Starting phenix.real_space_refine on Tue Jan 14 00:25:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b23_44095/01_2025/9b23_44095.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b23_44095/01_2025/9b23_44095.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b23_44095/01_2025/9b23_44095.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b23_44095/01_2025/9b23_44095.map" model { file = "/net/cci-nas-00/data/ceres_data/9b23_44095/01_2025/9b23_44095.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b23_44095/01_2025/9b23_44095.cif" } resolution = 3.2 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= 0.009 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 10 5.16 5 C 2975 2.51 5 N 748 2.21 5 O 937 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 4670 Number of models: 1 Model: "" Number of chains: 2 Chain: "D" Number of atoms: 2342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2342 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 12, 'TRANS': 272} Chain: "E" Number of atoms: 2328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2328 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 12, 'TRANS': 270} Time building chain proxies: 3.26, per 1000 atoms: 0.70 Number of scatterers: 4670 At special positions: 0 Unit cell: (69.72, 86.32, 123.67, 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 10 16.00 O 937 8.00 N 748 7.00 C 2975 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: 1.25 Conformation dependent library (CDL) restraints added in 587.5 milliseconds 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1080 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 4 sheets defined 56.9% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'D' and resid 81 through 88 Processing helix chain 'D' and resid 89 through 141 Proline residue: D 130 - end of helix Processing helix chain 'D' and resid 146 through 159 Processing helix chain 'D' and resid 162 through 166 Processing helix chain 'D' and resid 168 through 173 Processing helix chain 'D' and resid 175 through 180 Processing helix chain 'D' and resid 187 through 196 Processing helix chain 'D' and resid 196 through 201 removed outlier: 4.021A pdb=" N ASP D 201 " --> pdb=" O PRO D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 212 removed outlier: 3.804A pdb=" N VAL D 210 " --> pdb=" O ARG D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 316 Processing helix chain 'D' and resid 322 through 352 removed outlier: 4.070A pdb=" N GLU D 328 " --> pdb=" O GLU D 324 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLU D 331 " --> pdb=" O ASP D 327 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLU D 332 " --> pdb=" O GLU D 328 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU D 338 " --> pdb=" O LEU D 334 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ALA D 339 " --> pdb=" O GLU D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 362 Processing helix chain 'E' and resid 84 through 88 Processing helix chain 'E' and resid 89 through 140 removed outlier: 3.576A pdb=" N LYS E 127 " --> pdb=" O LYS E 123 " (cutoff:3.500A) Proline residue: E 130 - end of helix Processing helix chain 'E' and resid 146 through 161 Processing helix chain 'E' and resid 162 through 166 removed outlier: 3.543A pdb=" N LEU E 165 " --> pdb=" O GLU E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 173 Processing helix chain 'E' and resid 175 through 180 Processing helix chain 'E' and resid 187 through 196 Processing helix chain 'E' and resid 198 through 203 removed outlier: 3.936A pdb=" N THR E 202 " --> pdb=" O ILE E 198 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE E 203 " --> pdb=" O VAL E 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 198 through 203' Processing helix chain 'E' and resid 204 through 212 Processing helix chain 'E' and resid 259 through 263 removed outlier: 4.253A pdb=" N ASP E 263 " --> pdb=" O TYR E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 316 Processing helix chain 'E' and resid 324 through 326 No H-bonds generated for 'chain 'E' and resid 324 through 326' Processing helix chain 'E' and resid 327 through 351 removed outlier: 4.337A pdb=" N ASP E 333 " --> pdb=" O GLU E 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 356 through 362 Processing sheet with id=AA1, first strand: chain 'D' and resid 216 through 221 removed outlier: 4.429A pdb=" N ASP D 216 " --> pdb=" O ARG D 234 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG D 234 " --> pdb=" O ASP D 216 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N CYS D 249 " --> pdb=" O GLY D 271 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N GLY D 271 " --> pdb=" O CYS D 249 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N THR D 251 " --> pdb=" O ALA D 269 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N ALA D 269 " --> pdb=" O THR D 251 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N