Starting phenix.real_space_refine on Sat Aug 23 02:12:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p1u_17356/08_2025/8p1u_17356.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p1u_17356/08_2025/8p1u_17356.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8p1u_17356/08_2025/8p1u_17356.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p1u_17356/08_2025/8p1u_17356.map" model { file = "/net/cci-nas-00/data/ceres_data/8p1u_17356/08_2025/8p1u_17356.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p1u_17356/08_2025/8p1u_17356.cif" } resolution = 3.3 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= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 5898 2.51 5 N 1606 2.21 5 O 1603 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 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: 9149 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 751 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 3, 'TRANS': 89} Chain: "A" Number of atoms: 2836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2836 Classifications: {'peptide': 370} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 354} Chain breaks: 1 Chain: "B" Number of atoms: 4058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4058 Classifications: {'peptide': 530} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 498} Chain breaks: 2 Chain: "D" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 707 Classifications: {'peptide': 87} Link IDs: {'TRANS': 86} Chain: "E" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 797 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 94} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.32, per 1000 atoms: 0.25 Number of scatterers: 9149 At special positions: 0 Unit cell: (112.53, 90.21, 164.61, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 42 16.00 O 1603 8.00 N 1606 7.00 C 5898 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=0, symmetry=0 Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 380.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2140 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 9 sheets defined 56.6% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'C' and resid 12 through 69 removed outlier: 3.975A pdb=" N THR C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N TRP C 68 " --> pdb=" O GLU C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 81 Processing helix chain 'A' and resid 21 through 51 removed outlier: 5.127A pdb=" N GLU A 45 " --> pdb=" O SER A 41 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VAL A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN A 50 " --> pdb=" O VAL A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 78 Processing helix chain 'A' and resid 79 through 103 removed outlier: 3.656A pdb=" N TRP A 83 " --> pdb=" O PRO A 79 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N TRP A 88 " --> pdb=" O GLN A 84 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N LYS A 89 " --> pdb=" O ARG A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 146 removed outlier: 4.180A pdb=" N ILE A 129 " --> pdb=" O GLN A 125 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS A 131 " --> pdb=" O SER A 127 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN A 146 " --> pdb=" O LEU A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 157 removed outlier: 3.874A pdb=" N PHE A 157 " --> pdb=" O TRP A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 161 Processing helix chain 'A' and resid 162 through 173 removed outlier: 3.803A pdb=" N GLU A 173 " --> pdb=" O LEU A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 193 Processing helix chain 'A' and resid 196 through 215 Processing helix chain 'A' and resid 238 through 253 removed outlier: 4.464A pdb=" N LEU A 242 " --> pdb=" O ALA A 238 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE A 247 " --> pdb=" O SER A 243 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA A 248 " --> pdb=" O GLN A 244 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE A 249 " --> pdb=" O ALA A 245 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY A 250 " --> pdb=" O LEU A 246 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLY A 253 " --> pdb=" O PHE A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 268 removed outlier: 3.792A pdb=" N PHE A 267 " --> pdb=" O ILE A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 285 Processing helix chain 'A' and resid 285 through 314 removed outlier: 3.644A pdb=" N GLY A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 342 Processing helix chain 'A' and resid 358 through 379 Processing helix chain 'B' and resid 11 through 38 removed outlier: 4.098A pdb=" N LEU B 36 " --> pdb=" O ARG B 32 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 90 Processing helix chain 'B' and resid 91 through 94 removed outlier: 5.842A pdb=" N GLU B 94 " --> pdb=" O THR B 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 