Starting phenix.real_space_refine on Thu Mar 13 18:13:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p1u_17356/03_2025/8p1u_17356.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p1u_17356/03_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_17356/03_2025/8p1u_17356.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p1u_17356/03_2025/8p1u_17356.map" model { file = "/net/cci-nas-00/data/ceres_data/8p1u_17356/03_2025/8p1u_17356.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p1u_17356/03_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-5624/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: 6.29, per 1000 atoms: 0.69 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: 2.52 Conformation dependent library (CDL) restraints added in 1.1 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: 0.99 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: 2.74 Time building geometry restraints manager: 2.95 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: 3.530 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: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.240 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 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:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.620 ------------------------------------------------------------------------------- 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= 0.192 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 *********************** 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 : 1.031 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: 0.2251 time to fit residues: 36.1838 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 : 1.030 ------------------------------------------------------------------------------- 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 = 0.219474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 117)---------------| | r_work = 0.3600 r_free = 0.3600 target = 0.143199 restraints weight = 8913.749| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.49 r_work: 0.3340 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 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= 0.224 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 *********************** 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 : 0.927 Fit side-chains REVERT: A 1 MET cc_start: 0.5003 (mpp) cc_final: 0.3769 (mtm) REVERT: A 371 MET cc_start: 0.8417 (mtp) cc_final: 0.8189 (mtp) REVERT: B 241 GLU cc_start: 0.6791 (mp0) cc_final: 0.6586 (mp0) REVERT: B 447 GLN cc_start: 0.7854 (tp40) cc_final: 0.7372 (mm-40) REVERT: D 64 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.6667 (tm-30) REVERT: D 79 GLU cc_start: 0.7309 (mm-30) cc_final: 0.7082 (mm-30) outliers start: 23 outliers final: 8 residues processed: 118 average time/residue: 0.2271 time to fit residues: 37.2199 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 : 0.895 ------------------------------------------------------------------------------- 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: 0.6980 chunk 96 optimal weight: 10.0000 chunk 18 optimal weight: 0.8980 chunk 46 optimal weight: 0.0870 chunk 99 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 114 optimal weight: 6.9990 chunk 20 optimal weight: 8.9990 chunk 72 optimal weight: 0.4980 chunk 79 optimal weight: 3.9990 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4309 r_free = 0.4309 target = 0.218055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 97)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.142124 restraints weight = 9024.097| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 2.38 r_work: 0.3346 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.1262 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= 0.199 Angle : 0.520 8.866 12662 Z= 0.262 Chirality : 0.041 0.161 1438 Planarity : 0.004 0.052 1613 Dihedral : 3.968 19.770 1288 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.52 % Allowed : 19.96 % Favored : 77.52 % 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: 0.82 (0.25), residues: 1163 helix: 1.73 (0.21), residues: 615 sheet: -0.40 (0.52), residues: 92 loop : -0.91 (0.28), residues: 456 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 0.014 0.001 PHE A 334 TYR 0.008 0.001 TYR B 422 ARG 0.004 0.000 ARG E 214 *********************** 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 120 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 96 time to evaluate : 0.947 Fit side-chains REVERT: A 1 MET cc_start: 0.5050 (mpp) cc_final: 0.3808 (mtt) REVERT: A 190 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.7494 (mp) REVERT: B 241 GLU cc_start: 0.6894 (mp0) cc_final: 0.6568 (mp0) REVERT: D 35 ARG cc_start: 0.6992 (ttp-170) cc_final: 0.6607 (ttp80) REVERT: