Starting phenix.real_space_refine on Mon May 12 15:39:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p1u_17356/05_2025/8p1u_17356.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p1u_17356/05_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_17356/05_2025/8p1u_17356.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p1u_17356/05_2025/8p1u_17356.map" model { file = "/net/cci-nas-00/data/ceres_data/8p1u_17356/05_2025/8p1u_17356.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p1u_17356/05_2025/8p1u_17356.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.032 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 6.20, per 1000 atoms: 0.68 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: 2.58 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.88 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: 2.81 Time building geometry restraints manager: 2.99 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: 1.350 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: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.250 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.440 ------------------------------------------------------------------------------- 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 : 10.25 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (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 TRP 0.014 0.001 TRP A 116 HIS 0.006 0.001 HIS B 480 PHE 0.018 0.001 PHE B 542 TYR 0.007 0.001 TYR A 56 ARG 0.005 0.000 ARG A 108 Details of bonding type rmsd hydrogen bonds : bond 0.13103 ( 531) hydrogen bonds : angle 6.26383 ( 1554) covalent geometry : bond 0.00296 ( 9340) covalent geometry : angle 0.55789 (12662) *********************** 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 : 0.925 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: 0.2198 time to fit residues: 35.1401 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 : 1.028 ------------------------------------------------------------------------------- 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 97 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 chunk 67 optimal weight: 0.5980 chunk 105 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 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 = 0.4326 r_free = 0.4326 target = 0.219475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 106)---------------| | r_work = 0.3610 r_free = 0.3610 target = 0.144495 restraints weight = 8913.716| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.36 r_work: 0.3342 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 moved from start: 0.1001 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= 0.149 Angle : 0.546 9.822 12662 Z= 0.279 Chirality : 0.042 0.184 1438 Planarity : 0.004 0.052 1613 Dihedral : 4.151 30.776 1292 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.42 % Allowed : 19.85 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.25), residues: 1163 helix: 1.58 (0.21), residues: 621 sheet: -0.36 (0.53), residues: 92 loop : -0.99 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 83 HIS 0.004 0.001 HIS B 480 PHE 0.018 0.001 PHE A 334 TYR 0.013 0.001 TYR B 409 ARG 0.003 0.000 ARG D 77 Details of bonding type rmsd hydrogen bonds : bond 0.03927 ( 531) hydrogen bonds : angle 4.86127 ( 1554) covalent geometry : bond 0.00347 ( 9340) covalent geometry : angle 0.54620 (12662) *********************** 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 126 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 1.039 Fit side-chains REVERT: A 1 MET cc_start: 0.5015 (mpp) cc_final: 0.3781 (mtm) REVERT: A 371 MET cc_start: 0.8404 (mtp) cc_final: 0.8174 (mtp) REVERT: B 241 GLU cc_start: 0.6784 (mp0) cc_final: 0.6576 (mp0) REVERT: B 447 GLN cc_start: 0.7857 (tp40) cc_final: 0.7375 (mm-40) REVERT: D 64 GLU cc_start: 0.7227 (OUTLIER) cc_final: 0.6625 (tm-30) REVERT: D 79 GLU cc_start: 0.7279 (mm-30) cc_final: 0.7056 (mm-30) outliers start: 23 outliers final: 8 residues processed: 118 average time/residue: 0.2129 time to fit residues: 35.3158 Evaluate side-chains 101 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.925 ------------------------------------------------------------------------------- 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 210 THR 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 49 optimal weight: 0.9990 chunk 96 optimal weight: 10.0000 chunk 18 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 99 optimal weight: 0.4980 chunk 6 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 114 optimal weight: 7.9990 chunk 20 optimal weight: 8.9990 chunk 72 optimal weight: 5.9990 chunk 79 optimal weight: 8.