Starting phenix.real_space_refine on Thu Mar 6 03:35:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b23_44095/03_2025/9b23_44095.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b23_44095/03_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_44095/03_2025/9b23_44095.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b23_44095/03_2025/9b23_44095.map" model { file = "/net/cci-nas-00/data/ceres_data/9b23_44095/03_2025/9b23_44095.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b23_44095/03_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 3.77, per 1000 atoms: 0.81 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: 1.19 Conformation dependent library (CDL) restraints added in 642.5 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: 0.51 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: 1.34 Time building geometry restraints manager: 1.41 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: 1.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.060 Process input model: 16.160 Find NCS groups from input model: 0.180 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.020 ------------------------------------------------------------------------------- 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 : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 58 average time/residue: 0.2202 time to fit residues: 15.8781 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 : 0.533 ------------------------------------------------------------------------------- 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 = 0.081599 restraints weight = 17412.179| |-----------------------------------------------------------------------------| 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 : 0.541 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: 0.7728 (mt-10) cc_final: 0.7221 (mp0) REVERT: E 349 LYS cc_start: 0.7944 (tttt) cc_final: 0.7716 (tttp) outliers start: 4 outliers final: 3 residues processed: 46 average time/residue: 0.2111 time to fit residues: 12.2809 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 : 0.530 ------------------------------------------------------------------------------- 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: 0.0370 chunk 3 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 52 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 chunk 18 optimal weight: 0.5980 overall best weight: 0.6862 ------------------------------------------------------------------------------- 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 = 0.4325 r_free = 0.4325 target = 0.105655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.082547 restraints weight = 17455.142| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 6.32 r_work (final): 0.3873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4764 Z= 0.188 Angle : 0.601 6.825 6433 Z= 0.322 Chirality : 0.042 0.142 690 Planarity : 0.005 0.044 851 Dihedral : 5.990 27.142 606 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % 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: 1.22 (0.36), residues: 564 helix: 1.34 (0.31), residues: 256 sheet: 1.40 (0.47), residues: 92 loop : 0.01 (0.48), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 359 HIS 0.001 0.000 HIS E 281 PHE 0.017 0.002 PHE E 188 TYR 0.023 0.002 TYR D 84 ARG 0.006 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 55 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 335 GLU cc_start: 0.8872 (mm-30) cc_final: 0.8534 (mm-30) REVERT: D 346 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7261 (mp0) REVERT: E 266 TYR cc_start: 0.7851 (p90) cc_final: 0.7624 (p90) REVERT: E 346 GLU cc_start: 0.8745 (tp30) cc_final: 0.8455 (tp30) outliers start: 6 outliers final: 4 residues processed: 51 average time/residue: 0.2036 time to fit residues: 13.2296 Evaluate side-chains 43 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.598 ------------------------------------------------------------------------------- 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: 0.6980 chunk 53 optimal weight: 0.8980 chunk 35 optimal weight: 9.9990 chunk 1 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 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 = 0.4320 r_free = 0.4320 target = 0.105190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.082096 restraints weight = 17770.627| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 6.29 r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.2642 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= 0.193 Angle : 0.587 7.357 6433 Z= 0.312 Chirality : 0.042 0.150 690 Planarity : 0.004 0.039 851 Dihedral : 5.803 26.975 606 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.74 % Allowed : 9.27 % Favored : 89.00 % 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: 1.46 (0.32), residues: 251 sheet: 1.60 (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 0.014 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 50 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 335 GLU cc_start: 0.8967 (mm-30) cc_final: 0.8589 (mm-30) REVERT: E 266 TYR cc_start: 0.8049 (p90) cc_final: 0.7786 (p90) REVERT: E 346 GLU cc_start: 0.8731 (tp30) cc_final: 0.8409 (tp30) outliers start: 9 outliers final: 5 residues processed: 47 average time/residue: 0.2123 time to fit residues: 13.0144 Evaluate side-chains 42 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 240 ASN Chi-restraints excluded: chain E residue 118 PHE Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain E residue 348 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 20 optimal weight: 0.9980 chunk 52 optimal weight: 10.0000 chunk 32 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 23 optimal weight: 0.4980 chunk 5 optimal weight: 0.7980 chunk 35 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4310 r_free = 