Starting phenix.real_space_refine on Fri Aug 22 23:19:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yjn_33875/08_2025/7yjn_33875.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yjn_33875/08_2025/7yjn_33875.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7yjn_33875/08_2025/7yjn_33875.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yjn_33875/08_2025/7yjn_33875.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yjn_33875/08_2025/7yjn_33875.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yjn_33875/08_2025/7yjn_33875.map" } resolution = 3.4 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= 0.001 sd= 0.101 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 49 5.16 5 C 5476 2.51 5 N 1445 2.21 5 O 1557 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 92 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8528 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3230 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 17, 'TRANS': 400} Chain: "B" Number of atoms: 3592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3592 Classifications: {'peptide': 465} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 21, 'TRANS': 443} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'ARG:plan': 1, 'PHE:plan': 1, 'ASP:plan': 1, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "D" Number of atoms: 1122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1122 Classifications: {'peptide': 138} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 131} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "E" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 186 Classifications: {'peptide': 27} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 2, 'TRANS': 24} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 1, 'PHE:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "C" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 383 Classifications: {'peptide': 47} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'TRANS': 46} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'TRP:plan': 1, 'PHE:plan': 2, 'TYR:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'PLP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 2.24, per 1000 atoms: 0.26 Number of scatterers: 8528 At special positions: 0 Unit cell: (89.64, 82.08, 117.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 49 16.00 P 1 15.00 O 1557 8.00 N 1445 7.00 C 5476 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.65 Conformation dependent library (CDL) restraints added in 384.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2030 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 5 sheets defined 51.5% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 65 through 73 removed outlier: 3.857A pdb=" N ASP A 70 " --> pdb=" O GLU A 66 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLU A 71 " --> pdb=" O GLN A 67 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 72 " --> pdb=" O GLU A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 140 removed outlier: 3.546A pdb=" N LEU A 129 " --> pdb=" O HIS A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 168 removed outlier: 3.812A pdb=" N LEU A 157 " --> pdb=" O ILE A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 190 removed outlier: 3.615A pdb=" N THR A 181 " --> pdb=" O TYR A 177 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N MET A 182 " --> pdb=" O GLY A 178 " (cutoff:3.500A) Proline residue: A 187 - end of helix removed outlier: 3.711A pdb=" N CYS A 190 " --> pdb=" O ILE A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 213 removed outlier: 3.552A pdb=" N GLY A 209 " --> pdb=" O GLY A 205 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN A 211 " --> pdb=" O GLN A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 239 Processing helix chain 'A' and resid 263 through 275 removed outlier: 3.697A pdb=" N ILE A 267 " --> pdb=" O PRO A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 300 removed outlier: 3.777A pdb=" N HIS A 299 " --> pdb=" O GLY A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 338 Processing helix chain 'A' and resid 349 through 365 removed outlier: 3.618A pdb=" N ALA A 353 " --> pdb=" O PRO A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 385 Processing helix chain 'A' and resid 411 through 431 Processing helix chain 'A' and resid 460 through 480 removed outlier: 3.714A pdb=" N LEU A 464 " --> pdb=" O SER A 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 36 Processing helix chain 'B' and resid 54 through 63 Processing helix chain 'B' and resid 119 through 132 removed outlier: 3.913A pdb=" N ARG B 123 " --> pdb=" O TYR B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 160 Processing helix chain 'B' and resid 169 through 182 Proline residue: B 179 - end of helix Processing helix chain 'B' and resid 195 through 204 Processing helix chain 'B' and resid 216 through 230 Processing helix chain 'B' and resid 258 through 267 Processing helix chain 'B' and resid 290 through 295 removed outlier: 3.792A pdb=" N LEU B 294 " --> pdb=" O GLY B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 314 removed outlier: 3.884A pdb=" N GLY B 314 " --> pdb=" O THR B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 334 removed outlier: 3.682A pdb=" N GLN B 328 " --> pdb=" O LYS B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 339 Processing helix chain 