Starting phenix.real_space_refine on Thu Jul 2 20:37:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yjv_39351/07_2026/8yjv_39351.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yjv_39351/07_2026/8yjv_39351.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8yjv_39351/07_2026/8yjv_39351.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yjv_39351/07_2026/8yjv_39351.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8yjv_39351/07_2026/8yjv_39351.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yjv_39351/07_2026/8yjv_39351.map" } resolution = 3.51 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 404 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 64 5.49 5 S 61 5.16 5 C 6057 2.51 5 N 1667 2.21 5 O 2089 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9938 Number of models: 1 Model: "" Number of chains: 8 Chain: "C" Number of atoms: 1947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1947 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 7, 'TRANS': 245} Chain: "D" Number of atoms: 2779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2779 Classifications: {'peptide': 353} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 337} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 1946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1946 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 7, 'TRANS': 245} Chain: "B" Number of atoms: 1938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1938 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 7, 'TRANS': 244} Chain: "J" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 406 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "E" Number of atoms: 635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 635 Classifications: {'DNA': 31} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 30} Chain: "F" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 227 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Chain: "H" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Classifications: {'DNA': 3} Link IDs: {'rna3p': 2} Time building chain proxies: 2.05, per 1000 atoms: 0.21 Number of scatterers: 9938 At special positions: 0 Unit cell: (108.73, 107.07, 105.41, 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 61 16.00 P 64 15.00 O 2089 8.00 N 1667 7.00 C 6057 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 162 " distance=2.03 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 162 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.92 Conformation dependent library (CDL) restraints added in 304.5 milliseconds 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2098 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 14 sheets defined 31.9% alpha, 24.2% beta 12 base pairs and 48 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'C' and resid 8 through 19 removed outlier: 4.243A pdb=" N LEU C 12 " --> pdb=" O GLN C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 80 Processing helix chain 'C' and resid 141 through 155 removed outlier: 4.132A pdb=" N HIS C 153 " --> pdb=" O ARG C 149 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ILE C 154 " --> pdb=" O ASP C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 216 Processing helix chain 'C' and resid 217 through 222 Proline residue: C 220 - end of helix No H-bonds generated for 'chain 'C' and resid 217 through 222' Processing helix chain 'D' and resid 6 through 13 Processing helix chain 'D' and resid 23 through 27 removed outlier: 3.796A pdb=" N TYR D 26 " --> pdb=" O ILE D 23 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE D 27 " --> pdb=" O LYS D 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 23 through 27' Processing helix chain 'D' and resid 35 through 46 Processing helix chain 'D' and resid 61 through 77 removed outlier: 3.536A pdb=" N ASN D 77 " --> pdb=" O ARG D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 92 No H-bonds generated for 'chain 'D' and resid 90 through 92' Processing helix chain 'D' and resid 93 through 118 Processing helix chain 'D' and resid 120 through 129 Processing helix chain 'D' and resid 134 through 149 Processing helix chain 'D' and resid 158 through 169 removed outlier: 3.698A pdb=" N SER D 162 " --> pdb=" O GLU D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 186 removed outlier: 3.894A pdb=" N THR D 184 " --> pdb=" O MET D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 216 Processing helix chain 'D' and resid 219 through 231 Processing helix chain 'D' and resid 242 through 254 Processing helix chain 'D' and resid 256 through 262 Processing helix chain 'D' and resid 275 through 285 Processing helix chain 'D' and resid 302 through 313 Processing helix chain 'D' and resid 317 through 334 removed outlier: 3.802A pdb=" N ILE D 321 " --> pdb=" O SER D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 337 No H-bonds generated for 'chain 'D' and resid 335 through 337' Processing helix chain 'D' and resid 339 through 343 Processing helix chain 'A' and resid 8 through 19 removed outlier: 3.818A pdb=" N LEU A 12 " --> pdb=" O GLN A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 81 Processing helix chain 'A' and