Starting phenix.real_space_refine on Thu Jul 2 06:41:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fye_29571/07_2026/8fye_29571.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fye_29571/07_2026/8fye_29571.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fye_29571/07_2026/8fye_29571.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fye_29571/07_2026/8fye_29571.map" model { file = "/net/cci-nas-00/data/ceres_data/8fye_29571/07_2026/8fye_29571.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fye_29571/07_2026/8fye_29571.cif" } resolution = 2.85 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= 0.038 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: 6 Type Number sf(0) Gaussians P 2 5.49 5 S 54 5.16 5 C 4673 2.51 5 N 1234 2.21 5 O 1357 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7321 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1891 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 232} Chain breaks: 1 Chain: "B" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2584 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "G" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 442 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "R" Number of atoms: 2258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2258 Classifications: {'peptide': 286} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 273} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "R" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 146 Unusual residues: {'J40': 1, 'Y01': 2, 'YGH': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 1.67, per 1000 atoms: 0.23 Number of scatterers: 7321 At special positions: 0 Unit cell: (95.764, 76.396, 122.664, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 54 16.00 P 2 15.00 F 1 9.00 O 1357 8.00 N 1234 7.00 C 4673 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 109 " - pdb=" SG CYS R 187 " 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: 1.50 Conformation dependent library (CDL) restraints added in 449.1 milliseconds 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1726 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 8 sheets defined 47.6% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.378A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.935A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 329 through 352 Processing helix chain 'B' and resid 6 through 26 removed outlier: 3.972A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN B 13 " --> pdb=" O GLN B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 9 through 23 removed outlier: 3.606A pdb=" N LYS G 14 " --> pdb=" O ALA G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'R' and resid 36 through 64 Processing helix chain 'R' and resid 69 through 89 Processing helix chain 'R' and resid 89 through 100 Processing helix chain 'R' and resid 105 through 140 Processing helix chain 'R' and resid 140 through 147 Processing helix chain 'R' and resid 149 through 169 removed outlier: 3.646A pdb=" N ALA R 153 " --> pdb=" O THR R 149 " (cutoff:3.500A) Processing helix chain 'R' and resid 177 through 182 Processing helix chain 'R' and resid 192 through 204 Processing helix chain 'R' and resid 204 through 228 Processing helix chain 'R' and resid 325 through 368 removed outlier: 3.921A pdb=" N THR R 353 " --> pdb=" O ILE R 349 " (cutoff:3.500A) Proline residue: R 360 - end of helix removed outlier: 3.564A pdb=" N VAL R 364 " --> pdb=" O PRO R 360 " (cutoff:3.500A) Processing helix chain 'R' and resid 378 through 391 removed outlier: 3.559A pdb=" N GLY R 389 " --> pdb=" O ILE R 385 " (cutoff:3.500A) Processing helix chain 'R' and resid 391 through 401 Proline residue: R 397 - end of helix Processing helix chain 'R' and resid 404 through 415 Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 191 removed outlier: 3.874A pdb=" N VAL A 201 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLY A 40 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 9.258A pdb=" N ALA A 220 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 52 removed outlier: 3.563A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.656A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.433A 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: 5.938A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.856A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 192 removed outlier: 3.528A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.561A 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: 6.637A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.595A 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: 3.618A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 407 hydrogen bonds defined for protein. 