Starting phenix.real_space_refine on Thu Mar 5 05:43:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k5x_22683/03_2026/7k5x_22683.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k5x_22683/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7k5x_22683/03_2026/7k5x_22683.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k5x_22683/03_2026/7k5x_22683.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7k5x_22683/03_2026/7k5x_22683.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k5x_22683/03_2026/7k5x_22683.map" } 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-5986/lib/python3.9/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: 3.21, per 1000 atoms: 0.18 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: 1.30 Conformation dependent library (CDL) restraints added in 515.6 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: 3.03 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: 3.48 Time building geometry restraints manager: 1.75 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=" CA ASP F 24 " pdb=" CB ASP F 24 " ideal model delta sigma weight residual 1.527 1.539 -0.012 7.60e-03 1.73e+04 2.40e+00 bond pdb=" C3' DT J 153 " pdb=" O3' DT J 153 " ideal model delta sigma weight residual 1.422 1.463 -0.041 3.00e-02 1.11e+03 1.86e+00 bond pdb=" N ASP A 81 " pdb=" CA ASP A 81 " ideal model delta sigma weight residual 1.457 1.474 -0.016 1.29e-02 6.01e+03 1.59e+00 bond pdb=" CG1 ILE C 87 " pdb=" CD1 ILE C 87 " ideal model delta sigma weight residual 1.513 1.470 0.043 3.90e-02 6.57e+02 1.23e+00 bond pdb=" C3' DG J 119 " pdb=" O3' DG J 119 " ideal model delta sigma weight residual 1.422 1.454 -0.032 3.00e-02 1.11e+03 1.15e+00 ... (remaining 19439 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.16: 26207 1.16 - 2.31: 1502 2.31 - 3.47: 206 3.47 - 4.63: 32 4.63 - 5.78: 15 Bond angle restraints: 27962 Sorted by residual: angle pdb=" N ARG B 23 " pdb=" CA ARG B 23 " pdb=" C ARG B 23 " ideal model delta sigma weight residual 110.80 115.93 -5.13 2.13e+00 2.20e-01 5.80e+00 angle pdb=" C3' DC I 72 " pdb=" C2' DC I 72 " pdb=" C1' DC I 72 " ideal model delta sigma weight residual 101.60 98.05 3.55 1.50e+00 4.44e-01 5.61e+00 angle pdb=" CA GLN N 192 " pdb=" CB GLN N 192 " pdb=" CG GLN N 192 " ideal model delta sigma weight residual 114.10 118.75 -4.65 2.00e+00 2.50e-01 5.40e+00 angle pdb=" C TYR M 69 " pdb=" N ALA M 70 " pdb=" CA ALA M 70 " ideal model delta sigma weight residual 121.54 125.94 -4.40 1.91e+00 2.74e-01 5.31e+00 angle pdb=" CA ARG B 23 " pdb=" C ARG B 23 " pdb=" N ASP B 24 " ideal model delta sigma weight residual 116.84 120.66 -3.82 1.71e+00 3.42e-01 5.00e+00 ... (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: 2104 0.032 - 0.064: 792 0.064 - 0.095: 177 0.095 - 0.127: 67 0.127 - 0.159: 10 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=" 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 chirality pdb=" CA SER M 113 " pdb=" N SER M 113 " pdb=" C SER M 113 " pdb=" CB SER M 113 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.77e-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: 1.360 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: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.760 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 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 : 0.004 0.050 19448 Z= 0.172 Angle : 0.605 5.782 27970 Z= 0.373 Chirality : 0.037 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 covalent geometry : bond 0.00369 (19444) covalent geometry : angle 0.60487 (27962) SS BOND : bond 0.00271 ( 4) SS BOND : angle 0.74454 ( 8) hydrogen bonds : bond 0.09462 ( 1100) hydrogen bonds : angle 4.24947 ( 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 : 0.390 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: 0.7878 time to fit residues: 242.5746 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 : 0.543 ------------------------------------------------------------------------------- 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: 3.9990 chunk 107 optimal weight: 7.9990 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: 4.