Starting phenix.real_space_refine on Wed Aug 5 13:58:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ub8_42078/08_2026/8ub8_42078.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ub8_42078/08_2026/8ub8_42078.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ub8_42078/08_2026/8ub8_42078.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ub8_42078/08_2026/8ub8_42078.map" model { file = "/net/cci-nas-00/data/ceres_data/8ub8_42078/08_2026/8ub8_42078.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ub8_42078/08_2026/8ub8_42078.cif" } resolution = 3.28 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.026 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 143 5.49 5 S 37 5.16 5 C 6036 2.51 5 N 1861 2.21 5 O 2222 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 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: 10299 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2690 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 12, 'TRANS': 315} Chain: "B" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 976 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "C" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 914 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "D" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 893 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 107} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 876 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain: "F" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 888 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 4, 'TRANS': 106} Chain: "G" Number of atoms: 311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 311 Classifications: {'RNA': 14} Modifications used: {'rna3p_pur': 11, 'rna3p_pyr': 3} Link IDs: {'rna3p': 13} Chain: "H" Number of atoms: 270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 270 Classifications: {'RNA': 13} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 4, 'rna3p_pyr': 8} Link IDs: {'rna3p': 12} Chain: "I" Number of atoms: 2481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 2481 Classifications: {'RNA': 116} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 7, 'rna3p_pur': 51, 'rna3p_pyr': 48} Link IDs: {'rna2p': 17, 'rna3p': 98} Chain breaks: 2 Time building chain proxies: 2.42, per 1000 atoms: 0.23 Number of scatterers: 10299 At special positions: 0 Unit cell: (86, 98, 149, 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 37 16.00 P 143 15.00 O 2222 8.00 N 1861 7.00 C 6036 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: 0.76 Conformation dependent library (CDL) restraints added in 267.2 milliseconds 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1684 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 3 sheets defined 75.0% alpha, 3.6% beta 43 base pairs and 86 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 8 through 13 Processing helix chain 'A' and resid 14 through 27 removed outlier: 3.560A pdb=" N ASP A 20 " --> pdb=" O GLU A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 40 removed outlier: 3.857A pdb=" N GLU A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 54 removed outlier: 3.532A pdb=" N LEU A 47 " --> pdb=" O LEU A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 94 removed outlier: 3.957A pdb=" N ILE A 93 " --> pdb=" O ALA A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 98 Processing helix chain 'A' and resid 114 through 128 Processing helix chain 'A' and resid 129 through 131 No H-bonds generated for 'chain 'A' and resid 129 through 131' Processing helix chain 'A' and resid 142 through 146 removed outlier: 3.574A pdb=" N ILE A 146 " --> pdb=" O PHE A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 154 Processing helix chain 'A' and resid 163 through 172 Processing helix chain 'A' and resid 183 through 203 removed outlier: 3.588A pdb=" N ALA A 196 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N VAL A 197 " --> pdb=" O TYR A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 241 Processing helix chain 'A' and resid 273 through 289 Processing helix chain 'A' and resid 294 through 307 removed outlier: 3.842A pdb=" N ARG A 298 " --> pdb=" O GLU A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 324 Processing helix chain 'B' and resid 10 through 32 removed outlier: 3.682A pdb=" N ARG B 22 " --> pdb=" O GLU B 18 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL B 23 " --> pdb=" O ARG B 19 " (cutoff:3.500A) Proline residue: B 29 - end of helix Processing helix chain 'B' and resid 38 through 50 Processing helix chain 'B' and resid 51 through 61 Processing helix chain 'B' and resid 65 through 88 Processing helix chain 'B' and resid 95 through 122 Processing helix chain 'C' and resid 11 through 34 removed outlier: 3.657A pdb=" N ARG C 22 " --> pdb=" O GLU C 18 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL C 23 " --> pdb=" O ARG C 19 " (cutoff:3.500A) Proline residue: C 29 - end of helix Processing helix chain 'C' and resid 38 through 50 Processing helix chain 'C' and resid 51 through 62 removed outlier: 3.514A pdb=" N LEU C 55 " --> pdb=" O GLY C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 88 removed outlier: 3.592A pdb=" N LEU C 68 " --> pdb=" O