Starting phenix.real_space_refine on Fri Jun 6 18:32:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hj0_33482/06_2025/8hj0_33482.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hj0_33482/06_2025/8hj0_33482.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hj0_33482/06_2025/8hj0_33482.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hj0_33482/06_2025/8hj0_33482.map" model { file = "/net/cci-nas-00/data/ceres_data/8hj0_33482/06_2025/8hj0_33482.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hj0_33482/06_2025/8hj0_33482.cif" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.005 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 52 5.16 5 C 5250 2.51 5 N 1427 2.21 5 O 1531 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 8260 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1966 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 6, 'TRANS': 232} Chain breaks: 1 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "R" Number of atoms: 2297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2297 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 271} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Time building chain proxies: 5.15, per 1000 atoms: 0.62 Number of scatterers: 8260 At special positions: 0 Unit cell: (88.4, 102.96, 127.92, 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 52 16.00 O 1531 8.00 N 1427 7.00 C 5250 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.02 Simple disulfide: pdb=" SG CYS R 102 " - pdb=" SG CYS R 181 " distance=2.03 Simple disulfide: pdb=" SG CYS R 122 " - pdb=" SG CYS R 149 " distance=2.05 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: 2.38 Conformation dependent library (CDL) restraints added in 1.2 seconds 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1966 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 10 sheets defined 42.5% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 9 through 39 removed outlier: 4.105A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 63 Processing helix chain 'A' and resid 255 through 269 Processing helix chain 'A' and resid 283 through 294 Processing helix chain 'A' and resid 297 through 302 removed outlier: 3.905A pdb=" N TYR A 301 " --> pdb=" O LYS A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 306 removed outlier: 3.821A pdb=" N ALA A 306 " --> pdb=" O PRO A 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 303 through 306' Processing helix chain 'A' and resid 322 through 342 removed outlier: 3.836A pdb=" N ARG A 332 " --> pdb=" O LYS A 328 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA A 341 " --> pdb=" O ARG A 337 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N SER A 342 " --> pdb=" O ILE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 382 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.986A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 7 through 24 removed outlier: 4.887A pdb=" N GLU G 22 " --> pdb=" O GLN G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.507A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 65 removed outlier: 3.755A pdb=" N LYS N 65 " --> pdb=" O GLY N 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 62 through 65' Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'R' and resid 26 through 56 removed outlier: 4.382A pdb=" N ILE R 34 " --> pdb=" O LEU R 30 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ILE R 35 " --> pdb=" O GLU R 31 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N SER R 44 " --> pdb=" O VAL R 40 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLY R 45 " --> pdb=" O LEU R 41 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ASN R 46 " --> pdb=" O ILE R 42 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ILE R 47 " --> pdb=" O ILE R 43 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE R 48 " --> pdb=" O SER R 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 56 through 61 Processing helix chain 'R' and resid 62 through 80 removed outlier: 4.079A pdb=" N TYR R 66 " --> pdb=" O HIS R 62 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N PHE R 67 " --> pdb=" O THR R 63 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 91 removed outlier: 4.174A pdb=" N SER R 86 " --> pdb=" O CYS R 82 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N HIS R 91 " --> pdb=" O LEU R 87 " (cutoff:3.500A) Processing helix chain 'R' and resid 100 through 133 removed outlier: 4.286A pdb=" N ILE R 104 " --> pdb=" O LEU R 100 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL R 111 " --> pdb=" O PHE R 107 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER R 114 " --> pdb=" O SER R 110 " (cutoff:3.500A) Processing helix chain 'R' and resid 136 through 141 Processing helix chain 'R' and resid 142 through 161 removed outlier: 3.683A pdb=" N PHE R 161 " --> pdb=" O SER R 157 " (cutoff:3.500A) Processing helix chain 'R' and resid 