Starting phenix.real_space_refine on Tue Mar 3 20:34:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f8w_31494/03_2026/7f8w_31494.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f8w_31494/03_2026/7f8w_31494.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7f8w_31494/03_2026/7f8w_31494.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f8w_31494/03_2026/7f8w_31494.map" model { file = "/net/cci-nas-00/data/ceres_data/7f8w_31494/03_2026/7f8w_31494.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f8w_31494/03_2026/7f8w_31494.cif" } resolution = 3.1 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= 0.003 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: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 5421 2.51 5 N 1449 2.21 5 O 1556 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8486 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1850 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 5, 'TRANS': 218} Chain breaks: 1 Chain: "B" Number of atoms: 2347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2347 Classifications: {'peptide': 306} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 300} Chain: "C" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 245 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 4, 'TRANS': 28} Chain: "D" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Chain: "E" Number of atoms: 133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 133 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 15} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'PCA:plan-2': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 17 Chain: "R" Number of atoms: 2128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2128 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 261} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Time building chain proxies: 2.41, per 1000 atoms: 0.28 Number of scatterers: 8486 At special positions: 0 Unit cell: (128.535, 117.04, 90.915, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 60 16.00 O 1556 8.00 N 1449 7.00 C 5421 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS D 39 " - pdb=" SG CYS D 113 " distance=2.04 Simple disulfide: pdb=" SG CYS R 127 " - pdb=" SG CYS R 205 " 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: 0.57 Conformation dependent library (CDL) restraints added in 273.8 milliseconds 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2024 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 14 sheets defined 32.9% alpha, 18.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 8 through 30 removed outlier: 4.260A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ARG A 15 " --> pdb=" O ALA A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 57 removed outlier: 3.529A pdb=" N PHE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N HIS A 57 " --> pdb=" O MET A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 212 removed outlier: 4.224A pdb=" N TRP A 210 " --> pdb=" O GLU A 206 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N HIS A 212 " --> pdb=" O ARG A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 273 through 280 removed outlier: 4.412A pdb=" N SER A 280 " --> pdb=" O LYS A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 310 removed outlier: 3.662A pdb=" N GLU A 301 " --> pdb=" O GLN A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 350 Processing helix chain 'C' and resid 30 through 44 Processing helix chain 'D' and resid 45 through 49 Processing helix chain 'D' and resid 79 through 82 removed outlier: 4.014A pdb=" N LYS D 82 " --> pdb=" O ASP D 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 79 through 82' Processing helix chain 'R' and resid 56 through 81 removed outlier: 3.850A pdb=" N LEU R 81 " --> pdb=" O VAL R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 117 Proline residue: R 109 - end of helix Proline residue: R 114 - end of helix Processing helix chain 'R' and resid 123 through 157 Processing helix chain 'R' and resid 158 through 166 Processing helix chain 'R' and resid 167 through 186 removed outlier: 3.604A pdb=" N MET R 186 " --> pdb=" O SER R 182 " (cutoff:3.500A) Processing helix chain 'R' and resid 211 through 226 Processing helix chain 'R' and resid 227 through 249 removed outlier: 3.524A pdb=" N LEU R 249 " --> pdb=" O LEU R 245 " (cutoff:3.500A) Processing helix chain 'R' and resid 327 through 359 Proline residue: R 348 - end of helix Processing helix chain 'R' and resid 362 through 367 Processing helix chain 'R' and resid 369 through 391 removed outlier: 3.787A pdb=" N SER R 379 " --> pdb=" O ILE R 375 " (cutoff:3.500A) Proline residue: R 387 - end of helix Processing helix chain 'R' and resid 394 through 405 Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 187 removed outlier: 4.641A pdb=" N LEU A 36 " --> pdb=" O ARG A 196 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N PHE A 266 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N PHE A 