Starting phenix.real_space_refine on Sun Sep 13 00:54:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k5x_22683/09_2026/7k5x_22683.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k5x_22683/09_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_22683/09_2026/7k5x_22683.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k5x_22683/09_2026/7k5x_22683.map" model { file = "/net/cci-nas-00/data/ceres_data/7k5x_22683/09_2026/7k5x_22683.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k5x_22683/09_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-2.2.1-6174/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: 3.42, per 1000 atoms: 0.19 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: 1.48 Conformation dependent library (CDL) restraints added in 570.8 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: 2.75 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: 3.61 Time building geometry restraints manager: 1.98 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: 24853 1.16 - 2.31: 2511 2.31 - 3.47: 538 3.47 - 4.63: 45 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: 1.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.660 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.910 ------------------------------------------------------------------------------- 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 : 0.752 5.782 27970 Z= 0.646 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 / 0.49 (19444) covalent geometry : angle 0.75216 / 0.65 (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 : 0.531 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: 0.7608 (tp30) REVERT: C 95 LYS cc_start: 0.8778 (tttm) cc_final: 0.8361 (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: 0.8161 time to fit residues: 252.9451 Evaluate side-chains 213 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 0.487 ------------------------------------------------------------------------------- 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: 9.9990 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: 10.0000 chunk 77 optimal weight: 9.9990 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 = 0.4130 r_free = 0.4130 target = 0.157994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.105644 restraints weight = 27298.373| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.51 r_work: 0.3243 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 19448 Z= 0.155 Angle : 0.655 8.955 27970 Z= 0.379 Chirality : 0.046 0.269 3150 Planarity : 0.005 0.055 2162 Dihedral : 29.864 174.266 5714 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.09 % Allowed : 12.28 % Favored : 85.62 % 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: 1.65 (0.23), residues: 1270 helix: 2.18 (0.21), residues: 587 sheet: 0.51 (0.32), residues: 252 loop : 0.01 (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 90 TRP 0.007 0.001 TRP M 259 HIS 0.004 0.001 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.16 (19444) covalent geometry : angle 0.65494 / 0.38 (27962) SS BOND : bond 0.00569 / 0.29 ( 4) SS BOND : angle 1.08569 / 0.52 ( 8) hydrogen bonds : bond 0.04397 / 3.05 ( 1100) hydrogen bonds : angle 3.56223 / 2.67 ( 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 235 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 212 time to evaluate : 0.530 Fit side-chains REVERT: A 120 MET cc_start: 0.8236 (mtt) cc_final: 0.7695 (mtt) REVERT: B 93 GLN cc_start: 0.8565 (mt0) cc_final: 0.8364 (mt0) REVERT: C 32 ARG cc_start: 0.8810 (OUTLIER) cc_final: 0.8412 (tmm160) REVERT: C 61 GLU cc_start: 0.8558 (tp30) cc_final: 0.8279 (tp30) REVERT: D 68 ASP cc_start: 0.8980 (t0) cc_final: 0.8713 (t0) REVERT: D 93 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8136 (mp0) REVERT: E 73 GLU cc_start: 0.8652 (tt0) cc_final: 0.8362 (tt0) REVERT: F 26 ILE cc_start: 0.8890 (tp) cc_final: 0.8679 (tt) REVERT: G 62 ILE cc_start: 0.9218 (mt) cc_final: 0.8954 (mt) REVERT: G 95 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8321 (ttpp) REVERT: M 122 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7872 (tmtt) REVERT: M 154 GLN cc_start: 0.8440 (mm-40) cc_final: 0.8061 (tp-100) REVERT: N 162 GLU cc_start: 0.8031 (pp20) cc_final: 0.7688 (pm20) REVERT: N 210 ASN cc_start: 0.8691 (t0) cc_final: 0.8316 (t0) REVERT: U 30 MET cc_start: 0.6293 (mtp) cc_final: 0.6004 (mtp) REVERT: U 67 ILE cc_start: 0.7801 (mt) cc_final: 0.7559 (mt) outliers start: 23 outliers final: 9 residues processed: 218 average time/residue: 0.7598 time to fit residues: 181.9336 Evaluate side-chains 214 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 201 time to evaluate : 0.497 ------------------------------------------------------------------------------- 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 32 ARG 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 86 ARG Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain M residue 122 LYS 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: 2.9990 chunk 123 optimal weight: 7.9990 chunk 60 optimal weight: 1.9990 chunk 116 optimal weight: 8.9990 chunk 132 optimal weight: 6.9990 chunk 159 optimal weight: 9.9990 chunk 51 optimal weight: 0.0030 chunk 93 optimal weight: 40.0000 chunk 97 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 109 optimal weight: 50.0000 overall best weight: 3.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN D 47 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.153913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.099683 restraints weight = 27096.013| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.51 r_work: 0.3152 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 19448 Z= 0.283 Angle : 0.718 7.535 27970 Z= 0.399 Chirality : 0.050 0.273 3150 Planarity : 0.005 0.060 2162 Dihedral : 30.266 176.101 5714 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.28 % Allowed : 12.83 % 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: 1.03 (0.23), residues: 1270 helix: 1.49 (0.20), residues: 590 sheet: 0.45 (0.32), residues: 252 loop : -0.18 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG N 37 TYR 0.022 0.002 TYR C 50 PHE 0.016 0.002 PHE M 117 TRP 0.015 0.003 TRP M 259 HIS 0.010 0.002 HIS H 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00629 / 0.28 (19444) covalent geometry : angle 0.71737 / 0.40 (27962) SS BOND : bond 0.00546 / 0.28 ( 4) SS BOND : angle 1.40664 / 0.67 ( 8) hydrogen bonds : bond 0.05478 / 3.75 ( 1100) hydrogen bonds : angle 3.60837 / 2.69 ( 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 239 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 203 time to evaluate : 0.420 Fit side-chains REVERT: B 53 GLU cc_start: 0.8327 (mm-30) cc_final: 0.8123 (mm-30) REVERT: C 61 GLU cc_start: 0.8488 (tp30) cc_final: 0.8224 (tp30) REVERT: C 74 LYS cc_start: 0.8938 (OUTLIER) cc_final: 0.8466 (mtmm) REVERT: D 47 GLN cc_start: 0.8533 (mt0) cc_final: 0.8314 (mt0) REVERT: D 68 ASP cc_start: 0.8968 (t0) cc_final: 0.8740 (t0) REVERT: D 93 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8364 (mp0) REVERT: E 73 GLU cc_start: 0.8598 (tt0) cc_final: 0.8393 (tm-30) REVERT: F 26 ILE cc_start: 0.8941 (tp) cc_final: 0.8661 (tt) REVERT: G 62 ILE cc_start: 0.9243 (mt) cc_final: 0.8973 (mt) REVERT: G 95 LYS cc_start: 0.8949 (OUTLIER) cc_final: 0.8406 (ttpp) REVERT: N 230 MET cc_start: 0.8298 (OUTLIER) cc_final: 0.6671 (tpt) outliers start: 36 outliers final: 16 residues processed: 216 average time/residue: 0.7237 time to fit residues: 172.0384 Evaluate side-chains 209 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 189 time to evaluate : 0.489 ------------------------------------------------------------------------------- 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 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 88 THR Chi-restraints excluded: chain H residue 108 LYS 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 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: 0.5980 chunk 123 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 chunk 158 optimal weight: 9.9990 chunk 128 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 105 optimal weight: 10.0000 chunk 69 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN F 27 GLN 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.156350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.105642 restraints weight = 27170.005| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.74 r_work: 0.3179 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1626 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= 0.138 Angle : 0.631 8.913 27970 Z= 0.359 