91 through 94' Processing helix chain 'B' and resid 95 through 104 removed outlier: 3.638A pdb=" N ALA B 102 " --> pdb=" O GLN B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 117 Processing helix chain 'B' and resid 130 through 141 removed outlier: 4.432A pdb=" N GLY B 136 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 182 Processing helix chain 'B' and resid 182 through 187 Processing helix chain 'B' and resid 224 through 243 Processing helix chain 'B' and resid 277 through 282 Processing helix chain 'B' and resid 292 through 295 Processing helix chain 'B' and resid 296 through 309 removed outlier: 3.861A pdb=" N ARG B 309 " --> pdb=" O LEU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 348 Processing helix chain 'B' and resid 351 through 361 Processing helix chain 'B' and resid 362 through 373 removed outlier: 3.531A pdb=" N VAL B 373 " --> pdb=" O VAL B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 406 Processing helix chain 'B' and resid 415 through 427 Processing helix chain 'B' and resid 450 through 467 removed outlier: 3.662A pdb=" N VAL B 465 " --> pdb=" O LEU B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 538 Processing helix chain 'B' and resid 538 through 553 removed outlier: 3.798A pdb=" N GLY B 548 " --> pdb=" O LYS B 544 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 26 Processing helix chain 'D' and resid 30 through 66 removed outlier: 3.552A pdb=" N ARG D 56 " --> pdb=" O LEU D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 79 Processing helix chain 'E' and resid 184 through 200 removed outlier: 3.528A pdb=" N MET E 189 " --> pdb=" O GLN E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 203 No H-bonds generated for 'chain 'E' and resid 201 through 203' Processing helix chain 'E' and resid 233 through 248 removed outlier: 3.729A pdb=" N ARG E 239 " --> pdb=" O VAL E 235 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 93 through 94 removed outlier: 6.213A pdb=" N GLU E 226 " --> pdb=" O ILE E 259 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ARG E 177 " --> pdb=" O LEU E 209 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N MET E 211 " --> pdb=" O ARG E 177 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 53 through 58 removed outlier: 3.526A pdb=" N ARG B 54 " --> pdb=" O VAL B 195 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N LYS B 192 " --> pdb=" O GLN B 208 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N GLN B 208 " --> pdb=" O LYS B 192 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N GLN B 194 " --> pdb=" O ASP B 206 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N ASP B 206 " --> pdb=" O GLN B 194 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU B 196 " --> pdb=" O ILE B 204 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 123 through 124 Processing sheet with id=AA4, first strand: chain 'B' and resid 123 through 124 removed outlier: 6.353A pdb=" N ILE B 65 " --> pdb=" O LEU B 73 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 259 through 263 removed outlier: 6.154A pdb=" N ILE B 251 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N MET B 262 " --> pdb=" O LEU B 249 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU B 249 " --> pdb=" O MET B 262 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 289 through 290 Processing sheet with id=AA7, first strand: chain 'B' and resid 315 through 316 Processing sheet with id=AA8, first strand: chain 'B' and resid 322 through 325 Processing sheet with id=AA9, first strand: chain 'B' and resid 430 through 431 533 hydrogen bonds defined for protein. 1554 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: 1.65 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1698 1.33 - 1.45: 2236 1.45 - 1.57: 5329 1.57 - 1.69: 0 1.69 - 1.81: 77 Bond restraints: 9340 Sorted by residual: bond pdb=" CA MET A 189 " pdb=" C MET A 189 " ideal model delta sigma weight residual 1.523 1.484 0.039 1.30e-02 5.92e+03 9.22e+00 bond pdb=" CA LEU A 190 " pdb=" C LEU A 190 " ideal model delta sigma weight residual 1.524 1.488 0.035 1.29e-02 6.01e+03 7.50e+00 bond pdb=" CA ASP D 36 " pdb=" C ASP D 36 " ideal model delta sigma weight residual 1.524 1.493 0.032 1.24e-02 6.50e+03 6.47e+00 bond pdb=" C LEU A 190 " pdb=" O LEU A 190 " ideal model delta sigma weight residual 1.237 1.207 0.030 1.19e-02 7.06e+03 6.25e+00 bond pdb=" N ASP D 36 " pdb=" CA ASP D 36 " ideal model delta sigma weight residual 1.459 1.434 0.025 1.17e-02 7.31e+03 4.55e+00 ... (remaining 9335 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 12439 1.76 - 3.51: 185 3.51 - 5.27: 25 5.27 - 7.02: 11 7.02 - 8.78: 2 Bond angle restraints: 12662 Sorted by residual: angle pdb=" C GLN B 277 " pdb=" N PRO B 278 " pdb=" CA PRO B 278 " ideal model delta sigma weight residual 119.84 114.61 5.23 1.25e+00 6.40e-01 1.75e+01 angle pdb=" CA GLN E 252 " pdb=" CB GLN E 252 " pdb=" CG GLN E 252 " ideal model delta sigma