Starting phenix.real_space_refine on Tue Mar 3 18:35:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uke_26578/03_2026/7uke_26578.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uke_26578/03_2026/7uke_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_2026/7uke_26578.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uke_26578/03_2026/7uke_26578.map" model { file = "/net/cci-nas-00/data/ceres_data/7uke_26578/03_2026/7uke_26578.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uke_26578/03_2026/7uke_26578.cif" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8000 Number of models: 1 Model: "" Number of chains: 5 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: {'HIS:plan': 1, 'GLU:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 22 Chain: "B" 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: {'HIS:plan': 1, 'GLU:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 22 Chain: "C" 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: {'HIS:plan': 1, 'GLU:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 22 Chain: "D" 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: {'HIS:plan': 1, 'GLU:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 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} Time building chain proxies: 1.74, per 1000 atoms: 0.22 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: 0.73 Conformation dependent library (CDL) restraints added in 250.6 milliseconds 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: 0.25 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: 1.28 Time building geometry restraints manager: 0.88 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: 3.090 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: 0.130 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 8.310 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.010 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.990 ------------------------------------------------------------------------------- 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= 0.152 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.005 0.000 ARG D 296 TYR 0.008 0.001 TYR B 274 PHE 0.008 0.001 PHE D 329 TRP 0.012 0.002 TRP D 172 HIS 0.002 0.001 HIS C 306 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 8188) covalent geometry : angle 0.62643 (11124) hydrogen bonds : bond 0.13063 ( 629) hydrogen bonds : angle 4.89134 ( 1791) *********************** 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 : 0.291 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: 0.5859 (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: 0.1040 time to fit residues: 23.5189 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 : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.2980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 0.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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 = 0.4363 r_free = 0.4363 target = 0.198181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.128276 restraints weight = 9445.326| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 2.45 r_work: 0.3429 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 8188 Z= 0.195 Angle : 0.633 9.777 11124 Z= 0.322 Chirality : 0.042 0.145 1320 Planarity : 0.006 0.072 1360 Dihedral : 4.054 13.617 1148 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.59 % Allowed : 8.53 % Favored : 90.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.26), residues: 1028 helix: 1.46 (0.18), residues: 784 sheet: None (None), residues: 0 loop : -0.24 (0.42), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 305 TYR 0.011 0.001 TYR A 188 PHE 0.012 0.001 PHE A 193 TRP 0.016 0.002 TRP C 172 HIS 0.003 0.001 HIS D 414 Details of bonding type rmsd covalent geometry : bond 0.00472 ( 8188) covalent geometry : angle 0.63333 (11124) hydrogen bonds : bond 0.04436 ( 629) hydrogen bonds : angle 4.22529 ( 1791) *********************** 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 150 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 145 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 256 ARG cc_start: 0.6442 (mpt180) cc_final: 0.5914 (mmt180) REVERT: A 326 PHE cc_start: 0.6856 (m-10) cc_final: 0.5430 (t80) REVERT: B 273 TYR cc_start: 0.8010 (t80) cc_final: 0.7717 (t80) REVERT: B 420 ASP cc_start: 0.8135 (m-30) cc_final: 0.7836 (m-30) REVERT: C 183 MET cc_start: 0.5486 (pmm) cc_final: 0.4623 (mpp) REVERT: C 256 ARG cc_start: 0.6500 (mpt180) cc_final: 0.5959 (mmt180) REVERT: C 326 PHE cc_start: 0.6885 (m-10) cc_final: 0.5412 (t80) REVERT: D 273 TYR cc_start: 0.7961 (t80) cc_final: 0.7696 (t80) REVERT: D 420 ASP cc_start: 0.8122 (m-30) cc_final: 0.7823 (m-30) outliers start: 5 outliers final: 3 residues processed: 145 average time/residue: 0.0864 time to fit residues: 16.9205 Evaluate side-chains 133 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 130 time to evaluate : 0.267 ------------------------------------------------------------------------------- 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 1 optimal weight: 0.0980 chunk 92 optimal weight: 0.5980 chunk 51 optimal weight: 0.1980 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 95 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.4388 r_free = 0.4388 target = 0.201244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.132821 restraints weight = 9409.013| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 2.60 r_work: 0.3465 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8188 Z= 0.127 Angle : 0.557 7.846 11124 Z= 0.283 Chirality : 0.039 0.138 1320 Planarity : 0.006 0.069 1360 Dihedral : 3.769 13.305 1148 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.59 % Allowed : 11.61 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.26), residues: 1028 helix: 1.79 (0.18), residues: 784 sheet: None (None), residues: 0 loop : 0.10 (0.42), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 311 TYR 0.012 0.001 TYR A 188 PHE 0.007 0.001 PHE B 257 TRP 0.012 0.002 TRP C 172 HIS 0.003 0.001 HIS C 306 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 8188) covalent geometry : angle 0.55748 (11124) hydrogen bonds : bond 0.03851 ( 629) hydrogen bonds : angle 3.96177 ( 1791) *********************** 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 149 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 144 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 MET cc_start: 0.7240 (mmp) cc_final: 0.7024 (mmp) REVERT: A 305 ARG cc_start: 0.5851 (mtp-110) cc_final: 0.5627 (mtm-85) REVERT: A 346 GLU cc_start: 0.8577 (mm-30) cc_final: 0.8344 (mm-30) REVERT: B 273 TYR cc_start: 0.7941 (t80) cc_final: 0.7556 (t80) REVERT: B 413 TYR cc_start: 0.6481 (t80) cc_final: 0.6177 (t80) REVERT: B 414 HIS cc_start: 0.6451 (m90) cc_final: 0.6243 (m90) REVERT: B 420 ASP cc_start: 0.8112 (m-30) cc_final: 0.7822 (m-30) REVERT: C 183 MET cc_start: 0.5466 (pmm) cc_final: 0.4431 (mtt) REVERT: C 238 MET cc_start: 0.7207 (mmp) cc_final: 0.6673 (mtm) REVERT: D 413 TYR cc_start: 0.6486 (t80) cc_final: 0.6184 (t80) REVERT: D 414 HIS cc_start: 0.6493 (m90) cc_final: 0.6276 (m90) REVERT: D 420 ASP cc_start: 0.8098 (m-30) cc_final: 0.7809 (m-30) outliers start: 5 outliers final: 3 residues processed: 145 average time/residue: 0.0801 time to fit residues: 16.1473 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 : 0.283 ------------------------------------------------------------------------------- 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 393 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 58 optimal weight: 0.5980 chunk 81 optimal weight: 3.9990 chunk 25 optimal weight: 10.0000 chunk 31 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 23 optimal weight: 0.0050 chunk 20 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 overall best weight: 0.7194 ------------------------------------------------------------------------------- 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 = 0.4506 r_free = 0.4506 target = 0.207947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.141777 restraints weight = 9669.514| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 2.51 r_work: 0.3593 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3437 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2331 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= 0.139 Angle : 0.549 8.805 11124 Z= 0.281 Chirality : 0.039 0.135 1320 Planarity : 0.006 0.067 1360 Dihedral : 3.717 13.255 1148 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.78 % Allowed : 12.91 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.25 (0.26), residues: 1028 helix: 1.90 (0.18), residues: 788 sheet: None (None), residues: 0 loop : 0.27 (0.43), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 247 TYR 0.013 0.001 TYR A 188 PHE 0.011 0.001 PHE B 257 TRP 0.013 0.002 TRP A 172 HIS 0.001 0.000 HIS C 306 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 8188) covalent geometry : angle 