 " -0.011 2.00e-02 2.50e+03 pdb=" OH TYR D 121 " -0.076 2.00e-02 2.50e+03 pdb=" HD1 TYR D 121 " 0.052 2.00e-02 2.50e+03 pdb=" HD2 TYR D 121 " 0.041 2.00e-02 2.50e+03 pdb=" HE1 TYR D 121 " 0.009 2.00e-02 2.50e+03 pdb=" HE2 TYR D 121 " 0.020 2.00e-02 2.50e+03 ... (remaining 2450 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 1125 2.19 - 2.79: 35207 2.79 - 3.39: 58402 3.39 - 4.00: 84592 4.00 - 4.60: 122283 Nonbonded interactions: 301609 Sorted by model distance: nonbonded pdb="H2'' DC J 54 " pdb=" H5' DG J 55 " model vdw 1.586 2.440 nonbonded pdb=" H ARG F 23 " pdb=" H ASP F 24 " model vdw 1.599 2.100 nonbonded pdb=" H THR C 16 " pdb=" HG1 THR C 16 " model vdw 1.621 2.100 nonbonded pdb=" HG1 THR H 52 " pdb=" H GLY H 53 " model vdw 1.631 2.100 nonbonded pdb="H2'' DT I 55 " pdb=" H5' DC I 56 " model vdw 1.639 2.440 ... (remaining 301604 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 37 through 132 or (resid 133 through 134 and (name N or na \ me CA or name C or name O or name CB or name H or name HA )))) selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = (chain 'C' and (resid 10 through 12 or (resid 13 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 14 through 117 or (resid \ 118 and (name N or name CA or name C or name O or name CB or name H or name HA \ )))) selection = (chain 'G' and ((resid 10 through 11 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 12 through 118)) } ncs_group { reference = chain 'D' selection = chain 'H' } 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: 1.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.120 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.960 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 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:5.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 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 : 0.009 0.071 13560 Z= 0.625 Angle : 1.366 18.548 19651 Z= 0.932 Chirality : 0.080 1.423 2244 Planarity : 0.012 0.109 1424 Dihedral : 27.880 160.541 5797 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 0.47 % Allowed : 1.40 % Favored : 98.14 % 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: -0.53 (0.25), residues: 804 helix: -0.22 (0.19), residues: 585 sheet: None (None), residues: 0 loop : -0.27 (0.34), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 35 TYR 0.102 0.017 TYR C 57 PHE 0.043 0.009 PHE D 70 TRP 0.081 0.034 TRP K 48 HIS 0.012 0.003 HIS G 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00945 / 0.63 (13560) covalent geometry : angle 1.36625 / 0.93 (19651) hydrogen bonds : bond 0.20470 / 14.17 ( 696) hydrogen bonds : angle 6.40671 / 4.61 ( 1798) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 37 is missing expected H atoms. Skipping. Residue ALA 110 is missing expected H atoms. Skipping. Residue THR 10 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue ALA 110 is missing expected H atoms. Skipping. Residue THR 10 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 11 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue VAL 35 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LYS 49 is missing expected H atoms. Skipping. Residue THR 50 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue MET 62 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue TYR 70 is missing expected H atoms. Skipping. Evaluate side-chains 230 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 227 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 68 ASP cc_start: 0.8757 (t0) cc_final: 0.8399 (t0) REVERT: F 93 GLN cc_start: 0.8653 (mt0) cc_final: 0.8404 (mt0) REVERT: H 62 MET cc_start: 0.9231 (mmm) cc_final: 0.8995 (mmm) outliers start: 3 outliers final: 1 residues processed: 228 average time/residue: 1.5068 time to fit residues: 363.9879 Evaluate side-chains 155 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 154 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 51 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 7.