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.2980 chunk 91 optimal weight: 30.0000 chunk 149 optimal weight: 0.0980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 H 95 GLN M 95 ASN M 261 GLN N 57 GLN N 95 ASN N 188 GLN ** N 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 36 GLN U 50 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.157677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.104221 restraints weight = 27117.998| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.49 r_work: 0.3235 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 19448 Z= 0.169 Angle : 0.580 8.669 27970 Z= 0.344 Chirality : 0.036 0.155 3150 Planarity : 0.004 0.068 2162 Dihedral : 29.549 174.998 5714 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.09 % Allowed : 11.92 % Favored : 85.99 % 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: 1.76 (0.23), residues: 1270 helix: 2.23 (0.21), residues: 588 sheet: 0.67 (0.33), residues: 240 loop : 0.07 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG N 37 TYR 0.015 0.001 TYR C 50 PHE 0.009 0.001 PHE N 117 TRP 0.011 0.002 TRP M 196 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00379 (19444) covalent geometry : angle 0.57970 (27962) SS BOND : bond 0.00431 ( 4) SS BOND : angle 0.68851 ( 8) hydrogen bonds : bond 0.03766 ( 1100) hydrogen bonds : angle 3.37721 ( 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 238 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 215 time to evaluate : 0.317 Fit side-chains REVERT: A 120 MET cc_start: 0.8189 (mtt) cc_final: 0.7662 (mtt) REVERT: B 93 GLN cc_start: 0.8609 (mt0) cc_final: 0.8396 (mt0) REVERT: C 61 GLU cc_start: 0.8546 (tp30) cc_final: 0.8325 (tp30) REVERT: C 95 LYS cc_start: 0.9084 (tttm) cc_final: 0.8761 (ttmp) REVERT: D 68 ASP cc_start: 0.8982 (t0) cc_final: 0.8731 (t0) REVERT: D 93 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.8204 (mp0) REVERT: E 73 GLU cc_start: 0.8501 (tt0) cc_final: 0.8266 (tt0) REVERT: F 26 ILE cc_start: 0.8884 (tp) cc_final: 0.8671 (tt) REVERT: G 62 ILE cc_start: 0.9256 (mt) cc_final: 0.9016 (mt) REVERT: G 75 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8548 (mtpp) REVERT: M 154 GLN cc_start: 0.8442 (mm-40) cc_final: 0.7973 (tp-100) REVERT: N 162 GLU cc_start: 0.7944 (pp20) cc_final: 0.7648 (pm20) REVERT: N 210 ASN cc_start: 0.8661 (t0) cc_final: 0.8283 (t0) REVERT: U 30 MET cc_start: 0.6384 (mtp) cc_final: 0.6089 (mtp) REVERT: U 67 ILE cc_start: 0.7818 (mt) cc_final: 0.7540 (mt) outliers start: 23 outliers final: 9 residues processed: 221 average time/residue: 0.7167 time to fit residues: 173.3949 Evaluate side-chains 209 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 198 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 34 LYS Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain M residue 38 VAL Chi-restraints excluded: chain N residue 100 ASP Chi-restraints excluded: chain N 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: 4.9990 chunk 60 optimal weight: 2.9990 chunk 116 optimal weight: 6.9990 chunk 132 optimal weight: 6.9990 chunk 159 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 93 optimal weight: 10.0000 chunk 97 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 109 optimal weight: 30.0000 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 47 GLN G 104 GLN ** N 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4084 r_free = 0.4084 target = 0.154082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.099872 restraints weight = 27060.460| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.49 r_work: 0.3156 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 19448 Z= 0.256 Angle : 0.622 6.913 27970 Z= 0.362 Chirality : 0.039 0.163 3150 Planarity : 0.005 0.053 2162 Dihedral : 30.033 178.289 5714 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.55 % Allowed : 12.56 % Favored : 83.89 % 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: 1.39 (0.23), residues: 1270 helix: 1.81 (0.20), residues: 590 sheet: 0.68 (0.33), residues: 240 loop : -0.08 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 33 TYR 0.021 0.002 TYR H 40 PHE 0.014 0.002 PHE N 117 TRP 0.012 0.002 TRP M 259 HIS 0.006 0.001 HIS H 109 Details of bonding type rmsd covalent geometry : bond 0.00594 (19444) covalent geometry : angle 0.62201 (27962) SS BOND : bond 0.00433 ( 4) SS BOND : angle 1.03530 ( 8) hydrogen bonds : bond 0.04538 ( 1100) hydrogen bonds : angle 3.42939 ( 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 255 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 216 time to evaluate : 0.435 Fit side-chains revert: symmetry clash REVERT: A 37 LYS cc_start: 0.6852 (ptpp) cc_final: 0.6522 (ptpt) REVERT: C 13 