GLN C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 122 Processing helix chain 'D' and resid 14 through 34 removed outlier: 3.720A pdb=" N ARG D 22 " --> pdb=" O GLU D 18 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL D 23 " --> pdb=" O ARG D 19 " (cutoff:3.500A) Proline residue: D 29 - end of helix Processing helix chain 'D' and resid 35 through 37 No H-bonds generated for 'chain 'D' and resid 35 through 37' Processing helix chain 'D' and resid 38 through 50 Processing helix chain 'D' and resid 51 through 62 removed outlier: 3.590A pdb=" N LEU D 55 " --> pdb=" O GLY D 51 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER D 62 " --> pdb=" O VAL D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 86 removed outlier: 3.874A pdb=" N LEU D 68 " --> pdb=" O GLN D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 121 removed outlier: 3.810A pdb=" N GLN D 103 " --> pdb=" O VAL D 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 34 removed outlier: 3.697A pdb=" N ARG E 22 " --> pdb=" O GLU E 18 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL E 23 " --> pdb=" O ARG E 19 " (cutoff:3.500A) Proline residue: E 29 - end of helix Processing helix chain 'E' and resid 35 through 37 No H-bonds generated for 'chain 'E' and resid 35 through 37' Processing helix chain 'E' and resid 38 through 50 Processing helix chain 'E' and resid 51 through 62 removed outlier: 3.519A pdb=" N LEU E 55 " --> pdb=" O GLY E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 86 Processing helix chain 'E' and resid 95 through 121 Processing helix chain 'F' and resid 14 through 28 removed outlier: 3.605A pdb=" N GLU F 18 " --> pdb=" O MET F 14 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARG F 22 " --> pdb=" O GLU F 18 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL F 23 " --> pdb=" O ARG F 19 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 50 Processing helix chain 'F' and resid 51 through 61 Processing helix chain 'F' and resid 64 through 87 removed outlier: 3.631A pdb=" N GLY F 87 " --> pdb=" O ARG F 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 93 Proline residue: F 91 - end of helix No H-bonds generated for 'chain 'F' and resid 88 through 93' Processing helix chain 'F' and resid 95 through 122 removed outlier: 4.118A pdb=" N LEU F 105 " --> pdb=" O THR F 101 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 68 Processing sheet with id=AA2, first strand: chain 'A' and resid 210 through 213 removed outlier: 3.929A pdb=" N HIS A 248 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 258 through 260 484 hydrogen bonds defined for protein. 1425 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 109 hydrogen bonds 174 hydrogen bond angles 0 basepair planarities 43 basepair parallelities 86 stacking parallelities Total time for adding SS restraints: 1.55 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 1743 1.33 - 1.46: 4503 1.46 - 1.60: 4271 1.60 - 1.74: 241 1.74 - 1.87: 62 Bond restraints: 10820 Sorted by residual: bond pdb=" CA GLN F 64 " pdb=" CB GLN F 64 " ideal model delta sigma weight residual 1.529 1.641 -0.112 1.64e-02 3.72e+03 4.66e+01 bond pdb=" CA ARG E 36 " pdb=" CB ARG E 36 " ideal model delta sigma weight residual 1.529 1.442 0.086 1.64e-02 3.72e+03 2.77e+01 bond pdb=" O5' U I 24 " pdb=" C5' U I 24 " ideal model delta sigma weight residual 1.424 1.505 -0.081 1.60e-02 3.91e+03 2.58e+01 bond pdb=" O3' C I 68 " pdb=" P C I 69 " ideal model delta sigma weight residual 1.607 1.657 -0.050 1.20e-02 6.94e+03 1.77e+01 bond pdb=" C4 C I 128 " pdb=" C5 C I 128 " ideal model delta sigma weight residual 1.425 1.393 0.032 8.00e-03 1.56e+04 1.60e+01 ... (remaining 10815 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 13688 2.16 - 4.31: 1421 4.31 - 6.46: 174 6.46 - 8.62: 25 8.62 - 10.77: 8 Bond angle restraints: 15316 Sorted by residual: angle pdb=" C3' G G 370 " pdb=" O3' G G 370 " pdb=" P G G 371 " ideal model delta sigma weight residual 119.70 108.93 10.77 1.20e+00 6.94e-01 8.06e+01 angle pdb=" C3' G G 372 " pdb=" O3' G G 372 " pdb=" P C G 373 " ideal model delta sigma weight residual 119.70 108.93 10.77 1.20e+00 6.94e-01 8.05e+01 angle pdb=" N VAL A 170 " pdb=" CA VAL A 170 " pdb=" C VAL A 170 " ideal model delta sigma weight residual 112.96 104.20 8.76 1.00e+00 1.00e+00 7.67e+01 angle pdb=" C3' G G 371 " pdb=" O3' G G 371 " pdb=" P G G 372 " ideal model delta sigma weight residual 119.70 109.25 10.45 1.20e+00 6.94e-01 7.58e+01 angle pdb=" N ILE F 88 " pdb=" CA ILE F 88 " pdb=" C ILE F 88 " ideal model delta sigma weight residual 113.47 105.05 8.42 1.01e+00 9.80e-01 6.96e+01 ... (remaining 15311 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.75: 6022 35.75 - 71.49: 622 71.49 - 107.24: 63 107.24 - 142.98: 2 142.98 - 178.73: 3 Dihedral angle restraints: 6712 sinusoidal: 4101 harmonic: 2611 Sorted by residual: dihedral pdb=" O4' U I 94 " pdb=" C1' U I 94 " pdb=" N1 U I 94 " pdb=" C2 U I 94 " ideal model delta sinusoidal sigma weight residual 232.00 53.27 178.73 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U I 3 " pdb=" C1' U I 3 " pdb=" N1 U I 3 " pdb=" C2 U I 3 " ideal model delta sinusoidal sigma weight residual -160.00 -83.65 -76.35 1 1.50e+01 