0.54911 (11124) hydrogen bonds : bond 0.03888 ( 629) hydrogen bonds : angle 3.90226 ( 1791) *********************** 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 157 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 142 time to evaluate : 0.196 Fit side-chains revert: symmetry clash REVERT: B 273 TYR cc_start: 0.8051 (t80) cc_final: 0.7629 (t80) REVERT: B 413 TYR cc_start: 0.6645 (t80) cc_final: 0.6375 (t80) REVERT: B 420 ASP cc_start: 0.8021 (m-30) cc_final: 0.7659 (m-30) REVERT: B 421 LYS cc_start: 0.7741 (tptt) cc_final: 0.7170 (ttpt) REVERT: C 183 MET cc_start: 0.5587 (pmm) cc_final: 0.4627 (mtt) REVERT: C 238 MET cc_start: 0.7488 (mmp) cc_final: 0.6940 (mtm) REVERT: D 273 TYR cc_start: 0.8033 (t80) cc_final: 0.7655 (t80) REVERT: D 413 TYR cc_start: 0.6686 (t80) cc_final: 0.6431 (t80) REVERT: D 420 ASP cc_start: 0.8022 (m-30) cc_final: 0.7661 (m-30) REVERT: D 421 LYS cc_start: 0.7750 (tptt) cc_final: 0.7190 (ttpt) outliers start: 15 outliers final: 10 residues processed: 149 average time/residue: 0.0749 time to fit residues: 15.8658 Evaluate side-chains 144 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 134 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain B residue 326 PHE Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 320 CYS Chi-restraints excluded: chain C residue 328 LEU 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 87 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 75 optimal weight: 10.0000 chunk 37 optimal weight: 0.6980 chunk 65 optimal weight: 6.9990 chunk 88 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.4482 r_free = 0.4482 target = 0.206110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.137178 restraints weight = 9507.615| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 2.54 r_work: 0.3576 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3420 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8188 Z= 0.149 Angle : 0.552 9.071 11124 Z= 0.284 Chirality : 0.039 0.134 1320 Planarity : 0.006 0.067 1360 Dihedral : 3.719 13.067 1148 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.42 % Allowed : 15.88 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.32 (0.26), residues: 1028 helix: 1.92 (0.18), residues: 788 sheet: None (None), residues: 0 loop : 0.39 (0.44), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 168 TYR 0.014 0.001 TYR D 188 PHE 0.013 0.001 PHE B 257 TRP 0.013 0.002 TRP A 172 HIS 0.002 0.000 HIS C 306 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 8188) covalent geometry : angle 0.55170 (11124) hydrogen bonds : bond 0.03936 ( 629) hydrogen bonds : angle 3.88786 ( 1791) *********************** 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 151 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 139 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 238 MET cc_start: 0.7515 (mmp) cc_final: 0.7011 (mtm) REVERT: B 273 TYR cc_start: 0.8129 (t80) cc_final: 0.7694 (t80) REVERT: B 413 TYR cc_start: 0.6557 (t80) cc_final: 0.6328 (t80) REVERT: B 420 ASP cc_start: 0.7930 (m-30) cc_final: 0.7662 (m-30) REVERT: B 421 LYS cc_start: 0.7814 (tptt) cc_final: 0.7247 (ttpt) REVERT: C 183 MET cc_start: 0.5575 (pmm) cc_final: 0.4676 (mtt) REVERT: D 273 TYR cc_start: 0.8093 (t80) cc_final: 0.7696 (t80) REVERT: D 413 TYR cc_start: 0.6629 (t80) cc_final: 0.6392 (t80) REVERT: D 420 ASP cc_start: 0.7936 (m-30) cc_final: 0.7669 (m-30) REVERT: D 421 LYS cc_start: 0.7850 (tptt) cc_final: 0.7286 (ttpt) outliers start: 12 outliers final: 10 residues processed: 142 average time/residue: 0.0711 time to fit residues: 14.5845 Evaluate side-chains 148 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 138 time to evaluate : 0.280 ------------------------------------------------------------------------------- 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 B residue 326 PHE Chi-restraints excluded: chain C residue 270 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 36 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 39 optimal weight: 9.9990 chunk 61 optimal weight: 0.0050 chunk 28 optimal weight: 1.