resid 141 through 152 Processing helix chain 'A' and resid 209 through 216 Processing helix chain 'A' and resid 217 through 222 Proline residue: A 220 - end of helix No H-bonds generated for 'chain 'A' and resid 217 through 222' Processing helix chain 'B' and resid 8 through 20 removed outlier: 4.096A pdb=" N LEU B 12 " --> pdb=" O GLN B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 82 removed outlier: 3.682A pdb=" N ALA B 82 " --> pdb=" O ILE B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 152 Processing helix chain 'B' and resid 210 through 216 Processing helix chain 'B' and resid 217 through 222 Proline residue: B 220 - end of helix No H-bonds generated for 'chain 'B' and resid 217 through 222' Processing sheet with id=AA1, first strand: chain 'C' and resid 58 through 61 removed outlier: 4.924A pdb=" N THR C 59 " --> pdb=" O ARG C 5 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ARG C 5 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N SER B 172 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ALA B 157 " --> pdb=" O SER B 172 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 25 through 30 removed outlier: 3.779A pdb=" N MET C 68 " --> pdb=" O TRP C 28 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 34 through 40 removed outlier: 5.527A pdb=" N SER C 230 " --> pdb=" O PRO C 234 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LYS C 240 " --> pdb=" O THR C 224 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N THR C 224 " --> pdb=" O LYS C 240 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 126 through 127 removed outlier: 4.027A pdb=" N LYS D 345 " --> pdb=" O GLY C 127 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 204 through 208 Processing sheet with id=AA6, first strand: chain 'D' and resid 18 through 21 Processing sheet with id=AA7, first strand: chain 'D' and resid 152 through 154 removed outlier: 3.755A pdb=" N ALA D 174 " --> pdb=" O LYS D 30 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 47 through 48 Processing sheet with id=AA9, first strand: chain 'A' and resid 59 through 61 Processing sheet with id=AB1, first strand: chain 'A' and resid 66 through 71 removed outlier: 7.288A pdb=" N GLU A 25 " --> pdb=" O MET A 40 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N MET A 40 " --> pdb=" O GLU A 25 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N CYS A 27 " --> pdb=" O GLN A 38 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLN A 38 " --> pdb=" O CYS A 27 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU A 251 " --> pdb=" O LEU A 235 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N LYS A 240 " --> pdb=" O THR A 224 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N THR A 224 " --> pdb=" O LYS A 240 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 204 through 208 removed outlier: 3.735A pdb=" N LEU A 205 " --> pdb=" O ILE A 160 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ILE A 160 " --> pdb=" O LEU A 205 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 59 through 61 removed outlier: 3.904A pdb=" N THR B 59 " --> pdb=" O ARG B 5 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 25 through 30 Processing sheet with id=AB5, first strand: chain 'B' and resid 34 through 40 removed outlier: 3.728A pdb=" N LEU B 251 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU B 235 " --> pdb=" O LEU B 251 " (cutoff:3.500A) 425 hydrogen bonds defined for protein. 1182 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 24 hydrogen bonds 48 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 48 stacking parallelities Total time for adding SS restraints: 1.61 Time building geometry restraints manager: 1.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2315 1.33 - 1.45: 2144 1.45 - 1.57: 5536 1.57 - 1.69: 127 1.69 - 1.81: 98 Bond restraints: 10220 Sorted by residual: bond pdb=" C3' DT E 3 " pdb=" O3' DT E 3 " ideal model delta sigma weight residual 1.435 1.496 -0.061 1.30e-02 5.92e+03 2.22e+01 bond pdb=" C1' DT E 8 " pdb=" N1 DT E 8 " ideal model delta sigma weight residual 1.468 1.521 -0.053 1.40e-02 5.10e+03 1.42e+01 bond pdb=" C3' DT J 1 " pdb=" C2' DT J 1 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.18e+01 bond pdb=" C3' DA E 28 " pdb=" O3' DA E 28 " ideal model delta sigma weight residual 1.435 1.479 -0.044 1.30e-02 5.92e+03 1.17e+01 bond pdb=" C3' DT E 22 " pdb=" C2' DT E 22 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.17e+01 ... (remaining 10215 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.19: 13772 3.19 - 6.38: 248 6.38 - 9.58: 39 9.58 - 12.77: 7 12.77 - 15.96: 2 Bond angle restraints: 14068 Sorted by residual: angle pdb=" C ALA C 242 " pdb=" N ASP C 243 " pdb=" CA ASP C 243 " ideal model delta sigma weight residual 121.54 135.01 -13.47 1.91e+00 2.74e-01 4.97e+01 angle pdb=" CA PRO B 106 " pdb=" N PRO B 106 " pdb=" CD PRO B 106 " ideal model delta sigma weight residual 112.00 104.02 7.98 1.40e+00 5.10e-01 3.25e+01 angle pdb=" C ALA B 242 " pdb=" N ASP B 243 " pdb=" CA ASP B 243 " ideal model delta sigma weight residual 122.46 129.62 -7.16 1.41e+00 5.03e-01 2.58e+01 angle pdb=" CA LEU D 275 " pdb=" CB LEU D 275 " pdb=" CG LEU D 275 " ideal model delta sigma weight residual 116.30 132.26 -15.96 3.50e+00 8.16e-02 2.08e+01 angle pdb=" N LYS C 217 " pdb=" CA LYS C 217 " pdb=" C LYS C 217 " ideal model delta sigma weight residual 113.28 107.73 5.55 1.22e+00 6.72e-01 2.07e+01 ... (remaining 14063 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.35: 5746 35.35 - 70.69: 402 70.69 - 106.04: 17 106.04 - 141.39: 1 141.39 - 176.73: 1 Dihedral angle restraints: 6167 sinusoidal: 2933 harmonic: 3234 Sorted by residual: dihedral pdb=" CB CYS A 135 " pdb=" SG CYS A 135 " pdb=" SG CYS A 162 " pdb=" CB CYS A 162 " ideal model delta sinusoidal sigma weight residual 93.00 153.33 -60.33 1 1.00e+01 1.00e-02 4.85e+01 dihedral pdb=" CA ASP A 150 " pdb=" C ASP A 150 " pdb=" N LEU A 151 " pdb=" CA LEU A 151 " ideal model delta harmonic sigma weight residual 180.00 157.81 22.19 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA ILE B 241 " pdb=" C ILE B 241 " pdb=" N ALA B 242 " pdb=" CA ALA B 242 " ideal model delta harmonic sigma weight residual 180.00 160.21 19.79 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 6164 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1280 0.073 - 0.145: 290 0.145 - 0.218: 40 0.218 - 0.290: 6 0.290 - 0.363: 3 Chirality restraints: 1619 Sorted by residual: chirality pdb=" CB VAL A 233 " pdb=" CA VAL A 233 " pdb=" CG1 VAL A 233 " pdb=" CG2 VAL A 233 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.29e+00 chirality pdb=" CG LEU B 72 " pdb=" CB LEU B 72 " pdb=" CD1 LEU B 72 " pdb=" CD2 LEU B 72 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" CG LEU B 235 " pdb=" CB LEU B 235 " pdb=" CD1 LEU B 235 " pdb=" CD2 LEU B 235 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.20e+00 ... (remaining 1616 not shown) Planarity restraints: 1591 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 233 " 0.068 5.00e-02 4.00e+02 1.03e-01 1.71e+01 pdb=" N PRO A 234 " -0.179 5.00e-02 4.00e+02 pdb=" CA PRO A 234 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO A 234 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 214 " -0.019 2.00e-02 2.50e+03 2.60e-02 1.18e+01 pdb=" CG PHE B 214 " 0.059 2.00e-02 2.50e+03 pdb=" CD1 PHE B 214 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE B 214 " -0.023 2.00e-02 2.50e+03 pdb=" CE1 PHE B 214 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B 214 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE B 214 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 214 " 0.018 2.00e-02 2.50e+03 2.50e-02 1.09e+01 pdb=" CG PHE C 214 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 PHE C 214 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 PHE C 214 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE C 214 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE C 214 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE C 214 " 0.001 2.00e-02 2.50e+03 ... (remaining 1588 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 2804 2.83 - 3.35: 8286 3.35 - 3.87: 17788 3.87 - 4.38: 19625 4.38 - 4.90: 33050 Nonbonded interactions: 81553 Sorted by model distance: nonbonded pdb=" O MET D 67 " pdb=" OG1 THR D 71 " model vdw 2.317 3.040 nonbonded pdb=" O THR B 216 " pdb=" OG1 THR B 219 " model vdw 2.338 3.040 nonbonded pdb=" OG SER D 197 " pdb=" OP2 DA E 14 " model vdw 2.342 3.040 nonbonded pdb=" O ASN B 71 " pdb=" OG SER B 74 " model vdw 2.355 3.040 nonbonded pdb=" N GLY D 2 " pdb=" OD1 ASP D 179 " model vdw 2.383 3.120 ... (remaining 81548 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 2 through 253) selection = chain 'B' selection = (chain 'C' and resid 2 through 253) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.370 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 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:0.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 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 : 0.007 0.099 10222 Z= 0.416 Angle : 1.121 15.960 14072 Z= 0.682 Chirality : 0.062 0.363 1619 Planarity : 0.008 0.103 1591 Dihedral : 20.737 176.732 4063 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.10 % Allowed : 0.73 % Favored : 99.17 % 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: -3.60 (0.21), residues: 1103 helix: -2.47 (0.22), residues: 308 sheet: -2.02 (0.26), residues: 335 loop : -2.42 (0.22), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 5 TYR 0.030 0.003 TYR A 249 PHE 0.059 0.005 PHE B 214 TRP 0.051 0.005 TRP D 274 HIS 0.016 0.002 HIS D 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00744 / 0.42 (10220) covalent geometry : angle 1.12048 / 0.68 (14068) SS BOND : bond 0.00067 / 0.03 ( 2) SS BOND : angle 1.35529 / 1.10 ( 4) hydrogen bonds : bond 0.20225 / 13.64 ( 449) hydrogen bonds : angle 10.17809 / 7.04 ( 1230) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 157 time to evaluate : 0.366 Fit side-chains REVERT: C 53 ARG cc_start: 0.7826 (mtm180) cc_final: 0.7393 (mtm180) REVERT: C 97 ASP cc_start: 0.4939 (p0) cc_final: 0.4469 (p0) REVERT: C 244 MET cc_start: 0.8524 (mtp) cc_final: 0.8228 (mtp) REVERT: D 21 ASN cc_start: 0.7825 (m110) cc_final: 0.7594 (m110) REVERT: A 199 MET cc_start: 0.5303 (ttm) cc_final: 0.4907 (ttm) outliers start: 1 outliers final: 0 residues processed: 158 average time/residue: 0.0861 time to fit residues: 19.6424 Evaluate side-chains 118 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.4980 chunk 113 optimal weight: 10.0000 chunk 53 optimal weight: 0.0970 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.0470 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.0770 chunk 100 optimal weight: 0.9980 overall best weight: 0.2634 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 137 HIS ** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 HIS B 177 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.160819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.123670 restraints weight = 13133.