'B' and resid 344 through 359 Processing helix chain 'B' and resid 369 through 389 removed outlier: 3.596A pdb=" N GLY B 389 " --> pdb=" O LEU B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 421 removed outlier: 3.553A pdb=" N ALA B 413 " --> pdb=" O ALA B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 468 Processing helix chain 'D' and resid 25 through 45 removed outlier: 3.791A pdb=" N MET D 31 " --> pdb=" O TRP D 27 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER D 45 " --> pdb=" O VAL D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 71 Processing helix chain 'D' and resid 87 through 92 Processing helix chain 'D' and resid 93 through 96 Processing helix chain 'D' and resid 99 through 119 Proline residue: D 109 - end of helix Processing helix chain 'D' and resid 124 through 141 removed outlier: 3.708A pdb=" N LYS D 141 " --> pdb=" O LEU D 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 54 removed outlier: 3.563A pdb=" N ARG E 54 " --> pdb=" O ILE E 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 15 Processing helix chain 'C' and resid 21 through 47 removed outlier: 3.845A pdb=" N VAL C 32 " --> pdb=" O PHE C 28 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL C 33 " --> pdb=" O ASN C 29 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 174 through 175 removed outlier: 6.648A pdb=" N VAL A 278 " --> pdb=" O VAL A 309 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N THR A 311 " --> pdb=" O VAL A 278 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU A 280 " --> pdb=" O THR A 311 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N ALA A 313 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ARG A 247 " --> pdb=" O ARG A 277 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N ILE A 279 " --> pdb=" O ARG A 247 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE A 249 " --> pdb=" O ILE A 279 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N ASP A 281 " --> pdb=" O ILE A 249 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N ALA A 251 " --> pdb=" O ASP A 281 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL A 195 " --> pdb=" O TYR A 248 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N VAL A 250 " --> pdb=" O VAL A 195 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 390 through 392 removed outlier: 3.699A pdb=" N VAL A 435 " --> pdb=" O LYS A 452 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 82 through 85 removed outlier: 6.147A pdb=" N GLU B 83 " --> pdb=" O THR B 96 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR B 96 " --> pdb=" O GLU B 83 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR B 85 " --> pdb=" O LYS B 94 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 163 through 167 removed outlier: 3.636A pdb=" N ALA B 163 " --> pdb=" O GLY B 322 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY B 318 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL B 304 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASP B 191 " --> pdb=" O VAL B 245 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE B 212 " --> pdb=" O SER B 190 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 400 through 404 removed outlier: 3.501A pdb=" N MET B 401 " --> pdb=" O ILE B 442 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE B 442 " --> pdb=" O MET B 401 " (cutoff:3.500A) 413 hydrogen bonds defined for protein. 1224 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.18 Time building geometry restraints manager: 0.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 1363 1.27 - 1.40: 2196 1.40 - 1.54: 5003 1.54 - 1.67: 80 1.67 - 1.81: 76 Bond restraints: 8718 Sorted by residual: bond pdb=" CA THR D 64 " pdb=" C THR D 64 " ideal model delta sigma weight residual 1.522 1.396 0.126 1.37e-02 5.33e+03 8.46e+01 bond pdb=" C LEU B 103 " pdb=" N ASN B 104 " ideal model delta sigma weight residual 1.331 1.203 0.129 1.40e-02 5.10e+03 8.43e+01 bond pdb=" C LEU B 103 " pdb=" O LEU B 103 " ideal model delta sigma weight residual 1.234 1.130 0.105 1.15e-02 7.56e+03 8.31e+01 bond pdb=" CA LEU B 103 " pdb=" C LEU B 103 " ideal model delta sigma weight residual 1.520 1.414 0.107 1.20e-02 6.94e+03 7.89e+01 bond pdb=" C CYS B 102 " pdb=" O CYS B 102 " ideal model delta sigma weight residual 1.235 1.133 0.103 1.26e-02 6.30e+03 6.64e+01 ... (remaining 8713 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.26: 11388 4.26 - 8.51: 367 8.51 - 12.77: 45 12.77 - 17.03: 10 17.03 - 21.28: 6 Bond angle restraints: 11816 Sorted by residual: angle pdb=" N PHE A 189 " pdb=" CA PHE A 189 " pdb=" C PHE A 189 " ideal model delta sigma weight residual 113.16 130.33 -17.17 1.24e+00 6.50e-01 1.92e+02 angle pdb=" C ILE C 8 " pdb=" CA ILE C 8 " pdb=" CB ILE C 8 " ideal model delta sigma weight residual 111.97 98.11 13.86 1.28e+00 6.10e-01 1.17e+02 angle pdb=" C MET D 71 " pdb=" N LYS D 72 " pdb=" CA LYS D 72 " ideal model delta sigma weight residual 122.19 109.66 12.53 1.41e+00 5.03e-01 7.90e+01 angle pdb=" C PHE D 142 " pdb=" N PRO D 143 " pdb=" CA PRO D 143 " ideal model delta sigma weight residual 119.84 130.64 -10.80 1.25e+00 6.40e-01 7.46e+01 angle pdb=" C VAL B 223 " pdb=" CA VAL B 223 " pdb=" CB VAL B 223 " ideal model delta sigma weight residual 112.14 101.03 11.11 1.35e+00 5.49e-01 6.77e+01 ... (remaining 11811 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 4540 17.95 - 35.89: 499 