Chirality : 0.045 0.279 3150 Planarity : 0.004 0.045 2162 Dihedral : 30.195 177.649 5714 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.09 % Allowed : 14.56 % Favored : 82.35 % 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: 1.60 (0.23), residues: 1270 helix: 2.10 (0.21), residues: 590 sheet: 0.74 (0.34), residues: 240 loop : -0.12 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 33 TYR 0.017 0.001 TYR H 40 PHE 0.009 0.001 PHE M 178 TRP 0.009 0.001 TRP M 60 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.14 (19444) covalent geometry : angle 0.63076 / 0.36 (27962) SS BOND : bond 0.00366 / 0.18 ( 4) SS BOND : angle 0.82513 / 0.38 ( 8) hydrogen bonds : bond 0.04190 / 2.88 ( 1100) hydrogen bonds : angle 3.35783 / 2.50 ( 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 237 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 203 time to evaluate : 0.505 Fit side-chains revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8719 (tt0) cc_final: 0.8508 (tt0) REVERT: B 84 MET cc_start: 0.9139 (mmm) cc_final: 0.8825 (mmm) REVERT: C 74 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.8405 (mtmm) REVERT: D 68 ASP cc_start: 0.8944 (t0) cc_final: 0.8657 (t0) REVERT: D 76 GLU cc_start: 0.8780 (tp30) cc_final: 0.8460 (tp30) REVERT: D 93 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8432 (mp0) REVERT: F 26 ILE cc_start: 0.8880 (tp) cc_final: 0.8601 (tt) REVERT: G 62 ILE cc_start: 0.9245 (mt) cc_final: 0.9027 (mt) REVERT: M 154 GLN cc_start: 0.8606 (mm-40) cc_final: 0.8156 (tp-100) REVERT: M 261 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.8184 (pm20) REVERT: N 210 ASN cc_start: 0.8650 (t0) cc_final: 0.8173 (t0) REVERT: N 230 MET cc_start: 0.8335 (OUTLIER) cc_final: 0.6734 (tpt) outliers start: 34 outliers final: 17 residues processed: 216 average time/residue: 0.7123 time to fit residues: 169.8189 Evaluate side-chains 215 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 194 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 50 ILE 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 G residue 114 VAL Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain M residue 38 VAL 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 160 LEU 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: 3.9990 chunk 35 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 135 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 112 optimal weight: 8.9990 chunk 101 optimal weight: 10.0000 chunk 45 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 47 GLN F 27 GLN G 94 ASN G 104 GLN H 82 HIS ** 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 = 0.4119 r_free = 0.4119 target = 0.156795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.103584 restraints weight = 26984.589| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.52 r_work: 0.3211 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.1735 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= 0.137 Angle : 0.614 7.578 27970 Z= 0.351 Chirality : 0.044 0.274 3150 Planarity : 0.004 0.042 2162 Dihedral : 30.156 177.883 5714 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.91 % Allowed : 16.20 % Favored : 80.89 % 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: 1.71 (0.24), residues: 1270 helix: 2.17 (0.21), residues: 602 sheet: 0.98 (0.35), residues: 232 loop : -0.22 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 33 TYR 0.019 0.001 TYR H 40 PHE 0.010 0.001 PHE E 67 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 0.00260 / 0.14 (19444) covalent geometry : angle 0.61344 / 0.35 (27962) SS BOND : bond 0.00351 / 0.18 ( 4) SS BOND : angle 0.91835 / 0.43 ( 8) hydrogen bonds : bond 0.04019 / 2.78 ( 1100) hydrogen bonds : angle 3.27075 / 2.43 ( 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 239 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 207 time to evaluate : 0.525 Fit side-chains revert: symmetry clash REVERT: A 37 LYS cc_start: 0.7001 (ptpp) cc_final: 0.6616 (ptpt) REVERT: C 74 LYS cc_start: 0.8856 (OUTLIER) cc_final: 0.8388 (mtmm) REVERT: D 68 ASP cc_start: 0.8944 (t0) cc_final: 0.8730 (t0) REVERT: D 93 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.8367 (mp0) REVERT: F 26 ILE cc_start: 0.8905 (tp) cc_final: 0.8613 (tt) REVERT: G 13 LYS cc_start: 0.8192 (tppp) cc_final: 0.7856 (tppt) REVERT: G 95 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8282 (ttpp) REVERT: M 154 GLN cc_start: 0.8519 (mm-40) cc_final: 0.8059 (tp-100) REVERT: M 261 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.8191 (pm20) REVERT: N 46 GLN cc_start: 0.8395 (mt0) cc_final: 0.8161 (mt0) REVERT: N 210 ASN cc_start: 0.8612 (t0) cc_final: 0.8153 (t0) REVERT: N 230 MET cc_start: 0.8371 (OUTLIER) cc_final: 0.6713 (tpt) outliers start: 32 outliers final: 13 residues processed: 218 average time/residue: 0.7324 time to fit residues: 175.7397 Evaluate side-chains 214 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 196 time to evaluate : 0.507 ------------------------------------------------------------------------------- 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 50 ILE 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 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 160 LEU 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: 7.9990 chunk 94 optimal weight: 20.0000 chunk 43 optimal weight: 0.6980 chunk 2 optimal weight: 5.9990 chunk 97 optimal weight: 20.0000 chunk 149 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 60 optimal weight: 0.6980 chunk 141 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 47 GLN F 27 GLN 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.157272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.103457 restraints weight = 26835.357| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.48 r_work: 0.3228 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 19448 Z= 0.132 Angle : 0.601 9.652 27970 Z= 0.344 Chirality : 0.043 0.272 3150 Planarity : 0.004 0.046 2162 Dihedral : 30.136 179.128 5714 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.18 % Allowed : 17.47 % Favored : 79.34 % 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: 1.83 (0.24), residues: 1270 helix: 2.28 (0.21), residues: 602 sheet: 1.02 (0.35), residues: 232 loop : -0.16 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG H 33 TYR 0.017 0.001 TYR H 40 PHE 0.010 0.001 PHE E 67 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 0.00244 / 0.13 (19444) covalent geometry : angle 0.60104 / 0.34 (27962) SS BOND : bond 0.00350 / 0.18 ( 4) SS BOND : angle 0.79673 / 0.36 ( 8) hydrogen bonds : bond 0.03877 / 2.69 ( 1100) hydrogen bonds : angle 3.18712 / 2.36 ( 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 241 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 206 time to evaluate : 0.544 Fit side-chains REVERT: A 37 LYS cc_start: 0.7037 (ptpp) cc_final: 0.6620 (ptpt) REVERT: A 120 MET cc_start: 0.8339 (mtt) cc_final: 0.7806 (mtt) REVERT: B 84 MET cc_start: 0.9088 (mmm) cc_final: 0.8800 (mmm) REVERT: C 74 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8396 (mtmm) REVERT: D 68 ASP cc_start: 0.8935 (t0) cc_final: 0.8703 (t0) REVERT: D 93 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8338 (mp0) REVERT: F 26 ILE cc_start: 0.8929 (tp) cc_final: 0.8606 (tt) REVERT: G 95 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8288 (ttpp) REVERT: M 37 ARG cc_start: 0.8585 (ttm-80) cc_final: 0.8360 (mtm110) REVERT: M 154 GLN cc_start: 0.8546 (mm-40) cc_final: 0.8186 (tp-100) REVERT: M 261 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.8161 (pm20) REVERT: N 210 ASN cc_start: 0.8561 (t0) cc_final: 0.8099 (t0) REVERT: N 230 MET cc_start: 0.8388 (OUTLIER) cc_final: 0.6639 (tpt) outliers start: 35 outliers final: 16 residues processed: 217 average time/residue: 0.7127 time to fit residues: 170.4621 Evaluate side-chains 214 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 193 time to evaluate : 0.776 ------------------------------------------------------------------------------- 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 108 optimal weight: 40.0000 chunk 120 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 141 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 117 optimal weight: 5.9990 chunk 129 optimal weight: 10.0000 chunk 64 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 151 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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 = 0.4107 r_free = 0.4107 target = 0.155949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.103991 restraints weight = 