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.127375 restraints weight = 7662.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.129864 restraints weight = 5381.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.131415 restraints weight = 4262.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.132625 restraints weight = 3664.945| |-----------------------------------------------------------------------------| r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 10222 Z= 0.146 Angle : 0.649 8.513 14072 Z= 0.365 Chirality : 0.046 0.266 1619 Planarity : 0.005 0.087 1591 Dihedral : 21.735 177.824 1939 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.35 % Allowed : 7.17 % Favored : 91.48 % 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: -2.66 (0.22), residues: 1103 helix: -0.65 (0.27), residues: 311 sheet: -2.08 (0.26), residues: 326 loop : -2.18 (0.23), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 5 TYR 0.012 0.001 TYR A 114 PHE 0.032 0.002 PHE B 2 TRP 0.016 0.002 TRP D 274 HIS 0.004 0.001 HIS D 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.15 (10220) covalent geometry : angle 0.64892 / 0.36 (14068) SS BOND : bond 0.00488 / 0.26 ( 2) SS BOND : angle 0.77092 / 0.50 ( 4) hydrogen bonds : bond 0.05883 / 3.52 ( 449) hydrogen bonds : angle 7.25972 / 5.08 ( 1230) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 138 time to evaluate : 0.369 Fit side-chains REVERT: C 97 ASP cc_start: 0.4885 (p0) cc_final: 0.4176 (p0) REVERT: C 214 PHE cc_start: 0.8615 (m-10) cc_final: 0.8382 (m-10) REVERT: C 244 MET cc_start: 0.8260 (mtp) cc_final: 0.8032 (ttm) REVERT: D 77 ASN cc_start: 0.7916 (m-40) cc_final: 0.7490 (m110) REVERT: B 116 MET cc_start: 0.7576 (tpp) cc_final: 0.7358 (tpt) REVERT: B 131 GLN cc_start: 0.6473 (mm-40) cc_final: 0.6073 (mm-40) outliers start: 13 outliers final: 11 residues processed: 146 average time/residue: 0.0883 time to fit residues: 18.8546 Evaluate side-chains 127 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 321 ILE Chi-restraints excluded: chain D residue 329 SER Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain B residue 24 ASN Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 206 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 28 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 52 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 114 optimal weight: 10.0000 chunk 23 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 110 GLN D 137 HIS ** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.157378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.119614 restraints weight = 13195.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.123217 restraints weight = 7826.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.125668 restraints weight = 5565.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.127188 restraints weight = 4438.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.128333 restraints weight = 3836.103| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10222 Z= 0.186 Angle : 0.631 7.409 14072 Z= 0.348 Chirality : 0.046 0.293 1619 Planarity : 0.004 0.078 1591 Dihedral : 21.694 172.837 1939 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.97 % Allowed : 10.38 % Favored : 87.64 % 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: -2.20 (0.23), residues: 1103 helix: 0.18 (0.29), residues: 310 sheet: -2.02 (0.27), residues: 320 loop : -2.10 (0.24), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 53 TYR 0.013 0.002 TYR D 83 PHE 0.033 0.002 PHE B 214 TRP 0.013 0.001 TRP D 274 HIS 0.005 0.001 HIS D 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.19 (10220) covalent geometry : angle 0.63122 / 0.35 (14068) SS BOND : bond 0.00136 / 0.07 ( 2) SS BOND : angle 1.12907 / 0.78 ( 4) hydrogen bonds : bond 0.05112 / 3.14 ( 449) hydrogen bonds : angle 6.78226 / 4.72 ( 1230) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 0.247 Fit side-chains REVERT: C 97 ASP cc_start: 0.4978 (p0) cc_final: 0.4048 (p0) REVERT: C 214 PHE cc_start: 0.8713 (m-10) cc_final: 0.8379 (m-10) REVERT: B 131 GLN cc_start: 0.6701 (OUTLIER) cc_final: 0.6213 (mm-40) outliers start: 19 outliers final: 13 residues processed: 138 average time/residue: 0.0829 time to fit residues: 16.9331 Evaluate side-chains 133 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 243 ASP Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 321 ILE Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain B residue 24 ASN Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 224 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 62 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 43 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 36 ASN ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 GLN D 137 HIS ** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.153884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.116101 restraints weight = 13483.