Starting phenix.real_space_refine on Wed Mar 12 15:35:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uke_26578/03_2025/7uke_26578.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uke_26578/03_2025/7uke_26578.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7uke_26578/03_2025/7uke_26578.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uke_26578/03_2025/7uke_26578.map" model { file = "/net/cci-nas-00/data/ceres_data/7uke_26578/03_2025/7uke_26578.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uke_26578/03_2025/7uke_26578.cif" } resolution = 3.01 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= 0.005 sd= 0.060 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: 5 Type Number sf(0) Gaussians K 4 8.98 5 S 56 5.16 5 C 5252 2.51 5 N 1332 2.21 5 O 1356 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8000 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1999 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 10, 'TRANS': 248} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' K': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Restraints were copied for chains: B, C, D Time building chain proxies: 4.69, per 1000 atoms: 0.59 Number of scatterers: 8000 At special positions: 0 Unit cell: (116.466, 116.466, 83.426, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 4 19.00 S 56 16.00 O 1356 8.00 N 1332 7.00 C 5252 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: 1.99 Conformation dependent library (CDL) restraints added in 1.1 seconds 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1952 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 4 sheets defined 84.3% alpha, 1.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 166 through 177 Processing helix chain 'A' and resid 178 through 181 Processing helix chain 'A' and resid 182 through 205 Processing helix chain 'A' and resid 221 through 225 Processing helix chain 'A' and resid 225 through 250 Processing helix chain 'A' and resid 253 through 260 Processing helix chain 'A' and resid 260 through 279 Proline residue: A 272 - end of helix Processing helix chain 'A' and resid 287 through 296 Processing helix chain 'A' and resid 297 through 307 removed outlier: 3.578A pdb=" N ARG A 305 " --> pdb=" O LYS A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 320 Processing helix chain 'A' and resid 320 through 347 Processing helix chain 'A' and resid 356 through 369 removed outlier: 3.939A pdb=" N TRP A 362 " --> pdb=" O PRO A 358 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N TYR A 363 " --> pdb=" O ALA A 359 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR A 369 " --> pdb=" O ILE A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 398 Processing helix chain 'A' and resid 400 through 424 removed outlier: 4.749A pdb=" N VAL A 404 " --> pdb=" O LEU A 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 177 Processing helix chain 'B' and resid 178 through 181 Processing helix chain 'B' and resid 182 through 205 Processing helix chain 'B' and resid 221 through 225 Processing helix chain 'B' and resid 225 through 250 Processing helix chain 'B' and resid 253 through 260 Processing helix chain 'B' and resid 260 through 279 Proline residue: B 272 - end of helix Processing helix chain 'B' and resid 287 through 296 Processing helix chain 'B' and resid 297 through 307 removed outlier: 3.578A pdb=" N ARG B 305 " --> pdb=" O LYS B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 320 Processing helix chain 'B' and resid 320 through 347 Processing helix chain 'B' and resid 356 through 369 removed outlier: 3.939A pdb=" N TRP B 362 " --> pdb=" O PRO B 358 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N TYR B 363 " --> pdb=" O ALA B 359 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR B 369 " --> pdb=" O ILE B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 398 Processing helix chain 'B' and resid 400 through 424 removed outlier: 4.749A pdb=" N VAL B 404 " --> pdb=" O LEU B 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 177 Processing helix chain 'C' and resid 178 through 181 Processing helix chain 'C' and resid 182 through 205 Processing helix chain 'C' and resid 221 through 225 Processing helix