D 64 GLU cc_start: 0.7309 (OUTLIER) cc_final: 0.6748 (tm-30) REVERT: E 202 LEU cc_start: 0.7445 (mp) cc_final: 0.5988 (tt) outliers start: 24 outliers final: 14 residues processed: 113 average time/residue: 0.2027 time to fit residues: 32.9123 Evaluate side-chains 107 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 16 HIS 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 64 LEU 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 7 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- 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 = 0.4294 r_free = 0.4294 target = 0.216146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 113)---------------| | r_work = 0.3620 r_free = 0.3620 target = 0.143778 restraints weight = 8890.084| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 2.63 r_work: 0.3335 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9340 Z= 0.284 Angle : 0.553 8.635 12662 Z= 0.279 Chirality : 0.043 0.148 1438 Planarity : 0.004 0.051 1613 Dihedral : 4.077 19.757 1288 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.36 % Allowed : 19.43 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.63 (0.25), residues: 1163 helix: 1.55 (0.21), residues: 616 sheet: -0.38 (0.51), residues: 92 loop : -0.98 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 83 HIS 0.003 0.001 HIS B 61 PHE 0.021 0.001 PHE A 334 TYR 0.013 0.001 TYR A 306 ARG 0.002 0.000 ARG B 14 *********************** 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 135 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 103 time to evaluate : 1.094 Fit side-chains REVERT: A 1 MET cc_start: 0.5105 (mpp) cc_final: 0.3909 (mtt) REVERT: A 190 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.7467 (mp) REVERT: B 64 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8064 (tp) REVERT: B 354 ILE cc_start: 0.6960 (tp) cc_final: 0.6718 (tp) REVERT: D 35 ARG cc_start: 0.7051 (ttp-170) cc_final: 0.6699 (ttp80) REVERT: D 49 GLU cc_start: 0.7306 (mt-10) cc_final: 0.6705 (mp0) REVERT: D 64 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.6724 (tm-30) REVERT: E 202 LEU cc_start: 0.7438 (mp) cc_final: 0.6194 (tt) outliers start: 32 outliers final: 21 residues processed: 124 average time/residue: 0.2155 time to fit residues: 38.4299 Evaluate side-chains 121 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 97 time to evaluate : 1.018 ------------------------------------------------------------------------------- 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 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 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 D residue 64 GLU Chi-restraints excluded: chain E residue 209 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 55 optimal weight: 5.9990 chunk 83 optimal weight: 10.0000 chunk 0 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 = 0.4276 r_free = 0.4276 target = 0.214076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.152024 restraints weight = 8961.433| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 1.92 r_work: 0.3334 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9340 Z= 0.323 Angle : 0.582 10.297 12662 Z= 0.292 Chirality : 0.043 0.150 1438 Planarity : 0.004 0.051 1613 Dihedral : 4.178 19.759 1288 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.36 % Allowed : 19.75 % 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 (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: 0.48 (0.25), residues: 1163 helix: 1.38 (0.21), residues: 616 sheet: -0.28 (0.51), residues: 91 loop : -1.02 (0.29), residues: 456 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 0.022 0.002 PHE A 334 TYR 0.015 0.001 TYR A 306 ARG 0.002 0.000 ARG B 14 *********************** 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 132 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 100 time to evaluate : 1.588 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5038 (mpp) cc_final: 0.3920 (mtt) REVERT: A 190 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7593 (mp) REVERT: B 354 ILE cc_start: 0.7106 (tp) cc_final: 0.6904 (tp) REVERT: D 35 ARG cc_start: 0.6987 (ttp-170) cc_final: 0.6665 (ttp80) REVERT: D 49 GLU cc_start: 0.7322 (mt-10) cc_final: 0.6760 (mp0) REVERT: D 64 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.6755 (tm-30) REVERT: D 92 LEU cc_start: 0.5557 (OUTLIER) cc_final: 0.5061 (pt) outliers start: 32 outliers final: 23 residues processed: 124 average time/residue: 0.2517 time to fit residues: 45.7266 Evaluate side-chains 126 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 100 time to evaluate : 1.499 ------------------------------------------------------------------------------- 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 222 MET 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 