Starting phenix.real_space_refine on Sat Jul 4 08:41:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k5x_22683/07_2026/7k5x_22683.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k5x_22683/07_2026/7k5x_22683.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7k5x_22683/07_2026/7k5x_22683.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k5x_22683/07_2026/7k5x_22683.map" model { file = "/net/cci-nas-00/data/ceres_data/7k5x_22683/07_2026/7k5x_22683.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k5x_22683/07_2026/7k5x_22683.cif" } resolution = 2.93 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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 2242 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: 5 Type Number sf(0) Gaussians P 394 5.49 5 S 33 5.16 5 C 10258 2.51 5 N 3350 2.21 5 O 4256 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 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: 18291 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 799 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "B" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 799 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "F" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "G" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 4015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 4015 Classifications: {'DNA': 197} Link IDs: {'rna3p': 196} Chain: "J" Number of atoms: 4062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 4062 Classifications: {'DNA': 197} Link IDs: {'rna3p': 196} Chain: "M" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1777 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 10, 'TRANS': 216} Chain breaks: 1 Chain: "N" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1777 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 10, 'TRANS': 216} Chain breaks: 1 Chain: "U" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 568 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Time building chain proxies: 3.06, per 1000 atoms: 0.17 Number of scatterers: 18291 At special positions: 0 Unit cell: (133.875, 123.375, 200.812, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 33 16.00 P 394 15.00 O 4256 8.00 N 3350 7.00 C 10258 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS M 42 " - pdb=" SG CYS M 107 " distance=2.03 Simple disulfide: pdb=" SG CYS M 171 " - pdb=" SG CYS M 245 " distance=2.03 Simple disulfide: pdb=" SG CYS N 42 " - pdb=" SG CYS N 107 " distance=2.04 Simple disulfide: pdb=" SG CYS N 171 " - pdb=" SG CYS N 245 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.47 Conformation dependent library (CDL) restraints added in 551.8 milliseconds 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2408 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 23 sheets defined 48.6% alpha, 20.9% beta 197 base pairs and 340 stacking pairs defined. Time for finding SS restraints: 2.63 Creating SS restraints... Processing helix chain 'A' and resid 45 through 57 removed outlier: 3.694A pdb=" N ARG A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.849A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.633A pdb=" N ASP A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.526A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.626A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 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: 4.312A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 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 124 removed outlier: 3.719A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.660A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.249A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 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 104 through 124 removed outlier: 3.718A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) Processing helix chain 'M' and resid 98 through 102 removed outlier: 3.702A pdb=" N THR M 102 " --> pdb=" O SER M 99 " (cutoff:3.500A) Processing helix chain 'M' and resid 177 through 179 No H-bonds generated for 'chain 'M' and resid 177 through 179' Processing helix chain 'M' and resid 211 through 214 removed outlier: 3.721A pdb=" N LYS M 214 " --> pdb=" O GLU M 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 211 through 214' Processing helix chain 'M' and resid 236 through 240 Processing helix chain 'N' and resid 98 through 102 Processing helix chain 'N' and resid 177 through 179 No H-bonds generated for 'chain 'N' and resid 177 through 179' Processing helix chain 'N' and resid 211 through 214 removed outlier: 3.512A pdb=" N LYS N 214 " --> pdb=" O GLU N 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 211 through 214' Processing helix chain 'N' and resid 236 through 240 Processing helix chain 'U' and resid 26 through 38 removed outlier: 3.605A pdb=" N MET U 30 " --> pdb=" O LYS U 26 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU U 38 " --> pdb=" O ALA U 34 " (cutoff:3.500A) Processing helix chain 'U' and resid 46 through 57 removed outlier: 3.633A pdb=" N LYS U 54 " --> pdb=" O GLN U 50 " (cutoff:3.500A) Processing helix chain 'U' and resid 62 through 77 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.684A 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 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.327A 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 100 through 102 removed outlier: 6.624A 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: 6.672A 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: 7.241A 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 Processing sheet with id=AB2, first strand: chain 'M' and resid 23 through 25 removed outlier: 3.634A pdb=" N ASP M 89 " --> pdb=" O SER M 86 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 29 through 32 removed outlier: 3.566A pdb=" N GLU M 124 " --> pdb=" O MET M 30 