35.89 - 53.83: 132 53.83 - 71.78: 17 71.78 - 89.72: 4 Dihedral angle restraints: 5192 sinusoidal: 2029 harmonic: 3163 Sorted by residual: dihedral pdb=" C PHE A 183 " pdb=" N PHE A 183 " pdb=" CA PHE A 183 " pdb=" CB PHE A 183 " ideal model delta harmonic sigma weight residual -122.60 -151.10 28.50 0 2.50e+00 1.60e-01 1.30e+02 dihedral pdb=" N PHE A 183 " pdb=" C PHE A 183 " pdb=" CA PHE A 183 " pdb=" CB PHE A 183 " ideal model delta harmonic sigma weight residual 122.80 150.73 -27.93 0 2.50e+00 1.60e-01 1.25e+02 dihedral pdb=" N LEU B 259 " pdb=" C LEU B 259 " pdb=" CA LEU B 259 " pdb=" CB LEU B 259 " ideal model delta harmonic sigma weight residual 122.80 143.93 -21.13 0 2.50e+00 1.60e-01 7.14e+01 ... (remaining 5189 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.261: 1272 0.261 - 0.522: 51 0.522 - 0.782: 14 0.782 - 1.043: 0 1.043 - 1.304: 2 Chirality restraints: 1339 Sorted by residual: chirality pdb=" CA PHE A 183 " pdb=" N PHE A 183 " pdb=" C PHE A 183 " pdb=" CB PHE A 183 " both_signs ideal model delta sigma weight residual False 2.51 1.21 1.30 2.00e-01 2.50e+01 4.25e+01 chirality pdb=" CA LEU B 259 " pdb=" N LEU B 259 " pdb=" C LEU B 259 " pdb=" CB LEU B 259 " both_signs ideal model delta sigma weight residual False 2.51 1.38 1.13 2.00e-01 2.50e+01 3.18e+01 chirality pdb=" CG LEU D 129 " pdb=" CB LEU D 129 " pdb=" CD1 LEU D 129 " pdb=" CD2 LEU D 129 " both_signs ideal model delta sigma weight residual False -2.59 -1.84 -0.75 2.00e-01 2.50e+01 1.41e+01 ... (remaining 1336 not shown) Planarity restraints: 1486 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 186 " -0.145 5.00e-02 4.00e+02 2.18e-01 7.59e+01 pdb=" N PRO A 187 " 0.377 5.00e-02 4.00e+02 pdb=" CA PRO A 187 " -0.121 5.00e-02 4.00e+02 pdb=" CD PRO A 187 " -0.110 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE D 68 " -0.026 2.00e-02 2.50e+03 5.02e-02 2.52e+01 pdb=" C PHE D 68 " 0.087 2.00e-02 2.50e+03 pdb=" O PHE D 68 " -0.033 2.00e-02 2.50e+03 pdb=" N HIS D 69 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 229 " -0.023 2.00e-02 2.50e+03 4.88e-02 2.38e+01 pdb=" C ALA B 229 " 0.084 2.00e-02 2.50e+03 pdb=" O ALA B 229 " -0.033 2.00e-02 2.50e+03 pdb=" N GLU B 230 " -0.028 2.00e-02 2.50e+03 ... (remaining 1483 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.40: 45 2.40 - 3.03: 5810 3.03 - 3.65: 12168 3.65 - 4.28: 17359 4.28 - 4.90: 30608 Nonbonded interactions: 65990 Sorted by model distance: nonbonded pdb=" O GLY B 314 " pdb=" OE1 GLN B 350 " model vdw 1.776 3.040 nonbonded pdb=" OD1 ASP B 27 " pdb=" NH2 ARG B 58 " model vdw 1.869 3.120 nonbonded pdb=" OE1 GLN B 24 " pdb=" CE2 PHE B 54 " model vdw 1.908 3.340 nonbonded pdb=" O ALA B 229 " pdb=" N GLY B 231 " model vdw 1.910 3.120 nonbonded pdb=" O THR D 28 " pdb=" C THR D 29 " model vdw 1.946 3.270 ... (remaining 65985 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: 1.100 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: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.150 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 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 : 0.019 0.149 8719 Z= 1.216 Angle : 1.743 21.282 11816 Z= 1.050 Chirality : 0.133 1.304 1339 Planarity : 0.011 0.218 1486 Dihedral : 15.887 89.725 3162 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 26.04 Ramachandran Plot: Outliers : 1.94 % Allowed : 11.10 % Favored : 86.96 % Rotamer: Outliers : 8.37 % Allowed : 7.28 % Favored : 84.35 % Cbeta Deviations : 2.07 % 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 aren not related in a simple way. whole: -2.39 (0.25), residues: 1081 helix: -0.36 (0.22), residues: 543 sheet: -3.45 (0.48), residues: 80 loop : -2.75 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 26 TYR 0.029 0.003 TYR B 406 PHE 0.042 0.004 PHE B 20 TRP 0.029 0.004 TRP D 70 HIS 0.019 0.003 HIS B 61 Details of bonding type rmsd covalent geometry : bond 0.01860 ( 8718) covalent geometry : angle 1.74258 (11816) hydrogen bonds : bond 0.16383 ( 413) hydrogen bonds : angle 7.17996 ( 1224) Misc. bond : bond 0.07559 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 126 time to evaluate : 0.431 Fit side-chains revert: symmetry clash REVERT: A 89 MET cc_start: 0.8323 (OUTLIER) cc_final: 0.6702 (mmt) REVERT: A 368 ASP cc_start: 0.7614 (OUTLIER) cc_final: 0.7407 (t0) REVERT: A 388 LYS cc_start: 0.7788 (mttp) cc_final: 0.6983 (tttp) REVERT: A 473 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.7825 (ttm170) REVERT: B 28 PHE cc_start: 0.8085 (OUTLIER) cc_final: 0.7797 (m-80) REVERT: B 90 ASN cc_start: 0.7735 (OUTLIER) cc_final: 0.6954 (t0) REVERT: B 94 LYS cc_start: 0.8954 (OUTLIER) cc_final: 0.8333 (ttpp) REVERT: B 113 PHE cc_start: 0.8540 (OUTLIER) cc_final: 0.8286 (m-80) REVERT: B 222 ARG cc_start: 0.7878 (OUTLIER) cc_final: 0.7122 (ttm170) REVERT: D 24 PRO cc_start: 0.8738 (OUTLIER) cc_final: 0.8500 (Cg_endo) REVERT: D 30 TYR cc_start: 0.8213 (OUTLIER) cc_final: 0.7677 (t80) REVERT: D 72 LYS cc_start: 0.9003 (mtmm) cc_final: 0.8778 (mttt) REVERT: D 113 TYR cc_start: 0.8295 (t80) cc_final: 0.6948 (t80) REVERT: D 122 TYR cc_start: 0.7570 (OUTLIER) cc_final: 0.7336 (m-80) REVERT: D 128 PHE cc_start: 0.7853 (OUTLIER) cc_final: 0.7547 (t80) REVERT: C 2 ASN cc_start: 0.6587 (OUTLIER) cc_final: 0.6230 (p0) outliers start: 77 outliers final: 39 residues processed: 191 average time/residue: 0.1061 time to fit residues: 