162 through 165 Processing helix chain 'R' and resid 188 through 197 Processing helix chain 'R' and resid 199 through 231 removed outlier: 4.139A pdb=" N ALA R 203 " --> pdb=" O LEU R 199 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA R 204 " --> pdb=" O TYR R 200 " (cutoff:3.500A) Processing helix chain 'R' and resid 253 through 278 Proline residue: R 267 - end of helix Processing helix chain 'R' and resid 282 through 295 Processing helix chain 'R' and resid 298 through 308 removed outlier: 3.747A pdb=" N VAL R 302 " --> pdb=" O PHE R 298 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE R 303 " --> pdb=" O CYS R 299 " (cutoff:3.500A) Processing helix chain 'R' and resid 308 through 322 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 3.791A pdb=" N VAL A 214 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ILE A 244 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N PHE A 280 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N PHE A 246 " --> pdb=" O PHE A 280 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ASN A 282 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N VAL A 248 " --> pdb=" O ASN A 282 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.581A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.517A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 4.402A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 151 removed outlier: 4.066A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 192 removed outlier: 6.791A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 4.004A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.030A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 11 removed outlier: 4.136A pdb=" N THR N 125 " --> pdb=" O GLY N 10 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 412 hydrogen bonds defined for protein. 1179 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: 2.35 Time building geometry restraints manager: 2.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2702 1.35 - 1.48: 2214 1.48 - 1.62: 3457 1.62 - 1.75: 0 1.75 - 1.88: 70 Bond restraints: 8443 Sorted by residual: bond pdb=" CB CYS R 149 " pdb=" SG CYS R 149 " ideal model delta sigma weight residual 1.808 1.877 -0.069 3.30e-02 9.18e+02 4.38e+00 bond pdb=" CA ALA B 328 " pdb=" CB ALA B 328 " ideal model delta sigma weight residual 1.526 1.494 0.032 1.70e-02 3.46e+03 3.61e+00 bond pdb=" C VAL R 84 " pdb=" N PRO R 85 " ideal model delta sigma weight residual 1.335 1.358 -0.024 1.28e-02 6.10e+03 3.46e+00 bond pdb=" C ASN R 300 " pdb=" N PRO R 301 " ideal model delta sigma weight residual 1.335 1.361 -0.025 1.36e-02 5.41e+03 3.43e+00 bond pdb=" CB ASP R 126 " pdb=" CG ASP R 126 " ideal model delta sigma weight residual 1.516 1.562 -0.046 2.50e-02 1.60e+03 3.38e+00 ... (remaining 8438 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 10889 2.21 - 4.41: 474 4.41 - 6.62: 59 6.62 - 8.82: 18 8.82 - 11.03: 9 Bond angle restraints: 11449 Sorted by residual: angle pdb=" C ASP B 195 " pdb=" N THR B 196 " pdb=" CA THR B 196 " ideal model delta sigma weight residual 121.54 131.27 -9.73 1.91e+00 2.74e-01 2.60e+01 angle pdb=" C GLU R 97 " pdb=" N GLU R 98 " pdb=" CA GLU R 98 " ideal model delta sigma weight residual 121.54 130.46 -8.92 1.91e+00 2.74e-01 2.18e+01 angle pdb=" CA ASP R 126 " pdb=" CB ASP R 126 " pdb=" CG ASP R 126 " ideal model delta sigma weight residual 112.60 116.75 -4.15 1.00e+00 1.00e+00 1.72e+01 angle pdb=" CB ARG R 256 " pdb=" CG ARG R 256 " pdb=" CD ARG R 256 " ideal model delta sigma weight residual 111.30 119.61 -8.31 2.30e+00 1.89e-01 1.30e+01 angle pdb=" N CYS N 96 " pdb=" CA CYS N 96 " pdb=" C CYS N 96 " ideal model delta sigma weight residual 110.48 105.27 5.21 1.48e+00 4.57e-01 1.24e+01 ... (remaining 11444 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 4488 17.97 - 35.94: 410 35.94 - 53.91: 80 53.91 - 71.88: 13 71.88 - 89.84: 11 Dihedral angle restraints: 5002 sinusoidal: 1963 harmonic: 3039 Sorted by residual: dihedral pdb=" CB CYS N 22 " pdb=" SG CYS N 22 " pdb=" SG CYS N 96 " pdb=" CB CYS N 96 " ideal model delta sinusoidal sigma weight residual 93.00 14.33 78.67 1 1.00e+01 1.00e-02 7.71e+01 dihedral pdb=" CB CYS R 122 " pdb=" SG CYS R 122 " pdb=" SG CYS R 149 " pdb=" CB CYS R 149 " ideal model delta sinusoidal sigma weight residual 93.00 159.02 -66.02 1 1.00e+01 1.00e-02 5.70e+01 dihedral pdb=" CA SER R 307 " pdb=" C SER R 307 " pdb=" N ASP R 308 " pdb=" CA ASP R 308 " ideal model delta harmonic sigma weight residual -180.00 -156.42 -23.58 0 5.00e+00 4.00e-02 2.22e+01 ... (remaining 4999 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1091 0.078 - 0.155: 171 0.155 - 0.232: 21 0.232 - 0.310: 1 0.310 - 0.387: 3 Chirality restraints: 1287 Sorted by residual: chirality pdb=" CB THR B 47 " pdb=" CA THR B 47 " pdb=" OG1 THR B 47 " pdb=" CG2 THR B 47 " both_signs ideal model delta sigma weight residual False 