Starting phenix.real_space_refine on Thu Aug 6 00:38:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9igj_52852/08_2026/9igj_52852.cif Found real_map, /net/cci-nas-00/data/ceres_data/9igj_52852/08_2026/9igj_52852.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9igj_52852/08_2026/9igj_52852.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9igj_52852/08_2026/9igj_52852.map" model { file = "/net/cci-nas-00/data/ceres_data/9igj_52852/08_2026/9igj_52852.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9igj_52852/08_2026/9igj_52852.cif" } resolution = 3.8 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= 0.002 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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 250 5.49 5 S 22 5.16 5 C 7126 2.51 5 N 2332 2.21 5 O 2799 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 83 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12529 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 791 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 843 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 784 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "F" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 795 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "H" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 699 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "L" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 737 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 3, 'TRANS': 82} Chain: "K" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 737 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 3, 'TRANS': 82} Chain: "J" Number of atoms: 2560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 2560 Classifications: {'DNA': 125} Link IDs: {'rna3p': 124} Chain: "I" Number of atoms: 2565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 2565 Classifications: {'DNA': 125} Link IDs: {'rna3p': 124} Time building chain proxies: 2.20, per 1000 atoms: 0.18 Number of scatterers: 12529 At special positions: 0 Unit cell: (88.672, 138.224, 143.44, 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 22 16.00 P 250 15.00 O 2799 8.00 N 2332 7.00 C 7126 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 490.7 milliseconds 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1724 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 12 sheets defined 70.9% alpha, 5.0% beta 125 base pairs and 233 stacking pairs defined. Time for finding SS restraints: 2.07 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.709A 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: 3.772A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (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 46 through 73 Processing helix chain 'C' and resid 79 through 90 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: 3.653A pdb=" N ALA D 107 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 3.781A 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 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.753A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.558A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.501A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) 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 103 through 123 removed outlier: 3.575A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) Processing helix chain 'L' and resid 209 through 220 Processing helix chain 'L' and resid 223 through 227 Processing helix chain 'L' and resid 233 through 235 No H-bonds generated for 'chain 'L' and resid 233 through 235' Processing helix chain 'L' and resid 242 through 254 Processing helix chain 'L' and resid 260 through 274 removed outlier: 3.697A pdb=" N GLN L 273 " --> pdb=" O ARG L 269 " (cutoff:3.500A) Processing helix chain 'K' and resid 209 through 220 Processing helix chain 'K' and resid 223 through 227 Processing helix chain 'K' and resid 233 through 235 No H-bonds generated for 'chain 'K' and resid 233 through 235' Processing helix chain 'K' and resid 242 through 254 Processing helix chain 'K' and resid 260 through 274 removed outlier: 3.702A pdb=" N GLN K 273 " --> pdb=" O ARG K 269 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.897A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.945A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.550A 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: 6.907A 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: 7.095A 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 'L' and resid 228 through 232 removed outlier: 6.778A pdb=" N ILE L 237 " --> pdb=" O THR L 231 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 228 through 232 removed outlier: 5.671A pdb=" N TRP K 230 " --> pdb=" O LYS K 239 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N LYS K 239 " --> pdb=" O TRP K 230 " (cutoff:3.500A) 483 hydrogen bonds defined for protein. 1419 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 322 hydrogen bonds 644 hydrogen bond angles 0 basepair planarities 125 basepair parallelities 233 stacking parallelities Total time for adding SS restraints: 2.74 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1682 1.32 - 1.44: 4666 1.44 - 1.57: 6381 1.57 - 1.69: 500 1.69 - 1.81: 38 Bond restraints: 13267 Sorted by residual: bond pdb=" C1' DT J -72 " pdb=" N1 DT J -72 " ideal model delta sigma weight residual 1.468 1.549 -0.081 1.40e-02 5.10e+03 3.32e+01 bond pdb=" C1' DG I 58 " pdb=" N9 DG I 58 " ideal model delta sigma weight residual 1.468 1.388 0.080 1.40e-02 5.10e+03 3.27e+01 bond pdb=" C1' DC I 71 " pdb=" N1 DC I 71 " ideal model delta sigma weight residual 1.468 1.548 -0.080 1.40e-02 5.10e+03 3.26e+01 bond pdb=" C1' DA I 72 " pdb=" N9 DA I 72 " ideal model delta sigma weight residual 1.468 1.392 0.076 1.40e-02 5.10e+03 2.99e+01 bond pdb=" C1' DC I 70 " pdb=" N1 DC I 70 " ideal model delta sigma weight residual 1.468 1.543 -0.075 1.40e-02 5.10e+03 2.86e+01 ... (remaining 13262 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.18: 18647 3.18 - 6.36: 314 6.36 - 9.54: 14 9.54 - 12.72: 0 12.72 - 15.90: 2 Bond angle restraints: 18977 Sorted by residual: angle pdb=" O5' DT I -16 " pdb=" C5' DT I -16 " pdb=" C4' DT I -16 " ideal model delta sigma weight residual 109.40 115.28 -5.88 8.00e-01 1.56e+00 5.39e+01 angle pdb=" O4' DG J -56 " pdb=" C1' DG J -56 " pdb=" N9 DG J -56 " ideal model delta sigma weight residual 108.00 112.76 -4.76 7.00e-01 2.04e+00 4.62e+01 angle pdb=" O4' DG I 55 " pdb=" C1' DG I 55 " pdb=" N9 DG I 55 " ideal model delta sigma weight residual 108.00 112.42 -4.42 7.00e-01 2.04e+00 