weight residual 114.10 120.52 -6.42 2.00e+00 2.50e-01 1.03e+01 angle pdb=" C MET A 189 " pdb=" CA MET A 189 " pdb=" CB MET A 189 " ideal model delta sigma weight residual 110.79 105.46 5.33 1.66e+00 3.63e-01 1.03e+01 angle pdb=" N ILE B 287 " pdb=" CA ILE B 287 " pdb=" C ILE B 287 " ideal model delta sigma weight residual 112.96 109.76 3.20 1.00e+00 1.00e+00 1.02e+01 angle pdb=" CA LYS D 67 " pdb=" CB LYS D 67 " pdb=" CG LYS D 67 " ideal model delta sigma weight residual 114.10 120.06 -5.96 2.00e+00 2.50e-01 8.89e+00 ... (remaining 12657 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 4890 17.56 - 35.13: 518 35.13 - 52.69: 116 52.69 - 70.26: 18 70.26 - 87.82: 12 Dihedral angle restraints: 5554 sinusoidal: 2207 harmonic: 3347 Sorted by residual: dihedral pdb=" CA PHE A 267 " pdb=" C PHE A 267 " pdb=" N TYR A 268 " pdb=" CA TYR A 268 " ideal model delta harmonic sigma weight residual 180.00 -160.10 -19.90 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA ARG A 172 " pdb=" C ARG A 172 " pdb=" N GLU A 173 " pdb=" CA GLU A 173 " ideal model delta harmonic sigma weight residual 180.00 162.27 17.73 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA MET E 211 " pdb=" C MET E 211 " pdb=" N SER E 212 " pdb=" CA SER E 212 " ideal model delta harmonic sigma weight residual 180.00 163.21 16.79 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 5551 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 858 0.028 - 0.056: 347 0.056 - 0.083: 137 0.083 - 0.111: 69 0.111 - 0.139: 27 Chirality restraints: 1438 Sorted by residual: chirality pdb=" CG LEU D 65 " pdb=" CB LEU D 65 " pdb=" CD1 LEU D 65 " pdb=" CD2 LEU D 65 " both_signs ideal model delta sigma weight residual False -2.59 -2.73 0.14 2.00e-01 2.50e+01 4.84e-01 chirality pdb=" CA ILE A 117 " pdb=" N ILE A 117 " pdb=" C ILE A 117 " pdb=" CB ILE A 117 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.44e-01 chirality pdb=" CA ARG E 200 " pdb=" N ARG E 200 " pdb=" C ARG E 200 " pdb=" CB ARG E 200 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.42e-01 ... (remaining 1435 not shown) Planarity restraints: 1613 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN B 265 " -0.034 5.00e-02 4.00e+02 5.14e-02 4.23e+00 pdb=" N PRO B 266 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 266 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 266 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 345 " 0.032 5.00e-02 4.00e+02 4.83e-02 3.73e+00 pdb=" N PRO A 346 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 346 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 346 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 173 " -0.031 5.00e-02 4.00e+02 4.69e-02 3.52e+00 pdb=" N PRO A 174 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 174 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 174 " -0.026 5.00e-02 4.00e+02 ... (remaining 1610 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2229 2.79 - 3.32: 9057 3.32 - 3.85: 15536 3.85 - 4.37: 17354 4.37 - 4.90: 30819 Nonbonded interactions: 74995 Sorted by model distance: nonbonded pdb=" OG SER B 505 " pdb=" OG SER B 538 " model vdw 2.269 3.040 nonbonded pdb=" O THR B 295 " pdb=" OH TYR B 422 " model vdw 2.279 3.040 nonbonded pdb=" O GLY A 239 " pdb=" OG SER A 243 " model vdw 2.286 3.040 nonbonded pdb=" OD2 ASP B 253 " pdb=" OG1 THR B 256 " model vdw 2.301 3.040 nonbonded pdb=" OG SER C 26 " pdb=" OE1 GLN D 21 " model vdw 2.313 3.040 ... (remaining 74990 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: 1.730 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: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.190 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 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 : 0.003 0.039 9340 Z= 0.151 Angle : 0.558 8.778 12662 Z= 0.293 Chirality : 0.041 0.139 1438 Planarity : 0.004 0.051 1613 Dihedral : 15.309 87.823 3414 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.21 % Allowed : 19.54 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % 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: 0.73 (0.25), residues: 1163 helix: 1.64 (0.22), residues: 617 sheet: -0.02 (0.56), residues: 93 loop : -1.03 (0.27), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 108 TYR 0.007 0.001 TYR A 56 PHE 0.018 0.001 PHE B 542 TRP 0.014 0.001 TRP A 116 HIS 0.006 0.001 HIS B 480 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 9340) covalent geometry : angle 0.55789 (12662) hydrogen bonds : bond 0.13103 ( 531) hydrogen bonds : angle 6.26383 ( 1554) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 115 time to evaluate : 0.363 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4810 (mpp) cc_final: 0.3674 (mtm) REVERT: D 36 ASP cc_start: 0.7572 (OUTLIER) cc_final: 0.7288 (m-30) REVERT: E 202 LEU cc_start: 0.6327 (mp) cc_final: 0.5526 (tt) outliers start: 2 outliers final: 1 residues processed: 115 average time/residue: 0.1097 time to fit