LYS cc_start: 0.8013 (mmmm) cc_final: 0.7770 (mmmt) REVERT: C 73 ASN cc_start: 0.8589 (t0) cc_final: 0.8058 (t0) REVERT: C 74 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8447 (mtmm) REVERT: D 68 ASP cc_start: 0.8954 (t0) cc_final: 0.8719 (t0) REVERT: D 93 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.8603 (mp0) REVERT: E 73 GLU cc_start: 0.8593 (tt0) cc_final: 0.8357 (tm-30) REVERT: F 26 ILE cc_start: 0.8930 (tp) cc_final: 0.8628 (tt) REVERT: G 13 LYS cc_start: 0.8323 (tppp) cc_final: 0.8033 (tppt) REVERT: G 75 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8608 (mtpp) REVERT: G 95 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8386 (ttpp) REVERT: M 37 ARG cc_start: 0.8656 (ttm-80) cc_final: 0.8448 (mtm110) REVERT: M 97 LEU cc_start: 0.8866 (mt) cc_final: 0.8535 (mp) REVERT: M 112 GLU cc_start: 0.8262 (mm-30) cc_final: 0.8014 (mm-30) REVERT: M 230 MET cc_start: 0.8588 (OUTLIER) cc_final: 0.8074 (ttm) REVERT: M 256 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8910 (mp) REVERT: N 49 ARG cc_start: 0.7939 (mtm110) cc_final: 0.7667 (mtm110) REVERT: N 154 GLN cc_start: 0.8918 (mm-40) cc_final: 0.8700 (mm-40) REVERT: N 230 MET cc_start: 0.8414 (OUTLIER) cc_final: 0.6606 (tpt) outliers start: 39 outliers final: 20 residues processed: 228 average time/residue: 0.7430 time to fit residues: 184.8455 Evaluate side-chains 223 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 196 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain B residue 95 ARG 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 E residue 115 LYS Chi-restraints excluded: chain G residue 75 LYS 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 89 ILE Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 222 ASP Chi-restraints excluded: chain M residue 230 MET Chi-restraints excluded: chain M residue 256 LEU Chi-restraints excluded: chain N residue 100 ASP 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: 1.9990 chunk 123 optimal weight: 0.1980 chunk 52 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 112 optimal weight: 7.9990 chunk 158 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 105 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN D 47 GLN G 104 GLN H 82 HIS M 95 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.157566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.104031 restraints weight = 27369.305| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.49 r_work: 0.3235 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19448 Z= 0.147 Angle : 0.547 9.146 27970 Z= 0.324 Chirality : 0.034 0.156 3150 Planarity : 0.004 0.040 2162 Dihedral : 29.658 177.788 5714 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.91 % Allowed : 15.74 % Favored : 81.35 % 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: 1.90 (0.24), residues: 1270 helix: 2.37 (0.21), residues: 590 sheet: 0.90 (0.34), residues: 240 loop : -0.04 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 33 TYR 0.016 0.001 TYR H 40 PHE 0.010 0.001 PHE E 67 TRP 0.011 0.001 TRP M 60 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00321 (19444) covalent geometry : angle 0.54667 (27962) SS BOND : bond 0.00372 ( 4) SS BOND : angle 0.80526 ( 8) hydrogen bonds : bond 0.03379 ( 1100) hydrogen bonds : angle 3.14059 ( 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 248 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 216 time to evaluate : 0.527 Fit side-chains REVERT: A 37 LYS cc_start: 0.7178 (ptpp) cc_final: 0.6801 (ptpt) REVERT: B 84 MET cc_start: 0.9099 (mmm) cc_final: 0.8714 (mmm) REVERT: C 13 LYS cc_start: 0.8000 (mmmm) cc_final: 0.7790 (mmmt) REVERT: C 74 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8394 (mtmm) REVERT: D 68 ASP cc_start: 0.8933 (t0) cc_final: 0.8692 (t0) REVERT: D 93 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.8301 (mp0) REVERT: F 26 ILE cc_start: 0.8929 (tp) cc_final: 0.8576 (tt) REVERT: G 75 LYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8659 (mtpp) REVERT: M 154 GLN cc_start: 0.8446 (mm-40) cc_final: 0.8001 (tp-100) REVERT: M 230 MET cc_start: 0.8501 (OUTLIER) cc_final: 0.8034 (ttm) REVERT: N 43 LYS cc_start: 0.8395 (mmmm) cc_final: 0.8192 (tppp) REVERT: N 46 GLN cc_start: 0.8381 (mt0) cc_final: 0.8151 (mt0) REVERT: N 210 ASN cc_start: 0.8536 (t0) cc_final: 0.8083 (t0) REVERT: N 230 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.6430 (tpt) outliers start: 