3.98e+01 angle pdb=" O5' DC J 7 " pdb=" C5' DC J 7 " pdb=" C4' DC J 7 " ideal model delta sigma weight residual 109.40 114.05 -4.65 8.00e-01 1.56e+00 3.38e+01 angle pdb=" O5' DG J -70 " pdb=" C5' DG J -70 " pdb=" C4' DG J -70 " ideal model delta sigma weight residual 109.40 113.62 -4.22 8.00e-01 1.56e+00 2.78e+01 ... (remaining 18972 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 5052 17.66 - 35.32: 1001 35.32 - 52.97: 991 52.97 - 70.63: 275 70.63 - 88.29: 20 Dihedral angle restraints: 7339 sinusoidal: 4661 harmonic: 2678 Sorted by residual: dihedral pdb=" CA PRO H 103 " pdb=" C PRO H 103 " pdb=" N GLY H 104 " pdb=" CA GLY H 104 " ideal model delta harmonic sigma weight residual 180.00 151.87 28.13 0 5.00e+00 4.00e-02 3.17e+01 dihedral pdb=" CA LEU F 22 " pdb=" C LEU F 22 " pdb=" N ARG F 23 " pdb=" CA ARG F 23 " ideal model delta harmonic sigma weight residual -180.00 -158.00 -22.00 0 5.00e+00 4.00e-02 1.94e+01 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 180.00 158.43 21.57 0 5.00e+00 4.00e-02 1.86e+01 ... (remaining 7336 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 2022 0.119 - 0.238: 97 0.238 - 0.357: 9 0.357 - 0.477: 0 0.477 - 0.596: 11 Chirality restraints: 2139 Sorted by residual: chirality pdb=" P DG J -71 " pdb=" OP1 DG J -71 " pdb=" OP2 DG J -71 " pdb=" O5' DG J -71 " both_signs ideal model delta sigma weight residual True 2.34 -2.93 -0.60 2.00e-01 2.50e+01 8.87e+00 chirality pdb=" P DA J 29 " pdb=" OP1 DA J 29 " pdb=" OP2 DA J 29 " pdb=" O5' DA J 29 " both_signs ideal model delta sigma weight residual True 2.34 -2.87 -0.53 2.00e-01 2.50e+01 7.08e+00 chirality pdb=" P DT I -29 " pdb=" OP1 DT I -29 " pdb=" OP2 DT I -29 " pdb=" O5' DT I -29 " both_signs ideal model delta sigma weight residual True 2.34 -2.86 -0.52 2.00e-01 2.50e+01 6.86e+00 ... (remaining 2136 not shown) Planarity restraints: 1531 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT I -24 " 0.050 2.00e-02 2.50e+03 6.63e-02 1.10e+02 pdb=" N1 DT I -24 " 0.047 2.00e-02 2.50e+03 pdb=" C2 DT I -24 " -0.018 2.00e-02 2.50e+03 pdb=" O2 DT I -24 " -0.117 2.00e-02 2.50e+03 pdb=" N3 DT I -24 " 0.013 2.00e-02 2.50e+03 pdb=" C4 DT I -24 " 0.027 2.00e-02 2.50e+03 pdb=" O4 DT I -24 " 0.080 2.00e-02 2.50e+03 pdb=" C5 DT I -24 " -0.005 2.00e-02 2.50e+03 pdb=" C7 DT I -24 " -0.125 2.00e-02 2.50e+03 pdb=" C6 DT I -24 " 0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC J 5 " 0.101 2.00e-02 2.50e+03 6.31e-02 8.96e+01 pdb=" N1 DC J 5 " 0.023 2.00e-02 2.50e+03 pdb=" C2 DC J 5 " -0.008 2.00e-02 2.50e+03 pdb=" O2 DC J 5 " -0.067 2.00e-02 2.50e+03 pdb=" N3 DC J 5 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DC J 5 " -0.023 2.00e-02 2.50e+03 pdb=" N4 DC J 5 " 0.107 2.00e-02 2.50e+03 pdb=" C5 DC J 5 " -0.078 2.00e-02 2.50e+03 pdb=" C6 DC J 5 " -0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC J 7 " 0.111 2.00e-02 2.50e+03 5.98e-02 8.04e+01 pdb=" N1 DC J 7 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DC J 7 " -0.016 2.00e-02 2.50e+03 pdb=" O2 DC J 7 " -0.064 2.00e-02 2.50e+03 pdb=" N3 DC J 7 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DC J 7 " -0.004 2.00e-02 2.50e+03 pdb=" N4 DC J 7 " 0.089 2.00e-02 2.50e+03 pdb=" C5 DC J 7 " -0.067 2.00e-02 2.50e+03 pdb=" C6 DC J 7 " -0.056 2.00e-02 2.50e+03 ... (remaining 1528 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 3041 2.83 - 3.35: 10718 3.35 - 3.86: 24366 3.86 - 4.38: 28734 4.38 - 4.90: 40422 Nonbonded interactions: 107281 Sorted by model distance: nonbonded pdb=" NH2 ARG G 42 " pdb=" OP1 DA I -34 " model vdw 2.308 3.120 nonbonded pdb=" O CYS L 224 " pdb=" O ILE L 228 " model vdw 2.396 3.040 nonbonded pdb=" O CYS K 224 " pdb=" O ILE K 228 " model vdw 2.407 3.040 nonbonded pdb=" O MET L 292 " pdb=" CA PRO L 293 " model vdw 2.431 2.776 nonbonded pdb=" N ASP D 51 " pdb=" OD1 ASP D 51 " model vdw 2.444 3.120 ... (remaining 107276 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 40 through 133) selection = (chain 'E' and resid 40 through 133) } ncs_group { reference = (chain 'B' and resid 22 through 102) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 15 through 117) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 35 through 124) selection = chain 'H' } ncs_group { reference = chain 'K' selection = chain 'L' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.790 Find NCS groups from input model: 0.180 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:1.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6530 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 : 0.008 0.081 13267 Z= 0.708 Angle : 1.014 15.902 18977 Z= 0.824 Chirality : 0.071 0.596 2139 Planarity : 0.010 0.112 1531 Dihedral : 26.349 88.289 5615 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.44 % Allowed : 1.00 % Favored : 98.56 % Rotamer: Outliers : 0.77 % Allowed : 10.04 % Favored : 89.19 % 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 (0.27), residues: 900 helix: 1.76 (0.20), residues: 622 sheet: -2.68 (0.81), residues: 32 loop : 0.03 (0.36), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 35 TYR 0.036 0.003 TYR G 39 PHE 0.014 0.002 PHE L 289 TRP 0.014 0.002 TRP K 250 HIS 0.007 0.002 HIS G 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00820 / 0.71 (13267) covalent geometry : angle 1.01406 / 0.82 (18977) hydrogen bonds : bond 0.13008 / 8.63 ( 805) hydrogen bonds : angle 4.52164 / 3.28 ( 2063) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 367 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7570 (mm-30) REVERT: B 24 ASP cc_start: 0.4875 (m-30) cc_final: 0.3182 (m-30) REVERT: C 92 GLU cc_start: 0.6992 (mm-30) cc_final: 0.6428 (mm-30) REVERT: E 122 LYS cc_start: 0.7790 (ptpt) cc_final: 0.7515 (ptmm) REVERT: F 86 VAL cc_start: 0.7778 (t) cc_final: 0.7524 (t) REVERT: G 49 VAL cc_start: 0.6275 (t) cc_final: 0.6072 (t) outliers start: 6 outliers final: 0 residues processed: 367 average time/residue: 0.1551 time to fit residues: 75.7949 Evaluate side-chains 201 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 30.0000 chunk 49 optimal weight: 9.9990 chunk 97 optimal weight: 20.0000 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 50.0000 chunk 106 optimal weight: 20.0000 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN D 63 ASN E 113 HIS F 25 ASN F 93 GLN G 38 ASN G 73 ASN G 104 GLN K 232 GLN K 283 GLN K 288 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.036398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.028661 restraints weight = 133781.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.029443 restraints weight = 69079.