residues: 17.5156 Evaluate side-chains 99 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 97 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 PHE Chi-restraints excluded: chain D residue 36 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 10.0000 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 0.0970 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 ASN D 21 GLN E 193 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.218937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 100)---------------| | r_work = 0.3587 r_free = 0.3587 target = 0.141932 restraints weight = 8996.146| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.43 r_work: 0.3353 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 moved from start: 0.0989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9340 Z= 0.136 Angle : 0.541 10.008 12662 Z= 0.276 Chirality : 0.042 0.176 1438 Planarity : 0.004 0.052 1613 Dihedral : 4.127 30.907 1292 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.10 % Allowed : 20.06 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % 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 (0.25), residues: 1163 helix: 1.63 (0.21), residues: 621 sheet: -0.38 (0.53), residues: 92 loop : -0.98 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 77 TYR 0.013 0.001 TYR B 409 PHE 0.016 0.001 PHE A 334 TRP 0.018 0.001 TRP B 83 HIS 0.004 0.001 HIS B 480 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 9340) covalent geometry : angle 0.54074 (12662) hydrogen bonds : bond 0.03786 ( 531) hydrogen bonds : angle 4.82200 ( 1554) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 102 time to evaluate : 0.366 Fit side-chains REVERT: A 1 MET cc_start: 0.4917 (mpp) cc_final: 0.3682 (mtm) REVERT: D 64 GLU cc_start: 0.7253 (OUTLIER) cc_final: 0.6654 (tm-30) REVERT: D 79 GLU cc_start: 0.7272 (mm-30) cc_final: 0.7054 (mm-30) outliers start: 20 outliers final: 7 residues processed: 116 average time/residue: 0.1065 time to fit residues: 17.2476 Evaluate side-chains 99 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 91 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 265 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 67 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 77 optimal weight: 5.9990 chunk 83 optimal weight: 8.9990 chunk 62 optimal weight: 1.9990 chunk 54 optimal weight: 9.9990 chunk 114 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 377 GLN D 44 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.214400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 102)---------------| | r_work = 0.3537 r_free = 0.3537 target = 0.137601 restraints weight = 8952.325| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.32 r_work: 0.3258 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 9340 Z= 0.237 Angle : 0.600 8.648 12662 Z= 0.305 Chirality : 0.044 0.178 1438 Planarity : 0.005 0.053 1613 Dihedral : 4.238 19.822 1288 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.57 % Allowed : 19.54 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % 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 (0.24), residues: 1163 helix: 1.29 (0.21), residues: 615 sheet: -0.53 (0.51), residues: 92 loop : -1.09 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 172 TYR 0.017 0.001 TYR A 306 PHE 0.025 0.002 PHE A 334 TRP 0.021 0.001 TRP B 83 HIS 0.004 0.001 HIS B 420 Details of bonding type rmsd covalent geometry : bond 0.00577 ( 9340) covalent geometry : angle 0.60022 (12662) hydrogen bonds : bond 0.04109 ( 531) hydrogen bonds : angle 4.88539 ( 1554) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 96 time to evaluate : 0.360 Fit side-chains REVERT: A 1 MET cc_start: 0.5104 (mpp) cc_final: 0.3897 (mtt) REVERT: A 190 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7594 (mp) REVERT: B 64 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8027 (tp) REVERT: B 129 LEU cc_start: 0.7511 (mm) cc_final: 0.7186 (mm) REVERT: B 447 GLN cc_start: 0.7875 (tp40) cc_final: 0.7338 (mm-40) REVERT: D 35 ARG cc_start: 0.6892 (ttp-170) cc_final: 0.6558 (ttp80) REVERT: D 49 GLU cc_start: 0.7338 (mt-10) cc_final: 0.6750 (mp0) REVERT: D 64 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.6695 (tm-30) outliers start: 34 outliers final: 20 residues processed: 123 average time/residue: 0.0932 time to fit residues: 16.4173 Evaluate side-chains 117 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 38 MET Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 383 PHE Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 503 TYR Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain E residue 209 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 106 optimal weight: 0.2980 chunk 65 optimal weight: 0.4980 chunk 76 optimal weight: 10.0000 chunk 17 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 112 optimal weight: 7.9990 chunk 29 optimal weight: 0.7980 chunk 81 optimal weight: 5.9990 chunk 