D residue 92 LEU 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: 0.8980 chunk 110 optimal weight: 0.4980 chunk 99 optimal weight: 0.9980 chunk 79 optimal weight: 5.9990 chunk 108 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 92 optimal weight: 9.9990 chunk 40 optimal weight: 0.5980 chunk 102 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4301 r_free = 0.4301 target = 0.216832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.150308 restraints weight = 8881.307| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 1.95 r_work: 0.3384 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 moved from start: 0.1633 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= 0.201 Angle : 0.532 10.354 12662 Z= 0.266 Chirality : 0.041 0.159 1438 Planarity : 0.004 0.051 1613 Dihedral : 4.046 19.828 1288 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.78 % Allowed : 20.38 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.72 (0.25), residues: 1163 helix: 1.63 (0.21), residues: 617 sheet: -0.35 (0.51), residues: 92 loop : -0.95 (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 480 PHE 0.015 0.001 PHE A 334 TYR 0.012 0.001 TYR B 479 ARG 0.003 0.000 ARG A 251 *********************** 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 135 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 99 time to evaluate : 0.929 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5052 (mpp) cc_final: 0.3912 (mtt) REVERT: A 173 GLU cc_start: 0.5873 (OUTLIER) cc_final: 0.5189 (pm20) REVERT: A 190 LEU cc_start: 0.7658 (OUTLIER) cc_final: 0.7407 (mp) REVERT: B 354 ILE cc_start: 0.7031 (tp) cc_final: 0.6808 (tp) REVERT: B 546 MET cc_start: 0.7403 (tpp) cc_final: 0.7004 (tpp) REVERT: D 35 ARG cc_start: 0.7022 (ttp-170) cc_final: 0.6704 (ttp80) REVERT: D 49 GLU cc_start: 0.7318 (mt-10) cc_final: 0.6749 (mp0) REVERT: D 64 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.6753 (tm-30) REVERT: D 82 MET cc_start: 0.7221 (mtt) cc_final: 0.6812 (mtt) outliers start: 36 outliers final: 23 residues processed: 126 average time/residue: 0.1977 time to fit residues: 35.6171 Evaluate side-chains 123 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 97 time to evaluate : 0.947 ------------------------------------------------------------------------------- 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 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 265 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 114 optimal weight: 4.9990 chunk 68 optimal weight: 9.9990 chunk 26 optimal weight: 0.7980 chunk 84 optimal weight: 6.9990 chunk 11 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 chunk 104 optimal weight: 0.9990 chunk 100 optimal weight: 0.6980 chunk 8 optimal weight: 7.9990 chunk 44 optimal weight: 0.5980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.4301 r_free = 0.4301 target = 0.216914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.150977 restraints weight = 8988.430| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 1.93 r_work: 0.3378 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 moved from start: 0.1680 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= 0.221 Angle : 0.533 10.400 12662 Z= 0.266 Chirality : 0.041 0.152 1438 Planarity : 0.004 0.051 1613 Dihedral : 4.040 19.865 1288 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.26 % Allowed : 21.32 % Favored : 75.42 % 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: 0.75 (0.25), residues: 1163 helix: 1.65 (0.21), residues: 618 sheet: -0.34 (0.51), residues: 92 loop : -0.94 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 83 HIS 0.003 0.001 HIS B 480 PHE 0.016 0.001 PHE A 334 TYR 0.011 0.001 TYR B 479 ARG 0.002 0.000 ARG B 14 *********************** 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 133 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 102 time to evaluate : 1.174 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5028 (mpp) cc_final: 0.3886 (mtt) REVERT: A 173 GLU cc_start: 0.5853 (OUTLIER) cc_final: 0.5174 (pm20) REVERT: A 190 LEU cc_start: 0.7638 (OUTLIER) cc_final: 0.7391 (mp) REVERT: A 244 GLN cc_start: 0.6493 (mp10) cc_final: 0.6292 (mm-40) REVERT: B 354 ILE cc_start: 0.7017 (tp) cc_final: 0.6786 (tp) REVERT: B 546 MET cc_start: 0.7383 (tpp) cc_final: 0.6968 (tpp) REVERT: D 35 ARG cc_start: 0.6993 (ttp-170) cc_final: 0.6671 (ttp80) REVERT: D 49 GLU cc_start: 0.7303 (mt-10) cc_final: 0.6727 (mp0) REVERT: D 64 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.6782 (tm-30) outliers start: 31 outliers final: 22 residues processed: 125 average time/residue: 0.2683 time to fit residues: 50.3305 Evaluate side-chains 125 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 100 time to evaluate : 0.984 ------------------------------------------------------------------------------- 