27100.465| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.69 r_work: 0.3192 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 19448 Z= 0.173 Angle : 0.625 7.513 27970 Z= 0.352 Chirality : 0.044 0.271 3150 Planarity : 0.004 0.048 2162 Dihedral : 30.216 179.915 5714 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.91 % Allowed : 18.56 % 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: 1.64 (0.24), residues: 1270 helix: 2.07 (0.21), residues: 602 sheet: 0.96 (0.35), residues: 232 loop : -0.20 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG N 37 TYR 0.025 0.002 TYR H 40 PHE 0.009 0.001 PHE A 67 TRP 0.012 0.002 TRP M 60 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.17 (19444) covalent geometry : angle 0.62516 / 0.35 (27962) SS BOND : bond 0.00359 / 0.18 ( 4) SS BOND : angle 1.17781 / 0.56 ( 8) hydrogen bonds : bond 0.04277 / 2.95 ( 1100) hydrogen bonds : angle 3.24489 / 2.40 ( 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: 32 poor density : 200 time to evaluate : 0.429 Fit side-chains REVERT: A 37 LYS cc_start: 0.7158 (ptpp) cc_final: 0.6756 (ptpt) REVERT: B 92 ARG cc_start: 0.8814 (OUTLIER) cc_final: 0.7936 (ttp80) REVERT: C 74 LYS cc_start: 0.8913 (OUTLIER) cc_final: 0.8416 (mtmm) REVERT: D 68 ASP cc_start: 0.8927 (t0) cc_final: 0.8662 (t0) REVERT: D 93 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8375 (mp0) REVERT: F 25 ASN cc_start: 0.8510 (m110) cc_final: 0.8231 (m110) REVERT: F 26 ILE cc_start: 0.8950 (tp) cc_final: 0.8603 (tt) REVERT: G 90 ASP cc_start: 0.8995 (t70) cc_final: 0.8623 (t0) REVERT: G 95 LYS cc_start: 0.8874 (OUTLIER) cc_final: 0.8334 (ttpp) REVERT: M 154 GLN cc_start: 0.8591 (mm-40) cc_final: 0.8200 (tp-100) REVERT: M 261 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.8218 (pm20) REVERT: N 210 ASN cc_start: 0.8577 (t0) cc_final: 0.8089 (t0) REVERT: N 230 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.6644 (tpt) outliers start: 32 outliers final: 15 residues processed: 215 average time/residue: 0.7534 time to fit residues: 178.1764 Evaluate side-chains 216 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 195 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 93 GLU 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 H residue 119 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 Chi-restraints excluded: chain U residue 49 ILE 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: 0.0010 chunk 37 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 chunk 58 optimal weight: 0.7980 chunk 102 optimal weight: 9.9990 chunk 59 optimal weight: 0.7980 chunk 95 optimal weight: 20.0000 chunk 13 optimal weight: 0.4980 chunk 80 optimal weight: 10.0000 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN E 108 ASN G 104 GLN H 82 HIS M 95 ASN N 95 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.157913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.104213 restraints weight = 27102.016| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.48 r_work: 0.3236 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 19448 Z= 0.123 Angle : 0.601 10.817 27970 Z= 0.342 Chirality : 0.043 0.272 3150 Planarity : 0.004 0.059 2162 Dihedral : 30.134 178.617 5714 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.73 % Allowed : 19.38 % Favored : 77.89 % 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: 1.91 (0.24), residues: 1270 helix: 2.33 (0.21), residues: 602 sheet: 1.12 (0.35), residues: 232 loop : -0.14 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG N 37 TYR 0.027 0.001 TYR U 52 PHE 0.009 0.001 PHE E 67 TRP 0.011 0.001 TRP M 60 HIS 0.003 0.001 HIS M 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.12 (19444) covalent geometry : angle 0.60064 / 0.34 (27962) SS BOND : bond 0.00319 / 0.16 ( 4) SS BOND : angle 0.88538 / 0.41 ( 8) hydrogen bonds : bond 0.03783 / 2.63 ( 1100) hydrogen bonds : angle 3.15389 / 2.33 ( 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 232 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 202 time to evaluate : 0.555 Fit side-chains REVERT: A 37 LYS cc_start: 0.7152 (ptpp) cc_final: 0.6762 (ptpt) REVERT: A 120 MET cc_start: 0.8331 (mtt) cc_final: 0.7813 (mtt) REVERT: B 84 MET cc_start: 0.9128 (mmm) cc_final: 0.8764 (mmm) REVERT: B 92 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.7865 (ttp80) REVERT: C 32 