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.029958 restraints weight = 43950.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.030338 restraints weight = 32185.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.030560 restraints weight = 25512.070| |-----------------------------------------------------------------------------| r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 13267 Z= 0.191 Angle : 0.830 12.137 18977 Z= 0.460 Chirality : 0.049 0.212 2139 Planarity : 0.007 0.110 1531 Dihedral : 29.345 98.657 3758 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.96 % Allowed : 22.27 % Favored : 74.77 % 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: 1.38 (0.27), residues: 900 helix: 1.52 (0.20), residues: 637 sheet: -2.41 (0.89), residues: 32 loop : -0.12 (0.38), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 39 TYR 0.025 0.002 TYR B 88 PHE 0.039 0.003 PHE H 65 TRP 0.011 0.002 TRP L 211 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.19 (13267) covalent geometry : angle 0.83014 / 0.46 (18977) hydrogen bonds : bond 0.05521 / 3.67 ( 805) hydrogen bonds : angle 3.87763 / 2.86 ( 2063) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 238 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9372 (tt0) cc_final: 0.9102 (pt0) REVERT: A 81 ASP cc_start: 0.7270 (t0) cc_final: 0.6950 (t0) REVERT: A 105 GLU cc_start: 0.8944 (mm-30) cc_final: 0.8695 (mm-30) REVERT: B 44 LYS cc_start: 0.9393 (tttt) cc_final: 0.9029 (ttpt) REVERT: B 88 TYR cc_start: 0.8982 (m-10) cc_final: 0.8747 (m-10) REVERT: B 93 GLN cc_start: 0.8832 (mm110) cc_final: 0.8601 (mm110) REVERT: C 92 GLU cc_start: 0.8656 (mm-30) cc_final: 0.8314 (mt-10) REVERT: D 63 ASN cc_start: 0.9118 (OUTLIER) cc_final: 0.8867 (t0) REVERT: D 68 ASP cc_start: 0.9190 (t0) cc_final: 0.7613 (t0) REVERT: E 52 ARG cc_start: 0.9489 (OUTLIER) cc_final: 0.9027 (mtm-85) REVERT: E 94 GLU cc_start: 0.8723 (tp30) cc_final: 0.8258 (tp30) REVERT: E 120 MET cc_start: 0.8885 (mtp) cc_final: 0.8054 (mpp) REVERT: F 24 ASP cc_start: 0.8292 (t0) cc_final: 0.7942 (t0) REVERT: F 63 GLU cc_start: 0.9101 (pt0) cc_final: 0.8837 (pp20) REVERT: G 24 GLN cc_start: 0.8854 (mm-40) cc_final: 0.8617 (mp10) REVERT: H 42 TYR cc_start: 0.8663 (OUTLIER) cc_final: 0.8327 (m-80) REVERT: H 95 GLN cc_start: 0.9285 (pt0) cc_final: 0.8559 (pp30) REVERT: H 105 GLU cc_start: 0.9047 (tp30) cc_final: 0.8717 (tp30) REVERT: L 264 MET cc_start: 0.8937 (ppp) cc_final: 0.8595 (ppp) REVERT: K 229 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.7526 (mmmt) REVERT: K 264 MET cc_start: 0.9678 (ttp) cc_final: 0.9187 (mtt) outliers start: 23 outliers final: 12 residues processed: 250 average time/residue: 0.1504 time to fit residues: 50.2806 Evaluate side-chains 212 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 196 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 42 TYR Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain K residue 229 LYS Chi-restraints excluded: chain K residue 241 VAL Chi-restraints excluded: chain K residue 248 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 71 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 45 optimal weight: 9.9990 chunk 94 optimal weight: 30.0000 chunk 101 optimal weight: 50.0000 chunk 85 optimal weight: 6.9990 chunk 8 optimal weight: 7.9990 chunk 44 optimal weight: 0.9990 chunk 4 optimal weight: 10.0000 chunk 102 optimal weight: 40.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 108 ASN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 ASN G 24 GLN G 38 ASN H 84 ASN K 232 GLN K 255 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.034009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.026327 restraints weight = 141258.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.027065 restraints weight = 73451.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.027570 restraints weight = 47180.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.027911 restraints weight = 34397.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.028139 restraints weight = 27503.024| |-----------------------------------------------------------------------------| r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 13267 Z= 0.232 Angle : 0.794 11.184 18977 Z= 0.440 Chirality : 0.047 0.237 2139 Planarity : 0.005 0.070 1531 Dihedral : 29.495 100.354 3758 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.09 % Allowed : 22.39 % Favored : 74.52 % 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: 1.52 (0.27), residues: 900 helix: 1.63 (0.20), residues: 635 sheet: -3.30 (0.94), residues: 20 loop : -0.14 (0.37), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG G 32 TYR 0.032 0.003 TYR G 39 PHE 0.044 0.002 PHE H 65 TRP 0.049 0.004 TRP L 250 HIS 0.008 0.002 HIS H 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.23 (13267) covalent geometry : angle 0.79416 / 0.44 (18977) hydrogen bonds : bond 0.06522 / 4.37 ( 805) hydrogen bonds : angle 3.95700 / 2.90 ( 2063) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 209 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.7580 (t0) cc_final: 0.7361 (t0) REVERT: B 44 LYS cc_start: 0.9469 (tttt) cc_final: 0.9040 (ttpt) REVERT: B 74 GLU cc_start: 0.8933 (tm-30) cc_final: 0.8634 (tm-30) REVERT: B 77 LYS cc_start: 0.9226 (mmmm) cc_final: 0.8906 (mmmt) REVERT: B 88 TYR cc_start: 0.9069 (m-10) cc_final: 0.8815 (m-10) REVERT: D 63 ASN cc_start: 0.9235 (OUTLIER) cc_final: 0.8777 (t0) REVERT: D 76 GLU cc_start: 0.8995 (tp30) cc_final: 0.8576 (tp30) REVERT: D 83 TYR cc_start: 0.8875 (m-80) cc_final: 0.8259 (m-80) REVERT: E 94 GLU cc_start: 0.8737 (tp30) cc_final: 0.8255 (tp30) REVERT: E 120 MET cc_start: 0.8963 (mtp) cc_final: 0.8499 (mtp) REVERT: F 59 LYS cc_start: 0.9232 (tppt) cc_final: 0.8972 (tppt) REVERT: F 63 GLU cc_start: 0.9126 (pt0) cc_final: 0.8915 (pt0) REVERT: G 39 TYR cc_start: 0.8839 (m-80) cc_final: 0.8639 (m-10) REVERT: H 42 TYR cc_start: 0.8771 (OUTLIER) cc_final: 0.8464 (m-80) REVERT: H 68 ASP cc_start: 0.8953 (t0) cc_final: 0.8738 (t0) REVERT: H 109 HIS cc_start: 0.9128 (m170) cc_final: 0.8756 (m90) REVERT: L 264 MET cc_start: 0.9074 (ppp) cc_final: 0.8824 (ppp) REVERT: K 227 TYR cc_start: 0.9440 (m-10) cc_final: 0.9006 (m-10) REVERT: K 238 PHE cc_start: 0.8834 (p90) cc_final: 0.8110 (p90) REVERT: K 264 MET cc_start: 0.9459 (ttp) cc_final: 0.8960 (mtp) outliers start: 24 outliers final: 14 residues processed: 220 average time/residue: 0.1227 time to fit residues: 36.5912 Evaluate side-chains 198 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 182 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 42 TYR Chi-restraints excluded: chain K residue 241 VAL Chi-restraints excluded: chain K residue 259 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 74 optimal weight: 20.0000 chunk 23 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 72 optimal weight: 7.9990 chunk 99 optimal weight: 50.0000 chunk 64 optimal weight: 8.9990 chunk 34 optimal weight: 30.0000 chunk 73 optimal weight: 7.9990 chunk 103 optimal weight: 30.0000 chunk 6 optimal weight: 0.9990 chunk 16 optimal weight: 0.0170 overall best weight: 4.