32 outliers final: 7 residues processed: 225 average time/residue: 0.7207 time to fit residues: 177.6395 Evaluate side-chains 210 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 198 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain G residue 75 LYS 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 230 MET Chi-restraints excluded: chain M residue 257 ASP Chi-restraints excluded: chain N residue 230 MET Chi-restraints excluded: chain N residue 257 ASP 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: 0.8980 chunk 39 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 135 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 112 optimal weight: 6.9990 chunk 101 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN D 47 GLN E 68 GLN 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.157250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.103885 restraints weight = 27115.172| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.53 r_work: 0.3224 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 19448 Z= 0.160 Angle : 0.548 7.524 27970 Z= 0.323 Chirality : 0.034 0.156 3150 Planarity : 0.004 0.040 2162 Dihedral : 29.646 179.811 5714 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.46 % Allowed : 17.47 % Favored : 80.07 % 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: 1.86 (0.24), residues: 1270 helix: 2.29 (0.21), residues: 602 sheet: 1.05 (0.34), residues: 232 loop : -0.12 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG M 37 TYR 0.019 0.001 TYR U 52 PHE 0.008 0.001 PHE M 178 TRP 0.012 0.001 TRP M 60 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00357 (19444) covalent geometry : angle 0.54744 (27962) SS BOND : bond 0.00350 ( 4) SS BOND : angle 0.98998 ( 8) hydrogen bonds : bond 0.03473 ( 1100) hydrogen bonds : angle 3.10889 ( 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 241 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 214 time to evaluate : 0.516 Fit side-chains REVERT: A 37 LYS cc_start: 0.7085 (ptpp) cc_final: 0.6700 (ptpt) REVERT: A 73 GLU cc_start: 0.8572 (tt0) cc_final: 0.8362 (tt0) REVERT: A 120 MET cc_start: 0.8299 (mtt) cc_final: 0.7781 (mtt) REVERT: B 84 MET cc_start: 0.9060 (mmm) cc_final: 0.8762 (mmm) REVERT: C 13 LYS cc_start: 0.8038 (mmmm) cc_final: 0.7833 (mmmt) REVERT: C 74 LYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8393 (mtmm) REVERT: D 68 ASP cc_start: 0.8939 (t0) cc_final: 0.8717 (t0) REVERT: D 93 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8312 (mp0) REVERT: E 73 GLU cc_start: 0.8750 (tm-30) cc_final: 0.8518 (tt0) REVERT: F 25 ASN cc_start: 0.8545 (m110) cc_final: 0.8225 (m110) REVERT: F 26 ILE cc_start: 0.8909 (tp) cc_final: 0.8529 (tt) REVERT: G 75 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.8681 (mtpp) REVERT: M 154 GLN cc_start: 0.8544 (mm-40) cc_final: 0.7948 (tp-100) REVERT: M 230 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.8046 (ttm) REVERT: M 261 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.7396 (pm20) REVERT: N 30 MET cc_start: 0.8103 (mtm) cc_final: 0.7873 (mtm) REVERT: N 46 GLN cc_start: 0.8404 (mt0) cc_final: 0.8129 (mt0) REVERT: N 210 ASN cc_start: 0.8508 (t0) cc_final: 0.8042 (t0) REVERT: N 211 GLU cc_start: 0.8223 (pp20) cc_final: 0.8002 (pp20) REVERT: N 230 MET cc_start: 0.8425 (OUTLIER) cc_final: 0.6531 (tpt) outliers start: 27 outliers final: 10 residues processed: 224 average time/residue: 0.7447 time to fit residues: 182.4638 Evaluate side-chains 213 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 197 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain C residue 74 LYS 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 75 LYS Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 86 ARG Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain M residue 165 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 117 optimal weight: 0.0020 chunk 94 optimal weight: 7.9990 chunk 43 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 97 optimal weight: 5.9990 chunk 149 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 141 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN D 47 GLN G 104 GLN 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 = 0.4144 r_free = 0.4144 target = 0.158702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.106009 restraints weight = 26951.202| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.51 r_work: 0.3262 