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS B 93 GLN C 73 ASN G 112 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.076926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.057782 restraints weight = 84354.254| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 1.26 r_work: 0.2864 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13560 Z= 0.192 Angle : 0.761 8.130 19651 Z= 0.464 Chirality : 0.045 0.201 2244 Planarity : 0.006 0.048 1424 Dihedral : 31.211 163.931 4278 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 2.17 % Allowed : 14.42 % Favored : 83.41 % 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: 1.22 (0.28), residues: 804 helix: 1.32 (0.21), residues: 582 sheet: None (None), residues: 0 loop : -0.41 (0.34), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 63 TYR 0.015 0.002 TYR B 51 PHE 0.014 0.001 PHE E 67 TRP 0.010 0.003 TRP K 48 HIS 0.007 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.19 (13560) covalent geometry : angle 0.76109 / 0.46 (19651) hydrogen bonds : bond 0.06970 / 4.86 ( 696) hydrogen bonds : angle 3.63765 / 2.58 ( 1798) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 37 is missing expected H atoms. Skipping. Residue ALA 110 is missing expected H atoms. Skipping. Residue THR 10 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue ALA 110 is missing expected H atoms. Skipping. Residue THR 10 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 11 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue VAL 35 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LYS 49 is missing expected H atoms. Skipping. Residue THR 50 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue MET 62 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue TYR 70 is missing expected H atoms. Skipping. Evaluate side-chains 173 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 159 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.9304 (OUTLIER) cc_final: 0.8775 (mtmm) REVERT: C 64 GLU cc_start: 0.8527 (tm-30) cc_final: 0.8293 (tm-30) REVERT: D 68 ASP cc_start: 0.9162 (t0) cc_final: 0.8783 (t0) REVERT: E 125 GLN cc_start: 0.8783 (mt0) cc_final: 0.8298 (mp10) REVERT: F 93 GLN cc_start: 0.8808 (mt0) cc_final: 0.8594 (mt0) REVERT: G 104 GLN cc_start: 0.8939 (mm-40) cc_final: 0.8701 (mm-40) REVERT: H 85 LYS cc_start: 0.9363 (OUTLIER) cc_final: 0.9147 (mtmm) outliers start: 14 outliers final: 6 residues processed: 165 average time/residue: 1.3367 time to fit residues: 235.5663 Evaluate side-chains 152 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 144 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 85 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 98 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 86 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 chunk 89 optimal weight: 9.9990 chunk 100 optimal weight: 9.9990 chunk 12 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN E 68 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.075210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.055923 restraints weight = 84379.122| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 1.32 r_work: 0.2829 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 13560 Z= 0.242 Angle : 0.694 8.900 19651 Z= 0.426 Chirality : 0.043 0.193 2244 Planarity : 0.005 0.067 1424 Dihedral : 31.313 165.973 4276 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.64 % Allowed : 14.42 % Favored : 82.95 % 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: 1.46 (0.28), residues: 804 helix: 1.62 (0.21), residues: 584 sheet: None (None), residues: 0 loop : -0.76 (0.33), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 33 TYR 0.012 0.001 TYR B 51 PHE 0.009 0.001 PHE E 67 TRP 0.011 0.004 TRP K 48 HIS 0.005 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.24 (13560) covalent geometry : angle 0.69386 / 0.43 (19651) hydrogen bonds : bond 0.05952 / 4.16 ( 696) hydrogen bonds : angle 3.45344 / 2.46 ( 1798) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 37 is missing expected H atoms. Skipping. Residue ALA 110 is missing expected H atoms. Skipping. Residue THR 10 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue ALA 110 is missing expected H atoms. Skipping. Residue THR 10 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 11 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue VAL 35 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LYS 49 is missing expected H atoms. Skipping. Residue THR 50 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue MET 62 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue TYR 70 is missing expected H atoms. Skipping. Evaluate side-chains 164 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 147 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8175 (mt-10) REVERT: C 64 GLU cc_start: 0.8659 (tm-30) cc_final: 0.8311 (tm-30) REVERT: C 73 ASN cc_start: 0.8785 (t0) cc_final: 0.8571 (t0) REVERT: D 68 ASP cc_start: 0.9200 (t0) cc_final: 0.8824 (t0) REVERT: F 93 GLN cc_start: 0.8888 (mt0) cc_final: 0.8676 (mt0) REVERT: H 85 