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 416 ILE Chi-restraints excluded: chain B residue 503 TYR Chi-restraints excluded: chain D residue 64 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 80 optimal weight: 0.7980 chunk 114 optimal weight: 0.8980 chunk 94 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 35 optimal weight: 0.3980 chunk 48 optimal weight: 0.4980 chunk 19 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4308 r_free = 0.4308 target = 0.217700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.141822 restraints weight = 9051.428| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.47 r_work: 0.3340 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.1741 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= 0.204 Angle : 0.531 11.103 12662 Z= 0.265 Chirality : 0.041 0.147 1438 Planarity : 0.004 0.051 1613 Dihedral : 4.009 19.869 1288 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.47 % Allowed : 21.11 % Favored : 75.42 % 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: 0.81 (0.25), residues: 1163 helix: 1.71 (0.21), residues: 617 sheet: -0.28 (0.51), residues: 92 loop : -0.92 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 217 HIS 0.003 0.001 HIS B 480 PHE 0.015 0.001 PHE A 334 TYR 0.011 0.001 TYR B 479 ARG 0.002 0.000 ARG B 226 *********************** 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 135 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 102 time to evaluate : 1.114 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.5078 (mpp) cc_final: 0.3897 (mtt) REVERT: A 151 GLU cc_start: 0.4879 (OUTLIER) cc_final: 0.3816 (pm20) REVERT: A 173 GLU cc_start: 0.5679 (OUTLIER) cc_final: 0.5067 (pm20) REVERT: A 190 LEU cc_start: 0.7411 (OUTLIER) cc_final: 0.7174 (mp) REVERT: B 301 MET cc_start: 0.6955 (ttp) cc_final: 0.6583 (ppp) REVERT: B 473 ARG cc_start: 0.8331 (ttm-80) cc_final: 0.7943 (ttm110) REVERT: B 546 MET cc_start: 0.7165 (tpp) cc_final: 0.6764 (tpp) REVERT: D 35 ARG cc_start: 0.6972 (ttp-170) cc_final: 0.6645 (ttp80) REVERT: D 49 GLU cc_start: 0.7333 (mt-10) cc_final: 0.6723 (mp0) outliers start: 33 outliers final: 27 residues processed: 125 average time/residue: 0.2215 time to fit residues: 40.1796 Evaluate side-chains 131 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 101 time to evaluate : 0.958 ------------------------------------------------------------------------------- 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 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 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 210 THR Chi-restraints excluded: chain B residue 288 ASP 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 E residue 200 ARG Chi-restraints excluded: chain E residue 209 LEU 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: 0.1980 chunk 112 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 107 optimal weight: 8.9990 chunk 0 optimal weight: 4.9990 chunk 99 optimal weight: 0.2980 chunk 111 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 8 optimal weight: 0.1980 chunk 17 optimal weight: 1.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.4329 r_free = 0.4329 target = 0.220409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 123)---------------| | r_work = 0.3702 r_free = 0.3702 target = 0.153148 restraints weight = 8881.389| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 2.16 r_work: 0.3366 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 moved from start: 0.1797 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= 0.177 Angle : 0.522 11.278 12662 Z= 0.260 Chirality : 0.041 0.142 1438 Planarity : 0.004 0.050 1613 Dihedral : 3.934 19.746 1288 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.05 % Allowed : 21.53 % Favored : 75.42 % 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: 0.97 (0.25), residues: 1163 helix: 1.86 (0.21), residues: 617 sheet: -0.23 (0.51), residues: 92 loop : -0.88 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 217 HIS 0.003 0.001 HIS B 480 PHE 0.014 0.001 PHE A 267 TYR 0.010 0.001 TYR B 479 ARG 0.003 0.000 ARG A 374 *********************** 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 134 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 105 time to evaluate : 1.056 Fit side-chains REVERT: A 1 MET cc_start: 0.5013 (mpp) cc_final: 0.3880 (mtt) REVERT: A 80 MET cc_start: 0.8045 (mmt) cc_final: 0.7628 (mmt) REVERT: A 151 GLU cc_start: 0.4974 (OUTLIER) cc_final: 0.3903 (pm20) REVERT: A 173 GLU cc_start: 0.5800 (OUTLIER) cc_final: 0.5133 (pm20) REVERT: A 190 LEU cc_start: 0.7504 (OUTLIER) cc_final: 0.7259 (mp) REVERT: B 64 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8078 (tp) REVERT: B 129 LEU cc_start: 0.7682 (mm) cc_final: 0.7347 (mm) REVERT: B 301 MET cc_start: 