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 ASN ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 232 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.033515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.025581 restraints weight = 137840.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.026353 restraints weight = 69618.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.026868 restraints weight = 44379.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.027177 restraints weight = 32393.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.027427 restraints weight = 26288.430| |-----------------------------------------------------------------------------| r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.4093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13267 Z= 0.208 Angle : 0.743 10.260 18977 Z= 0.418 Chirality : 0.046 0.222 2139 Planarity : 0.005 0.071 1531 Dihedral : 29.606 100.732 3758 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.73 % Allowed : 22.39 % Favored : 73.87 % 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: 1.50 (0.27), residues: 900 helix: 1.61 (0.20), residues: 638 sheet: -2.65 (1.04), residues: 20 loop : -0.19 (0.37), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 284 TYR 0.035 0.002 TYR D 83 PHE 0.052 0.002 PHE H 65 TRP 0.043 0.004 TRP K 230 HIS 0.006 0.002 HIS K 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.21 (13267) covalent geometry : angle 0.74344 / 0.42 (18977) hydrogen bonds : bond 0.05421 / 3.62 ( 805) hydrogen bonds : angle 3.87659 / 2.85 ( 2063) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 203 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.8716 (tp-100) cc_final: 0.8383 (tm-30) REVERT: A 94 GLU cc_start: 0.8933 (OUTLIER) cc_final: 0.8697 (tt0) REVERT: A 105 GLU cc_start: 0.8840 (mm-30) cc_final: 0.8531 (mm-30) REVERT: B 44 LYS cc_start: 0.9443 (tttt) cc_final: 0.9022 (ttpt) REVERT: B 64 ASN cc_start: 0.9358 (m-40) cc_final: 0.9025 (m-40) REVERT: B 74 GLU cc_start: 0.9081 (tm-30) cc_final: 0.8680 (tm-30) REVERT: B 77 LYS cc_start: 0.9261 (mmmm) cc_final: 0.8959 (mmmt) REVERT: B 88 TYR cc_start: 0.9170 (m-10) cc_final: 0.8884 (m-10) REVERT: B 93 GLN cc_start: 0.9048 (OUTLIER) cc_final: 0.8805 (mm110) REVERT: C 92 GLU cc_start: 0.9111 (mm-30) cc_final: 0.8892 (mm-30) REVERT: D 63 ASN cc_start: 0.9207 (OUTLIER) cc_final: 0.8870 (t0) REVERT: D 68 ASP cc_start: 0.9008 (t0) cc_final: 0.8164 (t0) REVERT: D 71 GLU cc_start: 0.8791 (pp20) cc_final: 0.8324 (pp20) REVERT: D 79 ARG cc_start: 0.9335 (ttm-80) cc_final: 0.9047 (mtm-85) REVERT: E 52 ARG cc_start: 0.9539 (OUTLIER) cc_final: 0.9079 (mtm-85) REVERT: E 94 GLU cc_start: 0.8281 (tp30) cc_final: 0.7859 (tp30) REVERT: E 120 MET cc_start: 0.8879 (mtp) cc_final: 0.8374 (mtp) REVERT: F 59 LYS cc_start: 0.9176 (tppt) cc_final: 0.8848 (tppt) REVERT: F 63 GLU cc_start: 0.9144 (pt0) cc_final: 0.8895 (pt0) REVERT: G 41 GLU cc_start: 0.8929 (mp0) cc_final: 0.8723 (mp0) REVERT: G 56 GLU cc_start: 0.9090 (tt0) cc_final: 0.8538 (mt-10) REVERT: G 89 ASN cc_start: 0.9542 (m-40) cc_final: 0.9180 (m-40) REVERT: H 42 TYR cc_start: 0.8879 (OUTLIER) cc_final: 0.8640 (m-80) REVERT: H 68 ASP cc_start: 0.9127 (t0) cc_final: 0.8864 (t0) REVERT: H 113 GLU cc_start: 0.9397 (tt0) cc_final: 0.8903 (mt-10) REVERT: K 238 PHE cc_start: 0.8959 (p90) cc_final: 0.8117 (p90) REVERT: K 264 MET cc_start: 0.9439 (ttp) cc_final: 0.8918 (mtm) REVERT: K 292 MET cc_start: 0.3606 (ttp) cc_final: 0.1861 (mtp) outliers start: 29 outliers final: 13 residues processed: 218 average time/residue: 0.1148 time to fit residues: 34.9184 Evaluate side-chains 200 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 182 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 42 TYR Chi-restraints excluded: chain K residue 255 ASN Chi-restraints excluded: chain K residue 259 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 67 optimal weight: 10.0000 chunk 4 optimal weight: 7.9990 chunk 29 optimal weight: 9.9990 chunk 71 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 110 optimal weight: 30.0000 chunk 80 optimal weight: 1.9990 chunk 95 optimal weight: 30.0000 chunk 12 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 96 optimal weight: 30.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 ASN G 68 ASN ** L 288 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 = 0.3096 r_free = 0.3096 target = 0.033136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.025316 restraints weight = 140078.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.026029 restraints weight = 72003.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.026494 restraints weight = 46292.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.026840 restraints weight = 34253.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.027020 restraints weight = 27485.740| |-----------------------------------------------------------------------------| r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.4424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13267 Z= 0.195 Angle : 0.722 8.859 18977 Z= 0.409 Chirality : 0.044 0.225 2139 Planarity : 0.005 0.054 1531 Dihedral : 29.608 100.667 3758 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.60 % Allowed : 24.71 % Favored : 71.69 % 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: 1.38 (0.27), residues: 900 helix: 1.53 (0.20), residues: 634 sheet: -2.63 (1.03), residues: 20 loop : -0.25 (0.36), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 92 TYR 0.042 0.002 TYR D 83 PHE 0.046 0.002 PHE H 65 TRP 0.011 0.002 TRP K 230 HIS 0.006 0.002 HIS K 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.19 (13267) covalent geometry : angle 0.72198 / 0.41 (18977) hydrogen bonds : bond 0.05293 / 3.56 ( 805) hydrogen bonds : angle 3.89787 / 2.86 ( 2063) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 193 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.8660 (tp-100) cc_final: 0.8294 (tm-30) REVERT: A 94 GLU cc_start: 0.8913 (tp30) cc_final: 0.8659 (tt0) REVERT: A 105 GLU cc_start: 0.8896 (mm-30) cc_final: 0.8444 (mm-30) REVERT: A 106 ASP