chain 'C' and resid 225 through 250 Processing helix chain 'C' and resid 253 through 260 Processing helix chain 'C' and resid 260 through 279 Proline residue: C 272 - end of helix Processing helix chain 'C' and resid 287 through 296 Processing helix chain 'C' and resid 297 through 307 removed outlier: 3.578A pdb=" N ARG C 305 " --> pdb=" O LYS C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 320 Processing helix chain 'C' and resid 320 through 347 Processing helix chain 'C' and resid 356 through 369 removed outlier: 3.939A pdb=" N TRP C 362 " --> pdb=" O PRO C 358 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N TYR C 363 " --> pdb=" O ALA C 359 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR C 369 " --> pdb=" O ILE C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 398 Processing helix chain 'C' and resid 400 through 424 removed outlier: 4.749A pdb=" N VAL C 404 " --> pdb=" O LEU C 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 177 Processing helix chain 'D' and resid 178 through 181 Processing helix chain 'D' and resid 182 through 205 Processing helix chain 'D' and resid 221 through 225 Processing helix chain 'D' and resid 225 through 250 Processing helix chain 'D' and resid 253 through 260 Processing helix chain 'D' and resid 260 through 279 Proline residue: D 272 - end of helix Processing helix chain 'D' and resid 287 through 296 Processing helix chain 'D' and resid 297 through 307 removed outlier: 3.578A pdb=" N ARG D 305 " --> pdb=" O LYS D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 320 Processing helix chain 'D' and resid 320 through 347 Processing helix chain 'D' and resid 356 through 369 removed outlier: 3.938A pdb=" N TRP D 362 " --> pdb=" O PRO D 358 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N TYR D 363 " --> pdb=" O ALA D 359 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR D 369 " --> pdb=" O ILE D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 398 Processing helix chain 'D' and resid 400 through 424 removed outlier: 4.750A pdb=" N VAL D 404 " --> pdb=" O LEU D 400 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 210 removed outlier: 7.413A pdb=" N LEU A 219 " --> pdb=" O CYS A 209 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 208 through 210 removed outlier: 7.413A pdb=" N LEU B 219 " --> pdb=" O CYS B 209 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 208 through 210 removed outlier: 7.414A pdb=" N LEU C 219 " --> pdb=" O CYS C 209 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 208 through 210 removed outlier: 7.413A pdb=" N LEU D 219 " --> pdb=" O CYS D 209 " (cutoff:3.500A) 629 hydrogen bonds defined for protein. 1791 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.26 Time building geometry restraints manager: 2.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2436 1.34 - 1.46: 1837 1.46 - 1.58: 3827 1.58 - 1.69: 0 1.69 - 1.81: 88 Bond restraints: 8188 Sorted by residual: bond pdb=" CA ILE C 398 " pdb=" C ILE C 398 " ideal model delta sigma weight residual 1.518 1.530 -0.012 1.13e-02 7.83e+03 1.12e+00 bond pdb=" CA ILE A 398 " pdb=" C ILE A 398 " ideal model delta sigma weight residual 1.518 1.530 -0.012 1.13e-02 7.83e+03 1.10e+00 bond pdb=" CA ILE B 398 " pdb=" C ILE B 398 " ideal model delta sigma weight residual 1.518 1.530 -0.011 1.13e-02 7.83e+03 1.00e+00 bond pdb=" CA ILE D 398 " pdb=" C ILE D 398 " ideal model delta sigma weight residual 1.518 1.529 -0.011 1.13e-02 7.83e+03 9.57e-01 bond pdb=" CA VAL A 402 " pdb=" CB VAL A 402 " ideal model delta sigma weight residual 1.534 1.541 -0.006 6.80e-03 2.16e+04 8.62e-01 ... (remaining 8183 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 10863 1.60 - 3.20: 189 3.20 - 4.80: 59 4.80 - 6.41: 9 6.41 - 8.01: 4 Bond angle restraints: 11124 Sorted by residual: angle pdb=" N ILE C 398 " pdb=" CA ILE C 398 " pdb=" C ILE C 398 " ideal model delta sigma weight residual 112.98 109.12 3.86 1.25e+00 6.40e-01 9.52e+00 angle pdb=" N ILE A 398 " pdb=" CA ILE A 398 " pdb=" C ILE A 398 " ideal model delta sigma weight residual 112.98 109.19 3.79 1.25e+00 6.40e-01 9.19e+00 angle pdb=" N ILE B 398 " pdb=" CA ILE B 398 " pdb=" C ILE B 398 " ideal model delta sigma weight