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU M 52 " --> pdb=" O TYR M 68 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N TYR M 68 " --> pdb=" O LEU M 52 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N TRP M 54 " --> pdb=" O LEU M 66 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 29 through 32 removed outlier: 3.566A pdb=" N GLU M 124 " --> pdb=" O MET M 30 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'M' and resid 152 through 155 Processing sheet with id=AB6, first strand: chain 'M' and resid 159 through 161 removed outlier: 6.479A pdb=" N ILE M 183 " --> pdb=" O TYR M 199 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N TYR M 199 " --> pdb=" O ILE M 183 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N TRP M 185 " --> pdb=" O ILE M 197 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 159 through 161 removed outlier: 4.045A pdb=" N TYR M 258 " --> pdb=" O ARG M 247 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 23 through 24 removed outlier: 3.559A pdb=" N ASP N 89 " --> pdb=" O SER N 86 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 29 through 32 removed outlier: 6.785A pdb=" N LEU N 52 " --> pdb=" O TYR N 68 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N TYR N 68 " --> pdb=" O LEU N 52 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N TRP N 54 " --> pdb=" O LEU N 66 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 29 through 32 removed outlier: 3.528A pdb=" N THR N 116 " --> pdb=" O GLN N 109 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 152 through 155 Processing sheet with id=AC3, first strand: chain 'N' and resid 159 through 161 removed outlier: 8.076A pdb=" N TYR N 181 " --> pdb=" O TYR N 201 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N TYR N 201 " --> pdb=" O TYR N 181 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE N 183 " --> pdb=" O TYR N 199 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N TYR N 199 " --> pdb=" O ILE N 183 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N TRP N 185 " --> pdb=" O ILE N 197 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'N' and resid 159 through 161 removed outlier: 3.942A pdb=" N TYR N 258 " --> pdb=" O ARG N 247 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'U' and resid 44 through 45 removed outlier: 6.653A pdb=" N SER U 91 " --> pdb=" O THR U 83 " (cutoff:3.500A) 615 hydrogen bonds defined for protein. 1692 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 510 hydrogen bonds 1020 hydrogen bond angles 0 basepair planarities 197 basepair parallelities 340 stacking parallelities Total time for adding SS restraints: 3.49 Time building geometry restraints manager: 2.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 4002 1.33 - 1.45: 5933 1.45 - 1.57: 8669 1.57 - 1.69: 786 1.69 - 1.81: 54 Bond restraints: 19444 Sorted by residual: bond pdb=" C3' DG J 120 " pdb=" C2' DG J 120 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.19e+01 bond pdb=" C3' DT J 165 " pdb=" C2' DT J 165 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.31e+00 bond pdb=" C3' DG J 161 " pdb=" C2' DG J 161 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.20e+00 bond pdb=" C3' DA I 32 " pdb=" C2' DA I 32 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.15e+00 bond pdb=" C3' DG J 77 " pdb=" C2' DG J 77 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.04e+00 ... (remaining 19439 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.16: 24923 1.16 - 2.31: 2442 2.31 - 3.47: 538 3.47 - 4.63: 44 4.63 - 5.78: 15 Bond angle restraints: 27962 Sorted by residual: angle pdb=" N3 DT J 108 " pdb=" C4 DT J 108 " pdb=" O4 DT J 108 " ideal model delta sigma weight residual 119.90 122.71 -2.81 6.00e-01 2.78e+00 2.19e+01 angle pdb=" N3 DT J 83 " pdb=" C4 DT J 83 " pdb=" O4 DT J 83 " ideal model delta sigma weight residual 119.90 122.69 -2.79 6.00e-01 2.78e+00 2.16e+01 angle pdb=" N3 DT I 57 " pdb=" C4 DT I 57 " pdb=" O4 DT I 57 " ideal model delta sigma weight residual 119.90 122.59 -2.69 6.00e-01 2.78e+00 2.02e+01 angle pdb=" O4' DC J 74 " pdb=" C1' DC J 74 " pdb=" N1 DC J 74 " ideal model delta sigma weight residual 108.00 111.14 -3.14 7.00e-01 2.04e+00 2.01e+01 angle pdb=" N3 DT I 167 " pdb=" C4 DT I 167 " pdb=" O4 DT I 167 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.94e+01 ... (remaining 27957 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.54: 8737 34.54 - 69.07: 1865 69.07 - 103.61: 28 103.61 - 138.15: 0 138.15 - 172.69: 2 Dihedral angle restraints: 10632 sinusoidal: 6874 harmonic: 3758 Sorted by residual: dihedral pdb=" CA PRO D 103 " pdb=" C PRO D 103 " pdb=" N GLY D 104 " pdb=" CA GLY D 104 " ideal model delta harmonic sigma weight residual 180.00 160.05 19.95 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" C4' DT J 153 " pdb=" C3' DT J 153 " pdb=" O3' DT J 153 " pdb=" P DC J 154 " ideal model delta sinusoidal sigma weight residual 220.00 47.31 172.69 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DG J 119 " pdb=" C3' DG J 119 " pdb=" O3' DG J 119 " pdb=" P DG J 120 " ideal model delta sinusoidal sigma weight residual 220.00 67.79 152.21 1 3.50e+01 8.16e-04 1.48e+01 ... (remaining 10629 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1737 0.032 - 0.064: 942 0.064 - 0.095: 316 0.095 - 0.127: 140 0.127 - 0.159: 15 Chirality restraints: 3150 Sorted by residual: chirality pdb=" CB THR M 102 " pdb=" CA THR M 102 " pdb=" OG1 THR M 102 " pdb=" CG2 THR M 102 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.32e-01 chirality pdb=" C3' DT J 153 " pdb=" C4' DT J 153 " pdb=" O3' DT J 153 " pdb=" C2' DT J 153 " both_signs ideal model delta sigma weight residual False -2.73 -2.58 -0.15 2.00e-01 2.50e+01 5.88e-01 chirality pdb=" CA ASP A 81 " pdb=" N ASP A 81 " pdb=" C ASP A 81 " pdb=" CB ASP A 81 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.62e-01 ... (remaining 3147 not