LYS cc_start: 0.9381 (OUTLIER) cc_final: 0.9168 (mtmm) outliers start: 17 outliers final: 10 residues processed: 154 average time/residue: 1.2974 time to fit residues: 213.8690 Evaluate side-chains 150 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 138 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 85 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 2.9990 chunk 71 optimal weight: 20.0000 chunk 85 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 13 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 chunk 38 optimal weight: 0.7980 chunk 77 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN G 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.075779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.056594 restraints weight = 84037.838| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 1.26 r_work: 0.2847 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13560 Z= 0.177 Angle : 0.631 8.475 19651 Z= 0.395 Chirality : 0.040 0.201 2244 Planarity : 0.005 0.081 1424 Dihedral : 31.331 165.729 4276 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 1.55 % Allowed : 15.66 % Favored : 82.79 % 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: 1.82 (0.29), residues: 804 helix: 1.88 (0.22), residues: 590 sheet: None (None), residues: 0 loop : -0.69 (0.34), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 33 TYR 0.012 0.001 TYR B 51 PHE 0.009 0.001 PHE E 67 TRP 0.009 0.003 TRP K 48 HIS 0.006 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.18 (13560) covalent geometry : angle 0.63080 / 0.40 (19651) hydrogen bonds : bond 0.05175 / 3.61 ( 696) hydrogen bonds : angle 3.26291 / 2.31 ( 1798) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 37 is missing expected H atoms. Skipping. Residue ALA 110 is missing expected H atoms. Skipping. Residue THR 10 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue ALA 110 is missing expected H atoms. Skipping. Residue THR 10 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 11 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue VAL 35 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LYS 49 is missing expected H atoms. Skipping. Residue THR 50 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue MET 62 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue TYR 70 is missing expected H atoms. Skipping. Evaluate side-chains 157 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 147 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 64 GLU cc_start: 0.8697 (tm-30) cc_final: 0.8335 (tm-30) REVERT: D 68 ASP cc_start: 0.9201 (t0) cc_final: 0.8834 (t0) REVERT: E 125 GLN cc_start: 0.8771 (mt0) cc_final: 0.8239 (mp10) REVERT: H 47 GLN cc_start: 0.8674 (OUTLIER) cc_final: 0.8305 (mt0) REVERT: H 85 LYS cc_start: 0.9367 (OUTLIER) cc_final: 0.9144 (mtmm) outliers start: 10 outliers final: 7 residues processed: 150 average time/residue: 1.1689 time to fit residues: 188.4609 Evaluate side-chains 145 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 136 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 85 LYS Chi-restraints excluded: chain K residue 21 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 77 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 40 optimal weight: 0.0770 chunk 69 optimal weight: 3.9990 chunk 82 optimal weight: 10.0000 chunk 103 optimal weight: 20.0000 chunk 60 optimal weight: 0.0870 chunk 75 optimal weight: 9.9990 chunk 104 optimal weight: 9.9990 chunk 61 optimal weight: 5.9990 chunk 90 optimal weight: 10.0000 overall best weight: 4.0322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 93 GLN G 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.073900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.054586 restraints weight = 83216.250| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 1.32 r_work: 0.2793 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 13560 Z= 0.290 Angle : 0.679 8.354 19651 Z= 0.413 Chirality : 0.042 0.186 2244 Planarity : 0.005 0.055 1424 Dihedral : 31.416 165.357 4276 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.48 % Allowed : 16.59 % Favored : 80.93 % 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: 1.72 (0.29), residues: 804 helix: 1.87 (0.21), residues: 589 sheet: None (None), residues: 0 loop : -0.90 (0.35), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 42 TYR 0.013 0.002 TYR K 15 PHE 0.011 0.001 PHE E 67 TRP 0.010 0.004 TRP K 48 HIS 0.005 0.002 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00578 / 0.29 (13560) covalent