1173 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: 0.89 Time building geometry restraints manager: 0.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1217 1.32 - 1.44: 1939 1.44 - 1.57: 4231 1.57 - 1.69: 3 1.69 - 1.81: 76 Bond restraints: 7466 Sorted by residual: bond pdb=" O4 J40 R 502 " pdb=" P4 J40 R 502 " ideal model delta sigma weight residual 1.702 1.608 0.094 2.00e-02 2.50e+03 2.23e+01 bond pdb=" O42 J40 R 502 " pdb=" P4 J40 R 502 " ideal model delta sigma weight residual 1.548 1.484 0.064 2.00e-02 2.50e+03 1.01e+01 bond pdb=" N LEU R 90 " pdb=" CA LEU R 90 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.04e-02 9.25e+03 9.92e+00 bond pdb=" N MET R 211 " pdb=" CA MET R 211 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.28e-02 6.10e+03 9.24e+00 bond pdb=" C12 YGH R 501 " pdb=" N13 YGH R 501 " ideal model delta sigma weight residual 1.444 1.504 -0.060 2.00e-02 2.50e+03 9.04e+00 ... (remaining 7461 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.21: 10082 4.21 - 8.43: 27 8.43 - 12.64: 3 12.64 - 16.86: 0 16.86 - 21.07: 1 Bond angle restraints: 10113 Sorted by residual: angle pdb=" O1 J40 R 502 " pdb=" P1 J40 R 502 " pdb=" O13 J40 R 502 " ideal model delta sigma weight residual 92.86 113.93 -21.07 3.00e+00 1.11e-01 4.93e+01 angle pdb=" N CYS R 120 " pdb=" CA CYS R 120 " pdb=" C CYS R 120 " ideal model delta sigma weight residual 112.90 108.06 4.84 1.31e+00 5.83e-01 1.37e+01 angle pdb=" O1 J40 R 502 " pdb=" P1 J40 R 502 " pdb=" O11 J40 R 502 " ideal model delta sigma weight residual 108.88 97.80 11.08 3.00e+00 1.11e-01 1.36e+01 angle pdb=" CA PHE R 361 " pdb=" C PHE R 361 " pdb=" O PHE R 361 " ideal model delta sigma weight residual 120.42 116.60 3.82 1.06e+00 8.90e-01 1.30e+01 angle pdb=" O4 J40 R 502 " pdb=" P4 J40 R 502 " pdb=" O42 J40 R 502 " ideal model delta sigma weight residual 103.19 113.90 -10.71 3.00e+00 1.11e-01 1.27e+01 ... (remaining 10108 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.16: 4353 23.16 - 46.32: 221 46.32 - 69.48: 31 69.48 - 92.64: 5 92.64 - 115.80: 1 Dihedral angle restraints: 4611 sinusoidal: 1950 harmonic: 2661 Sorted by residual: dihedral pdb=" C40 J40 R 502 " pdb=" C41 J40 R 502 " pdb=" C42 J40 R 502 " pdb=" C43 J40 R 502 " ideal model delta sinusoidal sigma weight residual 178.73 62.93 115.80 1 3.00e+01 1.11e-03 1.53e+01 dihedral pdb=" CA LEU B 117 " pdb=" C LEU B 117 " pdb=" N ASP B 118 " pdb=" CA ASP B 118 " ideal model delta harmonic sigma weight residual 180.00 163.63 16.37 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 163.66 16.34 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 4608 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 784 0.039 - 0.078: 276 0.078 - 0.117: 79 0.117 - 0.156: 16 0.156 - 0.195: 4 Chirality restraints: 1159 Sorted by residual: chirality pdb=" CA VAL R 85 " pdb=" N VAL R 85 " pdb=" C VAL R 85 " pdb=" CB VAL R 85 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 9.54e-01 chirality pdb=" CA ILE R 415 " pdb=" N ILE R 415 " pdb=" C ILE R 415 " pdb=" CB ILE R 415 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.42e-01 chirality pdb=" CB VAL R 85 " pdb=" CA VAL R 85 " pdb=" CG1 VAL R 85 " pdb=" CG2 VAL R 85 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.13e-01 ... (remaining 1156 not shown) Planarity restraints: 1263 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE R 361 " -0.029 2.00e-02 2.50e+03 1.91e-02 6.36e+00 pdb=" CG PHE R 361 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE R 361 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE R 361 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE R 361 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE R 361 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE R 361 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET R 211 " 0.010 2.00e-02 2.50e+03 2.06e-02 4.23e+00 pdb=" C MET R 211 " -0.036 2.00e-02 2.50e+03 pdb=" O MET R 211 " 0.013 2.00e-02 2.50e+03 pdb=" N LEU R 212 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP R 125 " -0.010 2.00e-02 2.50e+03 2.03e-02 4.11e+00 pdb=" C TRP R 125 " 0.035 2.00e-02 2.50e+03 pdb=" O TRP R 125 " -0.013 2.00e-02 2.50e+03 pdb=" N HIS R 126 " -0.012 2.00e-02 2.50e+03 ... (remaining 1260 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 157 2.71 - 3.26: 7319 3.26 - 3.80: 12171 3.80 - 4.35: 15678 4.35 - 4.90: 26579 Nonbonded interactions: 61904 Sorted by model distance: nonbonded pdb=" OG SER G 57 " pdb=" OE1 GLU G 58 " model vdw 2.161 3.040 nonbonded pdb=" O GLN B 75 " pdb=" OG SER B 98 " model vdw 2.220 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.236 3.040 nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.328 3.040 nonbonded pdb=" OG1 THR B 159 " pdb=" NE1 TRP B 169 " model vdw 2.333 3.120 ... (remaining 61899 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: 1.580 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: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.960 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 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 0.094 7467 Z= 0.255 Angle : 0.713 21.071 10115 Z= 0.389 Chirality : 0.044 0.195 1159 Planarity : 0.004 0.039 1263 Dihedral : 13.645 115.798 2882 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % 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: 0.43 (0.28), residues: 902 helix: 1.86 (0.26), residues: 408 sheet: -0.53 (0.35), residues: 173 loop : -1.31 (0.33), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 227 TYR 0.011 0.001 TYR R 195 PHE 0.039 0.002 PHE R 361 TRP 0.026 0.002 TRP R 125 HIS 0.003 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.26 ( 7466) covalent geometry : angle 0.71303 / 0.39 (10113) SS BOND : bond 0.00095 / 0.05 ( 1) SS BOND : angle 0.09803 / 0.05 ( 2) hydrogen bonds : bond 0.13491 / 9.04 ( 407) hydrogen bonds : angle 5.82487 / 4.17 ( 1173) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.184 Fit side-chains REVERT: A 18 MET cc_start: 0.6458 (ttm) cc_final: 0.6229 (ttp) REVERT: B 45 MET cc_start: 0.8778 (mtt) cc_final: 0.8358 (mtt) REVERT: B 156 GLN cc_start: 0.8320 (mt0) cc_final: 0.8049 (mt0) REVERT: B 247 ASP cc_start: 0.7064 (t0) cc_final: 0.6854 (t0) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.5091 time to fit residues: 46.6628 Evaluate side-chains 66 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.0070 chunk 33 optimal weight: 0.0770 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 0.0010 overall best weight: 0.2562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 146 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.145959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.108505 restraints weight = 8065.567| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.32 r_work: 0.3019 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.0959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7467 Z= 0.100 Angle : 0.510 11.760 10115 Z= 0.259 Chirality : 0.041 0.233 1159 Planarity : 0.003 0.036 1263 Dihedral : 8.607 82.101 1215 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.03 % Allowed : 7.07 % Favored : 91.90 % 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 (0.28), residues: 902 helix: 2.35 (0.26), residues: 412 sheet: -0.30 (0.36), residues: 162 loop : -1.24 (0.32), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 227 TYR 0.009 0.001 TYR R 195 PHE 0.014 0.001 PHE B 234 TRP 0.011 0.001 TRP B 169 HIS 0.002 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 ( 7466) covalent geometry : angle 0.50980 / 0.26 (10113) SS BOND : bond 0.00047 / 0.02 ( 1) SS BOND : angle 0.26505 / 0.14 ( 2) hydrogen bonds : bond 0.03547 / 2.40 ( 407) hydrogen bonds : angle 4.44562 / 3.11 ( 1173) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.199 Fit side-chains REVERT: A 18 MET cc_start: 0.6266 (ttm) cc_final: 0.6059 (ttp) REVERT: B 45 MET cc_start: 0.8525 (mtt) cc_final: 0.8212 (mtt) REVERT: B 66 ASP cc_start: 0.7575 (p0) cc_final: 0.7260 (p0) REVERT: B 156 GLN cc_start: 0.8302 (mt0) cc_final: 0.8041 (mt0) REVERT: B 247 ASP cc_start: 0.7394 (t0) cc_final: 0.7137 (t0) outliers start: 8 outliers final: 1 residues processed: 82 average time/residue: 0.4048 time to fit residues: 35.6860 Evaluate side-chains 71 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 70 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 227 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 