27.3326 Evaluate side-chains 157 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 105 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 376 ASN Chi-restraints excluded: chain A residue 431 SER Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 477 GLU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain B residue 28 PHE Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 85 TYR Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 90 ASN Chi-restraints excluded: chain B residue 94 LYS Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 108 TYR Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 113 PHE Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 200 ASN Chi-restraints excluded: chain B residue 222 ARG Chi-restraints excluded: chain B residue 239 TRP Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain D residue 24 PRO Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 30 TYR Chi-restraints excluded: chain D residue 61 PHE Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 122 TYR Chi-restraints excluded: chain D residue 128 PHE Chi-restraints excluded: chain D residue 130 ASN Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain C residue 2 ASN Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 36 MET Chi-restraints excluded: chain C residue 40 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 38 optimal weight: 0.4980 chunk 61 optimal weight: 4.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 365 GLN A 375 GLN B 61 HIS B 195 HIS B 200 ASN B 227 GLN B 279 HIS D 84 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.139090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.114041 restraints weight = 12599.236| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.37 r_work: 0.3213 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 8719 Z= 0.208 Angle : 0.780 9.951 11816 Z= 0.410 Chirality : 0.049 0.186 1339 Planarity : 0.006 0.061 1486 Dihedral : 9.269 58.761 1296 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.46 % Allowed : 8.79 % Favored : 90.75 % Rotamer: Outliers : 4.89 % Allowed : 13.37 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.40 (0.25), residues: 1081 helix: 0.60 (0.22), residues: 558 sheet: -3.00 (0.52), residues: 80 loop : -2.59 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 246 TYR 0.020 0.002 TYR B 85 PHE 0.040 0.002 PHE A 183 TRP 0.023 0.002 TRP B 239 HIS 0.005 0.001 HIS D 124 Details of bonding type rmsd covalent geometry : bond 0.00488 ( 8718) covalent geometry : angle 0.78019 (11816) hydrogen bonds : bond 0.06413 ( 413) hydrogen bonds : angle 5.15382 ( 1224) Misc. bond : bond 0.00030 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 122 time to evaluate : 0.348 Fit side-chains revert: symmetry clash REVERT: A 125 HIS cc_start: 0.8001 (OUTLIER) cc_final: 0.7285 (t-170) REVERT: A 164 SER cc_start: 0.9235 (t) cc_final: 0.8966 (p) REVERT: A 368 ASP cc_start: 0.7348 (OUTLIER) cc_final: 0.7053 (t0) REVERT: A 473 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.8014 (ttp80) REVERT: B 107 SER cc_start: 0.8850 (OUTLIER) cc_final: 0.8488 (p) REVERT: B 113 PHE cc_start: 0.8596 (OUTLIER) cc_final: 0.8391 (m-80) REVERT: B 199 VAL cc_start: 0.8858 (t) cc_final: 0.8579 (p) REVERT: D 30 TYR cc_start: 0.8625 (OUTLIER) cc_final: 0.7540 (t80) outliers start: 45 outliers final: 22 residues processed: 156 average time/residue: 0.0958 time to fit residues: 20.7539 Evaluate side-chains 143 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 115 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 188 CYS Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 376 ASN Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 473 ARG Chi-restraints excluded: chain A residue 477 GLU Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 85 TYR Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 108 TYR Chi-restraints excluded: chain B residue 113 PHE Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain D residue 30 TYR Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain C residue 17 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 75 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 30 optimal weight: 5.9990 chunk 74 optimal weight: 0.0060 chunk 14 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 375 GLN B 195 HIS B 214 HIS D 84 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.145392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.121496 restraints weight = 12478.642| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.26 r_work: 0.3330 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8719 Z= 0.133 Angle : 0.637 7.045 11816 Z= 0.337 Chirality : 0.044 0.196 1339 Planarity : 0.005 0.058 1486 Dihedral : 7.342 59.901 1231 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.29 % Favored : 93.43 % Rotamer: Outliers : 3.48 % Allowed : 16.74 % Favored : 79.78 % 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 aren not related in a simple way. whole: -0.79 (0.26), residues: 1081 helix: 1.24 (0.22), residues: 561 sheet: -2.62 (0.53), residues: 87 loop : -2.53 (0.28), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 54 TYR 0.017 0.001 TYR D 83 PHE 0.031 0.001 PHE A 183 TRP 0.012 0.001 TRP D 126 HIS 0.003 0.001 HIS D 124 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 8718) covalent geometry : angle 0.63655 (11816) hydrogen bonds : bond 0.04749 ( 413) hydrogen