ARG cc_start: 0.8874 (OUTLIER) cc_final: 0.8474 (tmm160) REVERT: C 74 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8394 (mtmm) REVERT: D 68 ASP cc_start: 0.8936 (t0) cc_final: 0.8701 (t0) REVERT: D 93 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.8351 (mp0) REVERT: F 26 ILE cc_start: 0.8961 (tp) cc_final: 0.8609 (tt) REVERT: M 154 GLN cc_start: 0.8555 (mm-40) cc_final: 0.8167 (tp-100) REVERT: M 230 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.8163 (ttm) REVERT: M 261 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.8196 (pm20) REVERT: N 210 ASN cc_start: 0.8504 (t0) cc_final: 0.8048 (t0) REVERT: N 230 MET cc_start: 0.8396 (OUTLIER) cc_final: 0.6566 (tpt) REVERT: U 74 LEU cc_start: 0.7909 (mm) cc_final: 0.7683 (mm) outliers start: 30 outliers final: 14 residues processed: 215 average time/residue: 0.7603 time to fit residues: 179.6855 Evaluate side-chains 215 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 194 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 32 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 114 VAL 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 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 Chi-restraints excluded: chain U residue 49 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 49 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 77 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 107 optimal weight: 20.0000 chunk 127 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 25 ASN 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 = 0.4115 r_free = 0.4115 target = 0.156676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.103062 restraints weight = 27044.394| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.51 r_work: 0.3216 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.2157 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= 0.156 Angle : 0.611 8.208 27970 Z= 0.347 Chirality : 0.043 0.269 3150 Planarity : 0.004 0.055 2162 Dihedral : 30.162 178.394 5714 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.00 % Allowed : 20.75 % 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: 1.76 (0.24), residues: 1270 helix: 2.16 (0.21), residues: 606 sheet: 1.05 (0.35), residues: 232 loop : -0.16 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG N 37 TYR 0.022 0.002 TYR H 40 PHE 0.009 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 0.00317 / 0.16 (19444) covalent geometry : angle 0.61100 / 0.35 (27962) SS BOND : bond 0.00365 / 0.18 ( 4) SS BOND : angle 1.04068 / 0.49 ( 8) hydrogen bonds : bond 0.04067 / 2.82 ( 1100) hydrogen bonds : angle 3.19235 / 2.36 ( 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 222 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 200 time to evaluate : 0.537 Fit side-chains REVERT: A 37 LYS cc_start: 0.7172 (ptpp) cc_final: 0.6786 (ptpt) REVERT: B 84 MET cc_start: 0.9079 (mmm) cc_final: 0.8777 (mmm) REVERT: B 92 ARG cc_start: 0.8843 (OUTLIER) cc_final: 0.7927 (ttp80) REVERT: C 74 LYS cc_start: 0.8884 (OUTLIER) cc_final: 0.8380 (mtmm) REVERT: D 68 ASP cc_start: 0.8942 (t0) cc_final: 0.8687 (t0) REVERT: D 93 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8329 (mp0) REVERT: F 26 ILE cc_start: 0.8948 (tp) cc_final: 0.8565 (tt) REVERT: M 230 MET cc_start: 0.8436 (OUTLIER) cc_final: 0.8216 (ttm) REVERT: N 154 GLN cc_start: 0.8566 (mm110) cc_final: 0.8227 (mm-40) REVERT: N 210 ASN cc_start: 0.8519 (t0) cc_final: 0.8050 (t0) REVERT: N 230 MET cc_start: 0.8415 (OUTLIER) cc_final: 0.6578 (tpt) REVERT: U 74 LEU cc_start: 0.7830 (mm) cc_final: 0.7608 (mm) outliers start: 22 outliers final: 13 residues processed: 208 average time/residue: 0.7707 time to fit residues: 175.9584 Evaluate side-chains 215 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 197 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain B residue 50 ILE 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 F residue 50 ILE 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 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: 0.6980 chunk 15 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 85 optimal weight: 10.0000 chunk 73 optimal weight: 50.0000 chunk 98 optimal weight: 10.0000 chunk 14 optimal weight: 0.9990 chunk 122 optimal weight: 10.0000 chunk 107 optimal weight: 20.0000 chunk 130 