222 " --> pdb=" O PHE A 266 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 52 removed outlier: 5.958A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.951A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 103 through 105 removed outlier: 6.123A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.199A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 191 removed outlier: 6.890A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 231 through 234 removed outlier: 3.513A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 Processing sheet with id=AA9, first strand: chain 'D' and resid 21 through 24 removed outlier: 3.766A pdb=" N THR D 86 " --> pdb=" O GLN D 99 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 28 through 29 removed outlier: 4.057A pdb=" N VAL D 29 " --> pdb=" O THR D 135 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 76 through 77 removed outlier: 3.878A pdb=" N PHE D 127 " --> pdb=" O ARG D 115 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 158 through 159 Processing sheet with id=AB4, first strand: chain 'D' and resid 163 through 165 removed outlier: 6.294A pdb=" N VAL D 164 " --> pdb=" O GLU D 263 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'D' and resid 211 through 212 removed outlier: 5.337A pdb=" N LEU D 204 " --> pdb=" O LEU D 195 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N LEU D 195 " --> pdb=" O LEU D 204 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE D 206 " --> pdb=" O TRP D 193 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR D 245 " --> pdb=" O PHE D 194 " (cutoff:3.500A) 377 hydrogen bonds defined for protein. 1068 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.34 Time building geometry restraints manager: 0.80 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: 1835 1.33 - 1.45: 2081 1.45 - 1.58: 4667 1.58 - 1.70: 0 1.70 - 1.82: 91 Bond restraints: 8674 Sorted by residual: bond pdb=" N MET D 247 " pdb=" CA MET D 247 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.26e-02 6.30e+03 8.86e+00 bond pdb=" N GLN D 248 " pdb=" CA GLN D 248 " ideal model delta sigma weight residual 1.454 1.491 -0.037 1.27e-02 6.20e+03 8.42e+00 bond pdb=" N CYS R 107 " pdb=" CA CYS R 107 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.24e-02 6.50e+03 8.06e+00 bond pdb=" N MET R 108 " pdb=" CA MET R 108 " ideal model delta sigma weight residual 1.462 1.488 -0.026 9.50e-03 1.11e+04 7.66e+00 bond pdb=" N MET R 134 " pdb=" CA MET R 134 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.19e-02 7.06e+03 6.64e+00 ... (remaining 8669 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 11233 2.24 - 4.48: 439 4.48 - 6.72: 68 6.72 - 8.97: 24 8.97 - 11.21: 7 Bond angle restraints: 11771 Sorted by residual: angle pdb=" C ARG D 208 " pdb=" N MET D 209 " pdb=" CA MET D 209 " ideal model delta sigma weight residual 121.54 132.75 -11.21 1.91e+00 2.74e-01 3.44e+01 angle pdb=" N GLN D 248 " pdb=" CA GLN D 248 " pdb=" CB GLN D 248 " ideal model delta sigma weight residual 110.41 117.79 -7.38 1.63e+00 3.76e-01 2.05e+01 angle pdb=" CA ARG R 158 " pdb=" CB ARG R 158 " pdb=" CG ARG R 158 " ideal model delta sigma weight residual 114.10 123.09 -8.99 2.00e+00 2.50e-01 2.02e+01 angle pdb=" N PCA E 1 " pdb=" CA PCA E 1 " pdb=" CB PCA E 1 " ideal model delta sigma weight residual 110.50 103.43 7.07 1.70e+00 3.46e-01 1.73e+01 angle pdb=" CA LYS A 17 " pdb=" CB LYS A 17 " pdb=" CG LYS A 17 " ideal model delta sigma weight residual 114.10 122.19 -8.09 2.00e+00 2.50e-01 1.64e+01 ... (remaining 11766 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 4644 17.98 - 35.95: 390 35.95 - 53.93: 76 53.93 - 71.91: 7 71.91 - 89.89: 7 Dihedral angle restraints: 5124 sinusoidal: 1980 harmonic: 3144 Sorted by residual: dihedral pdb=" CA VAL R 164 " pdb=" C VAL R 164 " pdb=" N TRP R 165 " pdb=" CA TRP R 165 " ideal model delta harmonic sigma weight residual -180.00 -156.25 -23.75 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA GLU A 33 " pdb=" C GLU A 33 " pdb=" N LEU A 34 " pdb=" CA LEU A 34 " ideal model delta harmonic sigma weight residual 180.00 156.97 23.03 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA ASP B 66 " pdb=" C ASP B 66 " pdb=" N SER B 67 " pdb=" CA SER B 67 " ideal model delta harmonic sigma weight residual 180.00 157.79 22.21 0 5.00e+00 4.00e-02 1.97e+01 ... (remaining 5121 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1021 0.062 - 0.125: 251 0.125 - 0.187: 59 0.187 - 0.249: 5 0.249 - 0.311: 3 Chirality restraints: 1339 Sorted by residual: chirality pdb=" CB THR A 254 " pdb=" CA THR A 254 " pdb=" OG1 THR A 254 " pdb=" CG2 THR A 254 " both_signs ideal model delta sigma weight residual False 2.55 2.24 0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" CB ILE B 157 " pdb=" CA ILE B 157 " pdb=" CG1 ILE B 157 " pdb=" CG2 ILE B 157 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" CA ARG R 158 " pdb=" N ARG R 158 " pdb=" C ARG R 158 " pdb=" CB ARG R 158 