0.4310 target = 0.103856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.081581 restraints weight = 17341.578| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 6.17 r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.2952 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= 0.205 Angle : 0.592 7.934 6433 Z= 0.311 Chirality : 0.041 0.154 690 Planarity : 0.004 0.036 851 Dihedral : 5.718 26.574 606 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.35 % Allowed : 10.04 % Favored : 88.61 % 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: 1.37 (0.36), residues: 564 helix: 1.52 (0.32), residues: 251 sheet: 1.09 (0.50), residues: 98 loop : 0.23 (0.48), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 189 HIS 0.002 0.001 HIS E 268 PHE 0.014 0.002 PHE D 233 TYR 0.013 0.001 TYR D 84 ARG 0.004 0.001 ARG D 290 *********************** 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 48 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 335 GLU cc_start: 0.9052 (mm-30) cc_final: 0.8670 (mm-30) REVERT: E 249 CYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8611 (p) REVERT: E 266 TYR cc_start: 0.8098 (p90) cc_final: 0.7846 (p90) REVERT: E 346 GLU cc_start: 0.8799 (tp30) cc_final: 0.8502 (tp30) outliers start: 7 outliers final: 4 residues processed: 46 average time/residue: 0.1902 time to fit residues: 11.5206 Evaluate side-chains 44 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 240 ASN Chi-restraints excluded: chain E residue 118 PHE Chi-restraints excluded: chain E residue 249 CYS Chi-restraints excluded: chain E residue 274 ILE 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: 2.9990 chunk 12 optimal weight: 0.3980 chunk 27 optimal weight: 2.9990 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: 2.9990 chunk 49 optimal weight: 5.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- 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 = 0.4266 r_free = 0.4266 target = 0.101964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.079988 restraints weight = 17625.151| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 6.12 r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4764 Z= 0.284 Angle : 0.623 7.672 6433 Z= 0.330 Chirality : 0.043 0.146 690 Planarity : 0.004 0.037 851 Dihedral : 5.796 27.042 606 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.93 % Allowed : 11.20 % Favored : 86.87 % 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: 1.20 (0.37), residues: 564 helix: 1.34 (0.31), residues: 251 sheet: 1.02 (0.52), residues: 98 loop : 0.16 (0.48), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 189 HIS 0.003 0.001 HIS E 268 PHE 0.022 0.003 PHE D 233 TYR 0.012 0.002 TYR E 260 ARG 0.004 0.001 ARG D 135 *********************** 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 48 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 0.578 Fit side-chains REVERT: D 335 GLU cc_start: 0.9089 (mm-30) cc_final: 0.8689 (mm-30) REVERT: E 106 LEU cc_start: 0.8691 (tp) cc_final: 0.8305 (pp) REVERT: E 249 CYS cc_start: 0.8930 (OUTLIER) cc_final: 0.8662 (p) REVERT: E 266 TYR cc_start: 0.8156 (p90) cc_final: 0.7884 (p90) REVERT: E 346 GLU cc_start: 0.8809 (tp30) cc_final: 0.8535 (tp30) outliers start: 10 outliers final: 5 residues processed: 45 average time/residue: 0.1806 time to fit residues: 10.7295 Evaluate side-chains 41 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 343 SER 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: 0.9980 chunk 53 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 2 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 27 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 = 0.4298 r_free = 0.4298 target = 0.103815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.081743 restraints weight = 17542.609| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 6.25 r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4764 Z= 0.197 Angle : 0.620 9.254 6433 Z= 0.323 Chirality : 0.041 0.151 690 Planarity : 0.004 0.036 851 Dihedral : 5.666 26.898 606 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.35 % Allowed : 13.13 % Favored : 85.52 % 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: 1.29 (0.37), residues: 564 helix: 1.50 (0.32), residues: 248 sheet: 0.72 (0.53), residues: 102 loop : 0.31 (0.49), residues: 214 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 D 84 ARG 0.003 0.001 ARG D 135 *********************** 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 47 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.600 Fit side-chains revert: symmetry clash REVERT: D 335 GLU cc_start: 0.9130 (mm-30) cc_final: 0.8745 (mm-30) REVERT: E 117 MET cc_start: 0.8706 (ppp) cc_final: 0.8222 (ppp) REVERT: E 214 LEU cc_start: 0.8863 (tt) cc_final: 0.8648 (tt) REVERT: E 249 CYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8637 (p) REVERT: E 266 TYR cc_start: 0.8128 (p90) cc_final: 0.7902 (p90) outliers start: 7 outliers final: 3 residues processed: 45 average time/residue: 0.1665 time to fit residues: 10.3077 Evaluate side-chains 40 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 31 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 22 optimal weight: 9.9990 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 chunk 49 optimal weight: 20.