20 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 16 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 HIS A 204 GLN A 304 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.140418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.102460 restraints weight = 8058.321| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.34 r_work: 0.2957 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7467 Z= 0.165 Angle : 0.546 11.831 10115 Z= 0.278 Chirality : 0.043 0.231 1159 Planarity : 0.003 0.035 1263 Dihedral : 8.531 84.167 1215 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.54 % Allowed : 10.28 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.28), residues: 902 helix: 2.29 (0.26), residues: 416 sheet: -0.32 (0.36), residues: 162 loop : -1.17 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 219 TYR 0.012 0.001 TYR R 195 PHE 0.013 0.002 PHE A 189 TRP 0.009 0.001 TRP B 63 HIS 0.003 0.001 HIS B 62 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 ( 7466) covalent geometry : angle 0.54575 / 0.28 (10113) SS BOND : bond 0.00014 / 0.01 ( 1) SS BOND : angle 0.13771 / 0.07 ( 2) hydrogen bonds : bond 0.03939 / 2.69 ( 407) hydrogen bonds : angle 4.43955 / 3.10 ( 1173) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.261 Fit side-chains REVERT: A 18 MET cc_start: 0.6419 (ttm) cc_final: 0.6195 (ttp) REVERT: A 298 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7408 (mm-30) REVERT: B 45 MET cc_start: 0.8685 (mtt) cc_final: 0.8397 (mtt) REVERT: B 66 ASP cc_start: 0.7656 (p0) cc_final: 0.7412 (p0) REVERT: B 105 TYR cc_start: 0.9172 (t80) cc_final: 0.8872 (t80) REVERT: B 156 GLN cc_start: 0.8404 (mt0) cc_final: 0.8054 (mt0) REVERT: B 214 ARG cc_start: 0.7873 (mmp80) cc_final: 0.7621 (mmt180) REVERT: B 246 ASP cc_start: 0.8355 (m-30) cc_final: 0.7860 (m-30) outliers start: 12 outliers final: 6 residues processed: 84 average time/residue: 0.4643 time to fit residues: 41.5148 Evaluate side-chains 77 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 269 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 51 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 71 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 HIS B 220 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.140443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.102199 restraints weight = 8216.494| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.37 r_work: 0.2956 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7467 Z= 0.153 Angle : 0.537 11.987 10115 Z= 0.272 Chirality : 0.043 0.195 1159 Planarity : 0.003 0.034 1263 Dihedral : 8.604 88.321 1215 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.06 % Allowed : 11.70 % Favored : 86.25 % 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: 0.88 (0.28), residues: 902 helix: 2.25 (0.25), residues: 416 sheet: -0.39 (0.36), residues: 162 loop : -1.14 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 32 TYR 0.011 0.001 TYR R 205 PHE 0.012 0.002 PHE A 189 TRP 0.010 0.001 TRP R 387 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.15 ( 7466) covalent geometry : angle 0.53669 / 0.27 (10113) SS BOND : bond 0.00008 / 0.00 ( 1) SS BOND : angle 0.21364 / 0.11 ( 2) hydrogen bonds : bond 0.03782 / 2.58 ( 407) hydrogen bonds : angle 4.36367 / 3.04 ( 1173) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.250 Fit side-chains revert: symmetry clash REVERT: A 18 MET cc_start: 0.6417 (ttm) cc_final: 0.6193 (ttp) REVERT: B 45 MET cc_start: 0.8715 (mtt) cc_final: 0.8435 (mtt) REVERT: B 66 ASP cc_start: 0.7514 (p0) cc_final: 0.7258 (p0) REVERT: B 156 GLN cc_start: 0.8399 (mt0) cc_final: 0.8094 (mt0) REVERT: B 214 ARG cc_start: 0.7828 (mmp80) cc_final: 0.7587 (mmt180) REVERT: B 246 ASP cc_start: 0.8262 (m-30) cc_final: 0.7807 (m-30) outliers start: 16 outliers final: 7 residues processed: 86 average time/residue: 0.3665 time to fit residues: 33.9013 Evaluate side-chains 84 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 77 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 327 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 0 optimal weight: 10.0000 chunk 72 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 chunk 41 optimal weight: 0.5980 chunk 48 optimal weight: 0.9990 chunk 86 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 HIS B 220 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.140620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.102725 