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- 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 E 265 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.212658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 106)---------------| | r_work = 0.3515 r_free = 0.3515 target = 0.135155 restraints weight = 9096.338| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.36 r_work: 0.3262 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 9340 Z= 0.276 Angle : 0.636 8.609 12662 Z= 0.325 Chirality : 0.046 0.178 1438 Planarity : 0.005 0.054 1613 Dihedral : 4.387 19.865 1288 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 4.20 % Allowed : 18.38 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.24), residues: 1163 helix: 1.07 (0.21), residues: 616 sheet: -0.40 (0.52), residues: 91 loop : -1.18 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 83 HIS 0.005 0.001 HIS B 420 PHE 0.028 0.002 PHE A 334 TYR 0.021 0.002 TYR A 306 ARG 0.004 0.000 ARG A 172 Details of bonding type rmsd hydrogen bonds : bond 0.04309 ( 531) hydrogen bonds : angle 4.99805 ( 1554) covalent geometry : bond 0.00683 ( 9340) covalent geometry : angle 0.63616 (12662) *********************** 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 137 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 97 time to evaluate : 1.018 Fit side-chains REVERT: A 1 MET cc_start: 0.5115 (mpp) cc_final: 0.3903 (mtt) REVERT: A 190 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7582 (mp) REVERT: B 64 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8011 (tp) REVERT: B 129 LEU cc_start: 0.7576 (mm) cc_final: 0.7230 (mm) REVERT: B 447 GLN cc_start: 0.7905 (tp40) cc_final: 0.7399 (mm-40) REVERT: D 35 ARG cc_start: 0.6929 (ttp-170) cc_final: 0.6584 (ttp80) REVERT: D 49 GLU cc_start: 0.7340 (mt-10) cc_final: 0.6880 (mp0) REVERT: D 64 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.6716 (tm-30) outliers start: 40 outliers final: 24 residues processed: 128 average time/residue: 0.2080 time to fit residues: 38.0194 Evaluate side-chains 119 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 92 time to evaluate : 1.036 ------------------------------------------------------------------------------- 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 183 MET Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 222 MET 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 434 LEU 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 Chi-restraints excluded: chain E residue 265 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 7 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 46 optimal weight: 0.7980 chunk 90 optimal weight: 0.3980 chunk 31 optimal weight: 10.0000 chunk 56 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 64 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.214635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.148619 restraints weight = 8906.291| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 1.95 r_work: 0.3334 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.1488 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= 0.147 Angle : 0.542 8.751 12662 Z= 0.274 Chirality : 0.042 0.157 1438 Planarity : 0.004 0.053 1613 Dihedral : 4.196 20.332 1288 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.94 % Allowed : 20.06 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.25), residues: 1163 helix: 1.34 (0.21), residues: 616 sheet: -0.50 (0.51), residues: 92 loop : -1.13 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 83 HIS 0.003 0.001 HIS B 480 PHE 0.016 0.001 PHE A 334 TYR 0.010 0.001 TYR A 306 ARG 0.003 0.000 ARG A 251 Details of bonding type rmsd hydrogen bonds : bond 0.03752 ( 531) hydrogen bonds : angle 4.71557 ( 1554) covalent geometry : bond 0.00347 ( 9340) covalent geometry : angle 0.54223 (12662) *********************** 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 130 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 102 time to evaluate : 0.910 Fit side-chains REVERT: A 1 MET cc_start: 0.5112 (mpp) cc_final: 0.3914 (mtt) REVERT: A 190 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7636 (mp) REVERT: A 283 GLU cc_start: 0.8615 (tt0) cc_final: 0.8385 (tt0) REVERT: B 354 ILE cc_start: 0.7076 (tp) cc_final: 0.6829 (tp) REVERT: B 447 GLN cc_start: 0.7912 (tp40) cc_final: 0.7403 (mm-40) REVERT: B 546 MET cc_start: 0.7420 (tpp) cc_final: 0.7048 (tpp) REVERT: D 35 ARG cc_start: 0.7012 (ttp-170) cc_final: 0.6686 (ttp80) REVERT: D 49 GLU cc_start: 0.7278 (mt-10) cc_final: 0.6726 (mp0) REVERT: D 64 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.6760 (tm-30) REVERT: E 202 LEU cc_start: 0.7503 (mp) cc_final: 0.6154 (tt) outliers start: 28 outliers final: 21 residues processed: 124 average time/residue: 0.2039 time to fit residues: 36.1179 Evaluate side-chains 119 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 1.004 ------------------------------------------------------------------------------- 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 124 ILE Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 190 LEU 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 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 18 optimal weight: 0.6980 chunk 55 optimal weight: 5.9990 chunk 83 optimal weight: 8.9990 chunk 0 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.4279 r_free = 0.4279 target = 0.214421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.138644 restraints weight = 8922.934| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.40 r_work: 0.3299 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9340 Z= 0.171 Angle : 0.551 8.156 12662 Z= 0.279 Chirality : 0.042 0.148 1438 Planarity : 0.004 0.052 1613 Dihedral : 4.167 19.873 1288 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.99 % Allowed : 19.43 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.25), residues: 1163 helix: 1.38 (0.21), residues: 617 sheet: -0.44 (0.51), residues: 92 loop : -1.10 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 83 HIS 0.003 0.001 HIS B 61 PHE 0.019 0.001 PHE A 334 TYR 0.014 0.001 TYR B 479 ARG 0.002 0.000 ARG A 251 Details of bonding type rmsd hydrogen bonds : bond 0.03758 ( 531) hydrogen bonds : angle 4.64260 ( 1554) covalent geometry : bond 0.00409 ( 9340) covalent geometry : angle 0.55080 (12662) *********************** 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 140 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 102 time to evaluate : 1.025 Fit side-chains REVERT: A 1 MET cc_start: 0.5099 (mpp) cc_final: 0.3939 (mtt) REVERT: A 173 GLU cc_start: 0.5662 (OUTLIER) cc_final: 0.4780 (pm20) REVERT: A 190 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.7386 (mp) REVERT: B 447 GLN cc_start: 0.7811 (tp40) cc_final: 0.7348 (mm-40) REVERT: B 546 MET cc_start: 0.7421 (tpp) cc_final: 0.6899 (tpp) REVERT: D 35 ARG cc_start: 0.6947 (ttp-170) cc_final: 0.6618 (ttp80) REVERT: D 49 GLU cc_start: 0.7286 (mt-10) cc_final: 0.6675 (mp0) REVERT: D 64 GLU cc_start: 0.7283 (OUTLIER) cc_final: 0.6633 (tm-30) REVERT: E 202 LEU cc_start: 0.7656 (mp) cc_final: 0.6358 (tt) outliers start: 38 outliers final: 26 residues processed: 132 average time/residue: 0.2001 time to fit residues: 38.2462 Evaluate side-chains 128 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 99 time to evaluate : 0.991 ------------------------------------------------------------------------------- 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 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 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 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 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 66 optimal weight: 0.7980 chunk 110 optimal weight: 10.0000 chunk 99 optimal weight: 1.9990 chunk 79 optimal weight: 9.9990 chunk 108 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 92 optimal weight: 9.9990 chunk 40 optimal weight: 0.5980 chunk 102 optimal weight: 0.3980 chunk 1 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.216830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 96)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.142673 restraints weight = 8890.210| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.22 r_work: 0.3324 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9340 Z= 0.135 Angle : 0.536 10.415 12662 Z= 0.267 Chirality : 0.041 0.147 1438 Planarity : 0.004 0.052 1613 Dihedral : 4.088 19.880 1288 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.36 % Allowed : 20.90 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.25), residues: 1163 helix: 1.55 (0.21), residues: 616 sheet: -0.38 (0.51), residues: 92 loop : -1.02 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 83 HIS 0.002 0.001 HIS B 480 PHE 0.015 0.001 PHE A 334 TYR 0.012 0.001 TYR B 479 ARG 0.002 0.000 ARG A 251 Details of bonding type rmsd hydrogen bonds : bond 0.03589 ( 531) hydrogen bonds : angle 4.53743 ( 1554) covalent geometry : bond 0.00316 ( 9340) covalent geometry : angle 0.53597 (12662) *********************** 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 133 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 101 time to evaluate : 0.952 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5102 (mpp) cc_final: 0.3935 (mtt) REVERT: A 173 GLU cc_start: 0.5730 (OUTLIER) cc_final: 0.4879 (pm20) REVERT: A 190 LEU cc_start: 0.7523 (OUTLIER) cc_final: 0.7276 (mp) REVERT: B 546 MET cc_start: 0.7401 (tpp) cc_final: 0.6824 (tpp) REVERT: D 35 ARG cc_start: 0.6956 (ttp-170) cc_final: 0.6635 (ttp80) REVERT: D 49 GLU cc_start: 0.7343 (mt-10) cc_final: 0.6740 (mp0) REVERT: D 64 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.6634 (tm-30) outliers start: 32 outliers final: 23 residues processed: 123 average time/residue: 0.1999 time to fit residues: 35.4257 Evaluate side-chains 125 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 0.904 ------------------------------------------------------------------------------- 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 38 MET 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 183 MET Chi-restraints excluded: chain A residue 190 LEU 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 288 ASP 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 209 LEU Chi-restraints excluded: chain E residue 234 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 114 optimal weight: 2.9990 chunk 68 optimal weight: 10.0000 chunk 26 optimal weight: 0.9990 chunk 84 optimal weight: 7.9990 chunk 11 optimal weight: 0.5980 chunk 81 optimal weight: 2.9990 chunk 110 optimal weight: 20.0000 chunk 104 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 8 optimal weight: 0.2980 chunk 44 optimal weight: 0.6980 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.217258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 107)---------------| | r_work = 0.3589 r_free = 0.3589 target = 0.141783 restraints weight = 8990.673| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.23 r_work: 0.3320 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9340 Z= 0.135 Angle : 0.527 10.489 12662 Z= 0.263 Chirality : 0.041 0.145 1438 Planarity : 0.004 0.052 1613 Dihedral : 4.029 19.863 1288 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.99 % Allowed : 20.38 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.25), residues: 1163 helix: 1.64 (0.21), residues: 617 sheet: -0.34 (0.51), residues: 92 loop : -0.99 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 83 HIS 0.002 0.001 HIS B 61 PHE 0.016 0.001 PHE A 334 TYR 0.011 0.001 TYR B 479 ARG 0.002 0.000 ARG B 14 Details of bonding type rmsd hydrogen bonds : bond 0.03523 ( 531) hydrogen bonds : angle 4.46884 ( 1554) covalent geometry : bond 0.00318 ( 9340) covalent geometry : angle 0.52674 (12662) *********************** 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 141 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 103 time to evaluate : 1.058 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5020 (mpp) cc_final: 0.3836 (mtt) REVERT: A 151 GLU cc_start: 0.4973 (OUTLIER) cc_final: 0.3907 (pm20) REVERT: A 173 GLU cc_start: 0.5694 (OUTLIER) cc_final: 0.4843 (pm20) REVERT: A 190 LEU cc_start: 0.7360 (OUTLIER) cc_final: 0.7146 (mp) REVERT: B 546 MET cc_start: 0.7316 (tpp) cc_final: 0.6858 (tpp) REVERT: D 35 ARG cc_start: 0.6950 (ttp-170) cc_final: 0.6616 (ttp80) REVERT: D 49 GLU cc_start: 0.7312 (mt-10) cc_final: 0.6696 (mp0) REVERT: D 64 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.6637 (tm-30) outliers start: 38 outliers final: 27 residues processed: 132 average time/residue: 0.1940 time to fit residues: 37.0448 Evaluate side-chains 133 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 102 time to evaluate : 1.070 ------------------------------------------------------------------------------- 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 8 PHE Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 38 MET 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 134 VAL Chi-restraints excluded: chain A residue 151 GLU 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 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 80 optimal weight: 10.0000 chunk 114 optimal weight: 5.9990 chunk 94 optimal weight: 0.0970 chunk 17 optimal weight: 1.9990 chunk 113 optimal weight: 5.9990 chunk 104 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 59 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.217211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 96)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.144774 restraints weight = 9100.328| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.39 r_work: 0.3310 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9340 Z= 0.158 Angle : 0.550 11.196 12662 Z= 0.274 Chirality : 0.042 0.147 1438 Planarity : 0.004 0.052 1613 Dihedral : 4.080 19.981 1288 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.99 % Allowed : 21.11 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.25), residues: 1163 helix: 1.58 (0.21), residues: 617 sheet: -0.31 (0.51), residues: 92 loop : -0.99 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 217 HIS 0.002 0.001 HIS B 61 PHE 0.018 0.001 PHE A 334 TYR 0.011 0.001 TYR B 479 ARG 0.002 0.000 ARG B 14 Details of bonding type rmsd hydrogen bonds : bond 0.03604 ( 531) hydrogen bonds : angle 4.49486 ( 1554) covalent geometry : bond 0.00379 ( 9340) covalent geometry : angle 0.55012 (12662) *********************** 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 140 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 102 time to evaluate : 0.972 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5056 (mpp) cc_final: 0.3861 (mtt) REVERT: A 84 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7554 (tt0) REVERT: A 151 GLU cc_start: 0.4850 (OUTLIER) cc_final: 0.3795 (pm20) REVERT: A 173 GLU cc_start: 0.5688 (OUTLIER) cc_final: 0.4831 (pm20) REVERT: A 190 LEU cc_start: 0.7397 (OUTLIER) cc_final: 0.7155 (mp) REVERT: B 546 MET cc_start: 0.7303 (tpp) cc_final: 0.6815 (tpp) REVERT: D 35 ARG cc_start: 0.6970 (ttp-170) cc_final: 0.6629 (ttp80) REVERT: D 49 GLU cc_start: 0.7338 (mt-10) cc_final: 0.6723 (mp0) REVERT: D 64 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.6645 (tm-30) REVERT: D 65 LEU cc_start: 0.7698 (mt) cc_final: 0.7497 (mt) outliers start: 38 outliers final: 29 residues processed: 130 average time/residue: 0.2063 time to fit residues: 38.5578 Evaluate side-chains 138 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 104 time to evaluate : 1.065 ------------------------------------------------------------------------------- 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 8 PHE Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 38 MET Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 197 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 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 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 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 200 ARG Chi-restraints excluded: chain E residue 234 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 0.0030 chunk 112 optimal weight: 8.9990 chunk 7 optimal weight: 0.9990 chunk 107 optimal weight: 9.9990 chunk 0 optimal weight: 4.9990 chunk 99 optimal weight: 0.6980 chunk 111 optimal weight: 3.9990 chunk 77 optimal weight: 10.0000 chunk 40 optimal weight: 0.3980 chunk 8 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.218858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 100)---------------| | r_work = 0.3659 r_free = 0.3659 target = 0.149076 restraints weight = 8872.319| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 1.99 r_work: 0.3351 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6966 moved from start: 0.1796 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= 0.127 Angle : 0.527 11.079 12662 Z= 0.262 Chirality : 0.041 0.148 1438 Planarity : 0.004 0.051 1613 Dihedral : 4.018 19.898 1288 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.47 % Allowed : 21.74 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.25), residues: 1163 helix: 1.74 (0.21), residues: 618 sheet: -0.29 (0.51), residues: 92 loop : -0.94 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 83 HIS 0.003 0.001 HIS B 480 PHE 0.013 0.001 PHE A 334 TYR 0.010 0.001 TYR B 479 ARG 0.002 0.000 ARG A 251 Details of bonding type rmsd hydrogen bonds : bond 0.03455 ( 531) hydrogen bonds : angle 4.42168 ( 1554) covalent geometry : bond 0.00297 ( 9340) covalent geometry : angle 0.52700 (12662) *********************** 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 138 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 105 time to evaluate : 0.943 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5005 (mpp) cc_final: 0.3841 (mtt) REVERT: A 84 GLN cc_start: 0.8157 (OUTLIER) cc_final: 0.7562 (tt0) REVERT: A 151 GLU cc_start: 0.4871 (OUTLIER) cc_final: 0.3843 (pm20) REVERT: A 173 GLU cc_start: 0.5743 (OUTLIER) cc_final: 0.4876 (pm20) REVERT: A 190 LEU cc_start: 0.7394 (OUTLIER) cc_final: 0.7167 (mp) REVERT: B 301 MET cc_start: 0.6925 (ttp) cc_final: 0.6489 (ppp) REVERT: B 546 MET cc_start: 0.7354 (tpp) cc_final: 0.6840 (tpp) REVERT: D 35 ARG cc_start: 0.7006 (ttp-170) cc_final: 0.6673 (ttp80) REVERT: D 49 GLU cc_start: 0.7287 (mt-10) cc_final: 0.6692 (mp0) REVERT: D 79 GLU cc_start: 0.6575 (mm-30) cc_final: 0.6217 (mt-10) outliers start: 33 outliers final: 23 residues processed: 127 average time/residue: 0.2031 time to fit residues: 36.8483 Evaluate side-chains 130 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 103 time to evaluate : 1.001 ------------------------------------------------------------------------------- 