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.119695 restraints weight = 7962.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.122100 restraints weight = 5603.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.123686 restraints weight = 4478.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.124587 restraints weight = 3861.576| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 10222 Z= 0.235 Angle : 0.665 7.255 14072 Z= 0.364 Chirality : 0.047 0.308 1619 Planarity : 0.004 0.075 1591 Dihedral : 21.749 170.022 1939 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.97 % Allowed : 12.46 % Favored : 85.57 % 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: -2.25 (0.23), residues: 1103 helix: 0.26 (0.29), residues: 316 sheet: -2.18 (0.27), residues: 313 loop : -2.15 (0.24), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 146 TYR 0.017 0.002 TYR D 83 PHE 0.033 0.002 PHE B 214 TRP 0.008 0.002 TRP A 28 HIS 0.005 0.001 HIS D 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.23 (10220) covalent geometry : angle 0.66461 / 0.36 (14068) SS BOND : bond 0.00162 / 0.08 ( 2) SS BOND : angle 1.12617 / 0.73 ( 4) hydrogen bonds : bond 0.04967 / 3.05 ( 449) hydrogen bonds : angle 6.69948 / 4.65 ( 1230) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.208 Fit side-chains REVERT: C 36 ASN cc_start: 0.8468 (OUTLIER) cc_final: 0.7813 (m-40) REVERT: C 53 ARG cc_start: 0.8160 (mtm180) cc_final: 0.7947 (mtm180) REVERT: A 239 TYR cc_start: 0.8471 (m-80) cc_final: 0.8260 (m-80) outliers start: 19 outliers final: 16 residues processed: 132 average time/residue: 0.0855 time to fit residues: 16.7780 Evaluate side-chains 127 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 243 ASP Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 321 ILE Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain B residue 24 ASN Chi-restraints excluded: chain B residue 81 CYS Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 236 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 5 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 46 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 ASN D 110 GLN D 137 HIS ** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.154623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.117029 restraints weight = 13346.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.120647 restraints weight = 7863.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.123079 restraints weight = 5580.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.124671 restraints weight = 4451.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.125744 restraints weight = 3826.449| |-----------------------------------------------------------------------------| r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10222 Z= 0.186 Angle : 0.611 7.339 14072 Z= 0.337 Chirality : 0.046 0.314 1619 Planarity : 0.004 0.072 1591 Dihedral : 21.748 169.255 1939 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.97 % Allowed : 13.29 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.24), residues: 1103 helix: 0.55 (0.30), residues: 316 sheet: -2.21 (0.27), residues: 317 loop : -2.05 (0.24), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 146 TYR 0.013 0.002 TYR D 83 PHE 0.026 0.002 PHE B 214 TRP 0.010 0.002 TRP C 28 HIS 0.005 0.001 HIS C 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.19 (10220) covalent geometry : angle 0.61127 / 0.34 (14068) SS BOND : bond 0.00149 / 0.07 ( 2) SS BOND : angle 0.95465 / 0.61 ( 4) hydrogen bonds : bond 0.04656 / 2.82 ( 449) hydrogen bonds : angle 6.58282 / 4.57 ( 1230) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 0.453 Fit side-chains REVERT: C 53 ARG cc_start: 0.8156 (mtm180) cc_final: 0.7934 (mtm180) REVERT: C 225 VAL cc_start: 0.8494 (t) cc_final: 0.8271 (p) REVERT: A 239 TYR cc_start: 0.8420 (m-80) cc_final: 0.8178 (m-80) outliers start: 19 outliers final: 17 residues processed: 137 average time/residue: 0.0897 time to fit residues: 18.2094 Evaluate side-chains 131 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 243 ASP Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 321 ILE Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain B residue 24 ASN Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 236 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 102 optimal weight: 0.9990 chunk 115 optimal weight: 10.0000 chunk 101 optimal weight: 2.9990 chunk 108 optimal weight: 0.5980 chunk 58 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 60 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 26 optimal weight: 7.