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- 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 = 0.4494 r_free = 0.4494 target = 0.207493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.139064 restraints weight = 9507.151| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 2.47 r_work: 0.3606 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.3455 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2702 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= 0.134 Angle : 0.546 7.526 11124 Z= 0.278 Chirality : 0.038 0.130 1320 Planarity : 0.006 0.066 1360 Dihedral : 3.664 12.900 1148 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.30 % Allowed : 17.89 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.51 (0.26), residues: 1028 helix: 2.04 (0.18), residues: 788 sheet: None (None), residues: 0 loop : 0.53 (0.45), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 296 TYR 0.013 0.001 TYR D 188 PHE 0.013 0.001 PHE B 257 TRP 0.012 0.002 TRP A 172 HIS 0.002 0.000 HIS C 306 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 8188) covalent geometry : angle 0.54568 (11124) hydrogen bonds : bond 0.03792 ( 629) hydrogen bonds : angle 3.82170 ( 1791) *********************** 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 149 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 138 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 238 MET cc_start: 0.7497 (mmp) cc_final: 0.6957 (mtm) REVERT: B 262 MET cc_start: 0.6047 (OUTLIER) cc_final: 0.5761 (mmp) REVERT: B 273 TYR cc_start: 0.8099 (t80) cc_final: 0.7627 (t80) REVERT: B 413 TYR cc_start: 0.6505 (t80) cc_final: 0.6299 (t80) REVERT: B 414 HIS cc_start: 0.6596 (m90) cc_final: 0.6390 (m90) REVERT: B 420 ASP cc_start: 0.7913 (m-30) cc_final: 0.7648 (m-30) REVERT: C 183 MET cc_start: 0.5595 (pmm) cc_final: 0.4665 (mtt) REVERT: C 238 MET cc_start: 0.7587 (mmp) cc_final: 0.7369 (tpt) REVERT: D 413 TYR cc_start: 0.6563 (t80) cc_final: 0.6362 (t80) REVERT: D 414 HIS cc_start: 0.6635 (m90) cc_final: 0.6422 (m90) REVERT: D 420 ASP cc_start: 0.7887 (m-30) cc_final: 0.7621 (m-30) outliers start: 11 outliers final: 10 residues processed: 141 average time/residue: 0.0699 time to fit residues: 14.2386 Evaluate side-chains 149 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 138 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 393 SER Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain C residue 256 ARG Chi-restraints excluded: chain C residue 270 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 58 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 99 optimal weight: 0.5980 chunk 70 optimal weight: 0.6980 chunk 44 optimal weight: 0.5980 chunk 59 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4188 r_free = 0.4188 target = 0.193231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.129683 restraints weight = 9625.751| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.11 r_work: 0.3230 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2784 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= 0.139 Angle : 0.533 6.815 11124 Z= 0.276 Chirality : 0.038 0.128 1320 Planarity : 0.006 0.064 1360 Dihedral : 3.653 12.705 1148 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.90 % Allowed : 17.06 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.47 (0.26), residues: 1028 helix: 1.96 (0.18), residues: 800 sheet: None (None), residues: 0 loop : 0.66 (0.46), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 256 TYR 0.013 0.001 TYR D 188 PHE 0.016 0.001 PHE D 257 TRP 0.012 0.001 TRP A 172 HIS 0.002 0.000 HIS C 306 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 8188) covalent geometry : angle 0.53262 (11124) hydrogen bonds : bond 0.03819 ( 629) hydrogen bonds : angle 3.80189 ( 1791) *********************** 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 155 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 139 time to evaluate : 0.183 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 238 MET cc_start: 0.7514 (mmp) cc_final: 0.7023 (mtm) REVERT: B 262 MET cc_start: 0.6044 (OUTLIER) cc_final: 0.5495 (mmp) REVERT: B 273 TYR cc_start: 0.8086 (t80) cc_final: 0.7628 (t80) REVERT: B 420 ASP cc_start: 0.7825 (m-30) cc_final: 0.7588 (m-30) REVERT: B 421 LYS cc_start: 0.7801 (tptt) cc_final: 0.7243 (ttpt) REVERT: C 183 MET cc_start: 0.5638 (pmm) cc_final: 0.4779 (mtt) REVERT: C 238 MET cc_start: 0.7614 (mmp) cc_final: 0.7125 (mtm) REVERT: D 420 ASP cc_start: 0.7807 (m-30) cc_final: 0.7582 (m-30) outliers start: 16 outliers final: 14 residues processed: 146 average time/residue: 0.0731 time to fit residues: 15.3495 Evaluate side-chains 153 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 138 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 402 VAL Chi-restraints excluded: chain C residue 256 ARG Chi-restraints excluded: chain C residue 270 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 