bonds : angle 4.67452 ( 1224) Misc. bond : bond 0.00003 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 121 time to evaluate : 0.270 Fit side-chains revert: symmetry clash REVERT: A 125 HIS cc_start: 0.7957 (OUTLIER) cc_final: 0.7309 (t-170) REVERT: A 335 GLN cc_start: 0.8495 (tt0) cc_final: 0.8251 (tt0) REVERT: A 407 LYS cc_start: 0.8626 (mmtp) cc_final: 0.8006 (mttt) REVERT: A 413 LYS cc_start: 0.8239 (mmtm) cc_final: 0.7690 (tmtt) REVERT: B 199 VAL cc_start: 0.8748 (t) cc_final: 0.8430 (p) REVERT: D 30 TYR cc_start: 0.8613 (OUTLIER) cc_final: 0.7593 (t80) REVERT: D 92 MET cc_start: 0.8520 (mmm) cc_final: 0.8299 (tpt) outliers start: 32 outliers final: 20 residues processed: 146 average time/residue: 0.0873 time to fit residues: 17.8649 Evaluate side-chains 135 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 477 GLU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 85 TYR Chi-restraints excluded: chain B residue 90 ASN Chi-restraints excluded: chain B residue 108 TYR Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain D residue 30 TYR Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain C residue 40 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 57 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 84 optimal weight: 8.9990 chunk 36 optimal weight: 8.9990 chunk 30 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 99 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 HIS A 365 GLN A 375 GLN D 84 ASN D 144 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.141639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.116930 restraints weight = 12798.531| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.32 r_work: 0.3248 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 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 : 0.005 0.058 8719 Z= 0.223 Angle : 0.706 8.150 11816 Z= 0.370 Chirality : 0.046 0.169 1339 Planarity : 0.006 0.055 1486 Dihedral : 6.822 59.240 1214 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.14 % Favored : 91.58 % Rotamer: Outliers : 4.35 % Allowed : 17.17 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.26), residues: 1081 helix: 1.22 (0.22), residues: 561 sheet: -2.74 (0.54), residues: 80 loop : -2.35 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 54 TYR 0.016 0.002 TYR B 274 PHE 0.035 0.002 PHE A 183 TRP 0.015 0.001 TRP B 239 HIS 0.005 0.001 HIS B 214 Details of bonding type rmsd covalent geometry : bond 0.00542 ( 8718) covalent geometry : angle 0.70575 (11816) hydrogen bonds : bond 0.05730 ( 413) hydrogen bonds : angle 4.77263 ( 1224) Misc. bond : bond 0.00016 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 118 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 HIS cc_start: 0.7947 (OUTLIER) cc_final: 0.7497 (t-170) REVERT: A 407 LYS cc_start: 0.8565 (mmtp) cc_final: 0.8103 (mttt) REVERT: A 413 LYS cc_start: 0.8224 (mmtm) cc_final: 0.7648 (tmtt) REVERT: B 199 VAL cc_start: 0.8847 (t) cc_final: 0.8577 (p) REVERT: D 30 TYR cc_start: 0.8624 (OUTLIER) cc_final: 0.7438 (t80) REVERT: C 6 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.8362 (mtm180) outliers start: 40 outliers final: 28 residues processed: 149 average time/residue: 0.0801 time to fit residues: 16.6355 Evaluate side-chains 146 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 115 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 477 GLU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 108 TYR Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain D residue 30 TYR Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain C residue 6 ARG Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 40 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 104 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 69 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 49 optimal weight: 9.9990 chunk 90 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 375 GLN D 84 ASN D 94 ASN D 144 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.144189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.120194 restraints weight = 12576.212| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.27 r_work: 0.3313 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8719 Z= 0.134 Angle : 0.607 8.430 11816 Z= 0.319 Chirality : 0.043 0.156 1339 Planarity : 0.005 0.056 1486 Dihedral : 6.390 57.288 1212 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.83 % Favored : 93.89 % Rotamer: Outliers : 3.91 % Allowed : 19.13 % Favored : 76.96 % 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 aren not related in a simple way. whole: -0.41 (0.26), residues: 1081 helix: 1.49 (0.23), residues: 560 sheet: -2.13 (0.49), residues: 105 loop : -2.32 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 54 TYR 0.022 0.001 TYR B 85 PHE 0.028 0.001 PHE A 183 TRP 0.013 0.001 TRP B 239 HIS 0.005 0.001 HIS B 214 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 8718) covalent geometry : angle 0.60738 (11816) hydrogen bonds : bond 0.04487 ( 413) hydrogen bonds : angle 4.51402 ( 1224) Misc. bond : bond 0.00000 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 122 time to evaluate : 0.257 Fit side-chains revert: symmetry clash REVERT: A 125 HIS cc_start: 0.7807 (OUTLIER) cc_final: 0.7389 (t-170) REVERT: A 182 MET cc_start: 0.8233 (mmm) cc_final: 0.7468 (mmt) REVERT: A 388 LYS cc_start: 0.8110 (mttm) cc_final: 0.7205 (tttp) REVERT: A 407 LYS cc_start: 0.8525 (mmtp) cc_final: 0.8081 (mttt) REVERT: A 413 LYS cc_start: 0.8196 (mmtm) cc_final: 0.7637 (tmtt) REVERT: B 199 VAL cc_start: 0.8751 (t) cc_final: 0.8446 (p) REVERT: B 299 THR cc_start: 0.8666 (p) cc_final: 0.8372 (p) REVERT: B 417 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8319 (mm-30) REVERT: B 466 LEU cc_start: 0.8574 (tp) cc_final: 0.8349 (tt) REVERT: D 30 TYR cc_start: 0.8739 (OUTLIER) cc_final: 0.7741 (t80) REVERT: C 6 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.8452 (mtm180) outliers start: 36 outliers final: 25 residues processed: 151 average time/residue: 0.0817 time to fit residues: 17.1552 Evaluate side-chains 143 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 115 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 477 GLU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 85 TYR Chi-restraints excluded: chain B residue 108 TYR Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain D residue 30 TYR Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain C residue 6 ARG Chi-restraints excluded: chain C residue 40 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 55 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 45 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 19 optimal weight: 0.7980 chunk 87 optimal weight: 5.9990 chunk 3 optimal weight: 0.8980 chunk 65 optimal weight: 6.9990 chunk 90 optimal weight: 8.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 375 GLN B 24 GLN D 84 ASN D 144 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.142335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.117539 restraints weight = 12761.918| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.32 r_work: 0.3255 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 8719 Z= 0.219 Angle : 0.688 8.230 11816 Z= 0.359 Chirality : 0.046 0.164 1339 Planarity : 0.005 0.052 1486 Dihedral : 6.554 56.101 1212 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.23 % Favored : 91.49 % Rotamer: Outliers : 4.67 % Allowed : 20.11 % Favored : 75.22 % 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 aren not related in a simple way. whole: -0.47 (0.26), residues: 1081 helix: 1.34 (0.22), residues: 561 sheet: -2.12 (0.53), residues: 93 loop : -2.21 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 54 TYR 0.024 0.002 TYR B 85 PHE 0.033 0.002 PHE A 183 TRP 0.015 0.001 TRP B 239 HIS 0.005 0.001 HIS B 214 Details of bonding type rmsd covalent geometry : bond 0.00528 ( 8718) covalent geometry : angle 0.68824 (11816) hydrogen bonds : bond 0.05442 ( 413) hydrogen bonds : angle 4.66137 ( 1224) Misc. bond : bond 0.00020 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 118 time to evaluate : 0.285 Fit side-chains revert: symmetry clash REVERT: A 125 HIS cc_start: 0.7890 (OUTLIER) cc_final: 0.7527 (t-170) REVERT: A 388 LYS cc_start: 0.8112 (mttm) cc_final: 0.7299 (tttp) REVERT: A 413 LYS cc_start: 0.8183 (mmtm) cc_final: 0.7646 (tmtt) REVERT: B 199 VAL cc_start: 0.8807 (t) cc_final: 0.8523 (p) REVERT: B 299 THR cc_start: 0.8751 (OUTLIER) cc_final: 0.8465 (p) REVERT: D 30 TYR cc_start: 0.8779 (OUTLIER) cc_final: 0.7643 (t80) REVERT: C 6 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.8419 (mtm180) outliers start: 43 outliers final: 29 residues processed: 151 average time/residue: 0.0852 time to fit residues: 17.7654 Evaluate side-chains 147 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 114 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 477 GLU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 85 TYR Chi-restraints excluded: chain B residue 108 TYR Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain D residue 30 TYR Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain C residue 6 ARG Chi-restraints excluded: chain C residue 40 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 34 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 49 optimal weight: 0.2980 chunk 84 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 GLN A 375 GLN D 84 ASN D 144 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.144734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.120482 restraints weight = 12726.908| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 2.30 r_work: 0.3322 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 8719 Z= 0.127 Angle : 0.620 8.874 11816 Z= 0.320 Chirality : 0.043 0.157 1339 Planarity : 0.005 0.055 1486 Dihedral : 6.256 53.819 1212 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.38 % Favored : 93.34 % Rotamer: Outliers : 4.13 % Allowed : 20.54 % Favored : 75.33 % 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 aren not related in a simple way. whole: -0.30 (0.27), residues: 1081 helix: 1.55 (0.23), residues: 557 sheet: -2.05 (0.48), residues: 115 loop : -2.18 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 54 TYR 0.021 0.001 TYR B 85 PHE 0.026 0.001 PHE A 183 TRP 0.013 0.001 TRP B 239 HIS 0.004 0.001 HIS B 214 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 8718) covalent geometry : angle 0.61988 (11816) hydrogen bonds : bond 0.04281 ( 413) hydrogen bonds : angle 4.49813 ( 1224) Misc. bond : bond 0.00000 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 120 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: A 125 HIS cc_start: 0.7819 (OUTLIER) cc_final: 0.7518 (t-170) REVERT: A 388 LYS cc_start: 0.7969 (mttm) cc_final: 