2.55 2.16 0.39 2.00e-01 2.50e+01 3.75e+00 chirality pdb=" CB ILE N 51 " pdb=" CA ILE N 51 " pdb=" CG1 ILE N 51 " pdb=" CG2 ILE N 51 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.26e+00 chirality pdb=" CB ILE B 269 " pdb=" CA ILE B 269 " pdb=" CG1 ILE B 269 " pdb=" CG2 ILE B 269 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.73e+00 ... (remaining 1284 not shown) Planarity restraints: 1457 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN N 13 " -0.077 5.00e-02 4.00e+02 1.17e-01 2.18e+01 pdb=" N PRO N 14 " 0.202 5.00e-02 4.00e+02 pdb=" CA PRO N 14 " -0.063 5.00e-02 4.00e+02 pdb=" CD PRO N 14 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 215 " -0.024 2.00e-02 2.50e+03 2.69e-02 1.26e+01 pdb=" CG PHE R 215 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 PHE R 215 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE R 215 " -0.017 2.00e-02 2.50e+03 pdb=" CE1 PHE R 215 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE R 215 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE R 215 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER R 124 " -0.014 2.00e-02 2.50e+03 2.90e-02 8.40e+00 pdb=" C SER R 124 " 0.050 2.00e-02 2.50e+03 pdb=" O SER R 124 " -0.019 2.00e-02 2.50e+03 pdb=" N ILE R 125 " -0.017 2.00e-02 2.50e+03 ... (remaining 1454 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1882 2.78 - 3.31: 7840 3.31 - 3.84: 14430 3.84 - 4.37: 17211 4.37 - 4.90: 28894 Nonbonded interactions: 70257 Sorted by model distance: nonbonded pdb=" O VAL R 83 " pdb=" OG SER R 86 " model vdw 2.254 3.040 nonbonded pdb=" OG SER B 275 " pdb=" O SER B 316 " model vdw 2.256 3.040 nonbonded pdb=" O CYS B 204 " pdb=" OH TYR N 117 " model vdw 2.259 3.040 nonbonded pdb=" O TRP R 180 " pdb=" OG SER R 184 " model vdw 2.259 3.040 nonbonded pdb=" O ARG B 68 " pdb=" OG SER B 84 " model vdw 2.266 3.040 ... (remaining 70252 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: 0.500 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: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 23.140 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 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:3.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6438 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 8447 Z= 0.265 Angle : 1.074 11.028 11457 Z= 0.600 Chirality : 0.058 0.387 1287 Planarity : 0.008 0.117 1457 Dihedral : 14.888 89.844 3024 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.24), residues: 1029 helix: -0.90 (0.24), residues: 401 sheet: -0.79 (0.33), residues: 214 loop : -1.73 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP R 180 HIS 0.015 0.002 HIS A 220 PHE 0.063 0.004 PHE R 215 TYR 0.021 0.003 TYR A 348 ARG 0.026 0.002 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.15475 ( 412) hydrogen bonds : angle 7.19070 ( 1179) SS BOND : bond 0.01139 ( 4) SS BOND : angle 3.59672 ( 8) covalent geometry : bond 0.00564 ( 8443) covalent geometry : angle 1.07011 (11449) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 0.892 Fit side-chains revert: symmetry clash REVERT: B 111 TYR cc_start: 0.6383 (m-80) cc_final: 0.6142 (m-80) REVERT: G 21 MET cc_start: 0.4214 (mmm) cc_final: 0.2584 (mtm) REVERT: R 31 GLU cc_start: 0.5584 (mm-30) cc_final: 0.4817 (mm-30) REVERT: R 152 LEU cc_start: 0.6932 (mt) cc_final: 0.6605 (mp) REVERT: R 287 PHE cc_start: 0.5795 (t80) cc_final: 0.5311 (t80) outliers start: 0 outliers final: 0 residues processed: 201 average time/residue: 0.2395 time to fit residues: 62.9123 Evaluate side-chains 154 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 51 optimal weight: 0.5980 chunk 40 optimal weight: 6.9990 chunk 79 optimal weight: 0.4980 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 58 optimal weight: 7.9990 chunk 91 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN B 35 ASN ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.232968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.199848 restraints weight = 8729.589| |-----------------------------------------------------------------------------| r_work (start): 0.4255 rms_B_bonded: 1.79 r_work: 0.4144 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.4009 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.4009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6658 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8447 Z= 0.134 Angle : 0.589 5.754 11457 Z= 0.317 Chirality : 0.043 0.140 1287 Planarity : 0.005 0.083 1457 Dihedral : 5.275 22.001 1136 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.44 % Allowed : 8.97 % Favored : 89.