PHE D 253 " --> pdb=" O ASP D 267 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 285 through 294 Processing sheet with id=AA3, first strand: chain 'E' and resid 214 through 222 removed outlier: 3.993A pdb=" N GLY E 228 " --> pdb=" O LEU E 222 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N CYS E 249 " --> pdb=" O GLY E 271 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N GLY E 271 " --> pdb=" O CYS E 249 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N THR E 251 " --> pdb=" O ALA E 269 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ALA E 269 " --> pdb=" O THR E 251 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE E 253 " --> pdb=" O ASP E 267 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 285 through 293 removed outlier: 3.533A pdb=" N GLU E 288 " --> pdb=" O LYS E 305 " (cutoff:3.500A) 248 hydrogen bonds defined for protein. 711 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.19 Time building geometry restraints manager: 1.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1451 1.33 - 1.45: 616 1.45 - 1.57: 2683 1.57 - 1.69: 0 1.69 - 1.81: 14 Bond restraints: 4764 Sorted by residual: bond pdb=" N THR D 163 " pdb=" CA THR D 163 " ideal model delta sigma weight residual 1.457 1.490 -0.032 1.29e-02 6.01e+03 6.32e+00 bond pdb=" N GLU D 162 " pdb=" CA GLU D 162 " ideal model delta sigma weight residual 1.458 1.486 -0.029 1.25e-02 6.40e+03 5.21e+00 bond pdb=" N LEU D 160 " pdb=" CA LEU D 160 " ideal model delta sigma weight residual 1.457 1.486 -0.028 1.29e-02 6.01e+03 4.80e+00 bond pdb=" N LEU D 165 " pdb=" CA LEU D 165 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.33e-02 5.65e+03 4.73e+00 bond pdb=" N GLU D 164 " pdb=" CA GLU D 164 " ideal model delta sigma weight residual 1.458 1.485 -0.026 1.27e-02 6.20e+03 4.25e+00 ... (remaining 4759 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.04: 5994 1.04 - 2.08: 337 2.08 - 3.12: 72 3.12 - 4.15: 26 4.15 - 5.19: 4 Bond angle restraints: 6433 Sorted by residual: angle pdb=" C PRO E 308 " pdb=" CA PRO E 308 " pdb=" CB PRO E 308 " ideal model delta sigma weight residual 111.23 107.44 3.79 1.28e+00 6.10e-01 8.76e+00 angle pdb=" N GLU D 164 " pdb=" CA GLU D 164 " pdb=" C GLU D 164 " ideal model delta sigma weight residual 111.75 107.99 3.76 1.28e+00 6.10e-01 8.64e+00 angle pdb=" CA PRO E 308 " pdb=" C PRO E 308 " pdb=" O PRO E 308 " ideal model delta sigma weight residual 121.56 118.19 3.37 1.16e+00 7.43e-01 8.46e+00 angle pdb=" C PHE E 316 " pdb=" N ASP E 317 " pdb=" CA ASP E 317 " ideal model delta sigma weight residual 123.10 120.45 2.65 9.60e-01 1.09e+00 7.65e+00 angle pdb=" CA GLU D 162 " pdb=" C GLU D 162 " pdb=" O GLU D 162 " ideal model delta sigma weight residual 120.32 117.50 2.82 1.02e+00 9.61e-01 7.62e+00 ... (remaining 6428 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 2629 17.89 - 35.78: 211 35.78 - 53.67: 44 53.67 - 71.57: 15 71.57 - 89.46: 6 Dihedral angle restraints: 2905 sinusoidal: 1241 harmonic: 1664 Sorted by residual: dihedral pdb=" CA ILE D 265 " pdb=" C ILE D 265 " pdb=" N TYR D 266 " pdb=" CA TYR D 266 " ideal model delta harmonic sigma weight residual 180.00 -155.97 -24.03 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA TYR E 266 " pdb=" C TYR E 266 " pdb=" N ASP E 267 " pdb=" CA ASP E 267 " ideal model delta harmonic sigma weight residual 180.00 157.83 22.17 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA GLN D 322 " pdb=" C GLN D 322 " pdb=" N ASN D 323 " pdb=" CA ASN D 323 " ideal model delta harmonic sigma weight residual -180.00 -159.09 -20.91 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 2902 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 467 0.031 - 0.062: 136 0.062 - 0.092: 52 0.092 - 0.123: 29 0.123 - 0.154: 6 Chirality restraints: 690 Sorted by residual: chirality pdb=" CA LEU D 160 " pdb=" N LEU D 160 " pdb=" C LEU D 160 " pdb=" CB LEU D 160 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.90e-01 chirality pdb=" CA GLU D 164 " pdb=" N GLU D 164 " pdb=" C GLU D 164 " pdb=" CB GLU D 164 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 5.16e-01 chirality pdb=" CA PRO E 197 " pdb=" N PRO E 197 " pdb=" C PRO E 197 " pdb=" CB PRO E 197 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 5.03e-01 ... (remaining 687 not shown) Planarity restraints: 851 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU E 348 " -0.009 2.00e-02 2.50e+03 1.85e-02 3.43e+00 pdb=" C LEU E 348 " 0.032 2.00e-02 2.50e+03 pdb=" O LEU E 348 " -0.012 2.00e-02 2.50e+03 pdb=" N LYS E 349 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN D 240 " -0.030 5.00e-02 4.00e+02 4.60e-02 3.38e+00 pdb=" N PRO D 241 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO D 241 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 241 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 88 " -0.027 5.00e-02 4.00e+02 4.11e-02 2.70e+00 pdb=" N