Starting phenix.real_space_refine on Fri Sep 19 02:24:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cg9_45578/09_2025/9cg9_45578.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cg9_45578/09_2025/9cg9_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9cg9_45578/09_2025/9cg9_45578.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cg9_45578/09_2025/9cg9_45578.map" model { file = "/net/cci-nas-00/data/ceres_data/9cg9_45578/09_2025/9cg9_45578.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cg9_45578/09_2025/9cg9_45578.cif" } 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-2.0-5805/lib/python3.9/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: 3.69, per 1000 atoms: 0.16 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: 1.85 Conformation dependent library (CDL) restraints added in 463.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 4.26 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: 5.03 Time building geometry restraints manager: 2.69 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: 42103 5.99 - 11.99: 557 11.99 - 17.98: 15 17.98 - 23.97: 2 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 1.50e+00 4.44e-01 3.99e+02 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 1.50e+00 4.44e-01 3.27e+02 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 1.50e+00 4.44e-01 3.18e+02 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 1.50e+00 4.44e-01 2.30e+02 angle pdb=" C6 DA J 59 " pdb=" N6 DA J 59 " pdb=" H61 DA J 59 " ideal model delta sigma weight residual 120.00 100.21 19.79 1.50e+00 4.44e-01 1.74e+02 ... (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 - 0.270: 2239 0.270 - 0.541: 4 0.541 - 0.811: 0 0.811 - 1.082: 0 1.082 - 1.352: 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 -2.66 -1.31 -1.35 2.00e-01 2.50e+01 4.57e+01 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 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 -2.66 -2.32 -0.34 2.00e-01 2.50e+01 2.88e+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: 1.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.130 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 23.190 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 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:6.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 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 : 0.010 0.071 13560 Z= 0.598 Angle : 1.392 16.448 19651 Z= 0.935 Chirality : 0.076 1.352 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 aren 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 covalent geometry : bond 0.00977 (13560) covalent geometry : angle 1.39193 (19651) hydrogen bonds : bond 0.20470 ( 696) hydrogen bonds : angle 6.40671 ( 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 : 0.468 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: 1.8533 time to fit residues: 444.8408 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 : 0.381 ------------------------------------------------------------------------------- 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: 0.8980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 7.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN C 73 ASN E 68 GLN G 112 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.077682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.058784 restraints weight = 84542.189| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 1.25 r_work: 0.2908 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13560 Z= 0.183 Angle : 0.634 6.537 19651 Z= 0.393 Chirality : 0.039 0.140 2244 Planarity : 0.005 0.047 1424 Dihedral : 30.988 162.347 4278 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 1.71 % Allowed : 14.26 % Favored : 84.03 % 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 aren not related in a simple way. whole: 2.01 (0.29), residues: 804 helix: 1.87 (0.22), residues: 592 sheet: None (None), residues: 0 loop : -0.13 (0.35), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 33 TYR 0.016 0.002 TYR B 51 PHE 0.008 0.001 PHE E 67 TRP 0.006 0.002 TRP K 48 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00388 (13560) covalent geometry : angle 0.63415 (19651) hydrogen bonds : bond 0.05090 ( 696) hydrogen bonds : angle 3.16603 ( 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 175 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 164 time to evaluate : 0.505 Fit side-chains revert: symmetry clash REVERT: B 79 LYS cc_start: 0.9232 (OUTLIER) cc_final: 0.8675 (mtmm) REVERT: C 64 GLU cc_start: 0.8613 (tm-30) cc_final: 0.8302 (tm-30) REVERT: D 68 ASP cc_start: 0.9131 (t0) cc_final: 0.8810 (t0) REVERT: G 73 ASN cc_start: 0.8521 (t0) cc_final: 0.8112 (t0) REVERT: H 85 LYS cc_start: 0.9333 (OUTLIER) cc_final: 0.9117 (mtmm) outliers