cc_start: 0.9319 (m-30) cc_final: 0.9088 (m-30) REVERT: B 44 LYS cc_start: 0.9420 (tttt) cc_final: 0.8944 (ttpt) REVERT: B 53 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7946 (pt0) REVERT: B 64 ASN cc_start: 0.9340 (m-40) cc_final: 0.8997 (m-40) REVERT: B 74 GLU cc_start: 0.8972 (tm-30) cc_final: 0.8569 (tm-30) REVERT: B 77 LYS cc_start: 0.9322 (mmmm) cc_final: 0.9109 (mmmt) REVERT: D 63 ASN cc_start: 0.9144 (OUTLIER) cc_final: 0.8772 (t0) REVERT: D 68 ASP cc_start: 0.8968 (t0) cc_final: 0.8091 (t0) REVERT: D 71 GLU cc_start: 0.8782 (pp20) cc_final: 0.8389 (pp20) REVERT: D 76 GLU cc_start: 0.9092 (tp30) cc_final: 0.8792 (tp30) REVERT: D 79 ARG cc_start: 0.9174 (ttm-80) cc_final: 0.8706 (ttm110) REVERT: D 83 TYR cc_start: 0.8954 (m-80) cc_final: 0.8614 (m-80) REVERT: E 52 ARG cc_start: 0.9503 (OUTLIER) cc_final: 0.9051 (mtm-85) REVERT: E 120 MET cc_start: 0.8810 (mtp) cc_final: 0.8292 (mpp) REVERT: F 59 LYS cc_start: 0.9239 (tppt) cc_final: 0.8804 (tppt) REVERT: F 63 GLU cc_start: 0.9081 (pt0) cc_final: 0.8832 (pt0) REVERT: G 56 GLU cc_start: 0.9070 (tt0) cc_final: 0.8690 (mt-10) REVERT: H 42 TYR cc_start: 0.8857 (OUTLIER) cc_final: 0.8528 (m-80) REVERT: H 68 ASP cc_start: 0.9211 (t0) cc_final: 0.8966 (t0) REVERT: H 93 GLU cc_start: 0.9251 (mp0) cc_final: 0.9047 (mp0) REVERT: L 227 TYR cc_start: 0.9284 (m-80) cc_final: 0.8244 (m-80) REVERT: L 242 ASP cc_start: 0.8933 (t0) cc_final: 0.8215 (t0) REVERT: L 264 MET cc_start: 0.8667 (ppp) cc_final: 0.8429 (ppp) REVERT: K 238 PHE cc_start: 0.8883 (p90) cc_final: 0.8213 (p90) REVERT: K 264 MET cc_start: 0.9400 (ttp) cc_final: 0.8870 (mtm) outliers start: 28 outliers final: 21 residues processed: 207 average time/residue: 0.1166 time to fit residues: 33.6026 Evaluate side-chains 203 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 179 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 42 TYR Chi-restraints excluded: chain H residue 116 LYS Chi-restraints excluded: chain L residue 285 LEU Chi-restraints excluded: chain K residue 222 ASN Chi-restraints excluded: chain K residue 255 ASN Chi-restraints excluded: chain K residue 259 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 26 optimal weight: 0.6980 chunk 81 optimal weight: 10.0000 chunk 95 optimal weight: 30.0000 chunk 58 optimal weight: 6.9990 chunk 97 optimal weight: 40.0000 chunk 36 optimal weight: 9.9990 chunk 18 optimal weight: 0.0670 chunk 77 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 107 optimal weight: 30.0000 chunk 79 optimal weight: 20.0000 overall best weight: 2.3524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 288 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.033305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.025463 restraints weight = 139725.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.026195 restraints weight = 72042.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.026677 restraints weight = 46319.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.026969 restraints weight = 34181.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.027189 restraints weight = 27976.004| |-----------------------------------------------------------------------------| r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.4633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 13267 Z= 0.163 Angle : 0.713 10.545 18977 Z= 0.403 Chirality : 0.044 0.221 2139 Planarity : 0.005 0.055 1531 Dihedral : 29.563 100.851 3758 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.47 % Allowed : 25.48 % Favored : 71.04 % 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: 1.40 (0.28), residues: 900 helix: 1.66 (0.21), residues: 624 sheet: -2.16 (0.88), residues: 30 loop : -0.47 (0.37), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 226 TYR 0.035 0.002 TYR D 83 PHE 0.057 0.002 PHE H 65 TRP 0.012 0.002 TRP K 230 HIS 0.008 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.16 (13267) covalent geometry : angle 0.71266 / 0.40 (18977) hydrogen bonds : bond 0.04499 / 3.01 ( 805) hydrogen bonds : angle 3.80184 / 2.79 ( 2063) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 205 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.8601 (tp-100) cc_final: 0.8273 (tm-30) REVERT: A 94 GLU cc_start: 0.8904 (tp30) cc_final: 0.8648 (tt0) REVERT: A 105 GLU cc_start: 0.8960 (mm-30) cc_final: 0.8641 (mm-30) REVERT: B 26 ILE cc_start: 0.9111 (tt) cc_final: 0.8906 (tp) REVERT: B 44 LYS cc_start: 0.9382 (tttt) cc_final: 0.8933 (ttpt) REVERT: B 46 ILE cc_start: 0.9596 (tp) cc_final: 0.9350 (tp) REVERT: B 53 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7944 (pt0) REVERT: B 64 ASN cc_start: 0.9359 (m-40) cc_final: 0.9011 (m-40) REVERT: B 74 GLU cc_start: 0.8966 (tm-30) cc_final: 0.8563 (tm-30) REVERT: B 77 LYS cc_start: 0.9300 (mmmm) cc_final: 0.9093 (mmmt) REVERT: B 93 GLN cc_start: 0.9001 (OUTLIER) cc_final: 0.8731 (mm110) REVERT: D 68 ASP cc_start: 0.8929 (t0) cc_final: 0.8151 (t0) REVERT: D 71 GLU cc_start: 0.8794 (pp20) cc_final: 0.8567 (pp20) REVERT: D 83 TYR cc_start: 0.8826 (m-80) cc_final: 0.8623 (m-80) REVERT: E 52 ARG cc_start: 0.9508 (OUTLIER) cc_final: 0.9095 (mtm-85) REVERT: E 120 MET cc_start: 0.8838 (mtp) cc_final: 0.8389 (mpp) REVERT: F 59 LYS cc_start: 0.9231 (tppt) cc_final: 0.8751 (tppt) REVERT: F 63 GLU cc_start: 0.9093 (pt0) cc_final: 0.8833 (pt0) REVERT: G 56 GLU cc_start: 0.9066 (tt0) cc_final: 0.8635 (mt-10) REVERT: G 110 ASN cc_start: 0.9109 (t0) cc_final: 0.8668 (m110) REVERT: H 39 ILE cc_start: 0.9364 (OUTLIER) cc_final: 0.8989 (tp) REVERT: H 42 TYR cc_start: 0.8826 (OUTLIER) cc_final: 0.8503 (m-80) REVERT: H 68 ASP cc_start: 0.9264 (t0) cc_final: 0.8907 (t0) REVERT: H 71 GLU cc_start: 0.9318 (tp30) cc_final: 0.9073 (tp30) REVERT: H 82 HIS cc_start: 0.9269 (t-90) cc_final: 0.9063 (t-90) REVERT: L 242 ASP cc_start: 0.8816 (t0) cc_final: 0.8348 (t0) REVERT: L 264 MET cc_start: 0.8609 (ppp) cc_final: 0.8344 (ppp) REVERT: K 229 LYS cc_start: 0.8297 (OUTLIER) cc_final: 0.7657 (mmmt) REVERT: K 238 PHE cc_start: 0.8867 (p90) cc_final: 0.8202 (p90) REVERT: K 264 MET cc_start: 0.9326 (ttp) cc_final: 0.8796 (mtm) outliers start: 27 outliers final: 17 residues processed: 219 average time/residue: 0.1223 time to fit residues: 36.8523 Evaluate side-chains 210 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 188 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 42 TYR Chi-restraints excluded: chain H residue 79 ARG Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain H residue 116 LYS Chi-restraints excluded: chain K residue 229 LYS Chi-restraints excluded: chain K residue 255 ASN Chi-restraints excluded: chain K residue 259 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 5.9990 chunk 74 optimal weight: 20.0000 chunk 50 optimal weight: 10.0000 chunk 45 optimal weight: 0.9990 chunk 4 optimal weight: 9.9990 chunk 60 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 32 optimal weight: 8.9990 chunk 85 optimal weight: 5.9990 chunk 28 optimal weight: 9.9990 chunk 62 optimal weight: 30.