0.7003 (ttp) cc_final: 0.6501 (ppp) REVERT: B 473 ARG cc_start: 0.8386 (ttm-80) cc_final: 0.7999 (ttm110) REVERT: B 546 MET cc_start: 0.7296 (tpp) cc_final: 0.6940 (tpp) REVERT: D 35 ARG cc_start: 0.7032 (ttp-170) cc_final: 0.6706 (ttp80) REVERT: D 49 GLU cc_start: 0.7256 (mt-10) cc_final: 0.6681 (mp0) REVERT: E 202 LEU cc_start: 0.7817 (mp) cc_final: 0.6713 (tp) outliers start: 29 outliers final: 20 residues processed: 123 average time/residue: 0.2207 time to fit residues: 38.9245 Evaluate side-chains 127 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 103 time to evaluate : 1.037 ------------------------------------------------------------------------------- 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 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 334 PHE 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 416 ILE Chi-restraints excluded: chain B residue 503 TYR Chi-restraints excluded: chain E residue 200 ARG Chi-restraints excluded: chain E residue 209 LEU 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: 7.9990 chunk 59 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 113 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 77 optimal weight: 8.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 ** 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 = 0.4297 r_free = 0.4297 target = 0.216947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.158883 restraints weight = 9109.738| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 1.69 r_work: 0.3390 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9340 Z= 0.250 Angle : 0.554 11.200 12662 Z= 0.276 Chirality : 0.042 0.144 1438 Planarity : 0.004 0.051 1613 Dihedral : 4.023 19.995 1288 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.05 % Allowed : 22.06 % 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: 0.82 (0.25), residues: 1163 helix: 1.71 (0.21), residues: 618 sheet: -0.11 (0.52), residues: 91 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 0.019 0.001 PHE A 334 TYR 0.011 0.001 TYR B 479 ARG 0.002 0.000 ARG B 14 ********************** 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 131 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 102 time to evaluate : 0.891 Fit side-chains REVERT: A 1 MET cc_start: 0.4973 (mpp) cc_final: 0.3855 (mtt) REVERT: A 151 GLU cc_start: 0.4989 (OUTLIER) cc_final: 0.3931 (pm20) REVERT: A 173 GLU cc_start: 0.6026 (OUTLIER) cc_final: 0.5239 (pm20) REVERT: A 190 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7585 (mp) REVERT: B 64 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8202 (tp) REVERT: B 301 MET cc_start: 0.7112 (ttp) cc_final: 0.6649 (ppp) REVERT: B 473 ARG cc_start: 0.8511 (ttm-80) cc_final: 0.8160 (ttm110) REVERT: B 546 MET cc_start: 0.7428 (tpp) cc_final: 0.7061 (tpp) REVERT: D 35 ARG cc_start: 0.7080 (ttp-170) cc_final: 0.6766 (ttp80) REVERT: D 49 GLU cc_start: 0.7319 (mt-10) cc_final: 0.6824 (mp0) REVERT: E 202 LEU cc_start: 0.7754 (mp) cc_final: 0.6674 (tp) outliers start: 29 outliers final: 21 residues processed: 124 average time/residue: 0.2075 time to fit residues: 36.4699 Evaluate side-chains 125 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 100 time to evaluate : 0.930 ------------------------------------------------------------------------------- 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 65 LEU 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 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 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: 3.9990 chunk 3 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 8 optimal weight: 0.4980 chunk 74 optimal weight: 0.6980 chunk 77 optimal weight: 20.0000 chunk 28 optimal weight: 0.0870 chunk 62 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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 = 0.4329 r_free = 0.4329 target = 0.220164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.170823 restraints weight = 8943.631| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 1.60 r_work: 0.3426 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9340 Z= 0.211 Angle : 0.537 11.078 12662 Z= 0.268 Chirality : 0.041 0.144 1438 Planarity : 0.004 0.051 1613 Dihedral : 3.989 19.865 1288 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.63 % Allowed : 22.16 % 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 (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: 0.89 (0.25), residues: 1163 helix: 1.77 (0.21), residues: 618 sheet: -0.08 (0.52), residues: 91 loop : -0.92 (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 0.015 0.001 PHE A 334 TYR 0.010 0.001 TYR B 479 ARG 0.003 0.000 ARG B 14 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6549.72 seconds wall clock time: 115 minutes 41.61 seconds (6941.61 seconds total)