start: 11 outliers final: 3 residues processed: 169 average time/residue: 1.7269 time to fit residues: 309.7583 Evaluate side-chains 148 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 143 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 112 SER 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: 7.9990 chunk 41 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 86 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 100 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS E 68 GLN F 93 GLN G 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.074705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.055264 restraints weight = 84107.087| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 1.32 r_work: 0.2814 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 13560 Z= 0.274 Angle : 0.630 5.803 19651 Z= 0.388 Chirality : 0.045 0.136 2244 Planarity : 0.005 0.045 1424 Dihedral : 30.952 161.097 4276 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 3.10 % Allowed : 15.35 % Favored : 81.55 % 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 aren not related in a simple way. whole: 2.21 (0.29), residues: 804 helix: 2.14 (0.22), residues: 591 sheet: None (None), residues: 0 loop : -0.45 (0.34), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 128 TYR 0.012 0.001 TYR B 51 PHE 0.008 0.001 PHE F 100 TRP 0.010 0.003 TRP K 48 HIS 0.004 0.001 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00593 (13560) covalent geometry : angle 0.62973 (19651) hydrogen bonds : bond 0.04907 ( 696) hydrogen bonds : angle 3.13581 ( 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 166 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 146 time to evaluate : 0.506 Fit side-chains revert: symmetry clash REVERT: B 79 LYS cc_start: 0.9284 (OUTLIER) cc_final: 0.8760 (mtmm) REVERT: C 64 GLU cc_start: 0.8792 (tm-30) cc_final: 0.8479 (tm-30) REVERT: D 68 ASP cc_start: 0.9199 (t0) cc_final: 0.8760 (t0) REVERT: D 93 GLU cc_start: 0.8928 (mp0) cc_final: 0.8705 (mp0) REVERT: G 73 ASN cc_start: 0.8730 (t0) cc_final: 0.8373 (t0) REVERT: H 46 LYS cc_start: 0.9011 (mmmm) cc_final: 0.8800 (mmmt) REVERT: H 85 LYS cc_start: 0.9359 (OUTLIER) cc_final: 0.9135 (mtmm) outliers start: 20 outliers final: 9 residues processed: 154 average time/residue: 1.7209 time to fit residues: 281.4704 Evaluate side-chains 147 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 136 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain B residue 79 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 85 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 1.9990 chunk 71 optimal weight: 10.0000 chunk 85 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 38 optimal weight: 0.5980 chunk 77 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN G 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.075094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.055691 restraints weight = 83971.267| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 1.28 r_work: 0.2831 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 13560 Z= 0.224 Angle : 0.611 5.715 19651 Z= 0.377 Chirality : 0.042 0.132 2244 Planarity : 0.005 0.067 1424 Dihedral : 30.944 161.328 4276 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.02 % Allowed : 16.43 % Favored : 81.55 % 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 aren not related in a simple way. whole: 2.29 (0.29), residues: 804 helix: 2.20 (0.22), residues: 591 sheet: None (None), residues: 0 loop : -0.44 (0.35), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 33 TYR 0.010 0.001 TYR B 51 PHE 0.009 0.001 PHE E 67 TRP 0.008 0.003 TRP K 48 HIS 0.003 0.001 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00483 (13560) covalent geometry : angle 0.61107 (19651) hydrogen bonds : bond 0.04516 ( 696) hydrogen bonds : angle 3.07575 ( 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 155 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 142 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 79 LYS cc_start: 0.9295 (OUTLIER) cc_final: 0.8774 (mtmm) REVERT: C 99 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.8183 (mmp80) REVERT: D 68 ASP cc_start: 0.9185 (t0) cc_final: 0.8767 (t0) REVERT: D 93 GLU cc_start: 0.8879 (mp0) cc_final: 0.8662 (mp0) REVERT: G 73 ASN cc_start: 0.8624 (t0) cc_final: 0.8230 (t0) REVERT: H 47 GLN cc_start: 0.8647 (OUTLIER) cc_final: 0.8269 (mt0) REVERT: H 85 LYS cc_start: 0.9347 (OUTLIER) cc_final: 0.9130 (mtmm) outliers start: 13 outliers final: 7 residues processed: 148 average time/residue: 1.6115 time to fit residues: 253.1522 Evaluate side-chains 149 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 138 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 99 ARG 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 G residue 24 GLN Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 85 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 77 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 103 optimal weight: 20.0000 chunk 60 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 chunk 104 optimal weight: 6.9990 chunk 61 optimal weight: 0.0670 chunk 90 optimal weight: 4.9990 overall best weight: 2.