4.44e-03 3.26e+01 dihedral pdb=" CA HIS A 5 " pdb=" C HIS A 5 " pdb=" N ARG A 6 " pdb=" CA ARG A 6 " ideal model delta harmonic sigma weight residual -180.00 -152.74 -27.26 0 5.00e+00 4.00e-02 2.97e+01 ... (remaining 6709 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.133: 1492 0.133 - 0.266: 280 0.266 - 0.399: 29 0.399 - 0.532: 8 0.532 - 0.665: 4 Chirality restraints: 1813 Sorted by residual: chirality pdb=" P G H 117 " pdb=" OP1 G H 117 " pdb=" OP2 G H 117 " pdb=" O5' G H 117 " both_signs ideal model delta sigma weight residual True 2.41 3.08 -0.67 2.00e-01 2.50e+01 1.11e+01 chirality pdb=" P G G 369 " pdb=" OP1 G G 369 " pdb=" OP2 G G 369 " pdb=" O5' G G 369 " both_signs ideal model delta sigma weight residual True 2.41 -2.98 -0.57 2.00e-01 2.50e+01 8.06e+00 chirality pdb=" P U I 3 " pdb=" OP1 U I 3 " pdb=" OP2 U I 3 " pdb=" O5' U I 3 " both_signs ideal model delta sigma weight residual True 2.41 -2.97 -0.56 2.00e-01 2.50e+01 7.98e+00 ... (remaining 1810 not shown) Planarity restraints: 1402 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 28 " 0.091 2.00e-02 2.50e+03 4.79e-02 4.59e+01 pdb=" CG TYR F 28 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 TYR F 28 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR F 28 " -0.046 2.00e-02 2.50e+03 pdb=" CE1 TYR F 28 " -0.034 2.00e-02 2.50e+03 pdb=" CE2 TYR F 28 " -0.016 2.00e-02 2.50e+03 pdb=" CZ TYR F 28 " 0.034 2.00e-02 2.50e+03 pdb=" OH TYR F 28 " 0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 28 " 0.080 2.00e-02 2.50e+03 4.06e-02 3.30e+01 pdb=" CG TYR C 28 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 TYR C 28 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR C 28 " -0.034 2.00e-02 2.50e+03 pdb=" CE1 TYR C 28 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR C 28 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR C 28 " 0.015 2.00e-02 2.50e+03 pdb=" OH TYR C 28 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 81 " 0.005 2.00e-02 2.50e+03 3.57e-02 3.18e+01 pdb=" CG TRP E 81 " 0.004 2.00e-02 2.50e+03 pdb=" CD1 TRP E 81 " -0.047 2.00e-02 2.50e+03 pdb=" CD2 TRP E 81 " 0.072 2.00e-02 2.50e+03 pdb=" NE1 TRP E 81 " -0.028 2.00e-02 2.50e+03 pdb=" CE2 TRP E 81 " 0.038 2.00e-02 2.50e+03 pdb=" CE3 TRP E 81 " -0.019 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 81 " 0.033 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 81 " -0.030 2.00e-02 2.50e+03 pdb=" CH2 TRP E 81 " -0.027 2.00e-02 2.50e+03 ... (remaining 1399 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 47 2.49 - 3.09: 7487 3.09 - 3.69: 19014 3.69 - 4.30: 28523 4.30 - 4.90: 41089 Nonbonded interactions: 96160 Sorted by model distance: nonbonded pdb=" O ARG A 6 " pdb=" OD1 ASN A 7 " model vdw 1.887 3.040 nonbonded pdb=" O ASN F 121 " pdb=" NH1 ARG F 122 " model vdw 2.083 3.120 nonbonded pdb=" OE1 GLN D 52 " pdb=" CE2 PHE D 56 " model vdw 2.198 3.340 nonbonded pdb=" OE1 GLU F 108 " pdb=" NH2 ARG F 111 " model vdw 2.285 3.120 nonbonded pdb=" O GLU D 21 " pdb=" OG SER D 25 " model vdw 2.289 3.040 ... (remaining 96155 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 'B' and resid 13 through 121) selection = (chain 'C' and resid 13 through 121) selection = (chain 'D' and resid 13 through 121) selection = (chain 'E' and resid 13 through 121) selection = (chain 'F' and resid 13 through 121) } 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=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.280 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: 0.030 Set scattering table: 0.030 Process input model: 10.300 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 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 : 0.011 0.112 10820 Z= 0.713 Angle : 1.399 10.775 15316 Z= 0.974 Chirality : 0.106 0.665 1813 Planarity : 0.013 0.124 1402 Dihedral : 23.559 178.728 5028 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 27.19 Ramachandran Plot: Outliers : 2.26 % Allowed : 8.70 % Favored : 89.04 % Rotamer: Outliers : 6.27 % Allowed : 16.53 % Favored : 77.20 % 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: -4.02 (0.22), residues: 885 helix: -2.01 (0.16), residues: 656 sheet: -4.26 (0.80), residues: 26 loop : -4.02 (0.35), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.036 0.004 ARG A 127 TYR 0.091 0.014 TYR F 28 PHE 0.062 0.012 PHE E 84 TRP 0.072 0.013 TRP E 81 HIS 0.026 0.005 HIS A 88 Details of bonding type rmsd/Z covalent geometry : bond 0.01073 / 0.71 (10820) covalent geometry : angle 1.39877 / 0.97 (15316) hydrogen bonds : bond 0.19784 / 12.76 ( 593) hydrogen bonds : angle 9.02641 / 6.47 ( 1599) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 166 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TYR cc_start: 0.5413 (OUTLIER) cc_final: 0.5071 (p90) REVERT: A 111 PRO cc_start: 0.7939 (Cg_exo) cc_final: 0.7738 (Cg_endo) REVERT: A 112 ASP cc_start: 0.8570 (m-30) cc_final: 0.8269 (t0) REVERT: A 309 TRP cc_start: 0.6882 (m100) cc_final: 0.6657 (m100) REVERT: B 77 MET cc_start: 0.8180 (tpt) cc_final: 0.7837 (tpt) REVERT: B 108 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7527 (tt0) REVERT: C 91 PRO cc_start: 0.8287 (OUTLIER) cc_final: 0.7904 (Cg_endo) REVERT: D 18 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7220 (tp30) REVERT: D 26 TYR cc_start: 0.8019 (t80) cc_final: 0.7809 (t80) REVERT: D 95 THR cc_start: 0.7279 (p) cc_final: 0.7070 (p) REVERT: E 63 ASN cc_start: 0.7839 (t0) cc_final: 0.6734 (p0) outliers start: 47 outliers final: 16 residues processed: 195 average time/residue: 0.1373 time to fit residues: 34.8204 Evaluate side-chains 165 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 147 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 57 ASN Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 180 PRO Chi-restraints excluded: chain A residue 269 HIS Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain C residue 91 PRO Chi-restraints excluded: chain C residue 92 HIS Chi-restraints excluded: chain C residue 94 MET Chi-restraints excluded: chain D residue 36 ARG Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain F residue 14 MET Chi-restraints excluded: chain F residue 103 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 9.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.3980 chunk 100 optimal weight: 6.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 121 HIS A 306 HIS B 92 HIS C 92 HIS D 32 GLN ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 HIS F 92 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.167729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.128405 restraints weight = 13129.365| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.45 r_work: 0.3347 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10820 Z= 0.197 Angle : 0.738 8.211 15316 Z= 0.397 Chirality : 0.044 0.219 1813 Planarity : 0.006 0.055 1402 Dihedral : 23.852 176.577 3313 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.68 % Allowed : 6.10 % Favored : 93.22 % Rotamer: Outliers : 5.20 % Allowed : 17.20 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.10 (0.26), residues: 885 helix: -0.61 (0.18), residues: 667 sheet: -3.81 (0.75), residues: 26 loop : -3.44 (0.39), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 122 TYR 0.023 0.003 TYR A 152 PHE 0.023 0.003 PHE D 56 TRP 0.014 0.002 TRP F 81 HIS 0.013 0.002 HIS C 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.20 (10820) covalent geometry : angle 0.73771 / 0.40 (15316) hydrogen bonds : bond 0.06508 / 4.14 ( 593) hydrogen bonds : angle 4.96816 / 3.59 ( 1599) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 164 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: A 69 TYR cc_start: 0.5906 (OUTLIER) cc_final: 0.5195 (p90) REVERT: A 72 LYS cc_start: 0.8067 (OUTLIER) cc_final: 0.7744 (ttpp) REVERT: A 130 ARG cc_start: 0.7723 (mmt-90) cc_final: 0.7464 (mmt90) REVERT: A 278 LYS cc_start: 0.7421 (mtpt) cc_final: 0.6730 (mmtt) REVERT: B 44 MET cc_start: 0.8948 (mtp) cc_final: 0.8606 (mtp) REVERT: C 111 ARG cc_start: 0.8657 (ttm-80) cc_final: 0.8046 (ttp80) REVERT: D 14 MET cc_start: 0.7696 (ttt) cc_final: 0.7442 (ttm) REVERT: D 62 SER cc_start: 0.8282 (OUTLIER) cc_final: 0.7821 (p) REVERT: D 95 THR cc_start: 0.7524 (p) cc_final: 0.7155 (p) outliers start: 39 outliers final: 14 residues processed: 190 average time/residue: 0.1457 time to fit residues: 35.8038 Evaluate side-chains 165 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 148 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 72 LYS Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 36 ARG Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain F residue 14 MET Chi-restraints excluded: chain F residue 65 VAL Chi-restraints excluded: chain F residue 88 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 71 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 88 optimal weight: 9.9990 chunk 24 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 96 optimal weight: 20.0000 chunk 95 optimal weight: 20.0000 chunk 66 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.166623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.126568 restraints weight = 13488.447| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 1.48 r_work: 0.3326 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 10820 Z= 0.273 Angle : 0.721 9.878 15316 Z= 0.386 Chirality : 0.044 0.267 1813 Planarity : 0.006 0.042 1402 Dihedral : 23.561 179.619 3291 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.68 % Allowed : 7.12 % Favored : 92.20 % Rotamer: Outliers : 4.53 % Allowed : 18.40 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.27), residues: 885 helix: -0.15 (0.19), residues: 668 sheet: -3.15 (0.86), residues: 26 loop : -3.17 (0.44), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 111 TYR 0.026 0.003 TYR D 26 PHE 0.019 0.002 PHE A 231 TRP 0.018 0.002 TRP E 116 HIS 0.006 0.002 HIS F 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00615 / 0.27 (10820) covalent geometry : angle 0.72105 / 0.39 (15316) hydrogen bonds : bond 0.05998 / 3.84 ( 593) hydrogen bonds : angle 4.80311 / 3.45 ( 1599) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 149 time to evaluate : 0.185 Fit side-chains REVERT: A 69 TYR cc_start: 0.6005 (OUTLIER) cc_final: 0.5355 (p90) REVERT: A 130 ARG cc_start: 0.7921 (mmt-90) cc_final: 0.7710 (mmt180) REVERT: A 215 ASP cc_start: 0.8577 (p0) cc_final: 0.8356 (p0) REVERT: A 278 LYS cc_start: 0.7445 (mtpt) cc_final: 0.6733 (mmtt) REVERT: B 44 MET cc_start: 0.9032 (mtp) cc_final: 0.8754 (mtp) REVERT: C 111 ARG cc_start: 0.8627 (ttm-80) cc_final: 0.8101 (ttp80) REVERT: D 32 GLN cc_start: 0.8575 (mm110) cc_final: 0.8196 (mm-40) REVERT: D 42 ARG cc_start: 0.8577 (ttm170) cc_final: 0.8261 (ttp-170) REVERT: D 62 SER cc_start: 0.8475 (OUTLIER) cc_final: 0.7911 (p) REVERT: D 95 THR cc_start: 0.7642 (OUTLIER) cc_final: 0.7286 (p) outliers start: 34 outliers final: 14 residues processed: 176 average time/residue: 0.1172 time to fit residues: 26.9861 Evaluate side-chains 156 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 139 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain D residue 36 ARG Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain F residue 14 MET Chi-restraints excluded: chain F residue 88 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 88 optimal weight: 9.9990 chunk 86 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 58 optimal weight: 0.5980 chunk 61 optimal weight: 0.6980 chunk 70 optimal weight: 0.7980 chunk 85 optimal weight: 0.7980 chunk 84 optimal weight: 0.5980 chunk 32 optimal weight: 0.0770 chunk 23 optimal weight: 0.8980 chunk 73 optimal weight: 0.5980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 313 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.170456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.131169 restraints weight = 13420.986| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 1.48 r_work: 0.3388 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10820 Z= 0.155 Angle : 0.607 8.355 15316 Z= 0.329 Chirality : 0.039 0.226 1813 Planarity : 0.005 0.043 1402 Dihedral : 23.355 179.304 3288 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.56 % Allowed : 5.76 % Favored : 93.67 % Rotamer: Outliers : 4.13 % Allowed : 19.33 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.28), residues: 885 helix: 0.27 (0.19), residues: 667 sheet: -2.71 (0.89), residues: 26 loop : -3.16 (0.43), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 111 TYR 0.020 0.002 TYR A 193 PHE 0.018 0.002 PHE A 231 TRP 0.015 0.001 TRP E 116 HIS 0.007 0.001 HIS A 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (10820) covalent geometry : angle 0.60717 / 0.33 (15316) hydrogen bonds : bond 0.05089 / 3.30 ( 593) hydrogen bonds : angle 4.43562 / 3.17 ( 1599) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 155 time to evaluate : 0.310 Fit side-chains revert: symmetry clash REVERT: A 57 ASN cc_start: 0.8866 (m-40) cc_final: 0.8451 (m-40) REVERT: A 69 TYR cc_start: 0.5736 (OUTLIER) cc_final: 0.5172 (p90) REVERT: A 278 LYS cc_start: 0.7423 (mtpt) cc_final: 0.6672 (mmtt) REVERT: B 44 MET cc_start: 0.9026 (mtp) cc_final: 0.8704 (mtp) REVERT: B 108 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7613 (mm-30) REVERT: C 111 ARG cc_start: 0.8490 (ttm-80) cc_final: 0.8218 (ttp80) REVERT: D 62 SER cc_start: 0.8329 (OUTLIER) cc_final: 0.7784 (p) REVERT: D 95 THR cc_start: 0.7527 (p) cc_final: 0.7168 (p) REVERT: F 14 MET cc_start: 0.6284 (OUTLIER) cc_final: 0.5326 (tpt) REVERT: F 119 ARG cc_start: 0.8282 (ttp80) cc_final: 0.8046 (ttp80) outliers start: 31 outliers final: 17 residues processed: 176 average time/residue: 0.1262 time to fit residues: 28.6091 Evaluate side-chains 165 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 145 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 313 HIS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain D residue 19 ARG Chi-restraints excluded: chain D residue 36 ARG Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain F residue 14 MET Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 88 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 16 optimal weight: 0.8980 chunk 97 optimal weight: 20.0000 chunk 90 optimal weight: 10.0000 chunk 79 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 81 optimal weight: 0.3980 chunk 86 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.168261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.128133 restraints weight = 13283.950| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 1.52 r_work: 0.3342 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10820 Z= 0.157 Angle : 0.609 10.515 15316 Z= 0.329 Chirality : 0.039 0.233 1813 Planarity : 0.005 0.048 1402 Dihedral : 23.194 179.744 3286 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.44 % Favored : 92.99 % Rotamer: Outliers : 3.60 % Allowed : 20.80 % Favored : 75.60 % 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: -0.66 (0.28), residues: 885 helix: 0.44 (0.20), residues: 666 sheet: -2.40 (0.90), residues: 26 loop : -3.14 (0.43), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 111 TYR 0.018 0.002 TYR A 193 PHE 0.018 0.002 PHE A 231 TRP 0.010 0.001 TRP E 116 HIS 0.010 0.001 HIS A 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.16 (10820) covalent geometry : angle 0.60893 / 0.33 (15316) hydrogen bonds : bond 0.04949 / 3.21 ( 593) hydrogen bonds : angle 4.35045 / 3.10 ( 1599) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 149 time to evaluate : 0.300 Fit side-chains REVERT: A 57 ASN cc_start: 0.8902 (m-40) cc_final: 0.8507 (m-40) REVERT: A 69 TYR cc_start: 0.5676 (OUTLIER) cc_final: 0.5301 (p90) REVERT: A 278 LYS cc_start: 