PRO D 89 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO D 89 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 89 " -0.023 5.00e-02 4.00e+02 ... (remaining 848 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 65 2.57 - 3.15: 4141 3.15 - 3.73: 7324 3.73 - 4.32: 10238 4.32 - 4.90: 16541 Nonbonded interactions: 38309 Sorted by model distance: nonbonded pdb=" OH TYR E 252 " pdb=" OD1 ASP E 341 " model vdw 1.981 3.040 nonbonded pdb=" OH TYR D 252 " pdb=" OD1 ASP D 341 " model vdw 1.998 3.040 nonbonded pdb=" OH TYR D 260 " pdb=" OD2 ASP E 358 " model vdw 2.022 3.040 nonbonded pdb=" O LEU E 160 " pdb=" ND2 ASN E 161 " model vdw 2.061 3.120 nonbonded pdb=" O TYR E 260 " pdb=" OG SER E 261 " model vdw 2.128 3.040 ... (remaining 38304 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 Found NCS groups: ncs_group { reference = (chain 'D' and resid 83 through 365) selection = chain 'E' } 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: 0.920 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: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.000 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6860 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 0.032 4764 Z= 0.178 Angle : 0.592 5.193 6433 Z= 0.341 Chirality : 0.040 0.154 690 Planarity : 0.005 0.058 851 Dihedral : 14.698 89.457 1825 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.39 % Allowed : 0.39 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.35), residues: 564 helix: 1.50 (0.33), residues: 243 sheet: 0.82 (0.47), residues: 94 loop : -0.31 (0.43), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 189 HIS 0.003 0.001 HIS D 268 PHE 0.020 0.002 PHE E 188 TYR 0.014 0.002 TYR E 266 ARG 0.006 0.001 ARG E 135 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 57 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 58 average time/residue: 0.2153 time to fit residues: 15.4788 Evaluate side-chains 40 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 39 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 160 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 47 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 22 optimal weight: 20.0000 chunk 43 optimal weight: 1.9990 chunk 16 optimal weight: 0.0670 chunk 26 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 50 optimal weight: 6.9990 overall best weight: 1.3922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 161 ASN ** E 299 GLN ** 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 = 0.4286 r_free = 0.4286 target = 0.103971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.081600 restraints weight = 17412.180| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 6.12 r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 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 : 0.004 0.043 4764 Z= 0.267 Angle : 0.662 6.097 6433 Z= 0.361 Chirality : 0.045 0.156 690 Planarity : 0.005 0.047 851 Dihedral : 6.190 26.063 606 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.77 % Allowed : 7.34 % Favored : 91.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.03 (0.35), residues: 564 helix: 1.28 (0.31), residues: 250 sheet: 1.34 (0.45), residues: 92 loop : -0.20 (0.46), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 189 HIS 0.002 0.001 HIS E 281 PHE 0.028 0.003 PHE E 188 TYR 0.016 0.002 TYR D 84 ARG 0.015 0.001 ARG D 135 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 335 GLU cc_start: 0.8722 (mm-30) cc_final: 0.8393 (mm-30) REVERT: D 346 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7222 (mp0) REVERT: E 349 LYS cc_start: 0.7944 (tttt) cc_final: 0.7717 (tttp) outliers start: 4 outliers final: 3 residues processed: 46 average time/residue: 0.2096 time to fit residues: 12.1758 Evaluate side-chains 40 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 37 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain E residue 352 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 6 optimal weight: 8.9990 chunk 7 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 51 optimal weight: 0.0570 chunk 3 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 18 optimal weight: 0.5980 overall best weight: 0.8902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 294 ASN E 268 HIS ** E 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.104939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.082991 restraints weight = 17034.647| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 5.96 r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4764 Z= 0.203 Angle : 0.610 6.817 6433 Z= 0.326 Chirality : 0.042 0.139 690 Planarity : 0.005 0.046 851 Dihedral : 6.046 26.832 606 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.16 % Allowed : 8.11 % Favored : 90.