54 optimal weight: 8.9990 chunk 38 optimal weight: 0.5980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 265 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.216094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.148330 restraints weight = 9049.935| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 1.98 r_work: 0.3373 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9340 Z= 0.135 Angle : 0.525 8.672 12662 Z= 0.264 Chirality : 0.041 0.146 1438 Planarity : 0.004 0.053 1613 Dihedral : 4.059 20.143 1288 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.94 % Allowed : 20.27 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % 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: 0.58 (0.25), residues: 1163 helix: 1.56 (0.21), residues: 616 sheet: -0.54 (0.50), residues: 92 loop : -1.05 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 251 TYR 0.009 0.001 TYR A 64 PHE 0.014 0.001 PHE A 334 TRP 0.020 0.001 TRP B 83 HIS 0.003 0.001 HIS B 480 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 9340) covalent geometry : angle 0.52531 (12662) hydrogen bonds : bond 0.03632 ( 531) hydrogen bonds : angle 4.62957 ( 1554) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 101 time to evaluate : 0.351 Fit side-chains REVERT: A 1 MET cc_start: 0.5048 (mpp) cc_final: 0.3886 (mtt) REVERT: A 190 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7589 (mp) REVERT: B 64 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8154 (tp) REVERT: B 354 ILE cc_start: 0.7028 (tp) cc_final: 0.6791 (tp) REVERT: B 447 GLN cc_start: 0.7874 (tp40) cc_final: 0.7369 (mm-40) REVERT: B 546 MET cc_start: 0.7374 (tpp) cc_final: 0.6992 (tpp) REVERT: D 35 ARG cc_start: 0.7059 (ttp-170) cc_final: 0.6710 (ttp80) REVERT: D 49 GLU cc_start: 0.7263 (mt-10) cc_final: 0.6698 (mp0) REVERT: D 64 GLU cc_start: 0.7292 (OUTLIER) cc_final: 0.6797 (tm-30) REVERT: E 202 LEU cc_start: 0.7513 (mp) cc_final: 0.6162 (tt) outliers start: 28 outliers final: 16 residues processed: 120 average time/residue: 0.0964 time to fit residues: 16.5804 Evaluate side-chains 113 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 251 ARG Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 503 TYR Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain E residue 265 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 47 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 76 optimal weight: 8.9990 chunk 1 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 265 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.214799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.142421 restraints weight = 8977.163| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.12 r_work: 0.3310 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9340 Z= 0.184 Angle : 0.557 8.131 12662 Z= 0.282 Chirality : 0.042 0.147 1438 Planarity : 0.004 0.052 1613 Dihedral : 4.129 19.892 1288 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.89 % Allowed : 19.85 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % 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: 0.49 (0.25), residues: 1163 helix: 1.46 (0.21), residues: 616 sheet: -0.49 (0.50), residues: 92 loop : -1.07 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 14 TYR 0.015 0.001 TYR B 479 PHE 0.020 0.001 PHE A 334 TRP 0.021 0.001 TRP B 83 HIS 0.003 0.001 HIS B 61 Details of bonding type rmsd covalent geometry : bond 0.00446 ( 9340) covalent geometry : angle 0.55745 (12662) hydrogen bonds : bond 0.03776 ( 531) hydrogen bonds : angle 4.64320 ( 1554) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 93 time to evaluate : 0.413 Fit side-chains REVERT: A 1 MET cc_start: 0.5094 (mpp) cc_final: 0.3930 (mtt) REVERT: A 173 GLU cc_start: 0.5751 (OUTLIER) cc_final: 0.5143 (pm20) REVERT: A 190 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7519 (mp) REVERT: A 371 MET cc_start: 0.8450 (mtp) cc_final: 0.8245 (mtp) REVERT: B 64 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8087 (tp) REVERT: B 447 GLN cc_start: 0.7869 (tp40) cc_final: 0.7416 (mm-40) REVERT: B 546 MET cc_start: 0.7420 (tpp) cc_final: 0.6938 (tpp) REVERT: D 35 ARG cc_start: 0.6984 (ttp-170) cc_final: 0.6668 (ttp80) REVERT: D 49 GLU cc_start: 0.7300 (mt-10) cc_final: 0.6695 (mp0) REVERT: D 64 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.6706 (tm-30) REVERT: E 202 LEU cc_start: 0.7644 (mp) cc_final: 0.6381 (tt) outliers start: 37 outliers final: 26 residues processed: 122 average time/residue: 0.0962 time to fit residues: 16.9314 Evaluate side-chains 130 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 100 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 38 MET Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 251 ARG Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 383 PHE Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 503 TYR Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 234 VAL Chi-restraints excluded: chain E