residual 112.98 109.20 3.78 1.25e+00 6.40e-01 9.15e+00 angle pdb=" N ILE D 398 " pdb=" CA ILE D 398 " pdb=" C ILE D 398 " ideal model delta sigma weight residual 112.98 109.20 3.78 1.25e+00 6.40e-01 9.13e+00 angle pdb=" CA LEU D 271 " pdb=" CB LEU D 271 " pdb=" CG LEU D 271 " ideal model delta sigma weight residual 116.30 124.31 -8.01 3.50e+00 8.16e-02 5.23e+00 ... (remaining 11119 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.04: 4144 12.04 - 24.09: 408 24.09 - 36.13: 196 36.13 - 48.17: 32 48.17 - 60.22: 12 Dihedral angle restraints: 4792 sinusoidal: 1760 harmonic: 3032 Sorted by residual: dihedral pdb=" CA ASN A 408 " pdb=" CB ASN A 408 " pdb=" CG ASN A 408 " pdb=" OD1 ASN A 408 " ideal model delta sinusoidal sigma weight residual -90.00 -150.22 60.22 2 2.00e+01 2.50e-03 9.04e+00 dihedral pdb=" CA ASN D 408 " pdb=" CB ASN D 408 " pdb=" CG ASN D 408 " pdb=" OD1 ASN D 408 " ideal model delta sinusoidal sigma weight residual -90.00 -150.20 60.20 2 2.00e+01 2.50e-03 9.04e+00 dihedral pdb=" CA ASN B 408 " pdb=" CB ASN B 408 " pdb=" CG ASN B 408 " pdb=" OD1 ASN B 408 " ideal model delta sinusoidal sigma weight residual -90.00 -150.19 60.19 2 2.00e+01 2.50e-03 9.03e+00 ... (remaining 4789 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 617 0.024 - 0.047: 392 0.047 - 0.071: 188 0.071 - 0.095: 79 0.095 - 0.118: 44 Chirality restraints: 1320 Sorted by residual: chirality pdb=" CA VAL C 207 " pdb=" N VAL C 207 " pdb=" C VAL C 207 " pdb=" CB VAL C 207 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.50e-01 chirality pdb=" CA THR B 370 " pdb=" N THR B 370 " pdb=" C THR B 370 " pdb=" CB THR B 370 " both_signs ideal model delta sigma weight residual False 2.53 2.41 0.12 2.00e-01 2.50e+01 3.49e-01 chirality pdb=" CA VAL A 207 " pdb=" N VAL A 207 " pdb=" C VAL A 207 " pdb=" CB VAL A 207 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.44e-01 ... (remaining 1317 not shown) Planarity restraints: 1360 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 271 " 0.043 5.00e-02 4.00e+02 6.55e-02 6.87e+00 pdb=" N PRO D 272 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO D 272 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 272 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 271 " 0.043 5.00e-02 4.00e+02 6.54e-02 6.85e+00 pdb=" N PRO A 272 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO A 272 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 272 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 271 " -0.043 5.00e-02 4.00e+02 6.53e-02 6.82e+00 pdb=" N PRO C 272 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO C 272 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 272 " -0.036 5.00e-02 4.00e+02 ... (remaining 1357 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.74: 917 2.74 - 3.34: 10239 3.34 - 3.94: 15209 3.94 - 4.54: 21443 4.54 - 5.14: 31509 Nonbonded interactions: 79317 Sorted by model distance: nonbonded pdb=" OG SER D 319 " pdb=" OD1 ASN D 408 " model vdw 2.143 3.040 nonbonded pdb=" OG SER C 319 " pdb=" OD1 ASN C 408 " model vdw 2.143 3.040 nonbonded pdb=" OG SER B 319 " pdb=" OD1 ASN B 408 " model vdw 2.144 3.040 nonbonded pdb=" OG SER A 319 " pdb=" OD1 ASN A 408 " model vdw 2.144 3.040 nonbonded pdb=" O SER B 410 " pdb=" ND1 HIS B 414 " model vdw 2.207 3.120 ... (remaining 79312 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 'A' and resid 166 through 424) selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 2.890 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: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.430 Find NCS groups from input model: 0.320 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 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 0.041 8188 Z= 0.208 Angle : 0.626 8.007 11124 Z= 0.353 Chirality : 0.041 0.118 1320 Planarity : 0.006 0.066 1360 Dihedral : 12.429 60.217 2840 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.28 (0.27), residues: 1028 helix: 1.29 (0.18), residues: 784 sheet: None (None), residues: 0 loop : -0.40 (0.46), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 172 HIS 0.002 0.001 HIS C 306 PHE 0.008 0.001 PHE D 329 TYR 0.008 0.001 TYR B 274 ARG 0.005 0.000 ARG D 296 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 