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.06 (0.35), residues: 564 helix: 1.15 (0.31), residues: 262 sheet: 1.39 (0.47), residues: 92 loop : -0.07 (0.48), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 189 HIS 0.001 0.001 HIS E 281 PHE 0.018 0.002 PHE E 188 TYR 0.025 0.002 TYR D 84 ARG 0.004 0.000 ARG D 290 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 335 GLU cc_start: 0.8863 (mm-30) cc_final: 0.8511 (mm-30) REVERT: D 346 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7246 (mp0) REVERT: E 346 GLU cc_start: 0.8719 (tp30) cc_final: 0.8429 (tp30) outliers start: 6 outliers final: 4 residues processed: 48 average time/residue: 0.2097 time to fit residues: 12.7690 Evaluate side-chains 41 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain E residue 118 PHE Chi-restraints excluded: chain E residue 274 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 44 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 2 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 299 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 = 0.4317 r_free = 0.4317 target = 0.105033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.081907 restraints weight = 17818.526| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 6.37 r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4764 Z= 0.195 Angle : 0.585 6.963 6433 Z= 0.311 Chirality : 0.042 0.151 690 Planarity : 0.004 0.039 851 Dihedral : 5.830 26.547 606 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.54 % Allowed : 9.65 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.35 (0.36), residues: 564 helix: 1.41 (0.32), residues: 251 sheet: 1.66 (0.48), residues: 90 loop : 0.08 (0.47), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 189 HIS 0.002 0.001 HIS E 268 PHE 0.015 0.002 PHE D 124 TYR 0.015 0.002 TYR D 84 ARG 0.003 0.000 ARG D 135 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 335 GLU cc_start: 0.8971 (mm-30) cc_final: 0.8594 (mm-30) REVERT: E 266 TYR cc_start: 0.8050 (p90) cc_final: 0.7790 (p90) REVERT: E 346 GLU cc_start: 0.8756 (tp30) cc_final: 0.8449 (tp30) outliers start: 8 outliers final: 5 residues processed: 48 average time/residue: 0.1910 time to fit residues: 11.8299 Evaluate side-chains 43 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 240 ASN Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain E residue 118 PHE Chi-restraints excluded: chain E residue 274 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 20 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 35 optimal weight: 9.9990 chunk 29 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 299 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 = 0.4318 r_free = 0.4318 target = 0.104234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.081923 restraints weight = 17378.969| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 6.17 r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.2949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4764 Z= 0.192 Angle : 0.584 7.990 6433 Z= 0.306 Chirality : 0.041 0.154 690 Planarity : 0.004 0.036 851 Dihedral : 5.697 26.351 606 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.93 % Allowed : 10.42 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.38 (0.36), residues: 564 helix: 1.49 (0.32), residues: 251 sheet: 1.20 (0.51), residues: 98 loop : 0.21 (0.48), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 189 HIS 0.002 0.001 HIS E 268 PHE 0.013 0.002 PHE D 124 TYR 0.014 0.001 TYR D 84 ARG 0.003 0.000 ARG D 135 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 212 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7643 (mp0) REVERT: D 335 GLU cc_start: 0.9054 (mm-30) cc_final: 0.8672 (mm-30) REVERT: E 249 CYS cc_start: 0.8825 (OUTLIER) cc_final: 0.8613 (p) REVERT: E 266 TYR cc_start: 0.8068 (p90) cc_final: 0.7830 (p90) REVERT: E 346 GLU cc_start: 0.8762 (tp30) cc_final: 0.8456 (tp30) outliers start: 10 outliers final: 6 residues processed: 49 average time/residue: 0.1866 time to fit residues: 11.7610 Evaluate side-chains 46 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 38 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 212 GLU Chi-restraints excluded: chain D residue 240 ASN Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain E residue 118 PHE Chi-restraints excluded: chain E residue 249 CYS Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain E residue 348 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 32 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 37 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 chunk 49 optimal weight: 0.0980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 326 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.103207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.081164 restraints weight = 17685.081| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 6.19 r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4764 Z= 0.238 Angle : 0.606 7.891 6433 Z= 0.319 Chirality : 0.042 0.139 690 Planarity : 0.004 0.035 851 Dihedral : 5.688 26.463 606 