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19448 Z= 0.144 Angle : 0.538 9.367 27970 Z= 0.317 Chirality : 0.034 0.155 3150 Planarity : 0.004 0.039 2162 Dihedral : 29.475 179.096 5714 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.55 % Allowed : 18.20 % Favored : 79.25 % 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: 2.01 (0.24), residues: 1270 helix: 2.40 (0.21), residues: 602 sheet: 1.15 (0.35), residues: 232 loop : -0.07 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 33 TYR 0.015 0.001 TYR H 40 PHE 0.009 0.001 PHE E 67 TRP 0.014 0.001 TRP M 60 HIS 0.004 0.001 HIS M 110 Details of bonding type rmsd covalent geometry : bond 0.00314 (19444) covalent geometry : angle 0.53825 (27962) SS BOND : bond 0.00327 ( 4) SS BOND : angle 0.78117 ( 8) hydrogen bonds : bond 0.03244 ( 1100) hydrogen bonds : angle 3.01584 ( 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 235 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 207 time to evaluate : 0.435 Fit side-chains REVERT: A 37 LYS cc_start: 0.7040 (ptpp) cc_final: 0.6664 (ptpt) REVERT: A 120 MET cc_start: 0.8197 (mtt) cc_final: 0.7730 (mtt) REVERT: C 74 LYS cc_start: 0.8832 (OUTLIER) cc_final: 0.8340 (mtmm) REVERT: D 42 TYR cc_start: 0.8178 (t80) cc_final: 0.7872 (t80) REVERT: D 68 ASP cc_start: 0.8913 (t0) cc_final: 0.8658 (t0) REVERT: D 93 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8343 (mp0) REVERT: E 73 GLU cc_start: 0.8787 (tm-30) cc_final: 0.8453 (tt0) REVERT: F 25 ASN cc_start: 0.8537 (m110) cc_final: 0.8266 (m110) REVERT: F 26 ILE cc_start: 0.8927 (tp) cc_final: 0.8548 (tt) REVERT: G 75 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8676 (mtpp) REVERT: M 230 MET cc_start: 0.8461 (OUTLIER) cc_final: 0.8112 (ttm) REVERT: N 30 MET cc_start: 0.8107 (mtm) cc_final: 0.7822 (mtm) REVERT: N 46 GLN cc_start: 0.8384 (mt0) cc_final: 0.8104 (mt0) REVERT: N 154 GLN cc_start: 0.8838 (mm-40) cc_final: 0.8440 (mm-40) REVERT: N 210 ASN cc_start: 0.8415 (t0) cc_final: 0.7977 (t0) REVERT: N 211 GLU cc_start: 0.8238 (pp20) cc_final: 0.7988 (pp20) REVERT: N 230 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.6415 (tpt) outliers start: 28 outliers final: 10 residues processed: 219 average time/residue: 0.7234 time to fit residues: 173.8146 Evaluate side-chains 216 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 201 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 74 LYS 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 75 LYS Chi-restraints excluded: chain G residue 114 VAL 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 23 MET 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: 10.0000 chunk 120 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 141 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 chunk 117 optimal weight: 4.9990 chunk 129 optimal weight: 7.9990 chunk 64 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 151 optimal weight: 7.9990 chunk 17 optimal weight: 9.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN G 104 GLN H 63 ASN H 82 HIS N 95 ASN ** 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 = 0.4123 r_free = 0.4123 target = 0.157279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.104031 restraints weight = 27264.805| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.51 r_work: 0.3224 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 19448 Z= 0.171 Angle : 0.552 7.851 27970 Z= 0.323 Chirality : 0.035 0.158 3150 Planarity : 0.004 0.039 2162 Dihedral : 29.574 177.683 5714 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.18 % Allowed : 19.29 % Favored : 78.53 % 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: 1.98 (0.24), residues: 1270 helix: 2.39 (0.21), residues: 590 sheet: 1.06 (0.34), residues: 240 loop : 0.00 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG N 37 TYR 0.024 0.002 TYR U 52 PHE 0.007 0.001 PHE E 67 TRP 0.012 0.001 TRP M 60 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00385 (19444) covalent geometry : angle 0.55189 (27962) SS BOND : bond 0.00361 ( 4) SS BOND : angle 0.98743 ( 8) hydrogen bonds : bond 0.03574 ( 1100) hydrogen bonds : angle 3.07705 ( 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 237 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 213 time to evaluate : 0.517 Fit side-chains REVERT: A 37 LYS cc_start: 0.7059 (ptpp) cc_final: 0.6697 (ptpt) REVERT: A 73 GLU cc_start: 0.8576 (tt0) cc_final: 0.8353 (tt0) REVERT: A 120 MET cc_start: 0.8292 (mtt) cc_final: 0.7769 (mtt) REVERT: B 84 MET cc_start: 0.9114 (mmm) cc_final: 0.8704 (mmm) REVERT: C 73 ASN cc_start: 0.8516 (t0) cc_final: 0.8029 (t0) REVERT: C 74 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8354 (mtmm) REVERT: D 68 ASP cc_start: 0.8941 (t0) cc_final: 0.8689 (t0) REVERT: D 93 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.8320 (mp0) REVERT: E 73 GLU cc_start: 0.8743 (tm-30) cc_final: 0.8523 (tt0) REVERT: F 24 ASP cc_start: 0.7071 (t70) cc_final: 0.6664 (p0) REVERT: F 25 ASN cc_start: 0.8559 (m110) cc_final: 0.8277 (m110) REVERT: F 26 ILE cc_start: 0.8920 (tp) cc_final: 0.8566 (tt) REVERT: G 75 LYS cc_start: 0.8937 (OUTLIER) cc_final: 0.8699 (mtpp) REVERT: G 95 LYS cc_start: 0.8859 (OUTLIER) cc_final: 0.8202 (ttpp) REVERT: M 154 GLN cc_start: 0.8413 (mm-40) cc_final: 0.7970 (tp-100) REVERT: N 30 MET cc_start: 0.8106 (mtm) cc_final: 0.7894 (mtm) REVERT: N 46 GLN cc_start: 0.8440 (mt0) cc_final: 0.8098 (mt0) REVERT: N 154 GLN cc_start: 0.8705 (mm-40) cc_final: 0.8253 (mm-40) REVERT: N 210 ASN cc_start: 0.8486 (t0) cc_final: 0.8015 (t0) REVERT: N 211 GLU cc_start: 0.8242 (pp20) cc_final: 0.7999 (pp20) REVERT: N 230 MET cc_start: 0.8431 (OUTLIER) cc_final: 0.6542 (tpt) outliers start: 24 outliers final: 12 residues processed: 221 average time/residue: 0.7458 time to fit residues: 180.3596 Evaluate side-chains 221 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 204 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain D residue 34 LYS 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 75 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 57 LYS 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 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: 6.9990 chunk 155 optimal weight: 9.9990 chunk 37 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 84 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 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 = 0.4096 r_free = 0.4096 target = 0.155295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.102373 restraints weight = 27124.268| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.49 r_work: 0.3188 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 19448 Z= 0.221 Angle : 0.593 9.789 27970 Z= 0.343 Chirality : 0.037 0.162 3150 Planarity : 0.004 0.045 2162 Dihedral : 29.797 176.624 5714 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.46 % Allowed : 19.93 % Favored : 77.62 % 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: 1.67 (0.24), residues: 1270 helix: 2.08 (0.21), residues: 590 sheet: 0.91 (0.34), residues: 240 loop : -0.07 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG N 37 TYR 0.023 0.002 TYR H 40 PHE 0.009 0.002 PHE N 117 TRP 0.017 0.002 TRP M 60 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00510 (19444) covalent geometry : angle 0.59303 (27962) SS BOND : bond 0.00409 ( 4) SS BOND : angle 0.83342 ( 8) hydrogen bonds : bond 0.04071 ( 1100) hydrogen bonds : angle 3.22372 ( 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 229 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 202 time to evaluate : 0.504 Fit side-chains REVERT: A 37 LYS cc_start: 0.7080 (ptpp) cc_final: 0.6738 (ptpt) REVERT: A 73 GLU cc_start: 0.8631 (tt0) cc_final: 0.8414 (tt0) REVERT: B 84 MET cc_start: 0.9144 (mmm) cc_final: 0.8672 (mmm) REVERT: C 73 ASN cc_start: 0.8560 (t0) cc_final: 0.8023 (t0) REVERT: C 74 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8419 (mtmm) REVERT: D 68 ASP cc_start: 0.8893 (t0) cc_final: 0.8652 (t0) REVERT: D 93 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8440 (mp0) REVERT: E 73 GLU cc_start: 0.8734 (tm-30) cc_final: 0.8530 (tt0) REVERT: F 24 ASP cc_start: 0.7217 (t70) cc_final: 0.6937 (p0) REVERT: F 26 ILE cc_start: 0.8958 (tp) cc_final: 0.8611 (tt) REVERT: G 75 LYS cc_start: 0.8994 (OUTLIER) cc_final: 0.8722 (mtpp) REVERT: G 95 LYS cc_start: 0.8872 (OUTLIER) cc_final: 0.8213 (ttpp) REVERT: M 154 GLN cc_start: 0.8504 (mm-40) cc_final: 0.8034 (tp-100) REVERT: N 30 MET cc_start: 0.8089 (mtm) cc_final: 0.7849 (mtm) REVERT: N 46 GLN cc_start: 0.8365 (mt0) cc_final: 0.8069 (mt0) REVERT: N 154 GLN cc_start: 0.8740 (mm-40) cc_final: 0.8256 (mm-40) REVERT: N 230 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.6634 (tpt) outliers start: 27 outliers final: 13 residues processed: 213 average time/residue: 0.7697 time to fit residues: 178.9503 