residue 265 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 64 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 11 optimal weight: 0.1980 chunk 40 optimal weight: 0.4980 chunk 104 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 86 optimal weight: 0.1980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 265 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.218874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 99)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.144022 restraints weight = 8988.439| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.47 r_work: 0.3342 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6970 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9340 Z= 0.124 Angle : 0.515 7.887 12662 Z= 0.260 Chirality : 0.041 0.146 1438 Planarity : 0.004 0.051 1613 Dihedral : 4.011 19.904 1288 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.78 % Allowed : 20.17 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % 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: 0.74 (0.25), residues: 1163 helix: 1.68 (0.21), residues: 615 sheet: -0.42 (0.50), residues: 92 loop : -0.97 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 251 TYR 0.011 0.001 TYR B 479 PHE 0.014 0.001 PHE A 334 TRP 0.020 0.001 TRP B 83 HIS 0.002 0.001 HIS B 480 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 9340) covalent geometry : angle 0.51463 (12662) hydrogen bonds : bond 0.03516 ( 531) hydrogen bonds : angle 4.49175 ( 1554) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 102 time to evaluate : 0.359 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5107 (mpp) cc_final: 0.3924 (mtt) REVERT: A 190 LEU cc_start: 0.7499 (OUTLIER) cc_final: 0.7271 (mp) REVERT: B 546 MET cc_start: 0.7364 (tpp) cc_final: 0.6805 (tpp) REVERT: D 35 ARG cc_start: 0.6971 (ttp-170) cc_final: 0.6659 (ttp80) REVERT: D 49 GLU cc_start: 0.7330 (mt-10) cc_final: 0.6721 (mp0) REVERT: D 64 GLU cc_start: 0.7264 (OUTLIER) cc_final: 0.6620 (tm-30) outliers start: 36 outliers final: 27 residues processed: 125 average time/residue: 0.0925 time to fit residues: 16.7346 Evaluate side-chains 127 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 98 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 16 HIS Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 251 ARG Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 383 PHE Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 503 TYR Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 265 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 106 optimal weight: 6.9990 chunk 53 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 76 optimal weight: 0.1980 chunk 29 optimal weight: 4.9990 chunk 12 optimal weight: 0.4980 chunk 98 optimal weight: 0.7980 chunk 101 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 265 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.217771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.153248 restraints weight = 8986.274| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 1.95 r_work: 0.3385 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9340 Z= 0.133 Angle : 0.531 10.583 12662 Z= 0.264 Chirality : 0.041 0.147 1438 Planarity : 0.004 0.051 1613 Dihedral : 3.982 19.888 1288 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.89 % Allowed : 20.90 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % 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: 0.80 (0.25), residues: 1163 helix: 1.72 (0.21), residues: 617 sheet: -0.36 (0.50), residues: 92 loop : -0.96 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 14 TYR 0.010 0.001 TYR B 479 PHE 0.017 0.001 PHE A 267 TRP 0.020 0.001 TRP B 83 HIS 0.002 0.001 HIS B 480 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 9340) covalent geometry : angle 0.53088 (12662) hydrogen bonds : bond 0.03501 ( 531) hydrogen bonds : angle 4.47296 ( 1554) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 94 time to evaluate : 0.345 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5024 (mpp) cc_final: 0.3903 (mtt) REVERT: A 173 GLU cc_start: 0.5874 (OUTLIER) cc_final: 0.5001 (pm20) REVERT: A 190 LEU cc_start: 0.7658 (OUTLIER) cc_final: 0.7429 (mp) REVERT: B 546 MET cc_start: 0.7500 (tpp) cc_final: 0.6967 (tpp) REVERT: D 35 ARG cc_start: 0.7009 (ttp-170) cc_final: 0.6700 (ttp80) REVERT: D 49 GLU cc_start: 0.7309 (mt-10) cc_final: 0.6741 (mp0) REVERT: D 64 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.6712 (tm-30) outliers start: 37 outliers final: 27 residues processed: 120 average time/residue: 0.0996 time to fit residues: 17.1457 Evaluate side-chains 121 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 91 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 16 HIS Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 251 ARG Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 383 PHE Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 503 