0.7466 (mtpt) cc_final: 0.6669 (mmtt) REVERT: B 44 MET cc_start: 0.8985 (mtp) cc_final: 0.8686 (mtp) REVERT: B 108 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7534 (mm-30) REVERT: C 111 ARG cc_start: 0.8562 (ttm-80) cc_final: 0.8226 (ttp80) REVERT: D 62 SER cc_start: 0.8153 (OUTLIER) cc_final: 0.7622 (p) REVERT: D 95 THR cc_start: 0.7657 (OUTLIER) cc_final: 0.7305 (p) REVERT: F 14 MET cc_start: 0.6152 (OUTLIER) cc_final: 0.5949 (mmt) outliers start: 27 outliers final: 19 residues processed: 166 average time/residue: 0.1187 time to fit residues: 25.6861 Evaluate side-chains 162 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 139 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain D residue 19 ARG Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 36 ARG Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain F residue 14 MET Chi-restraints excluded: chain F residue 16 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 80 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 25 optimal weight: 0.3980 chunk 24 optimal weight: 0.0060 chunk 88 optimal weight: 10.0000 chunk 70 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 100 optimal weight: 9.9990 chunk 51 optimal weight: 0.9980 overall best weight: 0.8398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 290 HIS ** D 89 GLN ** 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 = 0.3995 r_free = 0.3995 target = 0.167643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.127066 restraints weight = 13429.435| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 1.53 r_work: 0.3324 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10820 Z= 0.174 Angle : 0.597 7.337 15316 Z= 0.321 Chirality : 0.039 0.240 1813 Planarity : 0.005 0.049 1402 Dihedral : 22.990 179.629 3286 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.56 % Allowed : 5.99 % Favored : 93.45 % Rotamer: Outliers : 4.13 % Allowed : 21.07 % Favored : 74.80 % 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: -0.50 (0.28), residues: 885 helix: 0.55 (0.20), residues: 666 sheet: -1.88 (0.96), residues: 26 loop : -3.09 (0.44), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 111 TYR 0.016 0.002 TYR A 193 PHE 0.018 0.002 PHE D 80 TRP 0.013 0.001 TRP E 116 HIS 0.004 0.001 HIS A 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 (10820) covalent geometry : angle 0.59675 / 0.32 (15316) hydrogen bonds : bond 0.04901 / 3.20 ( 593) hydrogen bonds : angle 4.32858 / 3.08 ( 1599) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 141 time to evaluate : 0.230 Fit side-chains REVERT: A 57 ASN cc_start: 0.8858 (m-40) cc_final: 0.8506 (m-40) REVERT: A 69 TYR cc_start: 0.5663 (OUTLIER) cc_final: 0.5280 (p90) REVERT: A 278 LYS cc_start: 0.7420 (mtpt) cc_final: 0.6653 (mmtt) REVERT: B 44 MET cc_start: 0.8977 (mtp) cc_final: 0.8708 (mtp) REVERT: B 108 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7510 (mm-30) REVERT: C 111 ARG cc_start: 0.8547 (ttm-80) cc_final: 0.8141 (ttp80) REVERT: D 62 SER cc_start: 0.8216 (OUTLIER) cc_final: 0.7543 (p) REVERT: D 67 LYS cc_start: 0.7676 (mtmt) cc_final: 0.7070 (mtmt) REVERT: D 95 THR cc_start: 0.7682 (OUTLIER) cc_final: 0.7338 (p) outliers start: 31 outliers final: 20 residues processed: 162 average time/residue: 0.1113 time to fit residues: 23.6883 Evaluate side-chains 158 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain D residue 19 ARG Chi-restraints excluded: chain D residue 36 ARG Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain F residue 16 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 89 optimal weight: 10.0000 chunk 26 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 15 optimal weight: 0.4980 chunk 17 optimal weight: 0.0770 chunk 82 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 14 optimal weight: 0.4980 chunk 100 optimal weight: 9.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.169094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.130307 restraints weight = 13104.685| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 1.41 r_work: 0.3369 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10820 Z= 0.140 Angle : 0.570 7.262 15316 Z= 0.308 Chirality : 0.037 0.218 1813 Planarity : 0.005 0.053 1402 Dihedral : 22.800 179.956 3283 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.88 % Favored : 93.67 % Rotamer: Outliers : 3.47 % Allowed : 21.47 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.29), residues: 885 helix: 0.72 (0.20), residues: 665 sheet: -1.38 (0.99), residues: 26 loop : -2.97 (0.44), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 111 TYR 0.015 0.002 TYR A 193 PHE 0.016 0.002 PHE A 231 TRP 0.014 0.001 TRP E 116 HIS 0.004 0.001 HIS A 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (10820) covalent geometry : angle 0.56990 / 0.31 (15316) hydrogen bonds : bond 0.04649 / 3.05 ( 593) hydrogen bonds : angle 4.18952 / 2.97 ( 1599) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 141 time to evaluate : 0.182 Fit side-chains REVERT: A 57 ASN cc_start: 0.8838 (m-40) cc_final: 0.8504 (m-40) REVERT: A 69 TYR cc_start: 0.5627 (OUTLIER) cc_final: 0.5374 (p90) REVERT: A 275 SER cc_start: 0.8749 (OUTLIER) cc_final: 0.8223 (t) REVERT: A 278 LYS cc_start: 