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.65e+00 ... (remaining 1336 not shown) Planarity restraints: 1484 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N PCA E 1 " 0.066 2.00e-02 2.50e+03 4.39e-02 2.41e+01 pdb=" CA PCA E 1 " -0.055 2.00e-02 2.50e+03 pdb=" CG PCA E 1 " 0.021 2.00e-02 2.50e+03 pdb=" CD PCA E 1 " 0.009 2.00e-02 2.50e+03 pdb=" OE PCA E 1 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 332 " 0.027 2.00e-02 2.50e+03 2.39e-02 1.43e+01 pdb=" CG TRP B 332 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP B 332 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP B 332 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 332 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 332 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 332 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 332 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 332 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP B 332 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR D 245 " 0.017 2.00e-02 2.50e+03 3.56e-02 1.27e+01 pdb=" C TYR D 245 " -0.062 2.00e-02 2.50e+03 pdb=" O TYR D 245 " 0.024 2.00e-02 2.50e+03 pdb=" N CYS D 246 " 0.021 2.00e-02 2.50e+03 ... (remaining 1481 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1991 2.80 - 3.32: 7783 3.32 - 3.85: 14432 3.85 - 4.37: 16155 4.37 - 4.90: 28184 Nonbonded interactions: 68545 Sorted by model distance: nonbonded pdb=" OH TYR B 264 " pdb=" O ALA B 299 " model vdw 2.273 3.040 nonbonded pdb=" O VAL A 13 " pdb=" OG SER A 16 " model vdw 2.294 3.040 nonbonded pdb=" OG SER D 47 " pdb=" OD1 ASP D 91 " model vdw 2.301 3.040 nonbonded pdb=" OG SER B 67 " pdb=" OD1 ASP B 323 " model vdw 2.307 3.040 nonbonded pdb=" NZ LYS A 209 " pdb=" OD2 ASP B 228 " model vdw 2.313 3.120 ... (remaining 68540 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.240 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.300 Find NCS groups from input model: 0.040 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5589 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 : 0.005 0.062 8676 Z= 0.250 Angle : 1.039 11.208 11775 Z= 0.554 Chirality : 0.059 0.311 1339 Planarity : 0.008 0.087 1484 Dihedral : 14.087 89.886 3094 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.23), residues: 1067 helix: -0.31 (0.26), residues: 308 sheet: -1.21 (0.33), residues: 242 loop : -2.00 (0.24), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 42 TYR 0.022 0.002 TYR A 279 PHE 0.041 0.003 PHE B 234 TRP 0.064 0.004 TRP B 332 HIS 0.013 0.002 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00491 ( 8674) covalent geometry : angle 1.03925 (11771) SS BOND : bond 0.00353 ( 2) SS BOND : angle 1.21971 ( 4) hydrogen bonds : bond 0.15301 ( 377) hydrogen bonds : angle 7.83424 ( 1068) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.338 Fit side-chains REVERT: A 26 ASP cc_start: 0.6145 (m-30) cc_final: 0.5893 (m-30) REVERT: A 242 MET cc_start: 0.4577 (tpt) cc_final: 0.4270 (tpt) REVERT: A 306 MET cc_start: 0.5356 (tmm) cc_final: 0.5114 (ttt) REVERT: B 111 TYR cc_start: 0.6260 (m-80) cc_final: 0.5894 (m-80) REVERT: D 115 ARG cc_start: 0.6902 (ttp-170) cc_final: 0.6208 (ptt180) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.0993 time to fit residues: 22.8384 Evaluate side-chains 120 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 0.1980 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.3980 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 10.0000 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN A 268 ASN ** B 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 56 GLN ** D 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 204 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4933 r_free = 0.4933 target = 0.225996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.191820 restraints weight = 10610.108| |-----------------------------------------------------------------------------| r_work (start): 0.4609 rms_B_bonded: 2.25 r_work: 0.4485 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.4485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6108 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8676 Z= 0.153 Angle : 0.678 10.232 11775 Z= 0.350 Chirality : 0.044 0.176 1339 Planarity : 0.005 0.058 1484 Dihedral : 5.146 21.814 1189 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.19 % Allowed : 10.86 % Favored : 87.95 % 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: -1.21 (0.25), residues: 1067 helix: 0.78 (0.27), residues: 321 sheet: -1.06 (0.33), residues: 251 loop : -1.72 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 15 TYR 0.016 0.001 TYR A 319 PHE 0.021 0.002 PHE A 302 TRP 0.023 0.002 TRP R 165 HIS 0.005 0.001 HIS B 142 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 8674) covalent geometry : angle 0.67793 (11771) SS BOND : bond 0.00437 ( 2) SS BOND : angle 0.90671 ( 4) hydrogen bonds : bond 0.04394 ( 377) hydrogen bonds : angle 5.72132 ( 