restraints weight = 8117.934| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 2.35 r_work: 0.2959 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7467 Z= 0.141 Angle : 0.525 11.925 10115 Z= 0.265 Chirality : 0.043 0.192 1159 Planarity : 0.003 0.033 1263 Dihedral : 8.331 89.316 1215 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.31 % Allowed : 11.95 % Favored : 85.73 % 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: 0.90 (0.28), residues: 902 helix: 2.28 (0.25), residues: 415 sheet: -0.35 (0.37), residues: 162 loop : -1.15 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 32 TYR 0.010 0.001 TYR R 195 PHE 0.011 0.002 PHE A 189 TRP 0.010 0.001 TRP R 387 HIS 0.002 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 ( 7466) covalent geometry : angle 0.52487 / 0.27 (10113) SS BOND : bond 0.00024 / 0.01 ( 1) SS BOND : angle 0.21646 / 0.11 ( 2) hydrogen bonds : bond 0.03688 / 2.52 ( 407) hydrogen bonds : angle 4.31071 / 3.01 ( 1173) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 0.217 Fit side-chains revert: symmetry clash REVERT: A 18 MET cc_start: 0.6500 (ttm) cc_final: 0.6280 (ttp) REVERT: B 45 MET cc_start: 0.8730 (mtt) cc_final: 0.8438 (mtt) REVERT: B 66 ASP cc_start: 0.7526 (p0) cc_final: 0.7311 (p0) REVERT: B 138 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8262 (mt-10) REVERT: B 156 GLN cc_start: 0.8502 (mt0) cc_final: 0.8202 (mt0) REVERT: B 214 ARG cc_start: 0.7843 (mmp80) cc_final: 0.7589 (mmt180) REVERT: B 246 ASP cc_start: 0.8336 (m-30) cc_final: 0.7884 (m-30) outliers start: 18 outliers final: 12 residues processed: 83 average time/residue: 0.3857 time to fit residues: 34.2493 Evaluate side-chains 85 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain R residue 89 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 33 optimal weight: 0.4980 chunk 4 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 9 optimal weight: 0.4980 chunk 64 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 HIS B 220 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.140770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.103053 restraints weight = 8060.733| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.33 r_work: 0.2970 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7467 Z= 0.133 Angle : 0.516 11.847 10115 Z= 0.261 Chirality : 0.042 0.192 1159 Planarity : 0.003 0.033 1263 Dihedral : 8.212 89.299 1215 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.31 % Allowed : 12.85 % Favored : 84.83 % 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: 0.93 (0.28), residues: 902 helix: 2.31 (0.25), residues: 415 sheet: -0.36 (0.36), residues: 170 loop : -1.14 (0.33), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 32 TYR 0.010 0.001 TYR R 195 PHE 0.011 0.002 PHE A 189 TRP 0.010 0.001 TRP R 387 HIS 0.002 0.001 HIS A 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 ( 7466) covalent geometry : angle 0.51567 / 0.26 (10113) SS BOND : bond 0.00017 / 0.01 ( 1) SS BOND : angle 0.20911 / 0.11 ( 2) hydrogen bonds : bond 0.03617 / 2.47 ( 407) hydrogen bonds : angle 4.26666 / 2.98 ( 1173) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 0.258 Fit side-chains revert: symmetry clash REVERT: A 18 MET cc_start: 0.6392 (ttm) cc_final: 0.6178 (ttp) REVERT: B 45 MET cc_start: 0.8716 (mtt) cc_final: 0.8419 (mtt) REVERT: B 156 GLN cc_start: 0.8479 (mt0) cc_final: 0.8087 (mt0) REVERT: B 214 ARG cc_start: 0.7693 (mmp80) cc_final: 0.7447 (mmt180) REVERT: B 220 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.8275 (mt0) REVERT: B 246 ASP cc_start: 0.8302 (m-30) cc_final: 0.7855 (m-30) outliers start: 18 outliers final: 13 residues processed: 85 average time/residue: 0.4397 time to fit residues: 40.1325 Evaluate side-chains 91 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 90 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 7 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 64 optimal weight: 0.2980 chunk 58 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 16 optimal weight: 6.9990 chunk 49 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN A 195 HIS B 220 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.140819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.102776 restraints weight = 8168.925| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.35 