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.075280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.055869 restraints weight = 82996.019| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 1.27 r_work: 0.2840 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.3890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 13560 Z= 0.215 Angle : 0.600 6.347 19651 Z= 0.371 Chirality : 0.042 0.134 2244 Planarity : 0.005 0.105 1424 Dihedral : 30.880 161.484 4276 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.02 % Allowed : 17.21 % Favored : 80.78 % 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 aren not related in a simple way. whole: 2.48 (0.29), residues: 804 helix: 2.34 (0.22), residues: 591 sheet: None (None), residues: 0 loop : -0.37 (0.36), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 33 TYR 0.010 0.001 TYR B 51 PHE 0.007 0.001 PHE E 67 TRP 0.008 0.003 TRP K 48 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00464 (13560) covalent geometry : angle 0.60001 (19651) hydrogen bonds : bond 0.04291 ( 696) hydrogen bonds : angle 2.98280 ( 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 158 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 145 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8701 (mt-10) cc_final: 0.8404 (mt-10) REVERT: C 90 ASP cc_start: 0.8687 (t0) cc_final: 0.8442 (t0) REVERT: C 99 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.8124 (mmp80) REVERT: D 68 ASP cc_start: 0.9186 (t0) cc_final: 0.8799 (t0) REVERT: D 93 GLU cc_start: 0.8933 (mp0) cc_final: 0.8687 (mp0) REVERT: H 42 TYR cc_start: 0.8629 (t80) cc_final: 0.8301 (t80) REVERT: H 47 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.8264 (mt0) REVERT: H 85 LYS cc_start: 0.9339 (OUTLIER) cc_final: 0.9128 (mtmm) outliers start: 13 outliers final: 8 residues processed: 150 average time/residue: 1.7064 time to fit residues: 271.2835 Evaluate side-chains 146 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 135 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 99 ARG Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 34 LYS 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 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 85 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 68 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.074359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.055062 restraints weight = 83474.609| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 1.29 r_work: 0.2815 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 13560 Z= 0.265 Angle : 0.609 4.849 19651 Z= 0.376 Chirality : 0.045 0.135 2244 Planarity : 0.005 0.074 1424 Dihedral : 30.851 161.713 4276 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.33 % Allowed : 17.83 % Favored : 79.84 % 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 aren not related in a simple way. whole: 2.33 (0.29), residues: 804 helix: 2.30 (0.22), residues: 591 sheet: None (None), residues: 0 loop : -0.67 (0.36), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 42 TYR 0.012 0.001 TYR A 41 PHE 0.009 0.001 PHE E 67 TRP 0.008 0.003 TRP K 48 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00573 (13560) covalent geometry : angle 0.60901 (19651) hydrogen bonds : bond 0.04591 ( 696) hydrogen bonds : angle 3.01835 ( 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 154 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 139 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.9501 (m-80) cc_final: 0.9284 (m-80) REVERT: A 50 GLU cc_start: 0.8718 (mt-10) cc_final: 0.8419 (mt-10) REVERT: C 99 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.8112 (mmp80) REVERT: D 68 ASP cc_start: 0.9171 (t0) cc_final: 0.8770 (t0) REVERT: D 93 GLU cc_start: 0.8924 (mp0) cc_final: 0.8633 (mp0) REVERT: G 73 ASN cc_start: 0.8648 (t0) cc_final: 0.8287 (t0) REVERT: H 85 LYS cc_start: 0.9341 (OUTLIER) cc_final: 0.9125 (mtmm) outliers start: 15 outliers final: 7 residues processed: 146 average time/residue: 1.5751 time to fit residues: 244.9128 Evaluate side-chains 144 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 135 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 99 ARG 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 85 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 19 optimal weight: 1.9990 chunk 103 optimal weight: 10.0000 chunk 27 