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 288 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.032581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.024778 restraints weight = 140538.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.025490 restraints weight = 72836.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.025951 restraints weight = 47139.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.026237 restraints weight = 34969.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.026459 restraints weight = 28657.433| |-----------------------------------------------------------------------------| r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.4987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 13267 Z= 0.195 Angle : 0.737 10.715 18977 Z= 0.413 Chirality : 0.044 0.229 2139 Planarity : 0.005 0.049 1531 Dihedral : 29.617 99.958 3758 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.60 % Allowed : 26.51 % Favored : 69.88 % 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: 1.45 (0.28), residues: 900 helix: 1.56 (0.21), residues: 631 sheet: -2.82 (0.90), residues: 20 loop : -0.09 (0.37), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG L 226 TYR 0.037 0.002 TYR D 83 PHE 0.049 0.002 PHE H 65 TRP 0.011 0.002 TRP K 230 HIS 0.006 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.19 (13267) covalent geometry : angle 0.73708 / 0.41 (18977) hydrogen bonds : bond 0.05426 / 3.65 ( 805) hydrogen bonds : angle 3.82524 / 2.81 ( 2063) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 192 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.9573 (OUTLIER) cc_final: 0.9185 (mmmm) REVERT: A 68 GLN cc_start: 0.8599 (tp-100) cc_final: 0.8064 (tp-100) REVERT: A 105 GLU cc_start: 0.8962 (mm-30) cc_final: 0.8703 (mm-30) REVERT: B 44 LYS cc_start: 0.9360 (tttt) cc_final: 0.8964 (ttpt) REVERT: B 46 ILE cc_start: 0.9656 (tp) cc_final: 0.9440 (tp) REVERT: B 53 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7981 (pt0) REVERT: B 59 LYS cc_start: 0.9502 (ttpp) cc_final: 0.8985 (tmmt) REVERT: B 64 ASN cc_start: 0.9364 (m-40) cc_final: 0.9018 (m-40) REVERT: B 93 GLN cc_start: 0.9052 (mm110) cc_final: 0.8782 (mm110) REVERT: D 79 ARG cc_start: 0.9428 (ttm110) cc_final: 0.8999 (mtm-85) REVERT: E 52 ARG cc_start: 0.9508 (OUTLIER) cc_final: 0.8998 (mtm-85) REVERT: E 94 GLU cc_start: 0.8221 (tp30) cc_final: 0.7732 (tp30) REVERT: E 120 MET cc_start: 0.8844 (mtp) cc_final: 0.8372 (mtp) REVERT: F 59 LYS cc_start: 0.9286 (tppt) cc_final: 0.8825 (tppt) REVERT: F 63 GLU cc_start: 0.9076 (pt0) cc_final: 0.8842 (pt0) REVERT: G 56 GLU cc_start: 0.9137 (tt0) cc_final: 0.8700 (mt-10) REVERT: H 42 TYR cc_start: 0.8951 (OUTLIER) cc_final: 0.8612 (m-80) REVERT: H 68 ASP cc_start: 0.9351 (t0) cc_final: 0.9008 (t0) REVERT: H 71 GLU cc_start: 0.9336 (tp30) cc_final: 0.9074 (tp30) REVERT: H 82 HIS cc_start: 0.9272 (t-90) cc_final: 0.9055 (t-90) REVERT: H 109 HIS cc_start: 0.9203 (m170) cc_final: 0.8809 (m90) REVERT: H 113 GLU cc_start: 0.9301 (tt0) cc_final: 0.9041 (mt-10) REVERT: L 227 TYR cc_start: 0.8780 (m-80) cc_final: 0.8510 (m-80) REVERT: L 242 ASP cc_start: 0.8986 (t0) cc_final: 0.8657 (t0) REVERT: L 264 MET cc_start: 0.8969 (ppp) cc_final: 0.8683 (ppp) REVERT: K 229 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.7563 (mmmt) REVERT: K 238 PHE cc_start: 0.8796 (p90) cc_final: 0.8181 (p90) REVERT: K 264 MET cc_start: 0.9256 (ttp) cc_final: 0.8726 (mtm) REVERT: K 292 MET cc_start: 0.2747 (mtp) cc_final: 0.2535 (mtt) outliers start: 28 outliers final: 18 residues processed: 208 average time/residue: 0.1215 time to fit residues: 34.7969 Evaluate side-chains 204 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 182 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 35 GLU Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain H residue 42 TYR Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain K residue 228 ILE Chi-restraints excluded: chain K residue 229 LYS Chi-restraints excluded: chain K residue 255 ASN Chi-restraints excluded: chain K residue 259 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 84 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 chunk 62 optimal weight: 7.9990 chunk 71 optimal weight: 6.9990 chunk 60 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 29 optimal weight: 10.0000 chunk 83 optimal weight: 3.9990 chunk 3 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.032132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.024419 restraints weight = 141649.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.025114 restraints weight = 73120.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.025553 restraints weight = 47320.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.025874 restraints weight = 35047.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.026061 restraints weight = 28486.955| |-----------------------------------------------------------------------------| r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.5295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 13267 Z= 0.210 Angle : 0.769 17.232 18977 Z= 0.426 Chirality : 0.044 0.235 2139 Planarity : 0.005 0.045 1531 Dihedral : 29.719 99.182 3758 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.22 % Allowed : 27.93 % Favored : 68.85 % 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: 1.41 (0.28), residues: 900 helix: 1.50 (0.20), residues: 629 sheet: -2.60 (0.96), residues: 20 loop : -0.04 (0.38), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 52 TYR 0.054 0.003 TYR D 83 PHE 0.046 0.002 PHE H 65 TRP 0.010 0.002 TRP L 230 HIS 0.006 0.002 HIS K 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.21 (13267) covalent geometry : angle 0.76872 / 0.43 (18977) hydrogen bonds : bond 0.05468 / 3.68 ( 805) hydrogen bonds : angle 3.93612 / 2.87 ( 2063) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 187 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.8662 (tp-100) cc_final: 0.8117 (tp-100) REVERT: A 105 GLU cc_start: 0.8967 (mm-30) cc_final: 0.8706 (mm-30) REVERT: B 44 LYS cc_start: 0.9385 (tttt) cc_final: 0.8983 (ttpt) REVERT: B 46 ILE cc_start: 0.9665 (tp) cc_final: 0.9463 (tp) REVERT: B 53 