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.25), residues: 1029 helix: 0.31 (0.25), residues: 410 sheet: -0.73 (0.33), residues: 223 loop : -1.50 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 169 HIS 0.008 0.001 HIS B 91 PHE 0.018 0.002 PHE R 272 TYR 0.010 0.001 TYR B 264 ARG 0.007 0.000 ARG N 67 Details of bonding type rmsd hydrogen bonds : bond 0.04158 ( 412) hydrogen bonds : angle 5.05002 ( 1179) SS BOND : bond 0.00798 ( 4) SS BOND : angle 1.84485 ( 8) covalent geometry : bond 0.00297 ( 8443) covalent geometry : angle 0.58752 (11449) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 180 time to evaluate : 0.924 Fit side-chains REVERT: A 60 MET cc_start: 0.6887 (mpp) cc_final: 0.6404 (mpp) REVERT: A 360 GLU cc_start: 0.6738 (mt-10) cc_final: 0.6386 (mp0) REVERT: B 111 TYR cc_start: 0.7093 (m-80) cc_final: 0.6880 (m-80) REVERT: B 118 ASP cc_start: 0.6289 (t70) cc_final: 0.5804 (t0) REVERT: B 325 MET cc_start: 0.7397 (mmt) cc_final: 0.6911 (mmt) REVERT: G 21 MET cc_start: 0.3930 (mmm) cc_final: 0.2420 (mtt) REVERT: R 152 LEU cc_start: 0.7181 (mt) cc_final: 0.6696 (mp) REVERT: R 194 PHE cc_start: 0.6643 (m-80) cc_final: 0.6398 (m-80) REVERT: R 256 ARG cc_start: 0.6630 (mtp-110) cc_final: 0.6412 (ptp-170) outliers start: 13 outliers final: 8 residues processed: 186 average time/residue: 0.2619 time to fit residues: 63.3233 Evaluate side-chains 163 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 155 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 123 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 7.9990 chunk 42 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 100 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 15 optimal weight: 0.0670 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 ASN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 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 = 0.4542 r_free = 0.4542 target = 0.232228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.198410 restraints weight = 8831.944| |-----------------------------------------------------------------------------| r_work (start): 0.4243 rms_B_bonded: 1.82 r_work: 0.4134 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3998 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6667 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8447 Z= 0.125 Angle : 0.555 5.790 11457 Z= 0.297 Chirality : 0.043 0.189 1287 Planarity : 0.004 0.067 1457 Dihedral : 4.874 21.137 1136 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.21 % Allowed : 13.84 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.25), residues: 1029 helix: 0.80 (0.26), residues: 407 sheet: -0.69 (0.32), residues: 221 loop : -1.38 (0.29), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.007 0.001 HIS B 91 PHE 0.016 0.002 PHE R 272 TYR 0.014 0.001 TYR B 264 ARG 0.010 0.000 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.03863 ( 412) hydrogen bonds : angle 4.68291 ( 1179) SS BOND : bond 0.00778 ( 4) SS BOND : angle 1.76766 ( 8) covalent geometry : bond 0.00281 ( 8443) covalent geometry : angle 0.55282 (11449) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 168 time to evaluate : 0.816 Fit side-chains REVERT: A 20 ARG cc_start: 0.6406 (mmt90) cc_final: 0.6094 (mtm-85) REVERT: A 59 GLN cc_start: 0.6304 (mp10) cc_final: 0.6066 (mp10) REVERT: A 60 MET cc_start: 0.6813 (OUTLIER) cc_final: 0.6289 (mpp) REVERT: A 360 GLU cc_start: 0.6835 (mt-10) cc_final: 0.6407 (mp0) REVERT: B 111 TYR cc_start: 0.6959 (m-80) cc_final: 0.6668 (m-80) REVERT: B 118 ASP cc_start: 0.6418 (t70) cc_final: 0.5937 (t70) REVERT: G 21 MET cc_start: 0.3933 (mmm) cc_final: 0.2525 (mtt) REVERT: R 152 LEU cc_start: 0.7249 (mt) cc_final: 0.6713 (mp) outliers start: 20 outliers final: 15 residues processed: 180 average time/residue: 0.2610 time to fit residues: 61.1473 Evaluate side-chains 171 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 155 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain R residue 84 VAL Chi-restraints excluded: chain R residue 110 SER Chi-restraints excluded: chain R residue 123 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 1 optimal weight: 0.8980 chunk 93 optimal weight: 6.9990 chunk 89 optimal weight: 0.6980 chunk 25 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 92 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 52 optimal weight: 6.9990 chunk 62 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 69 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.231646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.197911 restraints weight = 8730.549| |-----------------------------------------------------------------------------| r_work (start): 0.4212 rms_B_bonded: 1.82 r_work: 0.4107 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3972 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6674 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8447 Z= 0.132 Angle : 0.555 6.697 11457 Z= 0.297 Chirality : 0.043 0.238 1287 Planarity : 0.004 0.052 1457 Dihedral : 4.757 21.528 1136 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.99 % Allowed : 14.40 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.26), residues: 1029 helix: 1.03 (0.25), residues: 