shown) Planarity restraints: 2162 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY M 157 " -0.040 5.00e-02 4.00e+02 6.03e-02 5.81e+00 pdb=" N PRO M 158 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO M 158 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO M 158 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 125 " -0.026 2.00e-02 2.50e+03 1.09e-02 3.56e+00 pdb=" N9 DG I 125 " 0.025 2.00e-02 2.50e+03 pdb=" C8 DG I 125 " 0.004 2.00e-02 2.50e+03 pdb=" N7 DG I 125 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DG I 125 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DG I 125 " -0.002 2.00e-02 2.50e+03 pdb=" O6 DG I 125 " -0.008 2.00e-02 2.50e+03 pdb=" N1 DG I 125 " -0.004 2.00e-02 2.50e+03 pdb=" C2 DG I 125 " -0.000 2.00e-02 2.50e+03 pdb=" N2 DG I 125 " 0.006 2.00e-02 2.50e+03 pdb=" N3 DG I 125 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DG I 125 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 31 " -0.030 5.00e-02 4.00e+02 4.45e-02 3.17e+00 pdb=" N PRO B 32 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 32 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 32 " -0.025 5.00e-02 4.00e+02 ... (remaining 2159 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1905 2.75 - 3.29: 16528 3.29 - 3.82: 35552 3.82 - 4.36: 42582 4.36 - 4.90: 62107 Nonbonded interactions: 158674 Sorted by model distance: nonbonded pdb=" OE2 GLU D 113 " pdb=" NH1 ARG M 253 " model vdw 2.211 3.120 nonbonded pdb=" OE2 GLU C 41 " pdb=" OG SER D 87 " model vdw 2.226 3.040 nonbonded pdb=" OE1 GLU C 92 " pdb=" NH1 ARG M 251 " model vdw 2.238 3.120 nonbonded pdb=" OG1 THR F 82 " pdb=" OD2 ASP F 85 " model vdw 2.253 3.040 nonbonded pdb=" OD2 ASP D 68 " pdb=" OH TYR F 98 " model vdw 2.276 3.040 ... (remaining 158669 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' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'M' selection = chain 'N' } 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: 1.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.980 Find NCS groups from input model: 0.140 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:8.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 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 : 0.006 0.050 19448 Z= 0.485 Angle : 0.746 5.782 27970 Z= 0.640 Chirality : 0.045 0.159 3150 Planarity : 0.004 0.060 2162 Dihedral : 26.256 172.687 8212 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.09 % Allowed : 0.09 % Favored : 99.82 % 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: 1.31 (0.23), residues: 1270 helix: 1.84 (0.21), residues: 585 sheet: 0.07 (0.31), residues: 262 loop : 0.17 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 69 TYR 0.024 0.002 TYR C 50 PHE 0.010 0.001 PHE H 65 TRP 0.018 0.002 TRP M 196 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00552 / 0.48 (19444) covalent geometry : angle 0.74557 / 0.64 (27962) SS BOND : bond 0.00271 / 0.14 ( 4) SS BOND : angle 0.74454 / 0.34 ( 8) hydrogen bonds : bond 0.09462 / 6.50 ( 1100) hydrogen bonds : angle 4.24947 / 3.25 ( 2712) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 283 time to evaluate : 0.425 Fit side-chains REVERT: A 77 ASP cc_start: 0.7299 (m-30) cc_final: 0.6997 (t0) REVERT: A 120 MET cc_start: 0.7852 (mtt) cc_final: 0.7249 (mtt) REVERT: B 84 MET cc_start: 0.8172 (mmm) cc_final: 0.7886 (mmm) REVERT: B 93 GLN cc_start: 0.8346 (mt0) cc_final: 0.8081 (mt0) REVERT: C 19 SER cc_start: 0.8788 (p) cc_final: 0.8398 (p) REVERT: C 61 GLU cc_start: 0.8073 (tp30) cc_final: 0.7611 (tp30) REVERT: C 95 LYS cc_start: 0.8778 (tttm) cc_final: 0.8362 (ttmp) REVERT: E 73 GLU cc_start: 0.7940 (tt0) cc_final: 0.7705 (tt0) REVERT: F 26 ILE cc_start: 0.8793 (tp) cc_final: 0.8551 (tt) REVERT: G 62 ILE cc_start: 0.9050 (mt) cc_final: 0.8795 (mt) REVERT: N 30 MET cc_start: 0.7847 (mpp) cc_final: 0.7398 (mtm) REVERT: N 160 LEU cc_start: 0.7826 (mm) cc_final: 0.7602 (mm) REVERT: N 162 GLU cc_start: 0.7825 (pp20) cc_final: 0.7427 (pp20) REVERT: N 210 ASN cc_start: 0.8533 (t0) cc_final: 0.8136 (t0) REVERT: U 30 MET cc_start: 0.6633 (mtp) cc_final: 0.6317 (mtp) outliers start: 1 outliers final: 0 residues processed: 284 average time/residue: 0.6801 time to fit residues: 210.2559 Evaluate side-chains 211 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 0.2980 chunk 91 optimal weight: 50.0000 chunk 149 optimal weight: 0.0980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 24 GLN C 38 ASN D 95 GLN E 76 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN H 63 ASN M 95 ASN M 261 GLN N 95 ASN ** N 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 36 GLN U 50 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.157983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.104458 restraints weight = 27166.774| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.52 r_work: 0.3238 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 19448 Z= 0.156 Angle : 0.644 8.505 27970 Z= 0.374 Chirality : 0.046 0.246 3150 Planarity : 0.005 0.062 2162 Dihedral : 29.955 175.056 5714 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.00 % Allowed : 12.47 % Favored : 85.53 % 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: 1.65 (0.23), residues: 1270 helix: 2.18 (0.21), residues: 587 sheet: 0.51 (0.33), residues: 252 loop : 0.00 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG N 37 TYR 0.014 0.001 TYR G 57 PHE 0.007 0.001 PHE N 117 TRP 0.007 0.001 TRP M 196 HIS 0.004 0.001 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.16 (19444) covalent geometry : angle 0.64419 / 0.37 (27962) SS BOND : bond 0.00584 / 0.30 ( 4) SS BOND : angle 1.05660 / 0.50 ( 8) hydrogen bonds : bond 0.04394 / 3.04 ( 1100) hydrogen bonds : angle 3.54425 / 2.66 ( 2712) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 217 time to evaluate : 0.481 Fit side-chains revert: symmetry clash REVERT: A 120 MET cc_start: 0.8238 (mtt) cc_final: 