1068) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 121 time to evaluate : 0.361 Fit side-chains REVERT: A 26 ASP cc_start: 0.6571 (m-30) cc_final: 0.6176 (m-30) REVERT: A 306 MET cc_start: 0.5649 (tmm) cc_final: 0.5161 (ttt) REVERT: A 334 VAL cc_start: 0.6589 (m) cc_final: 0.6296 (m) REVERT: B 111 TYR cc_start: 0.6613 (m-80) cc_final: 0.6304 (m-80) REVERT: B 264 TYR cc_start: 0.5198 (m-10) cc_final: 0.4901 (m-10) REVERT: D 110 MET cc_start: 0.6530 (tpp) cc_final: 0.6192 (tpp) REVERT: R 186 MET cc_start: 0.1430 (tmm) cc_final: 0.0825 (ttt) REVERT: R 203 LEU cc_start: 0.4156 (tt) cc_final: 0.3649 (mt) REVERT: R 393 MET cc_start: 0.5184 (ttt) cc_final: 0.4818 (mmt) outliers start: 11 outliers final: 7 residues processed: 128 average time/residue: 0.0909 time to fit residues: 16.5289 Evaluate side-chains 117 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 110 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain R residue 204 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 74 optimal weight: 9.9990 chunk 5 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 91 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 18 optimal weight: 0.4980 chunk 83 optimal weight: 4.9990 chunk 64 optimal weight: 0.6980 chunk 49 optimal weight: 0.3980 chunk 10 optimal weight: 0.7980 chunk 77 optimal weight: 0.0970 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 HIS ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN ** D 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 204 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4915 r_free = 0.4915 target = 0.223962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.189707 restraints weight = 10496.237| |-----------------------------------------------------------------------------| r_work (start): 0.4585 rms_B_bonded: 2.23 r_work: 0.4478 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.4340 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.4340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6241 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8676 Z= 0.131 Angle : 0.617 8.533 11775 Z= 0.321 Chirality : 0.043 0.153 1339 Planarity : 0.004 0.043 1484 Dihedral : 4.849 22.595 1189 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.06 % Allowed : 13.79 % Favored : 84.15 % 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: -0.91 (0.25), residues: 1067 helix: 1.19 (0.27), residues: 327 sheet: -1.10 (0.32), residues: 251 loop : -1.56 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 15 TYR 0.013 0.001 TYR R 380 PHE 0.020 0.001 PHE B 292 TRP 0.019 0.002 TRP R 165 HIS 0.011 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 8674) covalent geometry : angle 0.61703 (11771) SS BOND : bond 0.00280 ( 2) SS BOND : angle 0.92767 ( 4) hydrogen bonds : bond 0.04010 ( 377) hydrogen bonds : angle 5.35610 ( 1068) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 ASP cc_start: 0.6482 (m-30) cc_final: 0.6109 (m-30) REVERT: A 228 GLU cc_start: 0.6966 (mt-10) cc_final: 0.6606 (mt-10) REVERT: A 306 MET cc_start: 0.5759 (tmm) cc_final: 0.5141 (ttt) REVERT: B 111 TYR cc_start: 0.6840 (m-80) cc_final: 0.6511 (m-80) REVERT: B 118 ASP cc_start: 0.7522 (t0) cc_final: 0.7292 (t0) REVERT: B 234 PHE cc_start: 0.6593 (OUTLIER) cc_final: 0.5511 (t80) REVERT: B 264 TYR cc_start: 0.5451 (m-10) cc_final: 0.4990 (m-10) REVERT: R 65 PHE cc_start: 0.5422 (t80) cc_final: 0.4966 (t80) REVERT: R 393 MET cc_start: 0.5428 (OUTLIER) cc_final: 0.4954 (mmt) outliers start: 19 outliers final: 8 residues processed: 138 average time/residue: 0.0915 time to fit residues: 17.8421 Evaluate side-chains 125 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 115 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 196 ARG Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain R residue 393 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 13 optimal weight: 0.0980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 204 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4869 r_free = 0.4869 target = 0.218711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.183462 restraints weight = 10644.210| |-----------------------------------------------------------------------------| r_work (start): 0.4483 rms_B_bonded: 2.25 r_work: 0.4371 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.4227 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.4227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6355 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8676 Z= 0.151 Angle : 0.637 11.101 11775 Z= 0.328 Chirality : 0.043 0.186 1339 Planarity : 0.004 0.041 1484 Dihedral : 4.858 27.276 1189 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.39 % Allowed : 15.74 % Favored : 81.87 % 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: -0.87 (0.25), residues: 1067 helix: 1.37 (0.27), residues: 327 sheet: -1.39 (0.31), residues: 271 loop : -1.44 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 15 TYR 0.012 0.001 TYR