GLU cc_start: 0.8279 (mt-10) cc_final: 0.8037 (pt0) REVERT: B 64 ASN cc_start: 0.9347 (m-40) cc_final: 0.9047 (m110) REVERT: B 77 LYS cc_start: 0.9324 (mmmm) cc_final: 0.9048 (mmmt) REVERT: B 88 TYR cc_start: 0.9168 (m-10) cc_final: 0.8945 (m-80) REVERT: B 93 GLN cc_start: 0.9081 (OUTLIER) cc_final: 0.8831 (mm110) REVERT: C 110 ASN cc_start: 0.8960 (t0) cc_final: 0.8489 (p0) REVERT: D 71 GLU cc_start: 0.8857 (pp20) cc_final: 0.8493 (pp20) REVERT: D 72 ARG cc_start: 0.9238 (OUTLIER) cc_final: 0.9020 (mmm-85) REVERT: D 79 ARG cc_start: 0.9457 (ttm110) cc_final: 0.9166 (ttm110) REVERT: E 59 GLU cc_start: 0.8667 (pm20) cc_final: 0.8432 (pm20) REVERT: F 59 LYS cc_start: 0.9278 (tppt) cc_final: 0.8834 (tppt) REVERT: F 63 GLU cc_start: 0.9078 (pt0) cc_final: 0.8847 (pt0) REVERT: G 56 GLU cc_start: 0.9143 (tt0) cc_final: 0.8723 (mt-10) REVERT: H 42 TYR cc_start: 0.8974 (OUTLIER) cc_final: 0.8600 (m-80) REVERT: H 64 SER cc_start: 0.9314 (m) cc_final: 0.9096 (p) REVERT: H 68 ASP cc_start: 0.9390 (t0) cc_final: 0.9101 (t0) REVERT: H 71 GLU cc_start: 0.9324 (tp30) cc_final: 0.9074 (tp30) REVERT: H 82 HIS cc_start: 0.9292 (t-90) cc_final: 0.9075 (t-90) REVERT: H 109 HIS cc_start: 0.9230 (m170) cc_final: 0.8832 (m90) REVERT: H 113 GLU cc_start: 0.9302 (tt0) cc_final: 0.9064 (mt-10) REVERT: L 227 TYR cc_start: 0.8860 (m-80) cc_final: 0.8564 (m-80) REVERT: L 242 ASP cc_start: 0.8742 (t0) cc_final: 0.8370 (t0) REVERT: L 264 MET cc_start: 0.8976 (ppp) cc_final: 0.8654 (ppp) REVERT: K 229 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7481 (mmmt) REVERT: K 238 PHE cc_start: 0.8720 (p90) cc_final: 0.8078 (p90) REVERT: K 264 MET cc_start: 0.9205 (ttp) cc_final: 0.8686 (mtm) outliers start: 25 outliers final: 20 residues processed: 202 average time/residue: 0.1262 time to fit residues: 35.2775 Evaluate side-chains 204 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 180 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 72 ARG Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 42 TYR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain K residue 228 ILE Chi-restraints excluded: chain K residue 229 LYS Chi-restraints excluded: chain K residue 255 ASN Chi-restraints excluded: chain K residue 258 ASP Chi-restraints excluded: chain K residue 259 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 58 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 7 optimal weight: 6.9990 chunk 3 optimal weight: 0.0000 chunk 108 optimal weight: 30.0000 chunk 27 optimal weight: 9.9990 chunk 40 optimal weight: 6.9990 chunk 75 optimal weight: 20.0000 chunk 41 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 39 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 288 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.032431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.024671 restraints weight = 142083.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.025385 restraints weight = 72941.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.025855 restraints weight = 47033.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.026165 restraints weight = 34698.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.026352 restraints weight = 27962.905| |-----------------------------------------------------------------------------| r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.5452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 13267 Z= 0.176 Angle : 0.765 17.014 18977 Z= 0.421 Chirality : 0.044 0.230 2139 Planarity : 0.004 0.038 1531 Dihedral : 29.689 99.164 3758 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.09 % Allowed : 27.80 % Favored : 69.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.28), residues: 900 helix: 1.56 (0.21), residues: 629 sheet: -2.62 (0.99), residues: 20 loop : -0.09 (0.38), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 226 TYR 0.060 0.002 TYR B 88 PHE 0.046 0.002 PHE H 65 TRP 0.008 0.002 TRP L 230 HIS 0.005 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.18 (13267) covalent geometry : angle 0.76536 / 0.42 (18977) hydrogen bonds : bond 0.04575 / 3.05 ( 805) hydrogen bonds : angle 3.88355 / 2.83 ( 2063) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 186 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.9596 (OUTLIER) cc_final: 0.9199 (mmmm) REVERT: A 68 GLN cc_start: 0.8647 (tp-100) cc_final: 0.8095 (tp-100) REVERT: A 105 GLU cc_start: 0.8996 (mm-30) cc_final: 0.8723 (mm-30) REVERT: B 44 LYS cc_start: 0.9370 (tttt) cc_final: 0.8971 (ttpt) REVERT: B 46 ILE cc_start: 0.9657 (tp) cc_final: 0.9453 (tp) REVERT: B 53 GLU cc_start: 0.8317 (mt-10) cc_final: 0.8062 (pt0) REVERT: B 59 LYS cc_start: 0.9498 (ttpp) cc_final: 0.8944 (tmmt) REVERT: B 64 ASN cc_start: 0.9403 (m-40) cc_final: 0.9139 (m-40) REVERT: B 91 LYS cc_start: 0.9112 (pptt) cc_final: 0.8575 (pttp) REVERT: C 110 ASN cc_start: 0.8980 (t0) cc_final: 0.8536 (p0) REVERT: D 79 ARG cc_start: 0.9421 (ttm110) cc_final: 0.9089 (ttm110) REVERT: D 83 TYR cc_start: 0.8913 (m-80) cc_final: 0.8679 (m-80) REVERT: E 59 GLU cc_start: 0.8787 (pm20) cc_final: 0.8555 (pm20) REVERT: E 120 MET cc_start: 0.8823 (mtp) cc_final: 0.8380 (mtp) REVERT: F 59 LYS cc_start: 0.9252 (tppt) cc_final: 0.8774 (tppt) REVERT: G 56 GLU cc_start: 0.9117 (tt0) cc_final: 0.8686 (mt-10) REVERT: H 39 ILE cc_start: 0.9173 (OUTLIER) cc_final: 0.8757 (tp) REVERT: H 42 TYR cc_start: 0.8963 (OUTLIER) cc_final: 0.8662 (m-80) REVERT: H 59 MET cc_start: 0.9079 (tpt) cc_final: 0.8869 (tpt) REVERT: H 68 ASP cc_start: 0.9443 (t0) cc_final: 0.9146 (t0) REVERT: H 71 GLU cc_start: 0.9325 (tp30) cc_final: 0.9044 (tp30) REVERT: H 82 HIS cc_start: 0.9300 (t-90) cc_final: 0.9094 (t-90) REVERT: H 109 HIS cc_start: 0.9220 (m170) cc_final: 0.8800 (m90) REVERT: H 113 GLU cc_start: 0.9303 (tt0) cc_final: 0.9073 (mt-10) REVERT: L 227 TYR cc_start: 0.8855 (m-80) cc_final: 0.8545 (m-80) REVERT: L 242 ASP cc_start: 0.8724 (t0) cc_final: 0.8326 (t0) REVERT: L 264 MET cc_start: 0.9036 (ppp) cc_final: 0.8711 (ppp) REVERT: K 238 PHE cc_start: 0.8707 (p90) cc_final: 0.8112 (p90) REVERT: K 264 MET cc_start: 0.9244 (ttp) cc_final: 0.8771 (mtm) outliers start: 24 outliers final: 16 residues processed: 199 average time/residue: 0.1228 time to fit residues: 34.1208 Evaluate side-chains 198 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 179 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 42 TYR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain K residue 228 ILE Chi-restraints excluded: chain K residue 229 LYS Chi-restraints excluded: chain K residue 255 ASN Chi-restraints excluded: chain K residue 258 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 90 optimal weight: 30.0000 chunk 38 optimal weight: 0.0270 chunk 37 optimal weight: 5.9990 chunk 40 optimal weight: 9.9990 chunk 78 optimal weight: 30.0000 chunk 109 optimal weight: 40.0000 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 20.0000 chunk 86 optimal weight: 3.9990 chunk 43 optimal weight: 9.9990 chunk 68 optimal weight: 9.9990 overall best weight: 5.