0.7702 (mtt) REVERT: D 47 GLN cc_start: 0.8523 (mt0) cc_final: 0.8274 (mt0) REVERT: D 68 ASP cc_start: 0.8991 (t0) cc_final: 0.8772 (t0) REVERT: D 93 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.8158 (mp0) REVERT: E 73 GLU cc_start: 0.8642 (tt0) cc_final: 0.8407 (tt0) REVERT: F 25 ASN cc_start: 0.8729 (m110) cc_final: 0.8206 (m110) REVERT: F 26 ILE cc_start: 0.8892 (tp) cc_final: 0.8682 (tt) REVERT: G 62 ILE cc_start: 0.9216 (mt) cc_final: 0.8948 (mt) REVERT: G 95 LYS cc_start: 0.8852 (OUTLIER) cc_final: 0.8314 (ttpp) REVERT: M 154 GLN cc_start: 0.8476 (mm-40) cc_final: 0.8096 (tp-100) REVERT: M 230 MET cc_start: 0.8373 (ttp) cc_final: 0.8123 (ttp) REVERT: N 154 GLN cc_start: 0.8838 (mm-40) cc_final: 0.8602 (mm-40) REVERT: N 162 GLU cc_start: 0.8017 (pp20) cc_final: 0.7690 (pm20) REVERT: N 210 ASN cc_start: 0.8684 (t0) cc_final: 0.8317 (t0) REVERT: U 30 MET cc_start: 0.6255 (mtp) cc_final: 0.5967 (mtp) REVERT: U 67 ILE cc_start: 0.7819 (mt) cc_final: 0.7562 (mt) outliers start: 22 outliers final: 9 residues processed: 223 average time/residue: 0.6866 time to fit residues: 168.3760 Evaluate side-chains 210 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 199 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain D residue 34 LYS Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain M residue 257 ASP Chi-restraints excluded: chain U residue 79 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 71 optimal weight: 1.9990 chunk 123 optimal weight: 7.9990 chunk 60 optimal weight: 1.9990 chunk 116 optimal weight: 10.0000 chunk 132 optimal weight: 4.9990 chunk 159 optimal weight: 6.9990 chunk 51 optimal weight: 0.4980 chunk 93 optimal weight: 40.0000 chunk 97 optimal weight: 20.0000 chunk 54 optimal weight: 3.9990 chunk 109 optimal weight: 50.0000 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 24 GLN D 84 ASN E 76 GLN G 104 GLN H 63 ASN H 95 GLN N 57 GLN N 188 GLN ** N 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.154191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.100100 restraints weight = 27043.938| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.53 r_work: 0.3157 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 19448 Z= 0.244 Angle : 0.686 7.432 27970 Z= 0.387 Chirality : 0.049 0.251 3150 Planarity : 0.005 0.061 2162 Dihedral : 30.428 177.718 5714 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.64 % Allowed : 12.37 % Favored : 83.99 % 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: 1.13 (0.23), residues: 1270 helix: 1.60 (0.20), residues: 588 sheet: 0.61 (0.34), residues: 240 loop : -0.24 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG M 37 TYR 0.030 0.002 TYR H 40 PHE 0.014 0.002 PHE N 117 TRP 0.014 0.002 TRP M 259 HIS 0.009 0.002 HIS H 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00532 / 0.24 (19444) covalent geometry : angle 0.68541 / 0.39 (27962) SS BOND : bond 0.00571 / 0.29 ( 4) SS BOND : angle 1.38129 / 0.67 ( 8) hydrogen bonds : bond 0.05398 / 3.69 ( 1100) hydrogen bonds : angle 3.55992 / 2.65 ( 2712) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 201 time to evaluate : 0.501 Fit side-chains revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8770 (tt0) cc_final: 0.8533 (tt0) REVERT: B 93 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.8248 (mt0) REVERT: C 73 ASN cc_start: 0.8610 (t0) cc_final: 0.8076 (t0) REVERT: C 74 LYS cc_start: 0.8948 (OUTLIER) cc_final: 0.8474 (mtmm) REVERT: D 68 ASP cc_start: 0.8954 (t0) cc_final: 0.8672 (t0) REVERT: D 93 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8378 (mp0) REVERT: E 73 GLU cc_start: 0.8587 (tt0) cc_final: 0.8374 (tm-30) REVERT: F 26 ILE cc_start: 0.8933 (tp) cc_final: 0.8648 (tt) REVERT: G 62 ILE cc_start: 0.9242 (mt) cc_final: 0.8970 (mt) REVERT: G 95 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8407 (ttpp) REVERT: N 230 MET cc_start: 0.8363 (OUTLIER) cc_final: 0.6494 (tpt) outliers start: 40 outliers final: 16 residues processed: 217 average time/residue: 0.6686 time to fit residues: 159.8993 Evaluate side-chains 212 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 191 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 34 LYS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 86 ARG Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain N residue 160 LEU Chi-restraints excluded: chain N residue 230 MET Chi-restraints excluded: chain U residue 79 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 125 optimal weight: 0.7980 chunk 123 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 112 optimal weight: 4.9990 chunk 158 optimal weight: 9.9990 chunk 128 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 105 optimal weight: 10.0000 chunk 69 optimal weight: 0.8980 chunk 48 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 27 GLN G 104 GLN H 82 HIS ** N 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.156814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.105933 restraints weight = 27202.180| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.69 r_work: 0.3200 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 19448 Z= 0.136 Angle : 0.615 9.054 27970 Z= 0.352 Chirality : 0.044 0.261 3150 Planarity : 0.004 0.051 2162 Dihedral : 30.318 179.341 5714 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.18 % Allowed : 14.56 % Favored : 82.26 % 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: 1.68 (0.23), residues: 1270 helix: 2.17 (0.21), residues: 590 sheet: 0.79 (0.34), residues: 240 loop : -0.12 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG M 37 TYR 0.019 0.001 TYR H 40 PHE 0.009 0.001 PHE M 178 TRP 0.010 0.001 TRP M 60 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.14 (19444) covalent geometry : angle 0.61523 / 0.35 (27962) SS BOND : bond 0.00404 / 0.20 ( 4) SS BOND : angle 0.84471 / 0.39 ( 8) hydrogen bonds : bond 0.04082 / 2.81 ( 