A 319 PHE 0.019 0.002 PHE B 292 TRP 0.021 0.002 TRP R 165 HIS 0.005 0.001 HIS R 207 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 8674) covalent geometry : angle 0.63718 (11771) SS BOND : bond 0.00306 ( 2) SS BOND : angle 0.91214 ( 4) hydrogen bonds : bond 0.03940 ( 377) hydrogen bonds : angle 5.25044 ( 1068) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 0.275 Fit side-chains REVERT: A 26 ASP cc_start: 0.6309 (m-30) cc_final: 0.5941 (m-30) REVERT: A 306 MET cc_start: 0.5974 (tmm) cc_final: 0.5177 (ttt) REVERT: B 69 LEU cc_start: 0.7168 (mt) cc_final: 0.6945 (mt) REVERT: B 118 ASP cc_start: 0.7835 (t0) cc_final: 0.7566 (t0) REVERT: B 217 MET cc_start: 0.6972 (ppp) cc_final: 0.6659 (ppp) REVERT: B 234 PHE cc_start: 0.7051 (OUTLIER) cc_final: 0.5992 (t80) REVERT: D 81 VAL cc_start: 0.3789 (OUTLIER) cc_final: 0.3387 (m) REVERT: R 65 PHE cc_start: 0.5833 (t80) cc_final: 0.5356 (t80) REVERT: R 393 MET cc_start: 0.5478 (OUTLIER) cc_final: 0.4873 (mmt) outliers start: 22 outliers final: 12 residues processed: 141 average time/residue: 0.0857 time to fit residues: 17.2967 Evaluate side-chains 130 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 196 ARG Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain R residue 204 GLN Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 393 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 24 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 14 optimal weight: 0.0970 chunk 72 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 63 optimal weight: 0.1980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 GLN ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 204 GLN ** R 207 HIS ** 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 = 0.4872 r_free = 0.4872 target = 0.219011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.183802 restraints weight = 10668.111| |-----------------------------------------------------------------------------| r_work (start): 0.4531 rms_B_bonded: 2.26 r_work: 0.4411 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.4411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6219 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8676 Z= 0.137 Angle : 0.629 10.419 11775 Z= 0.321 Chirality : 0.042 0.178 1339 Planarity : 0.004 0.039 1484 Dihedral : 4.781 27.743 1189 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.82 % Allowed : 16.72 % Favored : 80.46 % 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: -0.82 (0.25), residues: 1067 helix: 1.53 (0.28), residues: 321 sheet: -1.35 (0.31), residues: 269 loop : -1.49 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 96 TYR 0.029 0.001 TYR R 380 PHE 0.019 0.002 PHE B 292 TRP 0.021 0.002 TRP R 165 HIS 0.005 0.001 HIS C 44 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 8674) covalent geometry : angle 0.62844 (11771) SS BOND : bond 0.00253 ( 2) SS BOND : angle 0.89268 ( 4) hydrogen bonds : bond 0.03779 ( 377) hydrogen bonds : angle 5.15085 ( 1068) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 119 time to evaluate : 0.319 Fit side-chains REVERT: A 26 ASP cc_start: 0.6306 (m-30) cc_final: 0.5982 (m-30) REVERT: A 306 MET cc_start: 0.6011 (tmm) cc_final: 0.5193 (ttt) REVERT: B 42 ARG cc_start: 0.6225 (ttp80) cc_final: 0.5421 (mmt180) REVERT: B 111 TYR cc_start: 0.6731 (m-80) cc_final: 0.6397 (m-80) REVERT: B 234 PHE cc_start: 0.6953 (OUTLIER) cc_final: 0.5869 (t80) REVERT: B 264 TYR cc_start: 0.5580 (m-10) cc_final: 0.5309 (m-10) REVERT: D 81 VAL cc_start: 0.3749 (OUTLIER) cc_final: 0.3343 (m) REVERT: R 393 MET cc_start: 0.5384 (OUTLIER) cc_final: 0.4870 (mmt) outliers start: 26 outliers final: 16 residues processed: 138 average time/residue: 0.0818 time to fit residues: 16.4323 Evaluate side-chains 131 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 196 ARG Chi-restraints excluded: chain A residue 231 GLN Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain R residue 204 GLN Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 393 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 36 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 79 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 chunk 59 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 GLN ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 281 HIS ** B 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN D 130 GLN ** D 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 204 GLN ** R 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4858 r_free = 0.4858 target = 0.217496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.182352 restraints weight = 10563.571| |-----------------------------------------------------------------------------| r_work (start): 0.4513 rms_B_bonded: 2.23 r_work: 0.4403 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.4265 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.4265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6377 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8676 