geometry : angle 0.67914 / 0.41 (19651) hydrogen bonds : bond 0.05719 / 3.95 ( 696) hydrogen bonds : angle 3.32425 / 2.38 ( 1798) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 37 is missing expected H atoms. Skipping. Residue ALA 110 is missing expected H atoms. Skipping. Residue THR 10 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue ALA 110 is missing expected H atoms. Skipping. Residue THR 10 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 11 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue VAL 35 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LYS 49 is missing expected H atoms. Skipping. Residue THR 50 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue MET 62 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue TYR 70 is missing expected H atoms. Skipping. Evaluate side-chains 151 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8247 (mt-10) REVERT: C 64 GLU cc_start: 0.8852 (tm-30) cc_final: 0.8465 (tm-30) REVERT: D 34 LYS cc_start: 0.8586 (mmmt) cc_final: 0.8374 (mmmt) REVERT: D 68 ASP cc_start: 0.9228 (t0) cc_final: 0.8816 (t0) REVERT: D 93 GLU cc_start: 0.8857 (mp0) cc_final: 0.8606 (mp0) REVERT: H 85 LYS cc_start: 0.9375 (OUTLIER) cc_final: 0.9151 (mtmm) outliers start: 16 outliers final: 12 residues processed: 145 average time/residue: 1.2400 time to fit residues: 192.4513 Evaluate side-chains 142 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 85 LYS Chi-restraints excluded: chain K residue 21 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 68 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 95 optimal weight: 9.9990 chunk 62 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 73 optimal weight: 9.9990 chunk 86 optimal weight: 9.9990 chunk 32 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.074808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.055303 restraints weight = 83401.052| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 1.27 r_work: 0.2820 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13560 Z= 0.184 Angle : 0.618 8.070 19651 Z= 0.386 Chirality : 0.039 0.192 2244 Planarity : 0.005 0.078 1424 Dihedral : 31.416 165.265 4276 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.55 % Allowed : 19.07 % Favored : 79.38 % 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: 1.91 (0.29), residues: 804 helix: 1.99 (0.22), residues: 591 sheet: None (None), residues: 0 loop : -0.82 (0.35), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 33 TYR 0.011 0.001 TYR B 51 PHE 0.011 0.001 PHE E 67 TRP 0.007 0.003 TRP K 48 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.18 (13560) covalent geometry : angle 0.61827 / 0.39 (19651) hydrogen bonds : bond 0.04979 / 3.46 ( 696) hydrogen bonds : angle 3.17157 / 2.26 ( 1798) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 37 is missing expected H atoms. Skipping. Residue ALA 110 is missing expected H atoms. Skipping. Residue THR 10 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue ALA 110 is missing expected H atoms. Skipping. Residue THR 10 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 11 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue VAL 35 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LYS 49 is missing expected H atoms. Skipping. Residue THR 50 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue MET 62 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue TYR 70 is missing expected H atoms. Skipping. Evaluate side-chains 148 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 138 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8712 (mt-10) cc_final: 0.8447 (mt-10) REVERT: C 64 GLU cc_start: 0.8824 (tm-30) cc_final: 0.8434 (tm-30) REVERT: C 90 ASP cc_start: 0.8742 (t0) cc_final: 0.8527 (t0) REVERT: D 34 LYS cc_start: 0.8607 (mmmt) cc_final: 0.8363 (mmmt) REVERT: D 68 ASP cc_start: 0.9198 (t0) cc_final: 0.8809 (t0) REVERT: D 93 GLU cc_start: 0.8808 (mp0) cc_final: 0.8591 (mp0) REVERT: E 125 GLN cc_start: 0.8755 (OUTLIER) cc_final: 0.8269 (mp10) REVERT: H 42 TYR cc_start: 0.8634 (t80) cc_final: 0.8290 (t80) REVERT: H 47 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.8313 (mt0) REVERT: H 85 LYS cc_start: 0.9376 (OUTLIER) cc_final: 0.9149 (mtmm) outliers start: 10 outliers final: 7 residues processed: 141 average time/residue: 1.2603 time to fit residues: 190.6021 Evaluate side-chains 144 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 134 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 85 LYS Chi-restraints excluded: chain K residue 21 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 19 optimal weight: 3.9990 chunk 103 optimal weight: 8.9990 chunk 27 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 chunk 67 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 chunk 69 optimal weight: 2.9990 chunk 92 optimal weight: 9.