r_work: 0.2966 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7467 Z= 0.138 Angle : 0.520 11.919 10115 Z= 0.263 Chirality : 0.042 0.193 1159 Planarity : 0.003 0.033 1263 Dihedral : 8.132 89.031 1215 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.31 % Allowed : 13.24 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.93 (0.28), residues: 902 helix: 2.31 (0.25), residues: 414 sheet: -0.39 (0.36), residues: 170 loop : -1.12 (0.33), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 32 TYR 0.010 0.001 TYR R 205 PHE 0.011 0.002 PHE A 189 TRP 0.010 0.001 TRP B 82 HIS 0.002 0.001 HIS A 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 ( 7466) covalent geometry : angle 0.51972 / 0.26 (10113) SS BOND : bond 0.00017 / 0.01 ( 1) SS BOND : angle 0.18975 / 0.10 ( 2) hydrogen bonds : bond 0.03629 / 2.48 ( 407) hydrogen bonds : angle 4.25742 / 2.97 ( 1173) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.270 Fit side-chains revert: symmetry clash REVERT: A 18 MET cc_start: 0.6593 (ttm) cc_final: 0.6355 (ttp) REVERT: B 45 MET cc_start: 0.8792 (mtt) cc_final: 0.8494 (mtt) REVERT: B 156 GLN cc_start: 0.8613 (mt0) cc_final: 0.8252 (mt0) REVERT: B 220 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.8400 (mt0) REVERT: B 246 ASP cc_start: 0.8387 (m-30) cc_final: 0.7929 (m-30) outliers start: 18 outliers final: 14 residues processed: 87 average time/residue: 0.3910 time to fit residues: 36.6270 Evaluate side-chains 91 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 90 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 31 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 61 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 HIS A 294 ASN B 220 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.138573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.102660 restraints weight = 8179.419| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.19 r_work: 0.2974 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7467 Z= 0.164 Angle : 0.541 11.887 10115 Z= 0.274 Chirality : 0.043 0.195 1159 Planarity : 0.003 0.033 1263 Dihedral : 8.150 88.679 1215 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.31 % Allowed : 13.75 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.28), residues: 902 helix: 2.21 (0.25), residues: 414 sheet: -0.45 (0.36), residues: 170 loop : -1.14 (0.33), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 32 TYR 0.011 0.001 TYR R 195 PHE 0.012 0.002 PHE A 189 TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS A 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.16 ( 7466) covalent geometry : angle 0.54155 / 0.27 (10113) SS BOND : bond 0.00010 / 0.01 ( 1) SS BOND : angle 0.16064 / 0.08 ( 2) hydrogen bonds : bond 0.03782 / 2.59 ( 407) hydrogen bonds : angle 4.30504 / 3.01 ( 1173) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 0.253 Fit side-chains revert: symmetry clash REVERT: A 18 MET cc_start: 0.6453 (ttm) cc_final: 0.6208 (ttp) REVERT: B 45 MET cc_start: 0.8774 (mtt) cc_final: 0.8454 (mtt) REVERT: B 156 GLN cc_start: 0.8557 (mt0) cc_final: 0.8177 (mt0) REVERT: B 220 GLN cc_start: 0.8542 (OUTLIER) cc_final: 0.8287 (mt0) REVERT: B 246 ASP cc_start: 0.8333 (m-30) cc_final: 0.7838 (m-30) outliers start: 18 outliers final: 15 residues processed: 81 average time/residue: 0.4645 time to fit residues: 40.2999 Evaluate side-chains 88 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 90 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 17 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 chunk 64 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 HIS B 220 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.139454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.103640 restraints weight = 8053.600| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 2.19 r_work: 0.2981 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7467 Z= 0.146 Angle : 0.528 11.684 10115 Z= 0.268 Chirality : 0.043 0.194 1159 Planarity : 0.003 0.033 1263 Dihedral : 8.078 88.949 1215 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.44 % Allowed : 13.75 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.28), residues: 902 helix: 2.33 (0.25), residues: 408 sheet: -0.45 (0.36), residues: 171 loop : -1.10 (0.33), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 32 TYR 0.010 0.001 TYR R 195 PHE 0.011 0.002 PHE A 189 TRP 0.011 