Evaluate side-chains 217 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 199 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 ARG Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain D residue 34 LYS Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain G residue 75 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 49 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 26 optimal weight: 0.3980 chunk 77 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 107 optimal weight: 6.9990 chunk 127 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 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 = 0.4133 r_free = 0.4133 target = 0.158013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.105241 restraints weight = 27149.872| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.49 r_work: 0.3247 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19448 Z= 0.146 Angle : 0.552 9.539 27970 Z= 0.322 Chirality : 0.034 0.156 3150 Planarity : 0.004 0.051 2162 Dihedral : 29.533 178.023 5714 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.37 % Allowed : 20.11 % Favored : 77.53 % 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: 1.99 (0.24), residues: 1270 helix: 2.42 (0.21), residues: 590 sheet: 1.05 (0.35), residues: 240 loop : -0.02 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 35 TYR 0.028 0.001 TYR U 52 PHE 0.011 0.001 PHE E 67 TRP 0.019 0.001 TRP M 60 HIS 0.004 0.001 HIS M 31 Details of bonding type rmsd covalent geometry : bond 0.00321 (19444) covalent geometry : angle 0.55237 (27962) SS BOND : bond 0.00337 ( 4) SS BOND : angle 0.85442 ( 8) hydrogen bonds : bond 0.03327 ( 1100) hydrogen bonds : angle 3.03078 ( 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 234 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 208 time to evaluate : 0.423 Fit side-chains REVERT: A 37 LYS cc_start: 0.7101 (ptpp) cc_final: 0.6765 (ptpt) REVERT: A 73 GLU cc_start: 0.8599 (tt0) cc_final: 0.8394 (tt0) REVERT: C 73 ASN cc_start: 0.8529 (t0) cc_final: 0.8019 (t0) REVERT: C 74 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8393 (mtmm) REVERT: D 42 TYR cc_start: 0.8164 (t80) cc_final: 0.7871 (t80) REVERT: D 68 ASP cc_start: 0.8936 (t0) cc_final: 0.8655 (t0) REVERT: D 93 GLU cc_start: 0.8838 (OUTLIER) cc_final: 0.8400 (mp0) REVERT: E 73 GLU cc_start: 0.8723 (tm-30) cc_final: 0.8516 (tt0) REVERT: F 24 ASP cc_start: 0.7262 (t70) cc_final: 0.7034 (p0) REVERT: F 25 ASN cc_start: 0.8595 (m110) cc_final: 0.8298 (m110) REVERT: F 26 ILE cc_start: 0.8925 (tp) cc_final: 0.8563 (tt) REVERT: G 75 LYS cc_start: 0.8939 (OUTLIER) cc_final: 0.8703 (mtpp) REVERT: G 90 ASP cc_start: 0.8934 (t70) cc_final: 0.8540 (t0) REVERT: H 33 ARG cc_start: 0.7731 (mtp-110) cc_final: 0.7278 (mtm-85) REVERT: M 154 GLN cc_start: 0.8465 (mm-40) cc_final: 0.8003 (tp-100) REVERT: N 30 MET cc_start: 0.8092 (mtm) cc_final: 0.7762 (mtm) REVERT: N 46 GLN cc_start: 0.8361 (mt0) cc_final: 0.8096 (mt0) REVERT: N 154 GLN cc_start: 0.8713 (mm-40) cc_final: 0.8235 (mm-40) REVERT: N 210 ASN cc_start: 0.8464 (t0) cc_final: 0.8242 (t0) REVERT: N 230 MET cc_start: 0.8427 (OUTLIER) cc_final: 0.6443 (tpt) REVERT: U 30 MET cc_start: 0.5287 (ptt) cc_final: 0.4921 (pmt) outliers start: 26 outliers final: 12 residues processed: 216 average time/residue: 0.7350 time to fit residues: 174.0151 Evaluate side-chains 224 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 208 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain D residue 34 LYS 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 75 LYS Chi-restraints excluded: chain G residue 114 VAL 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 165 THR Chi-restraints excluded: chain M residue 195 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 26 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 73 optimal weight: 20.0000 chunk 98 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 122 optimal weight: 0.4980 chunk 107 optimal weight: 7.9990 chunk 130 optimal weight: 6.9990 chunk 143 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 93 GLN 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 = 0.4142 r_free = 0.4142 target = 0.158700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.106466 restraints weight = 27214.780| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.50 r_work: 0.3261 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19448 Z= 0.145 Angle : 