Z= 0.145 Angle : 0.649 11.120 11775 Z= 0.330 Chirality : 0.043 0.170 1339 Planarity : 0.004 0.042 1484 Dihedral : 4.757 28.541 1189 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.26 % Allowed : 16.94 % Favored : 79.80 % 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: -0.77 (0.25), residues: 1067 helix: 1.50 (0.28), residues: 327 sheet: -1.36 (0.31), residues: 271 loop : -1.41 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 15 TYR 0.026 0.001 TYR R 380 PHE 0.019 0.002 PHE B 292 TRP 0.020 0.002 TRP R 165 HIS 0.005 0.001 HIS C 44 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 8674) covalent geometry : angle 0.64850 (11771) SS BOND : bond 0.00249 ( 2) SS BOND : angle 0.78949 ( 4) hydrogen bonds : bond 0.03800 ( 377) hydrogen bonds : angle 5.15475 ( 1068) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 111 time to evaluate : 0.277 Fit side-chains REVERT: A 23 LEU cc_start: 0.5842 (OUTLIER) cc_final: 0.5472 (mp) REVERT: A 26 ASP cc_start: 0.6275 (m-30) cc_final: 0.5911 (m-30) REVERT: A 306 MET cc_start: 0.6146 (tmm) cc_final: 0.5323 (ttt) REVERT: B 42 ARG cc_start: 0.6263 (ttp80) cc_final: 0.5400 (mmt180) REVERT: B 111 TYR cc_start: 0.6943 (m-80) cc_final: 0.6565 (m-80) REVERT: B 234 PHE cc_start: 0.7109 (OUTLIER) cc_final: 0.5987 (t80) REVERT: B 264 TYR cc_start: 0.5759 (m-10) cc_final: 0.5343 (m-10) REVERT: C 50 LEU cc_start: 0.6459 (OUTLIER) cc_final: 0.6140 (mt) REVERT: D 81 VAL cc_start: 0.3893 (OUTLIER) cc_final: 0.3475 (m) REVERT: R 393 MET cc_start: 0.5570 (OUTLIER) cc_final: 0.4888 (mmt) outliers start: 30 outliers final: 18 residues processed: 133 average time/residue: 0.0807 time to fit residues: 15.5537 Evaluate side-chains 128 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 105 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 196 ARG Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain R residue 122 PHE Chi-restraints excluded: chain R residue 204 GLN Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 393 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 85 optimal weight: 0.0070 chunk 6 optimal weight: 0.0980 chunk 71 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 72 optimal weight: 0.1980 chunk 46 optimal weight: 0.6980 chunk 104 optimal weight: 7.9990 chunk 43 optimal weight: 0.6980 overall best weight: 0.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 ASN B 268 ASN ** D 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 204 GLN ** R 207 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 = 0.4877 r_free = 0.4877 target = 0.219742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.184974 restraints weight = 10608.860| |-----------------------------------------------------------------------------| r_work (start): 0.4542 rms_B_bonded: 2.23 r_work: 0.4433 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.4290 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.4290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6331 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8676 Z= 0.122 Angle : 0.621 9.639 11775 Z= 0.315 Chirality : 0.042 0.169 1339 Planarity : 0.004 0.041 1484 Dihedral : 4.637 30.003 1189 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.71 % Allowed : 17.92 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.70 (0.25), residues: 1067 helix: 1.59 (0.28), residues: 327 sheet: -1.35 (0.31), residues: 261 loop : -1.38 (0.27), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 96 TYR 0.021 0.001 TYR R 380 PHE 0.019 0.001 PHE B 292 TRP 0.019 0.002 TRP R 165 HIS 0.005 0.001 HIS C 44 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 8674) covalent geometry : angle 0.62103 (11771) SS BOND : bond 0.00279 ( 2) SS BOND : angle 0.76690 ( 4) hydrogen bonds : bond 0.03653 ( 377) hydrogen bonds : angle 5.03226 ( 1068) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 119 time to evaluate : 0.249 Fit side-chains REVERT: A 23 LEU cc_start: 0.5727 (OUTLIER) cc_final: 0.5404 (mp) REVERT: A 26 ASP cc_start: 0.6480 (m-30) cc_final: 0.6120 (m-30) REVERT: A 33 GLU cc_start: 0.5251 (mp0) cc_final: 0.4942 (mp0) REVERT: A 306 MET cc_start: 0.6065 (tmm) cc_final: 0.5402 (ttt) REVERT: B 42 ARG cc_start: 0.6282 (ttp80) cc_final: 0.5423 (mmt180) REVERT: B 111 TYR cc_start: 0.6844 (m-80) cc_final: 0.6490 (m-80) REVERT: B 132 ASN cc_start: 0.8382 (OUTLIER) cc_final: 0.8177 (p0) REVERT: B 234 PHE cc_start: 0.7047 (OUTLIER) cc_final: 0.6076 (t80) REVERT: B 264 TYR cc_start: 0.5720 (m-10) cc_final: 0.5304 (m-10) REVERT: C 50 LEU cc_start: 0.6445 (OUTLIER) cc_final: 0.6137 (mt) REVERT: D 81 VAL cc_start: 0.3827 (OUTLIER) cc_final: 0.3407 (m) REVERT: R 393 MET cc_start: 0.5624 (OUTLIER) cc_final: 0.4913 (mmt) outliers start: 25 outliers final: 16 residues processed: 138 average time/residue: 0.0856 time to fit residues: 16.8502 Evaluate side-chains 135 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 196 ARG Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain R residue 204 GLN Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 393 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 13 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 68 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 17 optimal weight: 0.0040 chunk 96 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 ASN B 155 ASN B 268 ASN R 204 GLN ** R 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4854 r_free = 0.4854 target = 0.217297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.181442 restraints weight = 10504.410| |-----------------------------------------------------------------------------| r_work (start): 0.4523 rms_B_bonded: 2.25 r_work: 0.4415 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.4276 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.4276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6351 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8676 Z= 0.136 Angle : 0.645 10.448 11775 Z= 0.327 Chirality : 0.043 0.178 1339 Planarity : 0.004 0.042 1484 Dihedral : 4.660 29.952 1189 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.04 % Allowed : 18.35 % Favored : 78.61 % 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: -0.72 (0.25), residues: 1067 helix: 1.58 (0.27), residues: 327 sheet: -1.36 (0.31), residues: 263 loop : -1.39 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 96 TYR 0.041 0.001 TYR R 380 PHE 0.019 0.002 PHE B 292 TRP 0.025 0.002 TRP R 165 HIS 0.005 0.001 HIS C 44 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 8674) covalent geometry : angle 0.64469 (11771) SS BOND : bond 0.00296 ( 2) SS BOND : angle 0.70545 ( 4) hydrogen bonds : bond 0.03698 ( 377) hydrogen bonds : angle 5.03036 ( 1068) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 121 time to evaluate : 0.318 Fit side-chains REVERT: A 26 ASP cc_start: 0.6430 (m-30) cc_final: 0.6059 (m-30) REVERT: A 306 MET cc_start: 0.6131 (tmm) cc_final: 0.5403 (ttt) REVERT: B 42 ARG cc_start: 0.6246 (ttp80) cc_final: 0.5492 (mmt180) REVERT: B 111 TYR cc_start: 0.6879 (m-80) cc_final: 0.6524 (m-80) REVERT: B 217 MET cc_start: 0.7177 (ppp) cc_final: 0.6840 (ppp) REVERT: B 234 PHE cc_start: 0.7028 (OUTLIER) cc_final: 0.6063 (t80) REVERT: B 264 TYR cc_start: 0.5770 (m-10) cc_final: 0.5349 (m-10) REVERT: B 284 LEU cc_start: 0.7798 (tt) cc_final: 0.7316 (tp) REVERT: D 100 MET cc_start: 0.6708 (mpp) cc_final: 0.6090 (ppp) REVERT: R 393 MET cc_start: 0.5618 (OUTLIER) cc_final: 0.4911 (mmt) outliers start: 28 outliers final: 17 residues processed: 140 average time/residue: 0.0832 time to fit residues: 16.7407 Evaluate side-chains 135 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 196 ARG Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain R residue 122 PHE Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 393 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 47 optimal weight: 0.4980 chunk 49 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 35 optimal weight: 0.1980 chunk 46 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 19 optimal weight: 8.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN B 268 ASN ** R 207 HIS ** 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 = 0.4781 r_free = 0.4781 target = 0.209294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.172747 restraints weight = 10644.605| |-----------------------------------------------------------------------------| r_work (start): 0.4434 rms_B_bonded: 2.25 r_work: 0.4322 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.4183 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.4183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6504 moved from start: 0.4021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8676 Z= 0.197 Angle : 0.749 14.802 11775 Z= 0.376 Chirality : 0.046 0.210 1339 Planarity : 0.005 0.049 1484 Dihedral : 5.129 30.621 1189 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 18.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.50 % Allowed : 19.33 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.92 (0.26), residues: 1067 helix: 1.39 (0.28), residues: 323 sheet: -1.31 (0.31), residues: 283 loop : -1.57 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 24 TYR 0.039 0.002 TYR R 380 PHE 0.019 0.002 PHE B 234 TRP 0.023 0.003 TRP R 165 HIS 0.005 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00453 ( 8674) covalent geometry : angle 0.74898 (11771) SS BOND : bond 0.00439 ( 2) SS BOND : angle 1.01566 ( 4) hydrogen bonds : bond 0.04169 ( 377) hydrogen bonds : angle 5.37761 ( 1068) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 0.276 Fit side-chains REVERT: A 26 ASP cc_start: 0.6511 (m-30) cc_final: 0.6194 (m-30) REVERT: B 42 ARG cc_start: 0.6258 (ttp80) cc_final: 0.5609 (mmt180) REVERT: B 217 MET cc_start: 0.7423 (ppp) cc_final: 0.7073 (ppp) REVERT: B 234 PHE cc_start: 0.7085 (OUTLIER) cc_final: 0.6202 (t80) REVERT: B 284 LEU cc_start: 0.7582 (tt) cc_final: 0.7266 (tp) REVERT: C 38 