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 65 LEU Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 173 GLU 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 38 VAL Chi-restraints excluded: chain B residue 53 VAL 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 110 optimal weight: 20.0000 chunk 108 optimal weight: 0.0070 chunk 59 optimal weight: 0.4980 chunk 85 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 113 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 77 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 377 GLN ** B 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.219315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.169290 restraints weight = 9094.155| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 1.54 r_work: 0.3427 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.1843 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= 0.135 Angle : 0.534 11.164 12662 Z= 0.265 Chirality : 0.041 0.145 1438 Planarity : 0.004 0.051 1613 Dihedral : 4.006 19.981 1288 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.36 % Allowed : 21.95 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.25), residues: 1163 helix: 1.71 (0.21), residues: 617 sheet: -0.24 (0.51), residues: 92 loop : -0.95 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 83 HIS 0.003 0.001 HIS B 480 PHE 0.016 0.001 PHE A 334 TYR 0.010 0.001 TYR B 479 ARG 0.002 0.000 ARG B 14 Details of bonding type rmsd hydrogen bonds : bond 0.03477 ( 531) hydrogen bonds : angle 4.41686 ( 1554) covalent geometry : bond 0.00318 ( 9340) covalent geometry : angle 0.53361 (12662) ********************** 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 135 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 103 time to evaluate : 1.039 Fit side-chains REVERT: A 1 MET cc_start: 0.5002 (mpp) cc_final: 0.3904 (mtt) REVERT: A 84 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.7806 (tt0) REVERT: A 151 GLU cc_start: 0.4978 (OUTLIER) cc_final: 0.3939 (pm20) REVERT: A 173 GLU cc_start: 0.6031 (OUTLIER) cc_final: 0.5097 (pm20) REVERT: A 190 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7585 (mp) REVERT: B 301 MET cc_start: 0.7120 (ttp) cc_final: 0.6562 (ppp) REVERT: B 546 MET cc_start: 0.7570 (tpp) cc_final: 0.7133 (tpp) REVERT: D 35 ARG cc_start: 0.7065 (ttp-170) cc_final: 0.6753 (ttp80) REVERT: D 49 GLU cc_start: 0.7264 (mt-10) cc_final: 0.6802 (mp0) REVERT: D 79 GLU cc_start: 0.6726 (mm-30) cc_final: 0.6354 (mt-10) REVERT: E 202 LEU cc_start: 0.7741 (mp) cc_final: 0.6667 (tp) outliers start: 32 outliers final: 25 residues processed: 126 average time/residue: 0.1994 time to fit residues: 36.0658 Evaluate side-chains 129 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 100 time to evaluate : 0.969 ------------------------------------------------------------------------------- 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 65 LEU Chi-restraints excluded: chain A residue 84 GLN Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 151 GLU Chi-restraints excluded: chain A residue 173 GLU 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 138 ILE Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 383 PHE 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 95 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 8 optimal weight: 6.9990 chunk 74 optimal weight: 0.8980 chunk 77 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 81 optimal weight: 0.1980 chunk 107 optimal weight: 10.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.216281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.170747 restraints weight = 9017.850| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 1.73 r_work: 0.3392 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.1891 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= 0.147 Angle : 0.542 11.047 12662 Z= 0.269 Chirality : 0.041 0.148 1438 Planarity : 0.004 0.052 1613 Dihedral : 4.035 20.018 1288 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.36 % Allowed : 22.16 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.25), residues: 1163 helix: 1.67 (0.21), residues: 617 sheet: -0.18 (0.51), residues: 92 loop : -0.96 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 83 HIS 0.003 0.001 HIS B 480 PHE 0.017 0.001 PHE A 334 TYR 0.010 0.001 TYR B 479 ARG 0.002 0.000 ARG A 251 Details of bonding type rmsd hydrogen bonds : bond 0.03524 ( 531) hydrogen bonds : angle 4.41829 ( 1554) covalent geometry : bond 0.00349 ( 9340) covalent geometry : angle 0.54242 (12662) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6356.29 seconds wall clock time: 110 minutes 9.05 seconds (6609.05 seconds total)