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 chunk 97 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.074998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.055624 restraints weight = 83390.928| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 1.26 r_work: 0.2829 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.4105 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= 0.191 Angle : 0.608 9.964 19651 Z= 0.373 Chirality : 0.040 0.136 2244 Planarity : 0.005 0.078 1424 Dihedral : 30.860 161.813 4276 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.02 % Allowed : 18.76 % 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 aren not related in a simple way. whole: 2.36 (0.29), residues: 804 helix: 2.33 (0.22), residues: 591 sheet: None (None), residues: 0 loop : -0.69 (0.36), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG H 33 TYR 0.009 0.001 TYR D 40 PHE 0.010 0.001 PHE E 67 TRP 0.006 0.002 TRP K 48 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00410 (13560) covalent geometry : angle 0.60825 (19651) hydrogen bonds : bond 0.04412 ( 696) hydrogen bonds : angle 2.97115 ( 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 152 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 139 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8702 (mt-10) cc_final: 0.8388 (mt-10) REVERT: C 99 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.8127 (mmp80) REVERT: D 68 ASP cc_start: 0.9164 (t0) cc_final: 0.8765 (t0) REVERT: D 93 GLU cc_start: 0.8916 (mp0) cc_final: 0.8637 (mp0) REVERT: G 73 ASN cc_start: 0.8605 (t0) cc_final: 0.8214 (t0) REVERT: H 47 GLN cc_start: 0.8605 (OUTLIER) cc_final: 0.8278 (mt0) REVERT: H 85 LYS cc_start: 0.9329 (OUTLIER) cc_final: 0.9112 (mtmm) outliers start: 13 outliers final: 8 residues processed: 144 average time/residue: 1.6574 time to fit residues: 254.2703 Evaluate side-chains 147 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 136 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 99 ARG 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 73 GLU 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 85 LYS 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: 3.9990 chunk 76 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 23 optimal weight: 0.4980 chunk 103 optimal weight: 8.9990 chunk 94 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 98 optimal weight: 7.9990 chunk 104 optimal weight: 10.0000 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.074284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.054860 restraints weight = 83061.707| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 1.29 r_work: 0.2811 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.4277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 13560 Z= 0.272 Angle : 0.617 8.227 19651 Z= 0.378 Chirality : 0.045 0.134 2244 Planarity : 0.005 0.093 1424 Dihedral : 30.872 161.277 4276 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.02 % Allowed : 19.07 % Favored : 78.91 % 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 aren not related in a simple way. whole: 2.28 (0.29), residues: 804 helix: 2.31 (0.22), residues: 591 sheet: None (None), residues: 0 loop : -0.84 (0.36), 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 0.013 0.004 TRP K 48 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00590 (13560) covalent geometry : angle 0.61725 (19651) hydrogen bonds : bond 0.04586 ( 696) hydrogen bonds : angle 3.02077 ( 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 151 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 138 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8733 (mt-10) cc_final: 0.8433 (mt-10) REVERT: C 99 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.8066 (mmp80) REVERT: D 68 ASP cc_start: 0.9162 (t0) cc_final: 0.8771 (t0) REVERT: D 93 GLU cc_start: 0.8930 (mp0) cc_final: 0.8710 (mp0) REVERT: H 85 LYS cc_start: 0.9338 (OUTLIER) cc_final: 0.9129 (mtmm) outliers start: 13 outliers final: 9 residues processed: 144 average time/residue: 1.5498 time to fit residues: 237.2645 Evaluate side-chains 143 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 132 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 99 ARG 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 73 GLU 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: 1.9990 chunk 13 optimal weight: 0.4980 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 70 optimal weight: 20.0000 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.075034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.055782 restraints weight = 83710.242| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 1.26 r_work: 0.2834 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.4322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13560 