TYR Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain E residue 200 ARG Chi-restraints excluded: chain E residue 234 VAL Chi-restraints excluded: chain E residue 265 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 0 optimal weight: 4.9990 chunk 102 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 113 optimal weight: 0.0870 chunk 89 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 105 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 265 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.219606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 101)---------------| | r_work = 0.3628 r_free = 0.3628 target = 0.146092 restraints weight = 8979.965| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 2.29 r_work: 0.3370 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9340 Z= 0.121 Angle : 0.519 10.400 12662 Z= 0.258 Chirality : 0.041 0.154 1438 Planarity : 0.004 0.051 1613 Dihedral : 3.940 19.837 1288 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 4.20 % Allowed : 20.48 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % 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: 0.88 (0.25), residues: 1163 helix: 1.81 (0.21), residues: 617 sheet: -0.32 (0.51), residues: 92 loop : -0.95 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 251 TYR 0.009 0.001 TYR B 479 PHE 0.015 0.001 PHE A 267 TRP 0.019 0.001 TRP B 83 HIS 0.002 0.001 HIS B 480 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 9340) covalent geometry : angle 0.51860 (12662) hydrogen bonds : bond 0.03427 ( 531) hydrogen bonds : angle 4.41086 ( 1554) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 96 time to evaluate : 0.348 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5039 (mpp) cc_final: 0.3867 (mtt) REVERT: A 151 GLU cc_start: 0.4902 (OUTLIER) cc_final: 0.4047 (pm20) REVERT: A 173 GLU cc_start: 0.5760 (OUTLIER) cc_final: 0.4923 (pm20) REVERT: A 190 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.7218 (mp) REVERT: B 546 MET cc_start: 0.7371 (tpp) cc_final: 0.6855 (tpp) REVERT: D 35 ARG cc_start: 0.6983 (ttp-170) cc_final: 0.6668 (ttp80) REVERT: D 49 GLU cc_start: 0.7310 (mt-10) cc_final: 0.6702 (mp0) outliers start: 40 outliers final: 29 residues processed: 125 average time/residue: 0.0925 time to fit residues: 16.6774 Evaluate side-chains 127 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 95 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 16 HIS Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 251 ARG Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 383 PHE Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 503 TYR Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain E residue 200 ARG Chi-restraints excluded: chain E residue 234 VAL Chi-restraints excluded: chain E residue 265 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 1 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 90 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 83 optimal weight: 9.9990 chunk 60 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 61 optimal weight: 0.6980 chunk 73 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 265 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.218249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.142238 restraints weight = 8938.915| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.32 r_work: 0.3347 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9340 Z= 0.139 Angle : 0.530 10.305 12662 Z= 0.263 Chirality : 0.041 0.147 1438 Planarity : 0.004 0.051 1613 Dihedral : 3.951 19.849 1288 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.78 % Allowed : 20.90 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % 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: 0.84 (0.25), residues: 1163 helix: 1.76 (0.21), residues: 617 sheet: -0.29 (0.51), residues: 92 loop : -0.95 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 14 TYR 0.009 0.001 TYR B 479 PHE 0.016 0.001 PHE A 334 TRP 0.019 0.001 TRP B 83 HIS 0.002 0.001 HIS B 480 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 9340) covalent geometry : angle 0.53022 (12662) hydrogen bonds : bond 0.03466 ( 531) hydrogen bonds : angle 4.41735 ( 1554) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 101 time to evaluate : 0.349 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5051 (mpp) cc_final: 0.3879 (mtt) REVERT: A 151 GLU cc_start: 0.4941 (OUTLIER) cc_final: 0.4029 (pm20) REVERT: A 173 GLU cc_start: 0.5653 (OUTLIER) cc_final: 0.4765 (pm20) REVERT: A 190 LEU cc_start: 0.7387 (OUTLIER) cc_final: 0.7161 (mp) REVERT: B 64 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8091 (tp) REVERT: B 546 MET cc_start: 0.7319 (tpp) cc_final: 0.6767 (tpp) REVERT: D 35 ARG cc_start: 0.6972 (ttp-170) cc_final: 0.6647 (ttp80) REVERT: D 49 GLU cc_start: 0.7315 (mt-10) cc_final: 0.6699 (mp0) outliers start: 36 outliers final: 31 residues processed: 126 average time/residue: 0.0896 time to fit residues: 16.3574 