247 ARG cc_start: 0.7060 (mtp85) cc_final: 0.6692 (mtp180) REVERT: A 326 PHE cc_start: 0.6874 (m-10) cc_final: 0.5860 (t80) REVERT: A 421 LYS cc_start: 0.8500 (mmpt) cc_final: 0.8278 (tttt) REVERT: B 420 ASP cc_start: 0.8004 (m-30) cc_final: 0.7738 (m-30) REVERT: C 247 ARG cc_start: 0.6966 (mtp85) cc_final: 0.6515 (mtp180) REVERT: D 420 ASP cc_start: 0.8016 (m-30) cc_final: 0.7753 (m-30) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.2339 time to fit residues: 52.8364 Evaluate side-chains 128 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 0.7980 chunk 75 optimal weight: 10.0000 chunk 42 optimal weight: 0.9990 chunk 25 optimal weight: 10.0000 chunk 51 optimal weight: 0.2980 chunk 40 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 408 ASN B 408 ASN C 408 ASN D 408 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.200050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.133425 restraints weight = 9345.910| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.73 r_work: 0.3444 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8188 Z= 0.225 Angle : 0.601 9.836 11124 Z= 0.304 Chirality : 0.040 0.137 1320 Planarity : 0.006 0.070 1360 Dihedral : 3.935 13.404 1148 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.47 % Allowed : 7.23 % Favored : 92.30 % 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: 1.73 (0.26), residues: 1028 helix: 1.58 (0.18), residues: 784 sheet: None (None), residues: 0 loop : -0.15 (0.41), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 172 HIS 0.003 0.001 HIS D 414 PHE 0.009 0.001 PHE A 193 TYR 0.011 0.001 TYR A 188 ARG 0.003 0.000 ARG D 305 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 147 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 238 MET cc_start: 0.7231 (mmp) cc_final: 0.6694 (mtm) REVERT: A 256 ARG cc_start: 0.6395 (mpt180) cc_final: 0.5911 (mmt180) REVERT: A 326 PHE cc_start: 0.6805 (m-10) cc_final: 0.5399 (t80) REVERT: A 346 GLU cc_start: 0.8640 (mm-30) cc_final: 0.8375 (mm-30) REVERT: B 420 ASP cc_start: 0.8140 (m-30) cc_final: 0.7823 (m-30) REVERT: C 183 MET cc_start: 0.5527 (pmm) cc_final: 0.4628 (mpp) REVERT: C 256 ARG cc_start: 0.6427 (mpt180) cc_final: 0.5889 (mmt180) REVERT: C 305 ARG cc_start: 0.5998 (mtp-110) cc_final: 0.5776 (mtm-85) REVERT: D 420 ASP cc_start: 0.8135 (m-30) cc_final: 0.7828 (m-30) outliers start: 4 outliers final: 3 residues processed: 148 average time/residue: 0.2575 time to fit residues: 50.9779 Evaluate side-chains 131 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 128 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 350 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 69 optimal weight: 0.4980 chunk 27 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 14 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.200106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.131312 restraints weight = 9431.255| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.63 r_work: 0.3453 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8188 Z= 0.213 Angle : 0.570 8.098 11124 Z= 0.290 Chirality : 0.039 0.137 1320 Planarity : 0.006 0.070 1360 Dihedral : 3.791 13.427 1148 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.24 % Allowed : 11.73 % Favored : 88.03 % 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: 2.04 (0.26), residues: 1028 helix: 1.76 (0.18), residues: 784 sheet: None (None), residues: 0 loop : 0.17 (0.42), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 172 HIS 0.003 0.001 HIS C 306 PHE 0.008 0.001 PHE B 257 TYR 0.013 0.001 TYR C 188 ARG 0.004 0.000 ARG C 311 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 138 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 238 MET cc_start: 0.7234 (mmp) cc_final: 0.6772 (mtm) REVERT: A 262 MET cc_start: 0.6775 (mpp) cc_final: 0.6564 (mpp) REVERT: B 273 TYR cc_start: 0.7971 (t80) cc_final: 0.7585 (t80) REVERT: B 413 TYR cc_start: 0.6449 (t80) cc_final: 0.6156 (t80) REVERT: B 414 HIS cc_start: 0.6482 (m90) cc_final: 0.6271 (m90) REVERT: B 420 ASP cc_start: 0.8101 (m-30) cc_final: 0.7807 (m-30) REVERT: C 183 MET cc_start: 0.5501 (pmm) cc_final: 0.4452 (mtt) REVERT: C 238 MET cc_start: 0.7218 (mmp) cc_final: 