0.7158 (tttp) REVERT: A 413 LYS cc_start: 0.8125 (mmtm) cc_final: 0.7642 (tmtt) REVERT: B 29 PHE cc_start: 0.7388 (t80) cc_final: 0.6994 (m-80) REVERT: B 199 VAL cc_start: 0.8712 (t) cc_final: 0.8441 (p) REVERT: B 299 THR cc_start: 0.8549 (p) cc_final: 0.8200 (p) REVERT: C 6 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.8316 (mtm180) outliers start: 38 outliers final: 30 residues processed: 151 average time/residue: 0.0917 time to fit residues: 18.9768 Evaluate side-chains 141 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 109 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 335 GLN Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 477 GLU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 85 TYR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 108 TYR Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain C residue 6 ARG Chi-restraints excluded: chain C residue 40 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 24 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 101 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 375 GLN D 84 ASN D 144 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.142500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.118193 restraints weight = 12547.278| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.28 r_work: 0.3290 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8719 Z= 0.178 Angle : 0.668 12.422 11816 Z= 0.342 Chirality : 0.045 0.157 1339 Planarity : 0.005 0.052 1486 Dihedral : 6.151 52.763 1208 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.77 % Favored : 91.95 % Rotamer: Outliers : 4.67 % Allowed : 20.87 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.26), residues: 1081 helix: 1.44 (0.23), residues: 559 sheet: -1.98 (0.51), residues: 103 loop : -2.17 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 54 TYR 0.022 0.002 TYR D 83 PHE 0.032 0.002 PHE A 183 TRP 0.013 0.001 TRP B 239 HIS 0.004 0.001 HIS B 214 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 8718) covalent geometry : angle 0.66809 (11816) hydrogen bonds : bond 0.04764 ( 413) hydrogen bonds : angle 4.55450 ( 1224) Misc. bond : bond 0.00013 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 112 time to evaluate : 0.291 Fit side-chains revert: symmetry clash REVERT: A 125 HIS cc_start: 0.7829 (OUTLIER) cc_final: 0.7510 (t-170) REVERT: A 182 MET cc_start: 0.8417 (mmp) cc_final: 0.8046 (mmt) REVERT: A 388 LYS cc_start: 0.8121 (mttm) cc_final: 0.7278 (tttp) REVERT: A 413 LYS cc_start: 0.8174 (mmtm) cc_final: 0.7655 (tmtt) REVERT: B 29 PHE cc_start: 0.7529 (t80) cc_final: 0.7141 (m-80) REVERT: B 199 VAL cc_start: 0.8765 (t) cc_final: 0.8466 (p) REVERT: B 299 THR cc_start: 0.8674 (OUTLIER) cc_final: 0.8356 (p) REVERT: B 466 LEU cc_start: 0.8244 (tt) cc_final: 0.7945 (tp) REVERT: D 30 TYR cc_start: 0.8801 (OUTLIER) cc_final: 0.7663 (t80) REVERT: C 6 ARG cc_start: 0.8650 (OUTLIER) cc_final: 0.8376 (mtm180) outliers start: 43 outliers final: 32 residues processed: 145 average time/residue: 0.0849 time to fit residues: 17.0290 Evaluate side-chains 145 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 109 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 477 GLU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 85 TYR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 108 TYR Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 279 HIS Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain D residue 30 TYR Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain C residue 6 ARG Chi-restraints excluded: chain C residue 40 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 14 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 35 optimal weight: 0.9980 chunk 84 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 4 optimal weight: 0.3980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 375 GLN D 84 ASN D 144 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.144492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.120338 restraints weight = 12526.241| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.27 r_work: 0.3320 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8719 Z= 0.137 Angle : 0.639 11.552 11816 Z= 0.327 Chirality : 0.043 0.153 1339 Planarity : 0.005 0.052 1486 Dihedral : 5.995 53.182 1208 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.20 % Favored : 93.62 % Rotamer: Outliers : 4.13 % Allowed : 21.41 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.33 (0.27), residues: 1081 helix: 1.44 (0.22), residues: 566 sheet: -2.00 (0.48), residues: 115 loop : -2.15 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 54 TYR 0.021 0.001 TYR D 83 PHE 0.028 0.001 PHE A 183 TRP 0.013 0.001 TRP B 239 HIS 0.004 0.001 HIS B 214 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 8718) covalent geometry : angle 0.63943 (11816) hydrogen bonds : bond 0.04280 ( 413) hydrogen bonds : angle 4.47970 ( 1224) Misc. bond : bond 0.00003 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 111 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: A 125 HIS cc_start: 0.7784 (OUTLIER) cc_final: 0.7458 (t-170) REVERT: A 182 MET cc_start: 0.8375 (mmp) cc_final: 0.8090 (mmt) REVERT: A 388 LYS cc_start: 0.8048 (mttm) cc_final: 0.7251 (tttp) REVERT: A 413 LYS cc_start: 0.8139 (mmtm) cc_final: 0.7645 (tmtt) REVERT: B 199 VAL cc_start: 0.8732 (t) cc_final: 0.8432 (p) REVERT: B 