MET cc_start: 0.4619 (mmt) cc_final: 0.4164 (mpp) REVERT: C 50 LEU cc_start: 0.6543 (OUTLIER) cc_final: 0.6338 (mt) REVERT: D 100 MET cc_start: 0.6645 (mpp) cc_final: 0.6181 (ppp) outliers start: 23 outliers final: 17 residues processed: 134 average time/residue: 0.0912 time to fit residues: 17.1981 Evaluate side-chains 136 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 117 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain R residue 122 PHE Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 207 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 85 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 chunk 84 optimal weight: 0.9990 chunk 35 optimal weight: 0.3980 chunk 28 optimal weight: 0.9990 chunk 6 optimal weight: 0.0030 chunk 23 optimal weight: 0.9980 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 HIS ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 281 HIS ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN ** R 207 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 = 0.4799 r_free = 0.4799 target = 0.211349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.172592 restraints weight = 10561.475| |-----------------------------------------------------------------------------| r_work (start): 0.4424 rms_B_bonded: 2.51 r_work: 0.4303 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.4303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6312 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8676 Z= 0.143 Angle : 0.668 10.899 11775 Z= 0.339 Chirality : 0.044 0.179 1339 Planarity : 0.004 0.049 1484 Dihedral : 4.907 30.193 1189 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.95 % Allowed : 19.98 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.92 (0.25), residues: 1067 helix: 1.42 (0.28), residues: 323 sheet: -1.37 (0.31), residues: 272 loop : -1.55 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 15 TYR 0.035 0.002 TYR R 380 PHE 0.022 0.002 PHE B 241 TRP 0.040 0.002 TRP B 99 HIS 0.006 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 8674) covalent geometry : angle 0.66826 (11771) SS BOND : bond 0.00305 ( 2) SS BOND : angle 0.87939 ( 4) hydrogen bonds : bond 0.03845 ( 377) hydrogen bonds : angle 5.15648 ( 1068) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 0.310 Fit side-chains REVERT: A 26 ASP cc_start: 0.6346 (m-30) cc_final: 0.6085 (m-30) REVERT: B 42 ARG cc_start: 0.6030 (ttp80) cc_final: 0.5502 (mmt180) REVERT: B 111 TYR cc_start: 0.6962 (m-80) cc_final: 0.6617 (m-80) REVERT: B 217 MET cc_start: 0.7156 (ppp) cc_final: 0.6878 (ppp) REVERT: B 234 PHE cc_start: 0.7078 (OUTLIER) cc_final: 0.6283 (t80) REVERT: B 264 TYR cc_start: 0.5832 (m-10) cc_final: 0.5569 (m-10) REVERT: B 284 LEU cc_start: 0.7560 (tt) cc_final: 0.7256 (tp) REVERT: C 38 MET cc_start: 0.4520 (mmt) cc_final: 0.4138 (mpp) REVERT: D 100 MET cc_start: 0.6459 (mpp) cc_final: 0.6084 (ppp) REVERT: R 134 MET cc_start: 0.5364 (mmp) cc_final: 0.4708 (mmp) REVERT: R 393 MET cc_start: 0.5835 (ttm) cc_final: 0.5245 (mmt) outliers start: 18 outliers final: 15 residues processed: 131 average time/residue: 0.0823 time to fit residues: 15.5925 Evaluate side-chains 131 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain R residue 122 PHE Chi-restraints excluded: chain R residue 206 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 42 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 103 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 281 HIS ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN ** R 207 HIS ** 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 = 0.4797 r_free = 0.4797 target = 0.210936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.172884 restraints weight = 10570.260| |-----------------------------------------------------------------------------| r_work (start): 0.4433 rms_B_bonded: 2.42 r_work: 0.4310 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.4310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6369 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8676 Z= 0.168 Angle : 0.688 13.293 11775 Z= 0.348 Chirality : 0.045 0.185 1339 Planarity : 0.004 0.051 1484 Dihedral : 4.951 29.139 1189 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 17.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.06 % Allowed : 20.96 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.26), residues: 1067 helix: 1.38 (0.28), residues: 323 sheet: -1.38 (0.31), residues: 272 loop : -1.57 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 68 TYR 0.034 0.002 TYR R 380 PHE 0.019 0.002 PHE B 292 TRP 0.029 0.002 TRP R 179 HIS 0.005 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 8674) covalent geometry : angle 0.68825 (11771) SS BOND : bond 0.00302 ( 2) SS BOND : angle 0.92917 ( 4) hydrogen bonds : bond 0.03962 ( 377) hydrogen bonds : angle 5.20445 ( 1068) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3276.12 seconds wall clock time: 56 minutes 35.39 seconds (3395.39 seconds total)