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 104 GLN G 112 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.074888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.055650 restraints weight = 83578.617| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 1.26 r_work: 0.2828 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13560 Z= 0.193 Angle : 0.613 10.911 19651 Z= 0.382 Chirality : 0.039 0.192 2244 Planarity : 0.005 0.039 1424 Dihedral : 31.411 165.020 4276 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.40 % Allowed : 19.07 % Favored : 79.53 % 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: 2.04 (0.29), residues: 804 helix: 2.10 (0.22), residues: 591 sheet: None (None), residues: 0 loop : -0.81 (0.35), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 33 TYR 0.011 0.001 TYR K 15 PHE 0.009 0.001 PHE E 67 TRP 0.004 0.002 TRP K 48 HIS 0.003 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.19 (13560) covalent geometry : angle 0.61327 / 0.38 (19651) hydrogen bonds : bond 0.04760 / 3.31 ( 696) hydrogen bonds : angle 3.11124 / 2.21 ( 1798) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 37 is missing expected H atoms. Skipping. Residue ALA 110 is missing expected H atoms. Skipping. Residue THR 10 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue ALA 110 is missing expected H atoms. Skipping. Residue THR 10 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 11 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue VAL 35 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LYS 49 is missing expected H atoms. Skipping. Residue THR 50 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue MET 62 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue TYR 70 is missing expected H atoms. Skipping. Evaluate side-chains 148 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 139 time to evaluate : 0.338 Fit side-chains REVERT: A 50 GLU cc_start: 0.8724 (mt-10) cc_final: 0.8461 (mt-10) REVERT: D 34 LYS cc_start: 0.8606 (mmmt) cc_final: 0.8357 (mmmt) REVERT: D 68 ASP cc_start: 0.9197 (t0) cc_final: 0.8827 (t0) REVERT: D 93 GLU cc_start: 0.8837 (mp0) cc_final: 0.8608 (mp0) REVERT: E 125 GLN cc_start: 0.8749 (OUTLIER) cc_final: 0.8248 (mp10) REVERT: H 42 TYR cc_start: 0.8634 (t80) cc_final: 0.8308 (t80) REVERT: H 47 GLN cc_start: 0.8639 (OUTLIER) cc_final: 0.8335 (mt0) REVERT: H 85 LYS cc_start: 0.9361 (OUTLIER) cc_final: 0.9140 (mtmm) outliers start: 9 outliers final: 6 residues processed: 142 average time/residue: 1.3172 time to fit residues: 200.0831 Evaluate side-chains 142 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 133 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 85 LYS Chi-restraints excluded: chain K residue 21 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 7 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 76 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 23 optimal weight: 0.3980 chunk 103 optimal weight: 20.0000 chunk 94 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 9 optimal weight: 0.7980 chunk 98 optimal weight: 10.0000 chunk 104 optimal weight: 0.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.075400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.056117 restraints weight = 83112.249| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 1.24 r_work: 0.2842 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13560 Z= 0.161 Angle : 0.600 7.665 19651 Z= 0.376 Chirality : 0.038 0.192 2244 Planarity : 0.005 0.053 1424 Dihedral : 31.395 164.977 4276 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.40 % Allowed : 19.38 % Favored : 79.22 % 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: 2.18 (0.29), residues: 804 helix: 2.20 (0.22), residues: 591 sheet: None (None), residues: 0 loop : -0.77 (0.36), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 33 TYR 0.010 0.001 TYR K 15 PHE 0.009 0.001 PHE E 67 TRP 0.004 0.001 TRP K 48 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.16 (13560) covalent geometry : angle 0.60002 / 0.38 (19651) hydrogen bonds : bond 0.04532 / 3.16 ( 696) hydrogen bonds : angle 3.03521 / 2.15 ( 1798) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 37 is missing expected