0.557 10.094 27970 Z= 0.322 Chirality : 0.034 0.154 3150 Planarity : 0.004 0.051 2162 Dihedral : 29.479 176.763 5714 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.36 % Allowed : 20.93 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.09 (0.24), residues: 1270 helix: 2.49 (0.21), residues: 590 sheet: 1.17 (0.35), residues: 240 loop : 0.01 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG N 37 TYR 0.016 0.001 TYR H 40 PHE 0.009 0.001 PHE E 67 TRP 0.023 0.002 TRP M 60 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00322 (19444) covalent geometry : angle 0.55646 (27962) SS BOND : bond 0.00291 ( 4) SS BOND : angle 0.95517 ( 8) hydrogen bonds : bond 0.03292 ( 1100) hydrogen bonds : angle 2.98837 ( 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 228 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 213 time to evaluate : 0.421 Fit side-chains REVERT: A 37 LYS cc_start: 0.7084 (ptpp) cc_final: 0.6774 (ptpt) REVERT: A 73 GLU cc_start: 0.8582 (tt0) cc_final: 0.8362 (tt0) REVERT: A 120 MET cc_start: 0.8188 (mtt) cc_final: 0.7647 (mtt) REVERT: C 73 ASN cc_start: 0.8522 (t0) cc_final: 0.8056 (t0) REVERT: C 74 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8433 (mtmm) REVERT: D 42 TYR cc_start: 0.8153 (t80) cc_final: 0.7858 (t80) REVERT: D 68 ASP cc_start: 0.8939 (t0) cc_final: 0.8684 (t0) REVERT: D 93 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8370 (mp0) REVERT: E 73 GLU cc_start: 0.8715 (tm-30) cc_final: 0.8444 (tt0) REVERT: F 25 ASN cc_start: 0.8610 (m110) cc_final: 0.8338 (m110) REVERT: F 26 ILE cc_start: 0.8948 (tp) cc_final: 0.8570 (tt) REVERT: G 13 LYS cc_start: 0.8250 (tppp) cc_final: 0.8011 (tptp) REVERT: M 154 GLN cc_start: 0.8424 (mm-40) cc_final: 0.7959 (tp-100) REVERT: M 165 THR cc_start: 0.5967 (OUTLIER) cc_final: 0.5515 (t) REVERT: M 230 MET cc_start: 0.8274 (OUTLIER) cc_final: 0.7859 (ttm) REVERT: N 46 GLN cc_start: 0.8318 (mt0) cc_final: 0.8043 (mt0) REVERT: N 154 GLN cc_start: 0.8712 (mm-40) cc_final: 0.8231 (mm-40) REVERT: N 210 ASN cc_start: 0.8391 (t0) cc_final: 0.7962 (t0) REVERT: N 230 MET cc_start: 0.8426 (OUTLIER) cc_final: 0.6268 (tpt) REVERT: U 30 MET cc_start: 0.5320 (ptt) cc_final: 0.5011 (pmt) outliers start: 15 outliers final: 10 residues processed: 217 average time/residue: 0.7594 time to fit residues: 179.9526 Evaluate side-chains 211 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 196 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain D residue 34 LYS 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 114 VAL Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain M residue 165 THR Chi-restraints excluded: chain M residue 230 MET Chi-restraints excluded: chain N residue 80 ARG Chi-restraints excluded: chain N residue 100 ASP Chi-restraints excluded: chain N residue 161 VAL Chi-restraints excluded: chain N residue 230 MET Chi-restraints excluded: chain U residue 79 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 26 optimal weight: 0.2980 chunk 69 optimal weight: 0.9990 chunk 141 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 151 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 chunk 153 optimal weight: 0.9990 chunk 154 optimal weight: 0.8980 chunk 99 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4148 r_free = 0.4148 target = 0.159231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.106466 restraints weight = 27228.408| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.51 r_work: 0.3269 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19448 Z= 0.144 Angle : 0.561 10.396 27970 Z= 0.324 Chirality : 0.034 0.155 3150 Planarity : 0.004 0.056 2162 Dihedral : 29.401 176.715 5714 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.55 % Allowed : 21.38 % 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: 2.04 (0.24), residues: 1270 helix: 2.44 (0.21), residues: 602 sheet: 1.24 (0.35), residues: 232 loop : -0.11 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG H 33 TYR 0.029 0.001 TYR U 52 PHE 0.009 0.001 PHE E 67 TRP 0.018 0.001 TRP M 60 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00318 (19444) covalent geometry : angle 0.56048 (27962) SS BOND : bond 0.00290 ( 4) SS BOND : angle 0.85479 ( 8) hydrogen bonds : bond 0.03246 ( 1100) hydrogen bonds : angle 2.95639 ( 2712) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8473.59 seconds wall clock time: 144 minutes 29.09 seconds (8669.09 seconds total)