0.001 TRP B 82 HIS 0.002 0.001 HIS A 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 ( 7466) covalent geometry : angle 0.52798 / 0.27 (10113) SS BOND : bond 0.00014 / 0.01 ( 1) SS BOND : angle 0.19388 / 0.10 ( 2) hydrogen bonds : bond 0.03704 / 2.53 ( 407) hydrogen bonds : angle 4.28028 / 2.99 ( 1173) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 73 time to evaluate : 0.244 Fit side-chains revert: symmetry clash REVERT: A 18 MET cc_start: 0.6292 (ttm) cc_final: 0.6066 (ttp) REVERT: B 45 MET cc_start: 0.8734 (mtt) cc_final: 0.8413 (mtt) REVERT: B 156 GLN cc_start: 0.8493 (mt0) cc_final: 0.8135 (mt0) REVERT: B 220 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.8163 (mt0) REVERT: B 246 ASP cc_start: 0.8256 (m-30) cc_final: 0.7762 (m-30) outliers start: 19 outliers final: 15 residues processed: 82 average time/residue: 0.3891 time to fit residues: 34.1674 Evaluate side-chains 89 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 90 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 18 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 HIS B 220 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.138140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.102368 restraints weight = 8124.630| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 2.17 r_work: 0.2971 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7467 Z= 0.171 Angle : 0.543 11.721 10115 Z= 0.276 Chirality : 0.043 0.196 1159 Planarity : 0.003 0.033 1263 Dihedral : 8.102 88.677 1215 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.31 % Allowed : 13.75 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.28), residues: 902 helix: 2.30 (0.25), residues: 411 sheet: -0.52 (0.36), residues: 173 loop : -1.06 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 32 TYR 0.011 0.001 TYR R 195 PHE 0.012 0.002 PHE A 189 TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS A 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.17 ( 7466) covalent geometry : angle 0.54348 / 0.28 (10113) SS BOND : bond 0.00003 / 0.00 ( 1) SS BOND : angle 0.16627 / 0.08 ( 2) hydrogen bonds : bond 0.03826 / 2.62 ( 407) hydrogen bonds : angle 4.32609 / 3.02 ( 1173) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 71 time to evaluate : 0.290 Fit side-chains revert: symmetry clash REVERT: A 18 MET cc_start: 0.6379 (ttm) cc_final: 0.6168 (ttp) REVERT: B 45 MET cc_start: 0.8791 (mtt) cc_final: 0.8457 (mtt) REVERT: B 156 GLN cc_start: 0.8591 (mt0) cc_final: 0.8220 (mt0) REVERT: B 220 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.8312 (pt0) REVERT: B 246 ASP cc_start: 0.8315 (m-30) cc_final: 0.7754 (m-30) outliers start: 18 outliers final: 15 residues processed: 80 average time/residue: 0.4380 time to fit residues: 37.5486 Evaluate side-chains 86 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 90 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 81 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 75 optimal weight: 0.3980 chunk 41 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 60 optimal weight: 0.3980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 195 HIS B 220 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.139831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.104048 restraints weight = 8140.936| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.20 r_work: 0.2987 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7467 Z= 0.130 Angle : 0.520 11.373 10115 Z= 0.264 Chirality : 0.042 0.192 1159 Planarity : 0.003 0.036 1263 Dihedral : 7.999 89.317 1215 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.19 % Allowed : 14.14 % Favored : 83.68 % 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: 0.97 (0.28), residues: 902 helix: 2.36 (0.25), residues: 408 sheet: -0.44 (0.37), residues: 178 loop : -1.01 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 32 TYR 0.010 0.001 TYR R 195 PHE 0.011 0.001 PHE A 189 TRP 0.011 0.001 TRP R 387 HIS 0.002 0.001 HIS A 322 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 ( 7466) covalent geometry : angle 0.51971 / 0.26 (10113) SS BOND : bond 0.00018 / 0.01 ( 1) SS BOND : angle 0.22474 / 0.12 ( 2) hydrogen bonds : bond 0.03619 / 2.47 ( 407) hydrogen bonds : angle 4.25913 / 2.97 ( 1173) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2092.91 seconds wall clock time: 36 minutes 32.37 seconds (2192.37 seconds total)