410 sheet: -0.67 (0.33), residues: 221 loop : -1.26 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 271 HIS 0.007 0.001 HIS B 91 PHE 0.016 0.002 PHE R 194 TYR 0.011 0.001 TYR B 264 ARG 0.007 0.000 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.03748 ( 412) hydrogen bonds : angle 4.57980 ( 1179) SS BOND : bond 0.00718 ( 4) SS BOND : angle 1.81260 ( 8) covalent geometry : bond 0.00299 ( 8443) covalent geometry : angle 0.55293 (11449) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 164 time to evaluate : 1.395 Fit side-chains revert: symmetry clash REVERT: A 239 ASN cc_start: 0.8228 (OUTLIER) cc_final: 0.7744 (t0) REVERT: A 346 ARG cc_start: 0.7035 (mpp80) cc_final: 0.6728 (mpp-170) REVERT: A 360 GLU cc_start: 0.6867 (mt-10) cc_final: 0.6402 (mp0) REVERT: B 43 ILE cc_start: 0.7999 (OUTLIER) cc_final: 0.7506 (mp) REVERT: B 111 TYR cc_start: 0.6929 (m-80) cc_final: 0.6645 (m-80) REVERT: B 118 ASP cc_start: 0.6446 (t70) cc_final: 0.5993 (t70) REVERT: B 254 ASP cc_start: 0.6949 (t70) cc_final: 0.6631 (t0) REVERT: B 275 SER cc_start: 0.8272 (t) cc_final: 0.7639 (m) REVERT: R 231 ARG cc_start: 0.6718 (tpm170) cc_final: 0.6376 (tpt-90) outliers start: 27 outliers final: 21 residues processed: 179 average time/residue: 0.2992 time to fit residues: 70.7291 Evaluate side-chains 180 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 157 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 110 SER Chi-restraints excluded: chain R residue 123 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 43 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 chunk 78 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 35 optimal weight: 0.3980 chunk 40 optimal weight: 1.9990 chunk 79 optimal weight: 7.9990 chunk 32 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN ** B 91 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 = 0.4525 r_free = 0.4525 target = 0.230186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.196124 restraints weight = 8711.310| |-----------------------------------------------------------------------------| r_work (start): 0.4223 rms_B_bonded: 1.83 r_work: 0.4116 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3980 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6690 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8447 Z= 0.140 Angle : 0.562 6.372 11457 Z= 0.300 Chirality : 0.044 0.240 1287 Planarity : 0.004 0.050 1457 Dihedral : 4.734 21.771 1136 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.32 % Allowed : 15.50 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.26), residues: 1029 helix: 1.21 (0.25), residues: 410 sheet: -0.64 (0.33), residues: 221 loop : -1.23 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 271 HIS 0.007 0.001 HIS B 91 PHE 0.020 0.002 PHE R 194 TYR 0.012 0.001 TYR B 264 ARG 0.009 0.000 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.03707 ( 412) hydrogen bonds : angle 4.55849 ( 1179) SS BOND : bond 0.00770 ( 4) SS BOND : angle 1.91613 ( 8) covalent geometry : bond 0.00320 ( 8443) covalent geometry : angle 0.56003 (11449) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 164 time to evaluate : 0.913 Fit side-chains revert: symmetry clash REVERT: A 59 GLN cc_start: 0.6325 (mt0) cc_final: 0.5997 (mp10) REVERT: A 239 ASN cc_start: 0.8268 (OUTLIER) cc_final: 0.7701 (t0) REVERT: A 326 ARG cc_start: 0.7284 (mtp-110) cc_final: 0.7061 (ttt-90) REVERT: A 360 GLU cc_start: 0.6819 (mt-10) cc_final: 0.6370 (mp0) REVERT: B 43 ILE cc_start: 0.7998 (OUTLIER) cc_final: 0.7526 (mp) REVERT: B 111 TYR cc_start: 0.7023 (m-80) cc_final: 0.6736 (m-80) REVERT: B 118 ASP cc_start: 0.6521 (t70) cc_final: 0.6070 (t70) REVERT: B 247 ASP cc_start: 0.7744 (p0) cc_final: 0.7307 (p0) REVERT: B 275 SER cc_start: 0.8294 (t) cc_final: 0.7609 (m) REVERT: R 231 ARG cc_start: 0.6716 (tpm170) cc_final: 0.6480 (tpt-90) REVERT: R 296 ASN cc_start: 0.6299 (p0) cc_final: 0.6051 (p0) outliers start: 30 outliers final: 22 residues processed: 180 average time/residue: 0.2326 time to fit residues: 55.0344 Evaluate side-chains 183 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 159 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 110 SER Chi-restraints excluded: chain R residue 123 ILE Chi-restraints excluded: chain R residue 177 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 14 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.230803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.196942 restraints weight = 8796.923| |-----------------------------------------------------------------------------| r_work (start): 0.4183 rms_B_bonded: 1.82 r_work: 0.4073 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3938 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6688 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8447 Z= 0.135 Angle : 0.559 6.155 11457 Z= 0.298 Chirality : 0.043 0.233 1287 Planarity : 0.004 