185 LEU Chi-restraints excluded: chain D residue 402 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 1.9990 chunk 75 optimal weight: 10.0000 chunk 66 optimal weight: 0.9990 chunk 5 optimal weight: 0.0010 chunk 99 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 67 optimal weight: 0.5980 chunk 56 optimal weight: 0.8980 overall best weight: 0.5986 ------------------------------------------------------------------------------- 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 = 0.4198 r_free = 0.4198 target = 0.194188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.148345 restraints weight = 9622.115| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 1.65 r_work: 0.3389 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2848 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= 0.129 Angle : 0.529 6.516 11124 Z= 0.273 Chirality : 0.038 0.128 1320 Planarity : 0.006 0.065 1360 Dihedral : 3.613 12.859 1148 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.01 % Allowed : 17.42 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.57 (0.26), residues: 1028 helix: 2.02 (0.18), residues: 800 sheet: None (None), residues: 0 loop : 0.71 (0.47), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 256 TYR 0.012 0.001 TYR D 188 PHE 0.014 0.001 PHE B 257 TRP 0.012 0.002 TRP A 172 HIS 0.002 0.000 HIS C 306 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 8188) covalent geometry : angle 0.52902 (11124) hydrogen bonds : bond 0.03715 ( 629) hydrogen bonds : angle 3.77099 ( 1791) *********************** 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 160 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 143 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 238 MET cc_start: 0.7404 (mmp) cc_final: 0.7004 (mtm) REVERT: B 262 MET cc_start: 0.6040 (OUTLIER) cc_final: 0.5708 (mmp) REVERT: B 420 ASP cc_start: 0.7624 (m-30) cc_final: 0.7407 (m-30) REVERT: B 421 LYS cc_start: 0.7838 (tptt) cc_final: 0.7361 (ttpt) REVERT: C 183 MET cc_start: 0.5635 (pmm) cc_final: 0.4857 (mtt) REVERT: C 238 MET cc_start: 0.7500 (mmp) cc_final: 0.7111 (mtm) REVERT: D 421 LYS cc_start: 0.7834 (tptt) cc_final: 0.7298 (ttpt) outliers start: 17 outliers final: 15 residues processed: 151 average time/residue: 0.0699 time to fit residues: 15.2034 Evaluate side-chains 155 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 139 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 397 VAL 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 270 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 185 LEU Chi-restraints excluded: chain D residue 402 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 33 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 26 optimal weight: 0.7980 chunk 75 optimal weight: 10.0000 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.4459 r_free = 0.4459 target = 0.203576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.141388 restraints weight = 9245.080| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 2.21 r_work: 0.3601 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3452 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8188 Z= 0.155 Angle : 0.553 7.405 11124 Z= 0.288 Chirality : 0.039 0.127 1320 Planarity : 0.006 0.064 1360 Dihedral : 3.669 13.453 1148 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.90 % Allowed : 17.54 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.50 (0.26), residues: 1028 helix: 1.98 (0.18), residues: 796 sheet: None (None), residues: 0 loop : 0.69 (0.47), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 256 TYR 0.013 0.001 TYR B 188 PHE 0.008 0.001 PHE C 298 TRP 0.011 0.001 TRP C 172 HIS 0.002 0.001 HIS A 306 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 8188) covalent geometry : angle 0.55300 (11124) hydrogen bonds : bond 0.03886 ( 629) hydrogen bonds : angle 3.84518 ( 1791) *********************** 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 158 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 142 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 238 MET cc_start: 0.7527 (mmp) cc_final: 0.6981 (mtm) REVERT: B 420 ASP cc_start: 0.7852 (m-30) cc_final: 0.7640 (m-30) REVERT: C 183 MET cc_start: 0.5575 (pmm) cc_final: 0.4671 (mtm) REVERT: C 238 MET cc_start: 0.7592 (mmp) cc_final: 0.7033 (mtm) REVERT: D 273 TYR cc_start: 0.8116 (t80) cc_final: 0.7703 (t80) REVERT: D 421 LYS cc_start: 0.7791 (tptt) cc_final: 0.7212 (ttpt) outliers start: 16 outliers final: 15 