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 36 ASN ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 GLN D 137 HIS ** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.154567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.117168 restraints weight = 13492.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.120824 restraints weight = 7818.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.123307 restraints weight = 5514.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.124913 restraints weight = 4368.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.125823 restraints weight = 3763.394| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10222 Z= 0.175 Angle : 0.603 7.452 14072 Z= 0.331 Chirality : 0.045 0.321 1619 Planarity : 0.004 0.071 1591 Dihedral : 21.742 168.039 1939 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.91 % Allowed : 13.29 % Favored : 83.80 % 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: -1.98 (0.24), residues: 1103 helix: 0.68 (0.30), residues: 317 sheet: -2.21 (0.27), residues: 314 loop : -1.99 (0.25), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 146 TYR 0.012 0.002 TYR D 83 PHE 0.026 0.002 PHE B 214 TRP 0.012 0.002 TRP C 28 HIS 0.006 0.001 HIS D 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.18 (10220) covalent geometry : angle 0.60278 / 0.33 (14068) SS BOND : bond 0.00105 / 0.05 ( 2) SS BOND : angle 0.92586 / 0.61 ( 4) hydrogen bonds : bond 0.04476 / 2.71 ( 449) hydrogen bonds : angle 6.45120 / 4.48 ( 1230) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 121 time to evaluate : 0.337 Fit side-chains REVERT: C 53 ARG cc_start: 0.8148 (mtm180) cc_final: 0.7924 (mtm180) REVERT: C 214 PHE cc_start: 0.8633 (m-10) cc_final: 0.8304 (m-10) REVERT: D 74 MET cc_start: 0.7781 (OUTLIER) cc_final: 0.7081 (mmt) REVERT: D 92 LEU cc_start: 0.7986 (mp) cc_final: 0.7769 (mp) REVERT: D 248 ASP cc_start: 0.6230 (m-30) cc_final: 0.5857 (t0) REVERT: D 327 ARG cc_start: 0.6812 (OUTLIER) cc_final: 0.6513 (ptt180) REVERT: A 139 MET cc_start: 0.7582 (ptt) cc_final: 0.7376 (ptt) REVERT: A 239 TYR cc_start: 0.8408 (m-80) cc_final: 0.8172 (m-80) outliers start: 28 outliers final: 22 residues processed: 138 average time/residue: 0.0823 time to fit residues: 16.8320 Evaluate side-chains 139 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 243 ASP Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 321 ILE Chi-restraints excluded: chain D residue 327 ARG Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain B residue 24 ASN Chi-restraints excluded: chain B residue 81 CYS Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 236 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 22 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 21 optimal weight: 0.2980 chunk 16 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 44 optimal weight: 0.0040 chunk 17 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 GLN D 137 HIS ** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 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 = 0.3962 r_free = 0.3962 target = 0.155795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.118536 restraints weight = 13296.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.122197 restraints weight = 7767.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.124682 restraints weight = 5477.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.126277 restraints weight = 4339.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.127378 restraints weight = 3726.449| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10222 Z= 0.150 Angle : 0.584 9.071 14072 Z= 0.320 Chirality : 0.045 0.328 1619 Planarity : 0.004 0.070 1591 Dihedral : 21.705 167.176 1939 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.39 % Allowed : 14.75 % Favored : 82.87 % 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: -1.85 (0.24), residues: 1103 helix: 0.79 (0.30), residues: 319 sheet: -2.11 (0.27), residues: 311 loop : -1.95 (0.25), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 70 TYR 0.010 0.001 TYR D 83 PHE 0.026 0.002 PHE B 214 TRP 0.011 0.001 TRP C 28 HIS 0.007 0.001 HIS C 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (10220) covalent geometry : angle 0.58422 / 0.32 (14068) SS BOND : bond 0.00143 / 0.07 ( 2) SS BOND : angle 0.81419 / 0.49 ( 4) hydrogen bonds : bond 0.04277 / 2.59 ( 449) hydrogen bonds : angle 6.32577 / 4.39 ( 1230) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 0.389 Fit side-chains REVERT: C 53 ARG cc_start: 0.8130 (mtm180) cc_final: 0.7903 (mtm180) REVERT: C 214 PHE cc_start: 0.8597 (m-10) cc_final: 0.8258 (m-10) REVERT: D 74 MET cc_start: 0.7741 (OUTLIER) cc_final: 0.7047 (mmt) REVERT: D 248 ASP cc_start: 0.6279 (m-30) cc_final: 0.5859 (t70) REVERT: D 327 ARG cc_start: 0.6839 (OUTLIER) cc_final: 0.6516 (ptt180) REVERT: A 239 TYR cc_start: 0.8333 (m-80) cc_final: 0.8113 (m-80) outliers start: 23 outliers final: 18 residues processed: 137 average time/residue: 0.0912 time to fit residues: 17.9947 Evaluate side-chains 136 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 243 ASP Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 321 ILE Chi-restraints excluded: chain D residue 327 ARG Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain B residue 24 ASN Chi-restraints excluded: chain B residue 81 CYS Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 219 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 90 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 chunk 96 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 80 optimal weight: 0.0980 chunk 7 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 GLN D 137 HIS ** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 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 = 0.3937 r_free = 0.3937 target = 0.154030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.117384 restraints weight = 13311.