0.048 1457 Dihedral : 4.654 21.993 1136 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.43 % Allowed : 17.05 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.26), residues: 1029 helix: 1.32 (0.25), residues: 410 sheet: -0.58 (0.33), residues: 220 loop : -1.22 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 271 HIS 0.007 0.001 HIS B 91 PHE 0.027 0.002 PHE R 287 TYR 0.014 0.001 TYR N 117 ARG 0.009 0.000 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.03625 ( 412) hydrogen bonds : angle 4.51013 ( 1179) SS BOND : bond 0.00739 ( 4) SS BOND : angle 1.86724 ( 8) covalent geometry : bond 0.00309 ( 8443) covalent geometry : angle 0.55667 (11449) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 165 time to evaluate : 0.820 Fit side-chains revert: symmetry clash REVERT: A 59 GLN cc_start: 0.6202 (mt0) cc_final: 0.5740 (mp10) REVERT: A 239 ASN cc_start: 0.8251 (OUTLIER) cc_final: 0.7733 (t0) REVERT: A 326 ARG cc_start: 0.7312 (mtp-110) cc_final: 0.7066 (ttt-90) REVERT: A 360 GLU cc_start: 0.6819 (mt-10) cc_final: 0.6381 (mp0) REVERT: B 43 ILE cc_start: 0.8068 (OUTLIER) cc_final: 0.7608 (mp) REVERT: B 111 TYR cc_start: 0.7040 (m-80) cc_final: 0.6704 (m-80) REVERT: B 118 ASP cc_start: 0.6518 (t70) cc_final: 0.6078 (t70) REVERT: B 275 SER cc_start: 0.8272 (t) cc_final: 0.7595 (m) REVERT: R 296 ASN cc_start: 0.6315 (p0) cc_final: 0.6074 (p0) outliers start: 31 outliers final: 25 residues processed: 183 average time/residue: 0.2279 time to fit residues: 55.1706 Evaluate side-chains 185 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 158 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 110 SER Chi-restraints excluded: chain R residue 123 ILE Chi-restraints excluded: chain R residue 153 ILE Chi-restraints excluded: chain R residue 177 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 97 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 75 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 32 optimal weight: 0.1980 chunk 8 optimal weight: 0.9980 chunk 86 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.231819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.197923 restraints weight = 8762.691| |-----------------------------------------------------------------------------| r_work (start): 0.4242 rms_B_bonded: 1.81 r_work: 0.4133 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3999 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6671 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8447 Z= 0.125 Angle : 0.553 8.797 11457 Z= 0.293 Chirality : 0.043 0.220 1287 Planarity : 0.004 0.051 1457 Dihedral : 4.550 21.790 1136 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.65 % Allowed : 17.28 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.26), residues: 1029 helix: 1.45 (0.25), residues: 410 sheet: -0.56 (0.34), residues: 210 loop : -1.15 (0.29), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 271 HIS 0.008 0.001 HIS B 91 PHE 0.023 0.002 PHE R 287 TYR 0.012 0.001 TYR N 117 ARG 0.007 0.000 ARG N 67 Details of bonding type rmsd hydrogen bonds : bond 0.03509 ( 412) hydrogen bonds : angle 4.46836 ( 1179) SS BOND : bond 0.00705 ( 4) SS BOND : angle 1.77239 ( 8) covalent geometry : bond 0.00285 ( 8443) covalent geometry : angle 0.55120 (11449) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 165 time to evaluate : 0.934 Fit side-chains revert: symmetry clash REVERT: A 59 GLN cc_start: 0.6008 (mt0) cc_final: 0.5645 (mp10) REVERT: A 239 ASN cc_start: 0.8195 (OUTLIER) cc_final: 0.7748 (t0) REVERT: A 326 ARG cc_start: 0.7232 (mtp-110) cc_final: 0.7023 (ttt-90) REVERT: A 346 ARG cc_start: 0.6952 (mpp80) cc_final: 0.6724 (mpp-170) REVERT: A 360 GLU cc_start: 0.6810 (mt-10) cc_final: 0.6375 (mp0) REVERT: B 43 ILE cc_start: 0.8022 (OUTLIER) cc_final: 0.7598 (mp) REVERT: B 111 TYR cc_start: 0.7019 (m-80) cc_final: 0.6698 (m-80) REVERT: B 118 ASP cc_start: 0.6411 (t70) cc_final: 0.5976 (t70) REVERT: B 275 SER cc_start: 0.8325 (t) cc_final: 0.7646 (m) REVERT: R 296 ASN cc_start: 0.6321 (p0) cc_final: 0.6109 (p0) outliers start: 33 outliers final: 23 residues processed: 185 average time/residue: 0.2395 time to fit residues: 58.2281 Evaluate side-chains 182 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 157 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 110 SER Chi-restraints excluded: chain R residue 123 ILE Chi-restraints excluded: chain R residue 153 ILE Chi-restraints excluded: chain R residue 177 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 16 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 92 optimal weight: 0.6980 chunk 70 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 60 optimal weight: 0.0670 chunk 97 optimal weight: 5.