0.6676 (mtm) REVERT: D 273 TYR cc_start: 0.7935 (t80) cc_final: 0.7587 (t80) REVERT: D 413 TYR cc_start: 0.6493 (t80) cc_final: 0.6189 (t80) REVERT: D 414 HIS cc_start: 0.6498 (m90) cc_final: 0.6284 (m90) REVERT: D 420 ASP cc_start: 0.8098 (m-30) cc_final: 0.7801 (m-30) outliers start: 2 outliers final: 2 residues processed: 138 average time/residue: 0.1832 time to fit residues: 35.6752 Evaluate side-chains 133 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 131 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain C residue 328 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 44 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 1 optimal weight: 0.0980 chunk 85 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.208604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.143367 restraints weight = 9612.834| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 2.59 r_work: 0.3596 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3441 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8188 Z= 0.188 Angle : 0.535 8.491 11124 Z= 0.275 Chirality : 0.039 0.132 1320 Planarity : 0.006 0.068 1360 Dihedral : 3.687 13.246 1148 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.18 % Allowed : 12.56 % Favored : 86.26 % 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: 2.31 (0.26), residues: 1028 helix: 1.92 (0.18), residues: 788 sheet: None (None), residues: 0 loop : 0.35 (0.43), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 172 HIS 0.001 0.000 HIS C 306 PHE 0.010 0.001 PHE B 257 TYR 0.013 0.001 TYR A 188 ARG 0.003 0.000 ARG A 305 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 146 time to evaluate : 1.229 Fit side-chains revert: symmetry clash REVERT: A 262 MET cc_start: 0.6967 (mpp) cc_final: 0.6750 (mpp) REVERT: B 273 TYR cc_start: 0.8018 (t80) cc_final: 0.7564 (t80) REVERT: B 420 ASP cc_start: 0.8028 (m-30) cc_final: 0.7644 (m-30) REVERT: B 421 LYS cc_start: 0.7736 (tptt) cc_final: 0.7146 (ttpt) REVERT: C 183 MET cc_start: 0.5616 (pmm) cc_final: 0.4636 (mtt) REVERT: C 238 MET cc_start: 0.7488 (mmp) cc_final: 0.6939 (mtm) REVERT: D 420 ASP cc_start: 0.8019 (m-30) cc_final: 0.7632 (m-30) REVERT: D 421 LYS cc_start: 0.7743 (tptt) cc_final: 0.7168 (ttpt) outliers start: 10 outliers final: 6 residues processed: 151 average time/residue: 0.1631 time to fit residues: 35.4082 Evaluate side-chains 141 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 135 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain C residue 320 CYS Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 393 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 9 optimal weight: 3.9990 chunk 85 optimal weight: 0.0770 chunk 88 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 60 optimal weight: 0.9980 chunk 86 optimal weight: 10.0000 chunk 48 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.204209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.142382 restraints weight = 9287.946| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 2.23 r_work: 0.3617 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3469 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8188 Z= 0.200 Angle : 0.551 9.162 11124 Z= 0.283 Chirality : 0.039 0.131 1320 Planarity : 0.006 0.069 1360 Dihedral : 3.678 12.896 1148 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.30 % Allowed : 15.88 % Favored : 82.82 % 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: 2.40 (0.26), residues: 1028 helix: 1.97 (0.18), residues: 788 sheet: None (None), residues: 0 loop : 0.45 (0.44), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 172 HIS 0.003 0.000 HIS B 414 PHE 0.014 0.001 PHE B 257 TYR 0.013 0.001 TYR D 188 ARG 0.003 0.000 ARG C 168 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 139 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 262 MET cc_start: 0.6915 (mpp) cc_final: 0.6698 (mpp) REVERT: B 273 TYR cc_start: 0.8069 (t80) cc_final: 0.7607 (t80) REVERT: B 420 ASP cc_start: 0.7933 (m-30) cc_final: 0.7651 (m-30) REVERT: B 421 LYS cc_start: 0.7842 (tptt) cc_final: 0.7290 (ttpt) REVERT: C 183 MET cc_start: 0.5612 (pmm) cc_final: 0.4691 (mtt) REVERT: D 420 ASP cc_start: 0.7916 (m-30) cc_final: 0.7638 (m-30) REVERT: D 421 LYS cc_start: 0.7837 (tptt) cc_final: 0.7287 (ttpt) outliers start: 11 outliers final: 9 residues processed: 143 average time/residue: 0.1814 time to fit residues: 36.0670 Evaluate side-chains 143 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 134 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 320 CYS Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain D residue 326 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 2 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 64 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 11 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 414 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.201767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.136304 restraints weight = 9395.744| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 2.47 r_work: 0.3504 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 8188 Z= 0.428 Angle : 0.649 7.336 11124 Z= 0.335 Chirality : 0.044 0.143 1320 Planarity : 0.006 0.068 1360 Dihedral : 4.055 13.431 1148 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.01 % Allowed : 16.82 % Favored : 81.16 % 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: 1.86 (0.26), residues: 1028 helix: 1.60 (0.18), residues: 780 sheet: None (None), residues: 0 loop : 0.25 (0.44), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 172 HIS 0.008 0.001 HIS D 414 PHE 0.016 0.002 PHE A 257 TYR 0.019 0.002 TYR C 188 ARG 0.004 0.000 ARG C 256 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 139 time to evaluate : 2.318 Fit side-chains REVERT: A 262 MET cc_start: 0.6957 (mpp) cc_final: 0.6753 (mpp) REVERT: B 262 MET cc_start: 0.6094 (OUTLIER) cc_final: 0.5689 (mmp) REVERT: B 393 SER cc_start: 0.9122 (t) cc_final: 0.8914 (m) REVERT: B 420 ASP cc_start: 0.7958 (m-30) cc_final: 0.7728 (m-30) REVERT: C 183 MET cc_start: 0.5588 (pmm) cc_final: 0.4693 (mtm) REVERT: C 238 MET cc_start: 0.7663 (mmp) cc_final: 0.7185 (mtm) REVERT: D 262 MET cc_start: 0.5989 (OUTLIER) cc_final: 0.5644 (mmp) REVERT: D 393 SER cc_start: 0.9132 (t) cc_final: 0.8923 (m) REVERT: D 420 ASP cc_start: 0.7921 (m-30) cc_final: 0.7689 (m-30) outliers start: 17 outliers final: 13 residues processed: 145 average time/residue: 0.2152 time to fit residues: 46.1053 Evaluate side-chains 150 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 135 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain C residue 256 ARG Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 320 CYS Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 326 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 0.0270 chunk 36 optimal weight: 0.0070 chunk 14 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 68 optimal weight: 0.3980 chunk 74 optimal weight: 1.9990 chunk 51 optimal weight: 0.4980 chunk 49 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 overall best weight: 0.3856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.194469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 100)---------------| | r_work = 0.3509 r_free = 0.3509 target = 0.130119 restraints weight = 9607.600| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.18 r_work: 0.3245 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8188 Z= 0.167 Angle : 0.542 7.479 11124 Z= 0.279 Chirality : 0.038 0.133 1320 Planarity : 0.006 0.065 1360 Dihedral : 3.716 12.588 1148 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.95 % Allowed : 19.31 % Favored : 79.74 % 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: 2.42 (0.26), residues: 1028 helix: 1.99 (0.18), residues: 780 sheet: None (None), residues: 0 loop : 0.49 (0.44), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 172 HIS 0.001 0.000 HIS D 414 PHE 0.015 0.001 PHE D 257 TYR 0.014 0.001 TYR D 273 ARG 0.002 0.000 ARG A 305 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 139 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 420 ASP cc_start: 0.7739 (m-30) cc_final: 0.7509 (m-30) REVERT: B 421 LYS cc_start: 0.7880 (tptt) cc_final: 0.7283 (ttpt) REVERT: C 183 MET cc_start: 0.5630 (pmm) cc_final: 0.4769 (mtt) REVERT: C 238 MET cc_start: 0.7593 (mmp) cc_final: 0.7163 (mtm) REVERT: D 420 ASP cc_start: 0.7766 (m-30) cc_final: 0.7540 (m-30) REVERT: D 421 LYS cc_start: 0.7864 (tptt) cc_final: 0.7276 (ttpt) outliers start: 8 outliers final: 5 residues processed: 143 average time/residue: 0.1725 time to fit residues: 34.9186 Evaluate side-chains 142 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 137 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain C residue 320 CYS Chi-restraints excluded: chain C residue 350 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 96 optimal weight: 0.0970 chunk 43 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.206221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.137831 restraints weight = 9519.704| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 2.49 r_work: 0.3588 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3429 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8188 Z= 0.206 Angle : 0.548 7.311 11124 Z= 0.283 Chirality : 0.039 0.130 1320 Planarity : 0.006 0.063 1360 Dihedral : 3.712 12.957 1148 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.78 % Allowed : 18.01 % Favored : 80.21 % 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: 2.39 (0.26), residues: 1028 helix: 1.93 (0.18), residues: 792 sheet: None (None), residues: 0 loop : 0.56 (0.45), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 172 HIS 0.001 0.000 HIS A 306 PHE 0.016 0.001 PHE D 257 TYR 0.023 0.001 TYR B 273 ARG 0.002 0.000 ARG C 256 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 141 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 262 MET cc_start: 0.5941 (OUTLIER) cc_final: 0.5462 (mmp) REVERT: B 420 ASP cc_start: 0.7838 (m-30) cc_final: 0.7592 (m-30) REVERT: B 421 LYS cc_start: 0.7751 (tptt) cc_final: 0.7161 (ttpt) REVERT: C 183 MET cc_start: 0.5548 (pmm) cc_final: 0.4632 (mtm) REVERT: C 238 MET cc_start: 0.7604 (mmp) cc_final: 0.7043 (mtm) REVERT: D 420 ASP cc_start: 0.7837 (m-30) cc_final: 0.7607 (m-30) REVERT: D 421 LYS cc_start: 0.7746 (tptt) cc_final: 0.7164 (ttpt) outliers start: 15 outliers final: 14 residues processed: 146 average time/residue: 0.1749 time to fit residues: 36.2549 Evaluate side-chains 152 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 137 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain C residue 256 ARG Chi-restraints excluded: chain C residue 320 CYS Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain D residue 185 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 5 optimal weight: 0.0570 chunk 35 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 73 optimal weight: 0.0050 chunk 60 optimal weight: 0.6980 chunk 67 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 6 optimal weight: 0.6980 chunk 69 optimal weight: 0.6980 overall best weight: 0.4312 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.207182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.147918 restraints weight = 9612.367| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 2.20 r_work: 0.3656 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3510 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8188 Z= 0.168 Angle : 0.528 7.067 11124 Z= 0.272 Chirality : 0.038 0.133 1320 Planarity : 0.006 0.065 1360 Dihedral : 3.594 13.529 1148 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.66 % Allowed : 17.89 % Favored : 80.45 % 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: 2.64 (0.26), residues: 1028 helix: 2.15 (0.18), residues: 784 sheet: None (None), residues: 0 loop : 0.56 (0.44), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 172 HIS 0.001 0.000 HIS A 306 PHE 0.016 0.001 PHE D 257 TYR 0.024 0.001 TYR B 273 ARG 0.002 0.000 ARG A 305 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 137 time to evaluate : 0.903 Fit side-chains REVERT: A 256 ARG cc_start: 0.6547 (OUTLIER) cc_final: 0.5992 (mmt180) REVERT: A 346 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7688 (tp30) REVERT: B 420 ASP cc_start: 0.7802 (m-30) cc_final: 0.7573 (m-30) REVERT: B 421 LYS cc_start: 0.7822 (tptt) cc_final: 0.7279 (ttpt) REVERT: C 183 MET cc_start: 0.5573 (pmm) cc_final: 0.4689 (mtt) REVERT: C 238 MET cc_start: 0.7621 (mmp) cc_final: 0.7089 (mtm) REVERT: C 256 ARG cc_start: 0.6515 (OUTLIER) cc_final: 0.5933 (mmt180) REVERT: D 420 ASP cc_start: 0.7856 (m-30) cc_final: 0.7625 (m-30) REVERT: D 421 LYS cc_start: 0.7817 (tptt) cc_final: 0.7280 (ttpt) outliers start: 14 outliers final: 12 residues processed: 142 average time/residue: 0.1795 time to fit residues: 36.4237 Evaluate side-chains 148 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 134 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain C residue 256 ARG Chi-restraints excluded: chain C residue 320 CYS Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 402 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 95 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 75 optimal weight: 10.0000 chunk 63 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 72 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 14 optimal weight: 5.9990 chunk 23 optimal weight: 0.4980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.206635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.139171 restraints weight = 9408.746| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 2.48 r_work: 0.3612 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3460 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8188 Z= 0.202 Angle : 0.545 7.491 11124 Z= 0.282 Chirality : 0.039 0.132 1320 Planarity : 0.006 0.064 1360 Dihedral : 3.614 14.217 1148 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.90 % Allowed : 16.82 % Favored : 81.28 % 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: 2.58 (0.26), residues: 1028 helix: 2.10 (0.18), residues: 784 sheet: None (None), residues: 0 loop : 0.55 (0.44), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 172 HIS 0.001 0.000 HIS A 306 PHE 0.008 0.001 PHE B 257 TYR 0.025 0.001 TYR B 273 ARG 0.002 0.000 ARG A 256 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2056 Ramachandran restraints generated. 1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 138 time to evaluate : 0.898 Fit side-chains REVERT: A 256 ARG cc_start: 0.6572 (OUTLIER) cc_final: 0.5969 (mmt180) REVERT: B 420 ASP cc_start: 0.7920 (m-30) cc_final: 0.7696 (m-30) REVERT: C 183 MET cc_start: 0.5506 (pmm) cc_final: 0.4628 (mtt) REVERT: C 238 MET cc_start: 0.7592 (mmp) cc_final: 0.7034 (mtm) REVERT: C 256 ARG cc_start: 0.6486 (OUTLIER) cc_final: 0.5894 (mmt180) REVERT: D 420 ASP cc_start: 0.7906 (m-30) cc_final: 0.7682 (m-30) outliers start: 16 outliers final: 12 residues processed: 144 average time/residue: 0.1694 time to fit residues: 34.6744 Evaluate side-chains 146 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 132 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain C residue 256 ARG Chi-restraints excluded: chain C residue 320 CYS Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 397 VAL Chi-restraints excluded: chain D residue 183 MET Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 402 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 40 optimal weight: 0.0050 chunk 61 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 12 optimal weight: 0.0470 chunk 26 optimal weight: 0.9990 chunk 92 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 79 optimal weight: 0.6980 chunk 37 optimal weight: 0.1980 chunk 72 optimal weight: 1.9990 overall best weight: 0.3492 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.196211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 100)---------------| | r_work = 0.3584 r_free = 0.3584 target = 0.136360 restraints weight = 9708.281| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.14 r_work: 0.3319 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8188 Z= 0.157 Angle : 0.534 7.548 11124 Z= 0.274 Chirality : 0.038 0.131 1320 Planarity : 0.006 0.064 1360 Dihedral : 3.504 14.037 1148 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.78 % Allowed : 17.18 % Favored : 81.04 % 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: 2.76 (0.26), residues: 1028 helix: 2.23 (0.18), residues: 784 sheet: None (None), residues: 0 loop : 0.62 (0.44), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 172 HIS 0.001 0.000 HIS A 306 PHE 0.011 0.001 PHE B 257 TYR 0.026 0.001 TYR B 273 ARG 0.002 0.000 ARG A 305 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5804.86 seconds wall clock time: 101 minutes 11.35 seconds (6071.35 seconds total)