Evaluate side-chains 134 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 99 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 16 HIS Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 251 ARG Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 288 ASP Chi-restraints excluded: chain B residue 383 PHE Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 503 TYR Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain E residue 200 ARG Chi-restraints excluded: chain E residue 234 VAL Chi-restraints excluded: chain E residue 265 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 4 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 113 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 49 optimal weight: 8.9990 chunk 93 optimal weight: 0.9990 chunk 31 optimal weight: 0.2980 chunk 30 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 554 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.217110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.167965 restraints weight = 8972.729| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 1.79 r_work: 0.3394 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9340 Z= 0.137 Angle : 0.537 11.088 12662 Z= 0.265 Chirality : 0.041 0.146 1438 Planarity : 0.004 0.051 1613 Dihedral : 3.968 19.888 1288 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.78 % Allowed : 21.01 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % 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: 0.83 (0.25), residues: 1163 helix: 1.75 (0.21), residues: 618 sheet: -0.28 (0.52), residues: 92 loop : -0.96 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 14 TYR 0.009 0.001 TYR B 479 PHE 0.015 0.001 PHE A 267 TRP 0.019 0.001 TRP B 83 HIS 0.002 0.001 HIS B 480 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 9340) covalent geometry : angle 0.53749 (12662) hydrogen bonds : bond 0.03471 ( 531) hydrogen bonds : angle 4.41491 ( 1554) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2326 Ramachandran restraints generated. 1163 Oldfield, 0 Emsley, 1163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 100 time to evaluate : 0.349 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5005 (mpp) cc_final: 0.3891 (mtt) REVERT: A 151 GLU cc_start: 0.5002 (OUTLIER) cc_final: 0.4139 (pm20) REVERT: A 173 GLU cc_start: 0.6045 (OUTLIER) cc_final: 0.5081 (pm20) REVERT: A 190 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7679 (mp) REVERT: B 64 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8223 (tp) REVERT: B 546 MET cc_start: 0.7604 (tpp) cc_final: 0.7135 (tpp) REVERT: D 35 ARG cc_start: 0.7081 (ttp-170) cc_final: 0.6786 (ttp80) REVERT: D 49 GLU cc_start: 0.7343 (mt-10) cc_final: 0.6874 (mp0) outliers start: 36 outliers final: 29 residues processed: 125 average time/residue: 0.0936 time to fit residues: 16.8765 Evaluate side-chains 134 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 101 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 16 HIS Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 182 MET Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 222 MET Chi-restraints excluded: chain A residue 251 ARG Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain B residue 16 CYS Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 383 PHE Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 503 TYR Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain E residue 200 ARG Chi-restraints excluded: chain E residue 234 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 75 optimal weight: 9.9990 chunk 106 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 chunk 78 optimal weight: 10.0000 chunk 38 optimal weight: 0.0770 chunk 89 optimal weight: 0.7980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 265 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.218176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.165447 restraints weight = 8914.832| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 1.68 r_work: 0.3411 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9340 Z= 0.138 Angle : 0.534 11.238 12662 Z= 0.264 Chirality : 0.041 0.145 1438 Planarity : 0.004 0.051 1613 Dihedral : 3.954 19.902 1288 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.78 % Allowed : 20.90 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % 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: 0.84 (0.25), residues: 1163 helix: 1.74 (0.21), residues: 618 sheet: -0.25 (0.52), residues: 92 loop : -0.94 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 14 TYR 0.009 0.001 TYR B 479 PHE 0.016 0.001 PHE A 334 TRP 0.019 0.001 TRP B 83 HIS 0.003 0.001 HIS B 480 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 9340) covalent geometry : angle 0.53384 (12662) hydrogen bonds : bond 0.03473 ( 531) hydrogen bonds : angle 4.40631 ( 1554) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3267.11 seconds wall clock time: 56 minutes 31.94 seconds (3391.94 seconds total)