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.232262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.198646 restraints weight = 8809.304| |-----------------------------------------------------------------------------| r_work (start): 0.4204 rms_B_bonded: 1.81 r_work: 0.4093 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3958 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6667 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8447 Z= 0.121 Angle : 0.569 14.604 11457 Z= 0.295 Chirality : 0.043 0.213 1287 Planarity : 0.004 0.051 1457 Dihedral : 4.484 21.790 1136 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.32 % Allowed : 18.16 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.26), residues: 1029 helix: 1.47 (0.25), residues: 416 sheet: -0.43 (0.35), residues: 204 loop : -1.16 (0.29), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.008 0.001 HIS B 91 PHE 0.022 0.002 PHE R 194 TYR 0.011 0.001 TYR N 117 ARG 0.009 0.000 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.03477 ( 412) hydrogen bonds : angle 4.44093 ( 1179) SS BOND : bond 0.00658 ( 4) SS BOND : angle 1.76330 ( 8) covalent geometry : bond 0.00273 ( 8443) covalent geometry : angle 0.56769 (11449) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 159 time to evaluate : 0.845 Fit side-chains revert: symmetry clash REVERT: A 13 ARG cc_start: 0.6728 (mtt180) cc_final: 0.6368 (mtt90) REVERT: A 59 GLN cc_start: 0.6148 (mt0) cc_final: 0.5746 (mp10) REVERT: A 239 ASN cc_start: 0.8194 (OUTLIER) cc_final: 0.7750 (t0) REVERT: A 326 ARG cc_start: 0.7282 (mtp-110) cc_final: 0.7057 (ttt-90) REVERT: A 346 ARG cc_start: 0.6918 (mpp80) cc_final: 0.6647 (mpp-170) REVERT: A 360 GLU cc_start: 0.6802 (mt-10) cc_final: 0.6382 (mp0) REVERT: B 43 ILE cc_start: 0.7966 (OUTLIER) cc_final: 0.7512 (mp) REVERT: B 111 TYR cc_start: 0.7030 (m-80) cc_final: 0.6661 (m-80) REVERT: B 118 ASP cc_start: 0.6385 (t70) cc_final: 0.5953 (t70) REVERT: B 275 SER cc_start: 0.8304 (t) cc_final: 0.7654 (m) REVERT: R 215 PHE cc_start: 0.7543 (m-80) cc_final: 0.7330 (m-80) REVERT: R 296 ASN cc_start: 0.6432 (p0) cc_final: 0.6208 (p0) outliers start: 30 outliers final: 26 residues processed: 177 average time/residue: 0.2366 time to fit residues: 55.7059 Evaluate side-chains 184 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 156 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 110 SER Chi-restraints excluded: chain R residue 123 ILE Chi-restraints excluded: chain R residue 153 ILE Chi-restraints excluded: chain R residue 177 VAL Chi-restraints excluded: chain R residue 266 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 36 optimal weight: 7.9990 chunk 94 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 44 optimal weight: 0.0570 chunk 28 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 90 optimal weight: 0.5980 overall best weight: 0.8500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.231069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.197099 restraints weight = 8878.043| |-----------------------------------------------------------------------------| r_work (start): 0.4235 rms_B_bonded: 1.82 r_work: 0.4125 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3993 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6682 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8447 Z= 0.133 Angle : 0.592 13.907 11457 Z= 0.304 Chirality : 0.044 0.198 1287 Planarity : 0.004 0.052 1457 Dihedral : 4.530 21.860 1136 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.54 % Allowed : 17.61 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.26), residues: 1029 helix: 1.48 (0.25), residues: 410 sheet: -0.47 (0.35), residues: 204 loop : -1.15 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.008 0.001 HIS B 91 PHE 0.031 0.002 PHE R 194 TYR 0.010 0.001 TYR N 95 ARG 0.008 0.000 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.03555 ( 412) hydrogen bonds : angle 4.48015 ( 1179) SS BOND : bond 0.00754 ( 4) SS BOND : angle 1.83423 ( 8) covalent geometry : bond 0.00304 ( 8443) covalent geometry : angle 0.59010 (11449) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 156 time to evaluate : 0.911 Fit side-chains revert: symmetry clash REVERT: A 59 GLN cc_start: 0.6160 (mt0) cc_final: 0.5761 (mp10) REVERT: A 239 ASN cc_start: 0.8234 (OUTLIER) cc_final: 0.7809 (t0) REVERT: A 346 ARG cc_start: 0.7067 (mpp80) cc_final: 0.6800 (mpp-170) REVERT: A 360 GLU cc_start: 0.6873 (mt-10) cc_final: 0.6428 (mp0) REVERT: B 43 ILE cc_start: 0.7977 (OUTLIER) cc_final: 0.7521 (mp) REVERT: B 111 TYR cc_start: 0.7012 (m-80) cc_final: 0.6641 (m-80) REVERT: B 118 ASP cc_start: 0.6472 (t70) cc_final: 0.6040 (t70) REVERT: B 275 SER cc_start: 0.8343 (t) cc_final: 0.7667 (m) REVERT: N 120 GLN cc_start: 0.6179 (mm-40) cc_final: 0.5918 (mm-40) REVERT: R 215 PHE cc_start: 0.7567 (m-80) cc_final: 0.7340 (m-80) REVERT: R 296 ASN cc_start: 0.6411 (p0) cc_final: 0.6185 (p0) outliers start: 32 outliers final: 27 residues processed: 178 average time/residue: 0.2189 time to fit residues: 52.5555 Evaluate side-chains 