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.93 % Allowed : 11.97 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.25 (0.36), residues: 564 helix: 1.37 (0.31), residues: 251 sheet: 1.15 (0.53), residues: 98 loop : 0.15 (0.47), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 189 HIS 0.003 0.001 HIS E 268 PHE 0.021 0.002 PHE D 233 TYR 0.011 0.002 TYR E 260 ARG 0.007 0.001 ARG D 234 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 335 GLU cc_start: 0.9113 (mm-30) cc_final: 0.8723 (mm-30) REVERT: E 249 CYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8655 (p) REVERT: E 266 TYR cc_start: 0.8148 (p90) cc_final: 0.7884 (p90) REVERT: E 346 GLU cc_start: 0.8838 (tp30) cc_final: 0.8546 (tp30) outliers start: 10 outliers final: 5 residues processed: 49 average time/residue: 0.1624 time to fit residues: 10.5670 Evaluate side-chains 45 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain E residue 118 PHE Chi-restraints excluded: chain E residue 249 CYS Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain E residue 348 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 54 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 2 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 154 GLN E 292 GLN ** E 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.103642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.081637 restraints weight = 17672.576| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 6.23 r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4764 Z= 0.207 Angle : 0.608 12.181 6433 Z= 0.311 Chirality : 0.041 0.141 690 Planarity : 0.004 0.036 851 Dihedral : 5.511 26.584 604 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.54 % Allowed : 13.13 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.31 (0.37), residues: 564 helix: 1.47 (0.32), residues: 248 sheet: 1.00 (0.55), residues: 100 loop : 0.24 (0.48), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 189 HIS 0.002 0.001 HIS E 268 PHE 0.013 0.002 PHE D 233 TYR 0.011 0.002 TYR E 260 ARG 0.004 0.001 ARG D 234 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 335 GLU cc_start: 0.9135 (mm-30) cc_final: 0.8748 (mm-30) REVERT: E 117 MET cc_start: 0.8707 (ppp) cc_final: 0.8210 (ppp) REVERT: E 249 CYS cc_start: 0.8888 (OUTLIER) cc_final: 0.8625 (p) REVERT: E 266 TYR cc_start: 0.8128 (p90) cc_final: 0.7904 (p90) outliers start: 8 outliers final: 5 residues processed: 47 average time/residue: 0.1783 time to fit residues: 11.1634 Evaluate side-chains 44 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain E residue 118 PHE Chi-restraints excluded: chain E residue 249 CYS Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain E residue 348 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 44 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 22 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 34 optimal weight: 6.9990 chunk 49 optimal weight: 20.0000 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 299 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 = 0.4295 r_free = 0.4295 target = 0.103617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.081675 restraints weight = 17740.352| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 6.24 r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4764 Z= 0.213 Angle : 0.629 11.030 6433 Z= 0.319 Chirality : 0.042 0.160 690 Planarity : 0.004 0.035 851 Dihedral : 5.477 26.668 604 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.93 % Allowed : 13.32 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.27 (0.37), residues: 564 helix: 1.45 (0.31), residues: 248 sheet: 0.96 (0.55), residues: 100 loop : 0.20 (0.48), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 189 HIS 0.002 0.001 HIS E 268 PHE 0.015 0.002 PHE D 233 TYR 0.012 0.002 TYR E 260 ARG 0.004 0.001 ARG D 234 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 335 GLU cc_start: 0.9158 (mm-30) cc_final: 0.8758 (mm-30) REVERT: E 117 MET cc_start: 0.8569 (ppp) cc_final: 0.8127 (ppp) REVERT: E 214 LEU cc_start: 0.8873 (tt) cc_final: 0.8645 (tt) REVERT: E 249 CYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8618 (p) REVERT: E 266 TYR cc_start: 0.8165 (p90) cc_final: 0.7965 (p90) REVERT: E 346 GLU cc_start: 0.8861 (tp30) cc_final: 0.8572 (tp30) outliers start: 10 outliers final: 6 residues processed: 47 average time/residue: 0.1727 time to fit residues: 10.8703 Evaluate side-chains 44 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 118 PHE Chi-restraints excluded: chain E residue 249 CYS Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain E residue 348 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 20 optimal weight: 0.0070 chunk 54 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 20.0000 chunk 23 optimal weight: 0.8980 chunk 22 optimal weight: 5.9990 chunk 28 optimal weight: 0.5980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 299 