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 292 GLN ** 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 = 0.4306 r_free = 0.4306 target = 0.104011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.080815 restraints weight = 17983.673| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 6.42 r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.3416 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= 0.198 Angle : 0.625 8.710 6433 Z= 0.322 Chirality : 0.042 0.155 690 Planarity : 0.004 0.035 851 Dihedral : 5.474 26.919 604 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.54 % Allowed : 13.51 % Favored : 84.94 % 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 (0.37), residues: 564 helix: 1.50 (0.32), residues: 248 sheet: 0.75 (0.53), residues: 101 loop : 0.21 (0.48), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 132 HIS 0.002 0.001 HIS D 268 PHE 0.013 0.002 PHE D 124 TYR 0.011 0.001 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: 8 poor density : 40 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 335 GLU cc_start: 0.9150 (mm-30) cc_final: 0.8750 (mm-30) REVERT: E 117 MET cc_start: 0.8575 (ppp) cc_final: 0.8130 (ppp) REVERT: E 214 LEU cc_start: 0.8892 (tt) cc_final: 0.8668 (tt) REVERT: E 249 CYS cc_start: 0.8818 (OUTLIER) cc_final: 0.8571 (p) outliers start: 8 outliers final: 4 residues processed: 47 average time/residue: 0.1578 time to fit residues: 10.1761 Evaluate side-chains 41 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 343 SER 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: 3.9990 chunk 54 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 6 optimal weight: 20.0000 chunk 23 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.4296 r_free = 0.4296 target = 0.103674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.081608 restraints weight = 17709.182| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 6.22 r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.3585 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= 0.198 Angle : 0.659 11.692 6433 Z= 0.329 Chirality : 0.041 0.188 690 Planarity : 0.004 0.036 851 Dihedral : 5.418 26.863 604 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.16 % Allowed : 14.48 % 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: 1.25 (0.37), residues: 564 helix: 1.51 (0.32), residues: 248 sheet: 0.77 (0.54), residues: 101 loop : 0.19 (0.47), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 132 HIS 0.002 0.001 HIS D 268 PHE 0.013 0.002 PHE D 124 TYR 0.011 0.002 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 45 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 335 GLU cc_start: 0.9164 (mm-30) cc_final: 0.8750 (mm-30) REVERT: E 117 MET cc_start: 0.8567 (ppp) cc_final: 0.8157 (ppp) REVERT: E 214 LEU cc_start: 0.8858 (tt) cc_final: 0.8626 (tt) REVERT: E 249 CYS cc_start: 0.8848 (OUTLIER) cc_final: 0.8606 (p) outliers start: 6 outliers final: 4 residues processed: 44 average time/residue: 0.1652 time to fit residues: 9.9127 Evaluate side-chains 41 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 343 SER 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: 1.9990 chunk 37 optimal weight: 30.0000 chunk 23 optimal weight: 0.4980 chunk 41 optimal weight: 6.9990 chunk 9 optimal weight: 8.9990 chunk 18 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 55 optimal weight: 0.0970 chunk 51 optimal weight: 0.0000 chunk 8 optimal weight: 0.0570 overall best weight: 0.2700 ------------------------------------------------------------------------------- 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 = 0.4339 r_free = 0.4339 target = 0.105532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.083375 restraints weight = 16923.347| |-----------------------------------------------------------------------------| r_work (start): 0.3905 rms_B_bonded: 6.19 r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.3733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 4764 Z= 0.169 Angle : 0.649 10.599 6433 Z= 0.323 Chirality : 0.041 0.215 690 Planarity : 0.004 0.037 851 Dihedral : 5.277 26.800 604 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.77 % Allowed : 15.06 % 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: 1.57 (0.31), residues: 253 sheet: 0.79 (0.54), residues: 100 loop : 0.10 (0.48), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 359 HIS 0.001 0.000 HIS E 268 PHE 0.015 0.001 PHE D 124 TYR 0.033 0.002 TYR D 266 ARG 0.005 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 46 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 335 GLU cc_start: 0.9160 (mm-30) cc_final: 0.8737 (mm-30) REVERT: E 117 MET cc_start: 0.8598 (ppp) cc_final: 0.8177 (ppp) REVERT: E 214 LEU cc_start: 0.8819 (tt) cc_final: 0.8595 (tt) outliers start: 4 outliers final: 4 residues processed: 44 average time/residue: 0.1900 time to fit residues: 11.0004 Evaluate side-chains 42 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain E residue 118 PHE 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: 5.9990 chunk 53 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 40 optimal weight: 0.0170 chunk 51 optimal weight: 0.8980 chunk 43 optimal weight: 0.4980 chunk 18 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 overall best weight: 0.6018 ------------------------------------------------------------------------------- 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 = 0.4326 r_free = 0.4326 target = 0.104686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.082776 restraints weight = 17035.808| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 6.09 r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.3890 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= 0.175 Angle : 0.638 10.714 6433 Z= 0.318 Chirality : 0.041 0.206 690 Planarity : 0.004 0.038 851 Dihedral : 5.242 26.787 604 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.97 % Allowed : 15.06 % Favored : 83.98 % 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 (0.36), residues: 564 helix: 1.56 (0.31), residues: 253 sheet: 0.59 (0.54), residues: 102 loop : 0.22 (0.48), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 189 HIS 0.002 0.001 HIS D 268 PHE 0.014 0.002 PHE E 188 TYR 0.018 0.002 TYR D 266 ARG 0.004 0.000 ARG D 234 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2837.96 seconds wall clock time: 49 minutes 16.09 seconds (2956.09 seconds total)