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.120891 restraints weight = 7836.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.123276 restraints weight = 5549.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.124861 restraints weight = 4417.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.125912 restraints weight = 3787.765| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10222 Z= 0.158 Angle : 0.595 7.633 14072 Z= 0.323 Chirality : 0.044 0.333 1619 Planarity : 0.004 0.070 1591 Dihedral : 21.659 166.056 1939 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.60 % Allowed : 15.47 % Favored : 81.93 % 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: -1.83 (0.24), residues: 1103 helix: 0.84 (0.30), residues: 319 sheet: -2.12 (0.26), residues: 318 loop : -1.94 (0.25), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 320 TYR 0.011 0.001 TYR D 83 PHE 0.025 0.002 PHE B 214 TRP 0.012 0.002 TRP C 28 HIS 0.006 0.001 HIS D 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 (10220) covalent geometry : angle 0.59475 / 0.32 (14068) SS BOND : bond 0.00121 / 0.06 ( 2) SS BOND : angle 0.82669 / 0.51 ( 4) hydrogen bonds : bond 0.04210 / 2.57 ( 449) hydrogen bonds : angle 6.24953 / 4.33 ( 1230) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 122 time to evaluate : 0.376 Fit side-chains REVERT: C 53 ARG cc_start: 0.8106 (mtm180) cc_final: 0.7897 (mtm180) REVERT: C 214 PHE cc_start: 0.8612 (m-10) cc_final: 0.8234 (m-10) REVERT: D 74 MET cc_start: 0.7762 (OUTLIER) cc_final: 0.7080 (mmt) REVERT: D 248 ASP cc_start: 0.6215 (m-30) cc_final: 0.5874 (t70) REVERT: D 327 ARG cc_start: 0.6865 (OUTLIER) cc_final: 0.6536 (ptt180) REVERT: A 239 TYR cc_start: 0.8358 (m-80) cc_final: 0.8157 (m-80) outliers start: 25 outliers final: 21 residues processed: 135 average time/residue: 0.1038 time to fit residues: 19.6545 Evaluate side-chains 137 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 243 ASP Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 321 ILE Chi-restraints excluded: chain D residue 327 ARG Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain B residue 24 ASN Chi-restraints excluded: chain B residue 81 CYS Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 236 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 50 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 5 optimal weight: 0.4980 chunk 49 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 HIS ** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 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 = 0.3933 r_free = 0.3933 target = 0.153640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.117108 restraints weight = 13339.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.120566 restraints weight = 7956.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.122936 restraints weight = 5668.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.124325 restraints weight = 4517.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.125451 restraints weight = 3927.541| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10222 Z= 0.164 Angle : 0.593 7.748 14072 Z= 0.323 Chirality : 0.045 0.338 1619 Planarity : 0.004 0.070 1591 Dihedral : 21.632 163.994 1939 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.91 % Allowed : 15.37 % Favored : 81.72 % 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: -1.81 (0.24), residues: 1103 helix: 0.86 (0.30), residues: 318 sheet: -2.15 (0.26), residues: 320 loop : -1.87 (0.25), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 320 TYR 0.012 0.001 TYR D 83 PHE 0.026 0.002 PHE B 214 TRP 0.012 0.002 TRP C 28 HIS 0.007 0.001 HIS D 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (10220) covalent geometry : angle 0.59331 / 0.32 (14068) SS BOND : bond 0.00148 / 0.07 ( 2) SS BOND : angle 0.85700 / 0.52 ( 4) hydrogen bonds : bond 0.04139 / 2.55 ( 449) hydrogen bonds : angle 6.24042 / 4.32 ( 1230) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 114 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: C 53 ARG cc_start: 0.8092 (mtm180) cc_final: 0.7874 (mtm180) REVERT: C 97 ASP cc_start: 0.5299 (p0) cc_final: 0.4385 (p0) REVERT: C 214 PHE cc_start: 0.8608 (m-10) cc_final: 0.8233 (m-10) REVERT: D 74 MET cc_start: 0.7749 (OUTLIER) cc_final: 0.6981 (mmt) REVERT: D 248 ASP cc_start: 0.6271 (m-30) cc_final: 0.5906 (t70) REVERT: D 327 ARG cc_start: 0.6889 (OUTLIER) cc_final: 0.6569 (ptt180) outliers start: 28 outliers final: 23 residues processed: 131 average