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 = 0.104153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.082607 restraints weight = 17733.905| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 6.12 r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.3565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4764 Z= 0.181 Angle : 0.642 11.349 6433 Z= 0.320 Chirality : 0.041 0.190 690 Planarity : 0.004 0.036 851 Dihedral : 5.426 26.779 604 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.54 % Allowed : 14.09 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.30 (0.37), residues: 564 helix: 1.51 (0.31), residues: 248 sheet: 0.90 (0.56), residues: 101 loop : 0.21 (0.48), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 359 HIS 0.002 0.001 HIS D 268 PHE 0.014 0.002 PHE D 124 TYR 0.010 0.001 TYR E 260 ARG 0.004 0.000 ARG D 234 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 335 GLU cc_start: 0.9166 (mm-30) cc_final: 0.8738 (mm-30) REVERT: E 117 MET cc_start: 0.8581 (ppp) cc_final: 0.8163 (ppp) REVERT: E 214 LEU cc_start: 0.8840 (tt) cc_final: 0.8614 (tt) REVERT: E 249 CYS cc_start: 0.8829 (OUTLIER) cc_final: 0.8600 (p) outliers start: 8 outliers final: 5 residues processed: 47 average time/residue: 0.1664 time to fit residues: 10.6747 Evaluate side-chains 42 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain E residue 118 PHE Chi-restraints excluded: chain E residue 249 CYS Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain E residue 348 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 21 optimal weight: 8.9990 chunk 17 optimal weight: 0.8980 chunk 37 optimal weight: 5.9990 chunk 23 optimal weight: 0.0030 chunk 41 optimal weight: 6.9990 chunk 9 optimal weight: 10.0000 chunk 18 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 55 optimal weight: 0.0770 chunk 51 optimal weight: 0.0570 chunk 8 optimal weight: 0.9980 overall best weight: 0.3466 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 299 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 = 0.4333 r_free = 0.4333 target = 0.105685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.083786 restraints weight = 17082.335| |-----------------------------------------------------------------------------| r_work (start): 0.3904 rms_B_bonded: 6.16 r_work (final): 0.3904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 4764 Z= 0.162 Angle : 0.624 10.716 6433 Z= 0.310 Chirality : 0.041 0.216 690 Planarity : 0.004 0.039 851 Dihedral : 5.282 26.686 604 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.35 % Allowed : 13.90 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.28 (0.37), residues: 564 helix: 1.52 (0.31), residues: 253 sheet: 0.89 (0.56), residues: 100 loop : 0.11 (0.47), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 359 HIS 0.002 0.000 HIS E 268 PHE 0.014 0.001 PHE D 124 TYR 0.023 0.002 TYR D 266 ARG 0.004 0.000 ARG D 234 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1128 Ramachandran restraints generated. 564 Oldfield, 0 Emsley, 564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 335 GLU cc_start: 0.9174 (mm-30) cc_final: 0.8754 (mm-30) REVERT: E 117 MET cc_start: 0.8603 (ppp) cc_final: 0.8206 (ppp) REVERT: E 214 LEU cc_start: 0.8813 (tt) cc_final: 0.8596 (tt) REVERT: E 249 CYS cc_start: 0.8723 (OUTLIER) cc_final: 0.8492 (p) outliers start: 7 outliers final: 5 residues processed: 50 average time/residue: 0.1642 time to fit residues: 10.9286 Evaluate side-chains 44 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 118 PHE Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 249 CYS Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain E residue 348 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 7 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 18 optimal weight: 0.0010 chunk 1 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 299 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 = 0.4330 r_free = 0.4330 target = 0.105471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.083512 restraints weight = 17201.711| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 6.17 r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.3913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 4764 Z= 0.173 Angle : 0.635 10.744 6433 Z= 0.314 Chirality : 0.040 0.201 690 Planarity : 0.004 0.038 851 Dihedral : 5.288 26.624 604 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.35 % Allowed : 14.48 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.27 (0.37), residues: 564 helix: 1.52 (0.31), residues: 253 sheet: 0.71 (0.56), residues: 102 loop : 0.20 (0.48), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 189 HIS 0.002 0.001 HIS D 268 PHE 0.016 0.002 PHE E 188 TYR 0.015 0.002 TYR D 266 ARG 0.006 0.001 ARG E 293 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2836.78 seconds wall clock time: 50 minutes 47.79 seconds (3047.79 seconds total)