299 THR cc_start: 0.8643 (p) cc_final: 0.8322 (p) REVERT: B 466 LEU cc_start: 0.8236 (tt) cc_final: 0.7973 (tp) REVERT: D 30 TYR cc_start: 0.8799 (OUTLIER) cc_final: 0.7785 (t80) REVERT: C 6 ARG cc_start: 0.8635 (OUTLIER) cc_final: 0.8361 (mtm180) outliers start: 38 outliers final: 32 residues processed: 138 average time/residue: 0.0942 time to fit residues: 17.9736 Evaluate side-chains 144 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 109 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 477 GLU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 85 TYR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 108 TYR Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 279 HIS Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain D residue 30 TYR Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain C residue 6 ARG Chi-restraints excluded: chain C residue 40 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 81 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 48 optimal weight: 8.9990 chunk 32 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 375 GLN D 84 ASN D 144 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.144746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.120495 restraints weight = 12475.861| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.28 r_work: 0.3322 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8719 Z= 0.136 Angle : 0.630 10.805 11816 Z= 0.322 Chirality : 0.043 0.158 1339 Planarity : 0.005 0.053 1486 Dihedral : 5.897 53.633 1208 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.94 % Favored : 92.88 % Rotamer: Outliers : 4.13 % Allowed : 21.41 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.26), residues: 1081 helix: 1.48 (0.22), residues: 567 sheet: -1.83 (0.49), residues: 103 loop : -2.10 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 54 TYR 0.021 0.001 TYR D 83 PHE 0.028 0.001 PHE A 183 TRP 0.012 0.001 TRP B 239 HIS 0.004 0.001 HIS B 214 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 8718) covalent geometry : angle 0.62997 (11816) hydrogen bonds : bond 0.04257 ( 413) hydrogen bonds : angle 4.46760 ( 1224) Misc. bond : bond 0.00006 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2162 Ramachandran restraints generated. 1081 Oldfield, 0 Emsley, 1081 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 110 time to evaluate : 0.327 Fit side-chains revert: symmetry clash REVERT: A 125 HIS cc_start: 0.7780 (OUTLIER) cc_final: 0.7442 (t-170) REVERT: A 182 MET cc_start: 0.8361 (mmp) cc_final: 0.8077 (mmt) REVERT: A 388 LYS cc_start: 0.8043 (mttm) cc_final: 0.7168 (tttp) REVERT: A 413 LYS cc_start: 0.8149 (mmtm) cc_final: 0.7643 (tmtt) REVERT: B 118 GLU cc_start: 0.8016 (mp0) cc_final: 0.7610 (tp30) REVERT: B 199 VAL cc_start: 0.8717 (t) cc_final: 0.8424 (p) REVERT: B 299 THR cc_start: 0.8651 (OUTLIER) cc_final: 0.8324 (p) REVERT: B 466 LEU cc_start: 0.8255 (tt) cc_final: 0.8022 (tp) REVERT: D 30 TYR cc_start: 0.8747 (OUTLIER) cc_final: 0.7717 (t80) REVERT: C 6 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.8347 (mtm180) outliers start: 38 outliers final: 33 residues processed: 138 average time/residue: 0.0997 time to fit residues: 19.0260 Evaluate side-chains 146 residues out of total 944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 109 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 477 GLU Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 85 TYR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 108 TYR Chi-restraints excluded: chain B residue 235 THR Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 279 HIS Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain D residue 30 TYR Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain C residue 6 ARG Chi-restraints excluded: chain C residue 40 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 98 optimal weight: 4.9990 chunk 86 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 6 optimal weight: 0.4980 chunk 101 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 80 optimal weight: 0.5980 chunk 58 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 84 ASN D 144 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.148191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.123559 restraints weight = 12522.585| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.33 r_work: 0.3339 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8719 Z= 0.122 Angle : 0.617 11.918 11816 Z= 0.314 Chirality : 0.042 0.169 1339 Planarity : 0.005 0.055 1486 Dihedral : 5.771 53.541 1208 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.11 % Favored : 93.71 % Rotamer: Outliers : 4.13 % Allowed : 21.63 % Favored : 74.24 % 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 aren not related in a simple way. whole: -0.09 (0.27), residues: 1081 helix: 1.59 (0.23), residues: 563 sheet: -1.82 (0.47), residues: 116 loop : -1.96 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 54 TYR 0.020 0.001 TYR D 83 PHE 0.027 0.001 PHE A 183 TRP 0.012 0.001 TRP B 239 HIS 0.003 0.001 HIS B 214 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 8718) covalent geometry : angle 0.61688 (11816) hydrogen bonds : bond 0.03960 ( 413) hydrogen bonds : angle 4.41084 ( 1224) Misc. bond : bond 0.00001 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1898.55 seconds wall clock time: 33 minutes 22.91 seconds (2002.91 seconds total)