time/residue: 0.0966 time to fit residues: 18.2212 Evaluate side-chains 137 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 112 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 243 ASP Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 321 ILE Chi-restraints excluded: chain D residue 327 ARG Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain B residue 24 ASN Chi-restraints excluded: chain B residue 81 CYS Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 236 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 65 optimal weight: 0.9980 chunk 39 optimal weight: 0.2980 chunk 107 optimal weight: 0.5980 chunk 9 optimal weight: 0.4980 chunk 43 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 36 optimal weight: 8.9990 chunk 32 optimal weight: 0.4980 chunk 97 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 69 optimal weight: 0.0970 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 HIS ** D 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 = 0.3955 r_free = 0.3955 target = 0.155450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.119296 restraints weight = 13252.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.122789 restraints weight = 7832.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.125126 restraints weight = 5558.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.126715 restraints weight = 4428.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.127736 restraints weight = 3810.777| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10222 Z= 0.130 Angle : 0.574 7.784 14072 Z= 0.312 Chirality : 0.044 0.340 1619 Planarity : 0.004 0.069 1591 Dihedral : 21.562 163.935 1939 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.87 % Allowed : 16.51 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.24), residues: 1103 helix: 0.94 (0.30), residues: 319 sheet: -2.04 (0.26), residues: 317 loop : -1.83 (0.25), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 146 TYR 0.010 0.001 TYR B 250 PHE 0.025 0.002 PHE B 214 TRP 0.010 0.002 TRP D 274 HIS 0.007 0.001 HIS D 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (10220) covalent geometry : angle 0.57368 / 0.31 (14068) SS BOND : bond 0.00146 / 0.07 ( 2) SS BOND : angle 0.66191 / 0.39 ( 4) hydrogen bonds : bond 0.03943 / 2.40 ( 449) hydrogen bonds : angle 6.10680 / 4.23 ( 1230) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: C 53 ARG cc_start: 0.8073 (mtm180) cc_final: 0.7505 (mtm180) REVERT: C 97 ASP cc_start: 0.5215 (p0) cc_final: 0.4344 (p0) REVERT: C 214 PHE cc_start: 0.8583 (m-10) cc_final: 0.8280 (m-10) REVERT: D 74 MET cc_start: 0.7799 (OUTLIER) cc_final: 0.7037 (mmt) REVERT: D 248 ASP cc_start: 0.6225 (m-30) cc_final: 0.5880 (t70) REVERT: D 327 ARG cc_start: 0.6869 (OUTLIER) cc_final: 0.6556 (ptt180) outliers start: 18 outliers final: 14 residues processed: 126 average time/residue: 0.1002 time to fit residues: 18.0166 Evaluate side-chains 125 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 327 ARG Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain B residue 24 ASN Chi-restraints excluded: chain B residue 81 CYS Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 236 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 67 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 84 optimal weight: 0.9980 chunk 81 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 51 optimal weight: 0.0470 chunk 38 optimal weight: 1.9990 chunk 12 optimal weight: 0.0040 chunk 36 optimal weight: 3.9990 chunk 54 optimal weight: 0.0270 chunk 19 optimal weight: 0.6980 overall best weight: 0.2748 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 137 HIS D 208 HIS ** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.156415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.120149 restraints weight = 13355.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.123716 restraints weight = 7762.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.126175 restraints weight = 5442.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.127719 restraints weight = 4297.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.128828 restraints weight = 3692.906| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10222 Z= 0.120 Angle : 0.564 8.028 14072 Z= 0.306 Chirality : 0.043 0.340 1619 Planarity : 0.004 0.070 1591 Dihedral : 21.508 163.995 1939 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.56 % Allowed : 17.13 % Favored : 81.31 % 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: -1.55 (0.24), residues: 1103 helix: 1.04 (0.30), residues: 319 sheet: -1.88 (0.27), residues: 309 loop : -1.82 (0.25), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 146 TYR 0.009 0.001 TYR B 250 PHE 0.025 0.001 PHE B 214 TRP 0.015 0.002 TRP A 28 HIS 0.007 0.001 HIS D 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (10220) covalent geometry : angle 0.56369 / 0.31 (14068) SS BOND : bond 0.00151 / 0.07 ( 2) SS BOND : angle 0.60302 / 0.35 ( 4) hydrogen bonds : bond 0.03864 / 2.35 ( 449) hydrogen bonds : angle 5.99075 / 4.16 ( 1230) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1803.77 seconds wall clock time: 32 minutes 0.81 seconds (1920.81 seconds total)