181 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 152 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 110 SER Chi-restraints excluded: chain R residue 123 ILE Chi-restraints excluded: chain R residue 153 ILE Chi-restraints excluded: chain R residue 177 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 81 optimal weight: 3.9990 chunk 67 optimal weight: 0.0470 chunk 96 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 62 optimal weight: 0.1980 chunk 91 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.233009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.199581 restraints weight = 8814.620| |-----------------------------------------------------------------------------| r_work (start): 0.4257 rms_B_bonded: 1.82 r_work: 0.4146 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.4010 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.4010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6652 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8447 Z= 0.118 Angle : 0.580 14.122 11457 Z= 0.298 Chirality : 0.043 0.188 1287 Planarity : 0.004 0.052 1457 Dihedral : 4.411 21.667 1136 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.21 % Allowed : 18.27 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.26), residues: 1029 helix: 1.60 (0.26), residues: 411 sheet: -0.28 (0.34), residues: 211 loop : -1.16 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.009 0.001 HIS B 91 PHE 0.032 0.002 PHE R 194 TYR 0.012 0.001 TYR N 117 ARG 0.008 0.000 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.03413 ( 412) hydrogen bonds : angle 4.38589 ( 1179) SS BOND : bond 0.00603 ( 4) SS BOND : angle 1.69520 ( 8) covalent geometry : bond 0.00264 ( 8443) covalent geometry : angle 0.57860 (11449) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2058 Ramachandran restraints generated. 1029 Oldfield, 0 Emsley, 1029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 161 time to evaluate : 0.903 Fit side-chains revert: symmetry clash REVERT: A 13 ARG cc_start: 0.6698 (mtt180) cc_final: 0.6364 (mtt90) REVERT: A 59 GLN cc_start: 0.5978 (mt0) cc_final: 0.5704 (mp10) REVERT: A 239 ASN cc_start: 0.8136 (OUTLIER) cc_final: 0.7788 (t0) REVERT: A 326 ARG cc_start: 0.7270 (mtp-110) cc_final: 0.6920 (ttt180) REVERT: A 360 GLU cc_start: 0.6887 (mt-10) cc_final: 0.6448 (mp0) REVERT: B 43 ILE cc_start: 0.7949 (OUTLIER) cc_final: 0.7508 (mp) REVERT: B 111 TYR cc_start: 0.7007 (m-80) cc_final: 0.6603 (m-80) REVERT: B 118 ASP cc_start: 0.6332 (t70) cc_final: 0.5909 (t70) REVERT: B 252 LEU cc_start: 0.7231 (tp) cc_final: 0.6996 (tp) REVERT: B 275 SER cc_start: 0.8196 (t) cc_final: 0.7562 (m) REVERT: R 178 PHE cc_start: 0.4513 (t80) cc_final: 0.4042 (t80) REVERT: R 215 PHE cc_start: 0.7531 (m-80) cc_final: 0.7313 (m-80) outliers start: 29 outliers final: 23 residues processed: 180 average time/residue: 0.2345 time to fit residues: 56.6026 Evaluate side-chains 179 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 154 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 213 GLN Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 110 SER Chi-restraints excluded: chain R residue 123 ILE Chi-restraints excluded: chain R residue 153 ILE Chi-restraints excluded: chain R residue 177 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 77 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 73 optimal weight: 0.4980 chunk 47 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 68 optimal weight: 0.4980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN N 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.232039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.198402 restraints weight = 8850.720| |-----------------------------------------------------------------------------| r_work (start): 0.4227 rms_B_bonded: 1.82 r_work: 0.4120 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3984 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6664 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8447 Z= 0.125 Angle : 0.587 13.699 11457 Z= 0.302 Chirality : 0.044 0.207 1287 Planarity : 0.004 0.052 1457 Dihedral : 4.424 21.656 1136 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.43 % Allowed : 18.49 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.26), residues: 1029 helix: 1.59 (0.26), residues: 411 sheet: -0.26 (0.36), residues: 203 loop : -1.14 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.009 0.001 HIS B 91 PHE 0.032 0.002 PHE R 194 TYR 0.016 0.001 TYR B 59 ARG 0.008 0.000 ARG N 67 Details of bonding type rmsd hydrogen bonds : bond 0.03501 ( 412) hydrogen bonds : angle 4.38598 ( 1179) SS BOND : bond 0.00703 ( 4) SS BOND : angle 1.73885 ( 8) covalent geometry : bond 0.00285 ( 8443) covalent geometry : angle 0.58513 (11449) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5201.47 seconds wall clock time: 90 minutes 12.50 seconds (5412.50 seconds total)