1100) hydrogen bonds : angle 3.30837 / 2.45 ( 2712) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 206 time to evaluate : 0.485 Fit side-chains revert: symmetry clash REVERT: A 37 LYS cc_start: 0.6743 (ptpp) cc_final: 0.6417 (ptpt) REVERT: B 53 GLU cc_start: 0.8272 (mm-30) cc_final: 0.8031 (mm-30) REVERT: B 84 MET cc_start: 0.9128 (mmm) cc_final: 0.8710 (mmm) REVERT: B 92 ARG cc_start: 0.8743 (OUTLIER) cc_final: 0.7850 (ttp80) REVERT: B 93 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.8193 (mt0) REVERT: C 74 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.8392 (mtmm) REVERT: D 68 ASP cc_start: 0.8968 (t0) cc_final: 0.8683 (t0) REVERT: D 93 GLU cc_start: 0.8843 (OUTLIER) cc_final: 0.8415 (mp0) REVERT: F 26 ILE cc_start: 0.8881 (tp) cc_final: 0.8595 (tt) REVERT: M 154 GLN cc_start: 0.8448 (mm-40) cc_final: 0.7632 (tp-100) REVERT: M 261 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.7398 (pm20) REVERT: N 210 ASN cc_start: 0.8634 (t0) cc_final: 0.8145 (t0) REVERT: N 230 MET cc_start: 0.8398 (OUTLIER) cc_final: 0.6654 (tpt) outliers start: 35 outliers final: 14 residues processed: 217 average time/residue: 0.6887 time to fit residues: 164.6068 Evaluate side-chains 215 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 195 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain D residue 34 LYS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 222 ASP Chi-restraints excluded: chain M residue 257 ASP Chi-restraints excluded: chain M residue 261 GLN Chi-restraints excluded: chain N residue 80 ARG Chi-restraints excluded: chain N residue 100 ASP Chi-restraints excluded: chain N residue 230 MET Chi-restraints excluded: chain U residue 79 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 59 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 135 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 112 optimal weight: 8.9990 chunk 101 optimal weight: 10.0000 chunk 45 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 104 GLN H 82 HIS N 95 ASN ** N 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.156473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.103276 restraints weight = 26931.747| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.51 r_work: 0.3208 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 19448 Z= 0.144 Angle : 0.600 9.185 27970 Z= 0.345 Chirality : 0.043 0.250 3150 Planarity : 0.004 0.039 2162 Dihedral : 30.285 179.270 5714 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.18 % Allowed : 16.56 % Favored : 80.25 % 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: 1.78 (0.24), residues: 1270 helix: 2.28 (0.21), residues: 590 sheet: 0.86 (0.34), residues: 240 loop : -0.09 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG H 33 TYR 0.021 0.001 TYR H 40 PHE 0.010 0.001 PHE E 67 TRP 0.010 0.001 TRP M 60 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.14 (19444) covalent geometry : angle 0.59945 / 0.35 (27962) SS BOND : bond 0.00346 / 0.17 ( 4) SS BOND : angle 0.92134 / 0.43 ( 8) hydrogen bonds : bond 0.04067 / 2.81 ( 1100) hydrogen bonds : angle 3.24962 / 2.41 ( 2712) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 219 time to evaluate : 0.488 Fit side-chains revert: symmetry clash REVERT: A 37 LYS cc_start: 0.6992 (ptpp) cc_final: 0.6622 (ptpt) REVERT: B 92 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.7880 (ttp80) REVERT: B 93 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.8255 (mt0) REVERT: C 73 ASN cc_start: 0.8515 (t0) cc_final: 0.7956 (t0) REVERT: C 74 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8420 (mtmm) REVERT: D 68 ASP cc_start: 0.8945 (t0) cc_final: 0.8676 (t0) REVERT: D 93 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8401 (mp0) REVERT: F 26 ILE cc_start: 0.8922 (tp) cc_final: 0.8621 (tt) REVERT: G 13 LYS cc_start: 0.8172 (tppp) cc_final: 0.7832 (tppt) REVERT: G 74 LYS cc_start: 0.9059 (OUTLIER) cc_final: 0.8751 (mttp) REVERT: G 95 LYS cc_start: 0.8852 (OUTLIER) cc_final: 0.8299 (ttpp) REVERT: M 154 GLN cc_start: 0.8520 (mm-40) cc_final: 0.7709 (tp-100) REVERT: M 261 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.7419 (pm20) REVERT: N 46 GLN cc_start: 0.8452 (mt0) cc_final: 0.8112 (mt0) REVERT: N 210 ASN cc_start: 0.8609 (t0) cc_final: 0.8135 (t0) REVERT: N 230 MET cc_start: 0.8386 (OUTLIER) cc_final: 0.6642 (tpt) outliers start: 35 outliers final: 11 residues processed: 230 average time/residue: 0.7008 time to fit residues: 176.8089 Evaluate side-chains 216 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 197 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 257 ASP Chi-restraints excluded: chain M residue 261 GLN Chi-restraints excluded: chain N residue 80 ARG Chi-restraints excluded: chain N residue 230 MET Chi-restraints excluded: chain U residue 79 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 117 optimal weight: 4.9990 chunk 94 optimal weight: 20.0000 chunk 43 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 97 optimal weight: 20.0000 chunk 149 optimal weight: 2.9990 chunk 45 optimal weight: 0.0980 chunk 47 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 141 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN E 108 ASN G 104 GLN H 82 HIS N 154 GLN ** N 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.157580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.103789 restraints weight = 26864.267| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.48 r_work: 0.3228 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 19448 Z= 0.124 Angle : 0.591 8.975 27970 Z= 0.341 Chirality : 0.042 0.251 3150 Planarity : 0.004 0.049 2162 Dihedral : 30.238 179.576 5714 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.00 % Allowed : 18.11 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.24), residues: 1270 helix: 2.33 (0.21), residues: 602 sheet: 1.03 (0.35), residues: 232 loop : -0.14 