H atoms. Skipping. Residue ALA 110 is missing expected H atoms. Skipping. Residue THR 10 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue ALA 110 is missing expected H atoms. Skipping. Residue THR 10 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 11 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue VAL 35 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LYS 49 is missing expected H atoms. Skipping. Residue THR 50 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue MET 62 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue TYR 70 is missing expected H atoms. Skipping. Evaluate side-chains 147 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 138 time to evaluate : 0.485 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8733 (mt-10) cc_final: 0.8463 (mt-10) REVERT: C 90 ASP cc_start: 0.8643 (t0) cc_final: 0.8415 (t0) REVERT: D 68 ASP cc_start: 0.9177 (t0) cc_final: 0.8825 (t0) REVERT: D 93 GLU cc_start: 0.8828 (mp0) cc_final: 0.8586 (mp0) REVERT: E 125 GLN cc_start: 0.8758 (OUTLIER) cc_final: 0.8271 (mp10) REVERT: H 42 TYR cc_start: 0.8672 (t80) cc_final: 0.8321 (t80) REVERT: H 47 GLN cc_start: 0.8639 (OUTLIER) cc_final: 0.8321 (mt0) REVERT: H 85 LYS cc_start: 0.9353 (OUTLIER) cc_final: 0.9131 (mtmm) outliers start: 9 outliers final: 6 residues processed: 142 average time/residue: 1.3554 time to fit residues: 206.3240 Evaluate side-chains 145 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 136 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 85 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 44 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 87 optimal weight: 10.9990 chunk 37 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 chunk 93 optimal weight: 8.9990 chunk 36 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 70 optimal weight: 50.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN G 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.075324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.055892 restraints weight = 84192.069| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 1.27 r_work: 0.2839 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.3923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13560 Z= 0.175 Angle : 0.608 7.593 19651 Z= 0.377 Chirality : 0.038 0.190 2244 Planarity : 0.005 0.056 1424 Dihedral : 31.385 164.885 4276 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.55 % Allowed : 19.69 % Favored : 78.76 % 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: 2.23 (0.29), residues: 804 helix: 2.26 (0.22), residues: 592 sheet: None (None), residues: 0 loop : -0.83 (0.36), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 33 TYR 0.011 0.001 TYR A 41 PHE 0.008 0.001 PHE E 67 TRP 0.004 0.002 TRP K 48 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.18 (13560) covalent geometry : angle 0.60754 / 0.38 (19651) hydrogen bonds : bond 0.04483 / 3.12 ( 696) hydrogen bonds : angle 3.00577 / 2.13 ( 1798) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 37 is missing expected H atoms. Skipping. Residue ALA 110 is missing expected H atoms. Skipping. Residue THR 10 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue ALA 110 is missing expected H atoms. Skipping. Residue THR 10 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 11 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue VAL 35 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LYS 49 is missing expected H atoms. Skipping. Residue THR 50 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue MET 62 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue TYR 70 is missing expected H atoms. Skipping. Evaluate side-chains 144 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 134 time to evaluate : 0.455 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8713 (mt-10) cc_final: 0.8426 (mt-10) REVERT: D 68 ASP cc_start: 0.9173 (t0) cc_final: 0.8825 (t0) REVERT: D 93 GLU cc_start: 0.8837 (mp0) cc_final: 0.8590 (mp0) REVERT: E 125 GLN cc_start: 0.8760 (OUTLIER) cc_final: 0.8268 (mp10) REVERT: H 42 TYR cc_start: 0.8676 (t80) cc_final: 0.8330 (t80) REVERT: H 47 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.8327 (mt0) REVERT: H 85 LYS cc_start: 0.9351 (OUTLIER) cc_final: 0.9136 (mtmm) outliers start: 10 outliers final: 6 residues processed: 139 average time/residue: 1.2419 time to fit residues: 185.4670 Evaluate side-chains 141 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 132 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 