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 253 HIS ** K 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.031315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.023596 restraints weight = 144529.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.024282 restraints weight = 74919.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.024721 restraints weight = 48421.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.024996 restraints weight = 35925.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.025206 restraints weight = 29240.158| |-----------------------------------------------------------------------------| r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.5833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.118 13267 Z= 0.239 Angle : 0.806 16.914 18977 Z= 0.442 Chirality : 0.045 0.245 2139 Planarity : 0.005 0.037 1531 Dihedral : 29.863 97.596 3758 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 17.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.35 % Allowed : 27.54 % Favored : 69.11 % 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: 1.19 (0.28), residues: 900 helix: 1.33 (0.20), residues: 636 sheet: -2.85 (0.95), residues: 20 loop : -0.13 (0.38), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 99 TYR 0.064 0.003 TYR D 83 PHE 0.036 0.003 PHE H 65 TRP 0.014 0.002 TRP K 250 HIS 0.011 0.002 HIS K 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.24 (13267) covalent geometry : angle 0.80602 / 0.44 (18977) hydrogen bonds : bond 0.06747 / 4.54 ( 805) hydrogen bonds : angle 4.07823 / 2.97 ( 2063) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 176 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.9646 (OUTLIER) cc_final: 0.9277 (mmmm) REVERT: A 68 GLN cc_start: 0.8722 (tp-100) cc_final: 0.8164 (tp-100) REVERT: A 126 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.8936 (tp) REVERT: B 44 LYS cc_start: 0.9392 (tttt) cc_final: 0.9124 (ttpt) REVERT: B 53 GLU cc_start: 0.8263 (mt-10) cc_final: 0.7977 (pt0) REVERT: B 59 LYS cc_start: 0.9497 (ttpp) cc_final: 0.8902 (ttpp) REVERT: B 63 GLU cc_start: 0.9300 (mt-10) cc_final: 0.8993 (mp0) REVERT: B 64 ASN cc_start: 0.9403 (m-40) cc_final: 0.9150 (m-40) REVERT: B 91 LYS cc_start: 0.9150 (pptt) cc_final: 0.8774 (pttt) REVERT: C 110 ASN cc_start: 0.9023 (t0) cc_final: 0.8609 (p0) REVERT: D 79 ARG cc_start: 0.9423 (ttm110) cc_final: 0.8906 (ttm110) REVERT: F 53 GLU cc_start: 0.8234 (pp20) cc_final: 0.7863 (pp20) REVERT: F 59 LYS cc_start: 0.9257 (tppt) cc_final: 0.8953 (tppt) REVERT: G 30 VAL cc_start: 0.9348 (t) cc_final: 0.9146 (p) REVERT: G 56 GLU cc_start: 0.9162 (tt0) cc_final: 0.8728 (mt-10) REVERT: G 89 ASN cc_start: 0.9540 (m-40) cc_final: 0.9262 (m110) REVERT: H 39 ILE cc_start: 0.9259 (OUTLIER) cc_final: 0.8856 (tp) REVERT: H 42 TYR cc_start: 0.9124 (OUTLIER) cc_final: 0.8774 (m-80) REVERT: H 59 MET cc_start: 0.9175 (tpt) cc_final: 0.8952 (tpt) REVERT: H 68 ASP cc_start: 0.9542 (t0) cc_final: 0.9230 (t0) REVERT: H 76 GLU cc_start: 0.9294 (mm-30) cc_final: 0.9061 (mm-30) REVERT: H 82 HIS cc_start: 0.9322 (t-90) cc_final: 0.9092 (t-90) REVERT: H 105 GLU cc_start: 0.9221 (tp30) cc_final: 0.9020 (tp30) REVERT: H 116 LYS cc_start: 0.9576 (OUTLIER) cc_final: 0.9362 (ptpp) REVERT: L 227 TYR cc_start: 0.8955 (m-80) cc_final: 0.8658 (m-80) REVERT: L 242 ASP cc_start: 0.8725 (t0) cc_final: 0.8345 (t0) REVERT: L 264 MET cc_start: 0.9048 (ppp) cc_final: 0.8719 (ppp) REVERT: K 229 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7467 (tppt) REVERT: K 238 PHE cc_start: 0.8795 (p90) cc_final: 0.8162 (p90) REVERT: K 264 MET cc_start: 0.9178 (ttp) cc_final: 0.8703 (mtm) REVERT: K 292 MET cc_start: 0.3420 (mtt) cc_final: 0.3092 (mtt) outliers start: 26 outliers final: 17 residues processed: 193 average time/residue: 0.1260 time to fit residues: 33.4906 Evaluate side-chains 193 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 170 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 42 TYR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain H residue 116 LYS Chi-restraints excluded: chain K residue 228 ILE Chi-restraints excluded: chain K residue 229 LYS Chi-restraints excluded: chain K residue 258 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 100 optimal weight: 50.0000 chunk 5 optimal weight: 1.9990 chunk 25 optimal weight: 8.9990 chunk 71 optimal weight: 6.9990 chunk 102 optimal weight: 30.0000 chunk 58 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 111 optimal weight: 40.0000 chunk 36 optimal weight: 8.9990 chunk 13 optimal weight: 1.9990 chunk 62 optimal weight: 30.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.031650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.023897 restraints weight = 143819.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.024602 restraints weight = 73774.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.025054 restraints weight = 47259.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.025334 restraints weight = 34662.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.025556 restraints weight = 28128.131| |-----------------------------------------------------------------------------| r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.5960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 13267 Z= 0.196 Angle : 0.790 16.550 18977 Z= 0.436 Chirality : 0.045 0.240 2139 Planarity : 0.005 0.052 1531 Dihedral : 29.888 97.494 3758 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.09 % Allowed : 28.44 % Favored : 68.47 % 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: 1.08 (0.28), residues: 900 helix: 1.23 (0.20), residues: 643 sheet: -2.91 (0.94), residues: 20 loop : -0.17 (0.39), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 79 TYR 0.090 0.003 TYR D 83 PHE 0.040 0.002 PHE H 65 TRP 0.008 0.002 TRP L 230 HIS 0.009 0.002 HIS K 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.20 (13267) covalent geometry : angle 0.79035 / 0.44 (18977) hydrogen bonds : bond 0.05035 / 3.33 ( 805) hydrogen bonds : angle 4.03978 / 2.95 ( 2063) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2116.38 seconds wall clock time: 37 minutes 11.03 seconds (2231.03 seconds total)