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG H 33 TYR 0.020 0.001 TYR U 27 PHE 0.010 0.001 PHE E 67 TRP 0.009 0.001 TRP M 60 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.12 (19444) covalent geometry : angle 0.59108 / 0.34 (27962) SS BOND : bond 0.00339 / 0.17 ( 4) SS BOND : angle 0.83734 / 0.40 ( 8) hydrogen bonds : bond 0.03805 / 2.64 ( 1100) hydrogen bonds : angle 3.17407 / 2.34 ( 2712) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 206 time to evaluate : 0.489 Fit side-chains REVERT: A 37 LYS cc_start: 0.7142 (ptpp) cc_final: 0.6745 (ptpt) REVERT: B 84 MET cc_start: 0.9104 (mmm) cc_final: 0.8741 (mmm) REVERT: B 92 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.7857 (ttp80) REVERT: C 73 ASN cc_start: 0.8477 (t0) cc_final: 0.7939 (t0) REVERT: C 74 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8401 (mtmm) REVERT: D 68 ASP cc_start: 0.8934 (t0) cc_final: 0.8662 (t0) REVERT: D 93 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8337 (mp0) REVERT: F 25 ASN cc_start: 0.8394 (m110) cc_final: 0.8116 (m110) REVERT: F 26 ILE cc_start: 0.8934 (tp) cc_final: 0.8599 (tt) REVERT: G 62 ILE cc_start: 0.9150 (OUTLIER) cc_final: 0.8758 (mt) REVERT: G 74 LYS cc_start: 0.9059 (OUTLIER) cc_final: 0.8742 (mttp) REVERT: G 95 LYS cc_start: 0.8829 (OUTLIER) cc_final: 0.8281 (ttpp) REVERT: M 154 GLN cc_start: 0.8558 (mm-40) cc_final: 0.8052 (tp-100) REVERT: M 230 MET cc_start: 0.8516 (OUTLIER) cc_final: 0.8075 (ttm) REVERT: N 46 GLN cc_start: 0.8414 (mt0) cc_final: 0.8091 (mt0) REVERT: N 210 ASN cc_start: 0.8558 (t0) cc_final: 0.8111 (t0) REVERT: N 230 MET cc_start: 0.8391 (OUTLIER) cc_final: 0.6557 (tpt) outliers start: 33 outliers final: 11 residues processed: 219 average time/residue: 0.6753 time to fit residues: 162.1369 Evaluate side-chains 216 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 197 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 195 GLU Chi-restraints excluded: chain M residue 230 MET Chi-restraints excluded: chain M residue 257 ASP Chi-restraints excluded: chain N residue 80 ARG Chi-restraints excluded: chain N residue 100 ASP Chi-restraints excluded: chain N residue 230 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 108 optimal weight: 40.0000 chunk 120 optimal weight: 10.0000 chunk 13 optimal weight: 0.9980 chunk 141 optimal weight: 6.9990 chunk 37 optimal weight: 0.9990 chunk 117 optimal weight: 3.9990 chunk 129 optimal weight: 9.9990 chunk 64 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 151 optimal weight: 4.9990 chunk 17 optimal weight: 8.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN G 104 GLN H 82 HIS N 95 ASN ** N 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.156259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.102654 restraints weight = 27139.918| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.52 r_work: 0.3196 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 19448 Z= 0.167 Angle : 0.608 10.280 27970 Z= 0.347 Chirality : 0.043 0.248 3150 Planarity : 0.004 0.047 2162 Dihedral : 30.298 178.816 5714 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.82 % Allowed : 19.02 % Favored : 78.16 % 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: 1.68 (0.24), residues: 1270 helix: 2.14 (0.21), residues: 602 sheet: 0.95 (0.35), residues: 232 loop : -0.20 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 33 TYR 0.025 0.002 TYR H 40 PHE 0.009 0.001 PHE A 67 TRP 0.010 0.002 TRP M 259 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.17 (19444) covalent geometry : angle 0.60823 / 0.35 (27962) SS BOND : bond 0.00406 / 0.20 ( 4) SS BOND : angle 1.04760 / 0.51 ( 8) hydrogen bonds : bond 0.04221 / 2.91 ( 1100) hydrogen bonds : angle 3.22916 / 2.39 ( 2712) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 201 time to evaluate : 0.345 Fit side-chains REVERT: A 37 LYS cc_start: 0.7170 (ptpp) cc_final: 0.6777 (ptpt) REVERT: B 92 ARG cc_start: 0.8824 (OUTLIER) cc_final: 0.7929 (ttp80) REVERT: B 93 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.8224 (mt0) REVERT: C 74 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8415 (mtmm) REVERT: D 68 ASP cc_start: 0.8912 (t0) cc_final: 0.8628 (t0) REVERT: D 93 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.8355 (mp0) REVERT: F 25 ASN cc_start: 0.8465 (m110) cc_final: 0.8188 (m110) REVERT: F 26 ILE cc_start: 0.8960 (tp) cc_final: 0.8614 (tt) REVERT: G 62 ILE cc_start: 0.9166 (OUTLIER) cc_final: 0.8773 (mt) REVERT: G 95 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8317 (ttpp) REVERT: M 154 GLN cc_start: 0.8570 (mm-40) cc_final: 0.7738 (tp-100) REVERT: M 261 GLN cc_start: 0.8387 (OUTLIER) cc_final: 0.7502 (pm20) REVERT: N 46 GLN cc_start: 0.8449 (mt0) cc_final: 0.8071 (mt0) REVERT: N 154 GLN cc_start: 0.8605 (mm110) cc_final: 0.8193 (mm-40) REVERT: N 192 GLN cc_start: 0.7179 (mp10) cc_final: 0.6681 (mp10) REVERT: N 210 ASN cc_start: 0.8586 (t0) cc_final: 0.8115 (t0) REVERT: N 230 MET cc_start: 0.8411 (OUTLIER) cc_final: 0.6670 (tpt) REVERT: U 74 LEU cc_start: 0.7769 (mm) cc_final: 0.7561 (mm) outliers start: 31 outliers final: 12 residues processed: 214 average time/residue: 0.6690 time to fit residues: 156.7874 Evaluate side-chains 215 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 195 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 195 GLU Chi-restraints excluded: chain M residue 257 ASP Chi-restraints excluded: chain M residue 261 GLN Chi-restraints excluded: chain N residue 80 ARG Chi-restraints excluded: chain N residue 100 ASP Chi-restraints excluded: chain N residue 230 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 87 optimal weight: 20.0000 chunk 155 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 84 optimal weight: 10.0000 chunk 58 optimal weight: 0.9980 chunk 102 optimal weight: 10.0000 chunk 59 optimal weight: 0.9980 chunk 95 optimal weight: 20.0000 chunk 13 optimal weight: 3.9990 chunk 80 optimal weight: 9.