0.7373 (mtpt) cc_final: 0.6618 (mmtt) REVERT: B 44 MET cc_start: 0.8959 (mtp) cc_final: 0.8670 (mtp) REVERT: B 108 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7351 (mm-30) REVERT: C 111 ARG cc_start: 0.8386 (ttm-80) cc_final: 0.8114 (ttp80) REVERT: D 67 LYS cc_start: 0.7680 (mtmt) cc_final: 0.7285 (mtmt) REVERT: D 95 THR cc_start: 0.7719 (OUTLIER) cc_final: 0.7370 (p) REVERT: F 69 TYR cc_start: 0.7947 (m-10) cc_final: 0.7603 (m-10) outliers start: 26 outliers final: 18 residues processed: 159 average time/residue: 0.1207 time to fit residues: 24.7504 Evaluate side-chains 155 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 134 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain D residue 19 ARG Chi-restraints excluded: chain D residue 36 ARG Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain F residue 16 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 89 optimal weight: 10.0000 chunk 18 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 93 optimal weight: 10.0000 chunk 79 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 95 optimal weight: 20.0000 chunk 52 optimal weight: 0.0470 overall best weight: 0.7482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 89 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 = 0.4009 r_free = 0.4009 target = 0.168894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.128192 restraints weight = 13357.517| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 1.53 r_work: 0.3346 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10820 Z= 0.162 Angle : 0.577 9.193 15316 Z= 0.310 Chirality : 0.038 0.231 1813 Planarity : 0.005 0.058 1402 Dihedral : 22.717 179.810 3282 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.99 % Favored : 93.56 % Rotamer: Outliers : 3.33 % Allowed : 21.87 % Favored : 74.80 % 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: -0.14 (0.28), residues: 885 helix: 0.76 (0.20), residues: 667 sheet: -1.13 (1.01), residues: 26 loop : -2.91 (0.45), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 111 TYR 0.014 0.002 TYR A 152 PHE 0.016 0.002 PHE D 80 TRP 0.012 0.001 TRP E 116 HIS 0.004 0.001 HIS D 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (10820) covalent geometry : angle 0.57663 / 0.31 (15316) hydrogen bonds : bond 0.04674 / 3.06 ( 593) hydrogen bonds : angle 4.23957 / 3.00 ( 1599) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 136 time to evaluate : 0.313 Fit side-chains REVERT: A 57 ASN cc_start: 0.8793 (m-40) cc_final: 0.8460 (m-40) REVERT: A 69 TYR cc_start: 0.5652 (OUTLIER) cc_final: 0.5390 (p90) REVERT: A 275 SER cc_start: 0.8771 (OUTLIER) cc_final: 0.8264 (t) REVERT: A 278 LYS cc_start: 0.7383 (mtpt) cc_final: 0.6620 (mmtt) REVERT: B 44 MET cc_start: 0.8967 (mtp) cc_final: 0.8708 (mtp) REVERT: B 108 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7352 (mm-30) REVERT: C 111 ARG cc_start: 0.8416 (ttm-80) cc_final: 0.8125 (ttp80) REVERT: D 13 GLN cc_start: 0.4628 (pm20) cc_final: 0.4388 (pm20) REVERT: D 67 LYS cc_start: 0.7717 (mtmt) cc_final: 0.7454 (mtmt) REVERT: D 95 THR cc_start: 0.7766 (OUTLIER) cc_final: 0.7413 (p) REVERT: F 69 TYR cc_start: 0.7941 (m-10) cc_final: 0.7548 (m-10) outliers start: 25 outliers final: 19 residues processed: 152 average time/residue: 0.1268 time to fit residues: 25.1039 Evaluate side-chains 152 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain D residue 19 ARG Chi-restraints excluded: chain D residue 36 ARG Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain F residue 16 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 0 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 chunk 79 optimal weight: 0.8980 chunk 52 optimal weight: 0.0970 chunk 77 optimal weight: 0.8980 chunk 85 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.169366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.129220 restraints weight = 13261.961| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 1.48 r_work: 0.3365 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10820 Z= 0.156 Angle : 0.570 7.859 15316 Z= 0.307 Chirality : 0.037 0.220 1813 Planarity : 0.005 0.057 1402 Dihedral : 22.619 179.955 3282 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.33 % Favored : 93.22 % Rotamer: Outliers : 3.33 % Allowed : 22.40 % Favored : 74.27 % 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: 0.01 (0.28), residues: 885 helix: 0.87 (0.20), residues: 660 sheet: -0.64 (1.03), residues: 26 loop : -2.80 (0.44), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 111 TYR 0.014 0.002 TYR A 152 PHE 0.017 0.002 PHE D 80 TRP 0.009 0.001 TRP E 116 HIS 0.004 0.001 HIS A 313 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 (10820) covalent geometry : angle 0.56986 / 0.31 (15316) hydrogen bonds : bond 0.04635 / 3.05 ( 593) hydrogen bonds : angle 4.22128 / 3.00 ( 1599) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 0.221 Fit side-chains REVERT: A 57 ASN cc_start: 0.8774 (m-40) cc_final: 0.8461 (m-40) REVERT: A 275 SER cc_start: 0.8798 (OUTLIER) cc_final: 0.8292 (t) REVERT: A 278 LYS cc_start: 0.7340 (mtpt) cc_final: 0.6583 (mmtt) REVERT: B 44 MET cc_start: 0.8956 (mtp) cc_final: 0.8703 (mtp) REVERT: B 108 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7337 (mm-30) REVERT: C 111 ARG cc_start: 0.8373 (ttm-80) cc_final: 0.8111 (ttp80) REVERT: D 13 GLN cc_start: 0.4660 (pm20) cc_final: 0.4403 (pm20) REVERT: D 67 LYS cc_start: 0.7679 (mtmt) cc_final: 0.7405 (mtmt) REVERT: D 95 THR cc_start: 0.7761 (OUTLIER) cc_final: 0.7409 (p) REVERT: F 69 TYR cc_start: 0.7940 (m-10) cc_final: 0.7540 (m-10) outliers start: 25 outliers final: 18 residues processed: 148 average time/residue: 0.1387 time to fit residues: 26.2507 Evaluate side-chains 154 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 134 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain C residue 64 GLN Chi-restraints excluded: chain D residue 19 ARG Chi-restraints excluded: chain D residue 36 ARG Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain F residue 16 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 58 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 64 optimal weight: 0.4980 chunk 1 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 chunk 95 optimal weight: 20.0000 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 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 = 0.4018 r_free = 0.4018 target = 0.169785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.129633 restraints weight = 13143.040| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 1.47 r_work: 0.3379 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10820 Z= 0.148 Angle : 0.567 7.827 15316 Z= 0.304 Chirality : 0.037 0.220 1813 Planarity : 0.005 0.057 1402 Dihedral : 22.556 179.712 3280 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.55 % Favored : 92.99 % Rotamer: Outliers : 3.07 % Allowed : 21.87 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.29), residues: 885 helix: 0.96 (0.20), residues: 659 sheet: -0.43 (1.04), residues: 26 loop : -2.78 (0.44), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 111 TYR 0.014 0.002 TYR A 152 PHE 0.016 0.002 PHE B 80 TRP 0.010 0.001 TRP E 116 HIS 0.004 0.001 HIS D 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (10820) covalent geometry : angle 0.56734 / 0.30 (15316) hydrogen bonds : bond 0.04583 / 3.03 ( 593) hydrogen bonds : angle 4.20344 / 2.98 ( 1599) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1770 Ramachandran restraints generated. 885 Oldfield, 0 Emsley, 885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 134 time to evaluate : 0.255 Fit side-chains REVERT: A 57 ASN cc_start: 0.8745 (m-40) cc_final: 0.8429 (m-40) REVERT: A 275 SER cc_start: 0.8800 (OUTLIER) cc_final: 0.8286 (t) REVERT: A 278 LYS cc_start: 0.7330 (mtpt) cc_final: 0.6598 (mmtt) REVERT: A 309 TRP cc_start: 0.6322 (m100) cc_final: 0.5632 (m-90) REVERT: B 44 MET cc_start: 0.8956 (mtp) cc_final: 0.8694 (mtp) REVERT: B 77 MET cc_start: 0.8888 (tpt) cc_final: 0.8226 (tpt) REVERT: B 108 GLU cc_start: 0.7748 (mm-30) cc_final: 0.7309 (mm-30) REVERT: C 111 ARG cc_start: 0.8357 (ttm-80) cc_final: 0.8105 (ttp80) REVERT: D 67 LYS cc_start: 0.7668 (mtmt) cc_final: 0.7422 (mtmt) REVERT: D 95 THR cc_start: 0.7764 (OUTLIER) cc_final: 0.7419 (p) REVERT: F 69 TYR cc_start: 0.7921 (m-10) cc_final: 0.7539 (m-10) outliers start: 23 outliers final: 18 residues processed: 148 average time/residue: 0.1359 time to fit residues: 26.1787 Evaluate side-chains 151 residues out of total 751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain C residue 64 GLN Chi-restraints excluded: chain D residue 19 ARG Chi-restraints excluded: chain D residue 36 ARG Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain E residue 108 GLU Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain F residue 16 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 48 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 31 optimal weight: 6.9990 chunk 42 optimal weight: 0.6980 chunk 29 optimal weight: 5.9990 chunk 44 optimal weight: 0.3980 chunk 24 optimal weight: 0.0980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 116 HIS C 92 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.170774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.130929 restraints weight = 13230.697| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 1.47 r_work: 0.3390 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.3989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10820 Z= 0.134 Angle : 0.560 7.391 15316 Z= 0.301 Chirality : 0.036 0.209 1813 Planarity : 0.005 0.058 1402 Dihedral : 22.480 179.453 3280 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.88 % Favored : 93.67 % Rotamer: Outliers : 3.07 % Allowed : 22.00 % Favored : 74.93 % 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: 0.22 (0.29), residues: 885 helix: 1.04 (0.20), residues: 658 sheet: -0.28 (1.05), residues: 26 loop : -2.81 (0.43), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG F 111 TYR 0.013 0.002 TYR A 152 PHE 0.015 0.002 PHE A 231 TRP 0.009 0.001 TRP E 116 HIS 0.005 0.001 HIS C 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (10820) covalent geometry : angle 0.55954 / 0.30 (15316) hydrogen bonds : bond 0.04516 / 2.98 ( 593) hydrogen bonds : angle 4.17237 / 2.96 ( 1599) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2335.85 seconds wall clock time: 40 minutes 45.18 seconds (2445.18 seconds total)