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- 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 = 0.4116 r_free = 0.4116 target = 0.156705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.102670 restraints weight = 27080.987| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.48 r_work: 0.3214 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.2234 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= 0.154 Angle : 0.617 10.633 27970 Z= 0.348 Chirality : 0.043 0.271 3150 Planarity : 0.004 0.057 2162 Dihedral : 30.178 177.243 5714 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.73 % Allowed : 21.29 % 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: 1.72 (0.24), residues: 1270 helix: 2.14 (0.21), residues: 606 sheet: 0.99 (0.35), residues: 232 loop : -0.17 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG N 37 TYR 0.028 0.002 TYR U 52 PHE 0.008 0.001 PHE E 67 TRP 0.014 0.001 TRP M 60 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.15 (19444) covalent geometry : angle 0.61698 / 0.35 (27962) SS BOND : bond 0.00395 / 0.20 ( 4) SS BOND : angle 1.25042 / 0.61 ( 8) hydrogen bonds : bond 0.04011 / 2.77 ( 1100) hydrogen bonds : angle 3.19431 / 2.36 ( 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 224 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 205 time to evaluate : 0.507 Fit side-chains REVERT: A 37 LYS cc_start: 0.7170 (ptpp) cc_final: 0.6787 (ptpt) REVERT: B 84 MET cc_start: 0.9078 (mmm) cc_final: 0.8781 (mmm) REVERT: B 92 ARG cc_start: 0.8818 (OUTLIER) cc_final: 0.7938 (ttp80) REVERT: C 74 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8389 (mtmm) REVERT: D 68 ASP cc_start: 0.8907 (t0) cc_final: 0.8697 (t0) REVERT: D 93 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.8352 (mp0) REVERT: F 26 ILE cc_start: 0.8912 (tp) cc_final: 0.8533 (tt) REVERT: G 13 LYS cc_start: 0.8136 (tppp) cc_final: 0.7842 (tppt) REVERT: G 90 ASP cc_start: 0.8975 (t70) cc_final: 0.8566 (t0) REVERT: M 154 GLN cc_start: 0.8391 (mm-40) cc_final: 0.7975 (tp-100) REVERT: N 49 ARG cc_start: 0.8009 (mtm110) cc_final: 0.7686 (mtm110) REVERT: N 154 GLN cc_start: 0.8589 (mm110) cc_final: 0.8248 (mm-40) REVERT: N 210 ASN cc_start: 0.8512 (t0) cc_final: 0.8041 (t0) REVERT: N 230 MET cc_start: 0.8414 (OUTLIER) cc_final: 0.6598 (tpt) REVERT: U 74 LEU cc_start: 0.8154 (mm) cc_final: 0.7926 (mm) outliers start: 19 outliers final: 14 residues processed: 211 average time/residue: 0.7522 time to fit residues: 174.3301 Evaluate side-chains 223 residues out of total 1099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 205 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain B residue 50 ILE 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 F residue 50 ILE 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 26 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 151 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 chunk 153 optimal weight: 0.8980 chunk 154 optimal weight: 0.9980 chunk 99 optimal weight: 9.9990 chunk 55 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 25 ASN 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 = 0.4121 r_free = 0.4121 target = 0.157138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.103810 restraints weight = 27145.719| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.48 r_work: 0.3224 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19448 Z= 0.138 Angle : 0.604 8.572 27970 Z= 0.343 Chirality : 0.042 0.268 3150 Planarity : 0.004 0.057 2162 Dihedral : 30.147 176.857 5714 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.64 % Allowed : 21.84 % Favored : 76.52 % 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: 2.22 (0.21), residues: 606 sheet: 1.03 (0.35), residues: 232 loop : -0.17 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG N 37 TYR 0.022 0.001 TYR H 40 PHE 0.009 0.001 PHE E 67 TRP 0.015 0.001 TRP M 60 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.14 (19444) covalent geometry : angle 0.60379 / 0.34 (27962) SS BOND : bond 0.00364 / 0.18 ( 4) SS BOND : angle 0.94449 / 0.43 ( 8) hydrogen bonds : bond 0.03896 / 2.70 ( 1100) hydrogen bonds : angle 3.16079 / 2.33 ( 2712) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8460.64 seconds wall clock time: 144 minutes 9.69 seconds (8649.69 seconds total)