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 104 GLN H 82 HIS ** N 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.156146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.102043 restraints weight = 27048.285| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.48 r_work: 0.3202 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 19448 Z= 0.164 Angle : 0.609 7.408 27970 Z= 0.346 Chirality : 0.043 0.252 3150 Planarity : 0.004 0.052 2162 Dihedral : 30.321 177.310 5714 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.91 % Allowed : 19.75 % Favored : 77.34 % 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: 1.63 (0.24), residues: 1270 helix: 2.06 (0.21), residues: 606 sheet: 0.92 (0.35), residues: 232 loop : -0.20 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG N 37 TYR 0.026 0.002 TYR H 40 PHE 0.008 0.001 PHE E 67 TRP 0.013 0.001 TRP M 60 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.16 (19444) covalent geometry : angle 0.60896 / 0.35 (27962) SS BOND : bond 0.00397 / 0.20 ( 4) SS BOND : angle 1.11493 / 0.51 ( 8) hydrogen bonds : bond 0.04102 / 2.83 ( 1100) hydrogen bonds : angle 3.23011 / 2.39 ( 2712) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 202 time to evaluate : 0.496 Fit side-chains REVERT: A 37 LYS cc_start: 0.7177 (ptpp) cc_final: 0.6790 (ptpt) REVERT: B 84 MET cc_start: 0.9100 (mmm) cc_final: 0.8697 (mmm) REVERT: B 93 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.8198 (mt0) REVERT: C 74 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.8388 (mtmm) REVERT: D 68 ASP cc_start: 0.8904 (t0) cc_final: 0.8664 (t0) REVERT: D 76 GLU cc_start: 0.8721 (tp30) cc_final: 0.8387 (tp30) REVERT: D 93 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.8354 (mp0) REVERT: F 25 ASN cc_start: 0.8462 (m110) cc_final: 0.8216 (m110) REVERT: F 26 ILE cc_start: 0.8931 (tp) cc_final: 0.8584 (tt) REVERT: G 62 ILE cc_start: 0.9164 (OUTLIER) cc_final: 0.8835 (mt) REVERT: G 90 ASP cc_start: 0.8960 (t70) cc_final: 0.8593 (t0) REVERT: G 95 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8331 (ttpp) REVERT: M 154 GLN cc_start: 0.8586 (mm-40) cc_final: 0.7746 (tp-100) REVERT: M 230 MET cc_start: 0.8438 (OUTLIER) cc_final: 0.8194 (ttm) REVERT: M 261 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.7518 (pm20) REVERT: N 30 MET cc_start: 0.8033 (mtm) cc_final: 0.7786 (mtm) REVERT: N 46 GLN cc_start: 0.8420 (mt0) cc_final: 0.8154 (mt0) REVERT: N 154 GLN cc_start: 0.8620 (mm110) cc_final: 0.8215 (mm-40) REVERT: N 192 GLN cc_start: 0.7156 (mp10) cc_final: 0.6672 (mp10) REVERT: N 210 ASN cc_start: 0.8568 (t0) cc_final: 0.8091 (t0) REVERT: N 230 MET cc_start: 0.8420 (OUTLIER) cc_final: 0.6687 (tpt) REVERT: U 74 LEU cc_start: 0.7883 (mm) cc_final: 0.7680 (mm) outliers start: 32 outliers final: 16 residues processed: 215 average time/residue: 0.6613 time to fit residues: 155.8795 Evaluate side-chains 222 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 198 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 195 GLU Chi-restraints excluded: chain M residue 230 MET Chi-restraints excluded: chain M residue 257 ASP Chi-restraints excluded: chain M residue 261 GLN Chi-restraints excluded: chain N residue 80 ARG Chi-restraints excluded: chain N residue 100 ASP Chi-restraints excluded: chain N residue 230 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 49 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 77 optimal weight: 9.9990 chunk 82 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 107 optimal weight: 20.0000 chunk 127 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 104 GLN H 82 HIS M 95 ASN ** N 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.157009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.103574 restraints weight = 27051.554| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.53 r_work: 0.3223 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19448 Z= 0.132 Angle : 0.596 9.405 27970 Z= 0.340 Chirality : 0.042 0.250 3150 Planarity : 0.004 0.062 2162 Dihedral : 30.270 176.834 5714 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.37 % Allowed : 20.38 % Favored : 77.25 % 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: 1.80 (0.24), residues: 1270 helix: 2.23 (0.21), residues: 606 sheet: 0.99 (0.35), residues: 232 loop : -0.15 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG N 37 TYR 0.026 0.001 TYR U 52 PHE 0.010 0.001 PHE E 67 TRP 0.013 0.001 TRP M 60 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.13 (19444) covalent geometry : angle 0.59562 / 0.34 (27962) SS BOND : bond 0.00372 / 0.19 ( 4) SS BOND : angle 1.10247 / 0.53 ( 8) hydrogen bonds : bond 0.03865 / 2.68 ( 1100) hydrogen bonds : angle 3.17365 / 2.34 ( 2712) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 212 time to evaluate : 0.486 Fit side-chains REVERT: A 37 LYS cc_start: 0.7178 (ptpp) cc_final: 0.6794 (ptpt) REVERT: B 84 MET cc_start: 0.9124 (mmm) cc_final: 0.8679 (mmm) REVERT: B 93 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.8206 (mt0) REVERT: C 74 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8377 (mtmm) REVERT: D 68 ASP cc_start: 0.8899 (t0) cc_final: 0.8636 (t0) REVERT: D 76 GLU cc_start: 0.8712 (tp30) cc_final: 0.8440 (tp30) REVERT: D 93 GLU cc_start: 0.8812 (OUTLIER) cc_final: 0.8415 (mp0) REVERT: F 26 ILE cc_start: 0.8928 (tp) cc_final: 0.8551 (tt) REVERT: G 90 ASP cc_start: 0.8958 (t70) cc_final: 0.8594 (t0) REVERT: G 95 LYS cc_start: 0.8837 (OUTLIER) cc_final: 0.8297 (ttpp) REVERT: M 154 GLN cc_start: 0.8567 (mm-40) cc_final: 0.7743 (tp-100) REVERT: M 230 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.8159 (ttm) REVERT: M 261 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.7503 (pm20) REVERT: N 30 MET cc_start: 0.8104 (mtm) cc_final: 0.7869 (mtm) REVERT: N 46 GLN cc_start: 0.8397 (mt0) cc_final: 0.8129 (mt0) REVERT: N 154 GLN cc_start: 0.8616 (mm110) cc_final: 0.8204 (mm-40) REVERT: N 210 ASN cc_start: 0.8529 (t0) cc_final: 0.8052 (t0) REVERT: N 230 MET cc_start: 0.8403 (OUTLIER) cc_final: 0.6574 (tpt) REVERT: U 74 LEU cc_start: 0.7948 (mm) cc_final: 0.7725 (mm) outliers start: 26 outliers final: 17 residues processed: 222 average time/residue: 0.7110 time to fit residues: 173.5619 Evaluate side-chains 229 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 205 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 195 GLU Chi-restraints excluded: chain M residue 230 MET Chi-restraints excluded: chain M residue 257 ASP Chi-restraints excluded: chain M residue 261 GLN Chi-restraints excluded: chain N residue 80 ARG Chi-restraints excluded: chain N residue 100 ASP Chi-restraints excluded: chain N residue 230 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 26 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 85 optimal weight: 10.0000 chunk 73 optimal weight: 50.0000 chunk 98 optimal weight: 9.9990 chunk 14 optimal weight: 0.7980 chunk 122 optimal weight: 10.0000 chunk 107 optimal weight: 20.0000 chunk 130 optimal weight: 3.9990 chunk 143 optimal weight: 5.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 25 ASN G 104 GLN H 63 ASN H 82 HIS ** N 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.155636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.101448 restraints weight = 27040.523| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.48 r_work: 0.3193 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 19448 Z= 0.184 Angle : 0.622 8.434 27970 Z= 0.351 Chirality : 0.044 0.249 3150 Planarity : 0.005 0.055 2162 Dihedral : 30.334 176.520 5714 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.09 % Allowed : 20.84 % Favored : 77.07 % 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: 1.54 (0.24), residues: 1270 helix: 1.98 (0.21), residues: 606 sheet: 0.87 (0.35), residues: 232 loop : -0.23 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG N 37 TYR 0.027 0.002 TYR H 40 PHE 0.009 0.002 PHE A 67 TRP 0.014 0.002 TRP M 60 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.18 (19444) covalent geometry : angle 0.62143 / 0.35 (27962) SS BOND : bond 0.00441 / 0.23 ( 4) SS BOND : angle 1.42645 / 0.70 ( 8) hydrogen bonds : bond 0.04352 / 3.00 ( 1100) hydrogen bonds : angle 3.26067 / 2.40 ( 2712) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 204 time to evaluate : 0.820 Fit side-chains REVERT: A 37 LYS cc_start: 0.7193 (ptpp) cc_final: 0.6811 (ptpt) REVERT: B 93 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.8243 (mt0) REVERT: C 73 ASN cc_start: 0.8514 (t0) cc_final: 0.8027 (t0) REVERT: C 74 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8409 (mtmm) REVERT: D 68 ASP cc_start: 0.8906 (t0) cc_final: 0.8631 (t0) REVERT: D 76 GLU cc_start: 0.8801 (tp30) cc_final: 0.8527 (tp30) REVERT: D 93 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8397 (mp0) REVERT: F 26 ILE cc_start: 0.8936 (tp) cc_final: 0.8571 (tt) REVERT: G 90 ASP cc_start: 0.8978 (t70) cc_final: 0.8618 (t0) REVERT: G 95 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8336 (ttpp) REVERT: M 154 GLN cc_start: 0.8665 (mm-40) cc_final: 0.8354 (mm-40) REVERT: M 230 MET cc_start: 0.8477 (OUTLIER) cc_final: 0.8182 (ttm) REVERT: M 261 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.7523 (pm20) REVERT: N 30 MET cc_start: 0.8096 (mtm) cc_final: 0.7865 (mtm) REVERT: N 46 GLN cc_start: 0.8400 (mt0) cc_final: 0.8135 (mt0) REVERT: N 49 ARG cc_start: 0.8104 (mtm110) cc_final: 0.7823 (mtm110) REVERT: N 154 GLN cc_start: 0.8626 (mm110) cc_final: 0.8220 (mm-40) REVERT: N 230 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.6687 (tpt) outliers start: 23 outliers final: 14 residues processed: 210 average time/residue: 0.7214 time to fit residues: 166.1547 Evaluate side-chains 228 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 207 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 195 GLU Chi-restraints excluded: chain M residue 230 MET Chi-restraints excluded: chain M residue 257 ASP Chi-restraints excluded: chain M residue 261 GLN Chi-restraints excluded: chain N residue 80 ARG Chi-restraints excluded: chain N residue 100 ASP Chi-restraints excluded: chain N residue 230 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 26 optimal weight: 0.3980 chunk 69 optimal weight: 0.6980 chunk 141 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 151 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 154 optimal weight: 0.1980 chunk 99 optimal weight: 9.9990 chunk 55 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 104 GLN H 82 HIS M 95 ASN ** N 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.157785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.104596 restraints weight = 27115.719| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 1.51 r_work: 0.3237 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 19448 Z= 0.122 Angle : 0.590 9.959 27970 Z= 0.337 Chirality : 0.042 0.249 3150 Planarity : 0.004 0.060 2162 Dihedral : 30.242 175.254 5714 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.91 % Allowed : 21.11 % Favored : 76.98 % 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: 1.88 (0.24), residues: 1270 helix: 2.32 (0.21), residues: 606 sheet: 1.03 (0.35), residues: 232 loop : -0.16 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG N 37 TYR 0.029 0.001 TYR U 52 PHE 0.009 0.001 PHE E 67 TRP 0.015 0.001 TRP M 60 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.12 (19444) covalent geometry : angle 0.58957 / 0.34 (27962) SS BOND : bond 0.00385 / 0.20 ( 4) SS BOND : angle 0.91365 / 0.41 ( 8) hydrogen bonds : bond 0.03752 / 2.60 ( 1100) hydrogen bonds : angle 3.13657 / 2.30 ( 2712) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7971.43 seconds wall clock time: 135 minutes 52.04 seconds (8152.04 seconds total)