Z= 0.183 Angle : 0.604 8.709 19651 Z= 0.371 Chirality : 0.040 0.135 2244 Planarity : 0.005 0.092 1424 Dihedral : 30.876 161.336 4276 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.86 % Allowed : 19.69 % Favored : 78.45 % 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 aren not related in a simple way. whole: 2.39 (0.29), residues: 804 helix: 2.39 (0.22), residues: 591 sheet: None (None), residues: 0 loop : -0.82 (0.36), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 42 TYR 0.010 0.001 TYR D 40 PHE 0.009 0.001 PHE E 67 TRP 0.009 0.003 TRP K 48 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00395 (13560) covalent geometry : angle 0.60422 (19651) hydrogen bonds : bond 0.04277 ( 696) hydrogen bonds : angle 2.95463 ( 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 153 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 141 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8699 (mt-10) cc_final: 0.8390 (mt-10) REVERT: D 68 ASP cc_start: 0.9161 (t0) cc_final: 0.8773 (t0) REVERT: D 93 GLU cc_start: 0.8921 (mp0) cc_final: 0.8700 (mp0) REVERT: E 59 GLU cc_start: 0.8876 (pt0) cc_final: 0.8540 (pm20) REVERT: H 85 LYS cc_start: 0.9324 (OUTLIER) cc_final: 0.9118 (mtmm) outliers start: 12 outliers final: 9 residues processed: 148 average time/residue: 1.4263 time to fit residues: 225.5682 Evaluate side-chains 145 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 135 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 110 ASN 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: 3.9990 chunk 66 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.073997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.054620 restraints weight = 83309.417| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 1.29 r_work: 0.2804 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.4357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 13560 Z= 0.290 Angle : 0.627 8.431 19651 Z= 0.382 Chirality : 0.046 0.134 2244 Planarity : 0.006 0.092 1424 Dihedral : 30.873 161.051 4276 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.71 % Allowed : 20.16 % Favored : 78.14 % 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 aren not related in a simple way. whole: 2.17 (0.29), residues: 804 helix: 2.25 (0.21), residues: 591 sheet: None (None), residues: 0 loop : -0.94 (0.35), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 42 TYR 0.010 0.001 TYR K 15 PHE 0.010 0.001 PHE E 67 TRP 0.009 0.003 TRP K 48 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00630 (13560) covalent geometry : angle 0.62684 (19651) hydrogen bonds : bond 0.04739 ( 696) hydrogen bonds : angle 3.05917 ( 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 143 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 132 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8717 (mt-10) cc_final: 0.8415 (mt-10) REVERT: D 68 ASP cc_start: 0.9175 (t0) cc_final: 0.8779 (t0) REVERT: D 93 GLU cc_start: 0.8937 (mp0) cc_final: 0.8704 (mp0) REVERT: G 73 ASN cc_start: 0.8586 (t0) cc_final: 0.8206 (t0) REVERT: H 42 TYR cc_start: 0.8654 (t80) cc_final: 0.8376 (t80) REVERT: H 85 LYS cc_start: 0.9340 (OUTLIER) cc_final: 0.9133 (mtmm) outliers start: 11 outliers final: 10 residues processed: 138 average time/residue: 1.5001 time to fit residues: 220.3046 Evaluate side-chains 143 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 132 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 C residue 110 ASN 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 10 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.073594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.054239 restraints weight = 83304.976| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 1.30 r_work: 0.2792 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.4441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 13560 Z= 0.317 Angle : 0.637 7.296 19651 Z= 0.387 Chirality : 0.048 0.137 2244 Planarity : 0.006 0.088 1424 Dihedral : 30.928 160.838 4276 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.71 % Allowed : 20.93 % Favored : 77.36 % 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 aren not related in a simple way. whole: 2.04 (0.29), residues: 804 helix: 2.18 (0.21), residues: 591 sheet: None (None), residues: 0 loop : -1.09 (0.36), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG H 33 TYR 0.012 0.002 TYR K 15 PHE 0.010 0.001 PHE E 67 TRP 0.010 0.003 TRP K 48 HIS 0.004 0.001 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00691 (13560) covalent geometry : angle 0.63657 (19651) hydrogen bonds : bond 0.04842 ( 696) hydrogen bonds : angle 3.11147 ( 1798) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8656.02 seconds wall clock time: 146 minutes 42.94 seconds (8802.94 seconds total)