85 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 4 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 89 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 88 optimal weight: 8.9990 chunk 84 optimal weight: 20.0000 chunk 36 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.074963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.055462 restraints weight = 83543.931| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 1.27 r_work: 0.2831 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13560 Z= 0.212 Angle : 0.621 7.614 19651 Z= 0.382 Chirality : 0.039 0.186 2244 Planarity : 0.005 0.060 1424 Dihedral : 31.389 164.903 4276 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.24 % Allowed : 20.00 % Favored : 78.76 % 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: 2.20 (0.29), residues: 804 helix: 2.25 (0.21), residues: 592 sheet: None (None), residues: 0 loop : -0.87 (0.36), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 33 TYR 0.013 0.001 TYR A 41 PHE 0.009 0.001 PHE E 67 TRP 0.005 0.002 TRP K 48 HIS 0.003 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.21 (13560) covalent geometry : angle 0.62051 / 0.38 (19651) hydrogen bonds : bond 0.04604 / 3.19 ( 696) hydrogen bonds : angle 3.04205 / 2.16 ( 1798) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 37 is missing expected H atoms. Skipping. Residue ALA 110 is missing expected H atoms. Skipping. Residue THR 10 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue ALA 110 is missing expected H atoms. Skipping. Residue THR 10 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 11 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue VAL 35 is missing expected H atoms. Skipping. Residue LYS 42 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LYS 49 is missing expected H atoms. Skipping. Residue THR 50 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue LYS 56 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue MET 62 is missing expected H atoms. Skipping. Residue LYS 64 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue TYR 70 is missing expected H atoms. Skipping. Evaluate side-chains 142 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 134 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8736 (mt-10) cc_final: 0.8448 (mt-10) REVERT: C 90 ASP cc_start: 0.8678 (t0) cc_final: 0.8451 (t0) REVERT: D 68 ASP cc_start: 0.9178 (t0) cc_final: 0.8813 (t0) REVERT: D 93 GLU cc_start: 0.8847 (mp0) cc_final: 0.8601 (mp0) REVERT: E 125 GLN cc_start: 0.8768 (OUTLIER) cc_final: 0.8278 (mp10) REVERT: H 42 TYR cc_start: 0.8686 (t80) cc_final: 0.8344 (t80) REVERT: H 47 GLN cc_start: 0.8635 (OUTLIER) cc_final: 0.8343 (mt0) REVERT: H 85 LYS cc_start: 0.9355 (OUTLIER) cc_final: 0.9143 (mtmm) outliers start: 8 outliers final: 7 residues processed: 138 average time/residue: 1.1960 time to fit residues: 177.1721 Evaluate side-chains 142 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 132 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 85 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 10 optimal weight: 1.9990 chunk 90 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 78 optimal weight: 9.9990 chunk 52 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 102 optimal weight: 20.0000 chunk 95 optimal weight: 9.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.074955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.055678 restraints weight = 83457.141| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 1.26 r_work: 0.2831 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.4005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13560 Z= 0.201 Angle : 0.613 7.546 19651 Z= 0.378 Chirality : 0.038 0.185 2244 Planarity : 0.005 0.059 1424 Dihedral : 31.394 164.954 4276 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.40 % Allowed : 19.84 % Favored : 78.76 % 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: 2.24 (0.29), residues: 804 helix: 2.28 (0.21), residues: 592 sheet: None (None), residues: 0 loop : -0.87 (0.36), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 33 TYR 0.016 0.001 TYR A 41 PHE 0.009 0.001 PHE E 67 TRP 0.005 0.002 TRP K 48 HIS 0.004 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.20 (13560) covalent geometry : angle 0.61288 / 0.38 (19651) hydrogen bonds : bond 0.04576 / 3.17 ( 696) hydrogen bonds : angle 3.02505 / 2.15 ( 1798) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7210.29 seconds wall clock time: 122 minutes 17.60 seconds (7337.60 seconds total)