residues processed: 148 average time/residue: 0.0715 time to fit residues: 15.3132 Evaluate side-chains 155 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 140 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 397 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain C residue 256 ARG Chi-restraints excluded: chain C residue 270 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 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 24 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 61 optimal weight: 0.0370 chunk 29 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 40 optimal weight: 7.9990 chunk 86 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 14 optimal weight: 0.0040 overall best weight: 0.5672 ------------------------------------------------------------------------------- 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 = 0.4201 r_free = 0.4201 target = 0.194452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.148070 restraints weight = 9610.108| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 1.75 r_work: 0.3384 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2993 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= 0.127 Angle : 0.535 7.372 11124 Z= 0.278 Chirality : 0.038 0.128 1320 Planarity : 0.006 0.065 1360 Dihedral : 3.585 13.812 1148 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.78 % Allowed : 17.54 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.63 (0.26), residues: 1028 helix: 2.07 (0.18), residues: 796 sheet: None (None), residues: 0 loop : 0.77 (0.47), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 256 TYR 0.012 0.001 TYR B 188 PHE 0.014 0.001 PHE B 257 TRP 0.013 0.002 TRP C 172 HIS 0.001 0.000 HIS C 306 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 8188) covalent geometry : angle 0.53536 (11124) hydrogen bonds : bond 0.03686 ( 629) hydrogen bonds : angle 3.78753 ( 1791) ********************** 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 150 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 135 time to evaluate : 0.263 Fit side-chains REVERT: A 238 MET cc_start: 0.7403 (mmp) cc_final: 0.6993 (mtm) REVERT: A 256 ARG cc_start: 0.6490 (OUTLIER) cc_final: 0.6058 (mmt180) REVERT: B 273 TYR cc_start: 0.7991 (t80) cc_final: 0.7571 (t80) REVERT: B 421 LYS cc_start: 0.7897 (tptt) cc_final: 0.7350 (ttpt) REVERT: C 183 MET cc_start: 0.5616 (pmm) cc_final: 0.4828 (mtt) REVERT: C 189 TYR cc_start: 0.7695 (m-80) cc_final: 0.7330 (m-80) REVERT: C 238 MET cc_start: 0.7553 (mmp) cc_final: 0.7123 (mtm) REVERT: C 256 ARG cc_start: 0.6428 (OUTLIER) cc_final: 0.5978 (mmt180) REVERT: D 273 TYR cc_start: 0.7991 (t80) cc_final: 0.7600 (t80) REVERT: D 421 LYS cc_start: 0.7761 (tptt) cc_final: 0.7284 (ttpt) outliers start: 15 outliers final: 12 residues processed: 142 average time/residue: 0.0671 time to fit residues: 13.9518 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 : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 397 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain C residue 256 ARG Chi-restraints excluded: chain C residue 270 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 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 77 optimal weight: 0.9980 chunk 34 optimal weight: 0.2980 chunk 81 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4195 r_free = 0.4195 target = 0.193882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.146215 restraints weight = 9511.341| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 1.63 r_work: 0.3383 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.3058 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= 0.133 Angle : 0.547 9.877 11124 Z= 0.282 Chirality : 0.038 0.128 1320 Planarity : 0.006 0.064 1360 Dihedral : 3.605 14.104 1148 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.90 % Allowed : 16.94 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.52 (0.26), residues: 1028 helix: 2.00 (0.18), residues: 800 sheet: None (None), residues: 0 loop : 0.64 (0.47), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 256 TYR 0.013 0.001 TYR B 188 PHE 0.008 0.001 PHE B 257 TRP 0.012 0.001 TRP C 172 HIS 0.001 0.000 HIS C 306 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 8188) covalent geometry : angle 0.54677 (11124) hydrogen bonds : bond 0.03739 ( 629) hydrogen bonds : angle 3.80964 ( 1791) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2761.06 seconds wall clock time: 47 minutes 44.30 seconds (2864.30 seconds total)