Starting phenix.real_space_refine on Tue Feb 13 22:52:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uke_26578/02_2024/7uke_26578.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uke_26578/02_2024/7uke_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uke_26578/02_2024/7uke_26578.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uke_26578/02_2024/7uke_26578.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uke_26578/02_2024/7uke_26578.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uke_26578/02_2024/7uke_26578.pdb" } 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 Residue "A TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/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: {'GLU:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 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: {'GLU:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 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: {'GLU:plan': 2, 'ASP:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 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: {'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} Time building chain proxies: 4.85, per 1000 atoms: 0.61 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 - 3.50 Amino acid : False - 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: 3.42 Conformation dependent library (CDL) restraints added in 1.5 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: 0.85 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: 2.33 Time building geometry restraints manager: 3.65 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: 100.09 - 106.88: 192 106.88 - 113.67: 4592 113.67 - 120.45: 3462 120.45 - 127.24: 2818 127.24 - 134.02: 60 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 2.440 nonbonded pdb=" OG SER C 319 " pdb=" OD1 ASN C 408 " model vdw 2.143 2.440 nonbonded pdb=" OG SER B 319 " pdb=" OD1 ASN B 408 " model vdw 2.144 2.440 nonbonded pdb=" OG SER A 319 " pdb=" OD1 ASN A 408 " model vdw 2.144 2.440 nonbonded pdb=" O SER B 410 " pdb=" ND1 HIS B 414 " model vdw 2.207 2.520 ... (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 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: 3.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 9.590 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 25.880 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.540 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 0.933 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: 0.2498 time to fit residues: 56.2661 Evaluate side-chains 128 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 0.899 ------------------------------------------------------------------------------- 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: 0.9980 chunk 75 optimal weight: 10.0000 chunk 42 optimal weight: 0.9990 chunk 25 optimal weight: 10.0000 chunk 51 optimal weight: 0.0010 chunk 40 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 30 optimal weight: 0.0070 chunk 47 optimal weight: 0.5980 chunk 58 optimal weight: 0.5980 chunk 90 optimal weight: 4.9990 overall best weight: 0.4404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8188 Z= 0.177 Angle : 0.568 9.894 11124 Z= 0.284 Chirality : 0.038 0.143 1320 Planarity : 0.006 0.069 1360 Dihedral : 3.789 13.046 1148 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.24 % Allowed : 7.82 % Favored : 91.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.26), residues: 1028 helix: 1.71 (0.18), residues: 784 sheet: None (None), residues: 0 loop : -0.14 (0.41), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 172 HIS 0.001 0.000 HIS D 306 PHE 0.009 0.001 PHE D 343 TYR 0.011 0.001 TYR A 188 ARG 0.002 0.000 ARG C 293 *********************** 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 148 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 146 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 326 PHE cc_start: 0.6900 (m-10) cc_final: 0.5874 (t80) REVERT: B 248 LEU cc_start: 0.7589 (tt) cc_final: 0.7355 (tt) REVERT: B 304 SER cc_start: 0.8241 (p) cc_final: 0.8038 (p) REVERT: B 413 TYR cc_start: 0.6961 (t80) cc_final: 0.6659 (t80) REVERT: B 420 ASP cc_start: 0.7899 (m-30) cc_final: 0.7649 (m-30) REVERT: C 183 MET cc_start: 0.5571 (pmm) cc_final: 0.4725 (mtt) REVERT: D 304 SER cc_start: 0.8273 (p) cc_final: 0.8066 (p) REVERT: D 413 TYR cc_start: 0.7011 (t80) cc_final: 0.6729 (t80) REVERT: D 420 ASP cc_start: 0.7918 (m-30) cc_final: 0.7667 (m-30) outliers start: 2 outliers final: 2 residues processed: 146 average time/residue: 0.2027 time to fit residues: 40.3483 Evaluate side-chains 133 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 131 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain C residue 328 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 chunk 75 optimal weight: 10.0000 chunk 61 optimal weight: 8.9990 chunk 25 optimal weight: 10.0000 chunk 90 optimal weight: 8.9990 chunk 98 optimal weight: 0.0000 chunk 81 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 89 optimal weight: 0.9990 overall best weight: 1.1390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1962 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= 0.270 Angle : 0.568 7.612 11124 Z= 0.291 Chirality : 0.040 0.132 1320 Planarity : 0.006 0.070 1360 Dihedral : 3.814 13.681 1148 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.47 % Allowed : 10.78 % Favored : 88.74 % 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: 1.96 (0.26), residues: 1028 helix: 1.73 (0.18), residues: 784 sheet: None (None), residues: 0 loop : 0.03 (0.41), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 172 HIS 0.003 0.001 HIS A 306 PHE 0.011 0.001 PHE C 257 TYR 0.014 0.001 TYR A 188 ARG 0.003 0.000 ARG A 305 *********************** 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 139 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 135 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 304 SER cc_start: 0.8330 (p) cc_final: 0.8112 (p) REVERT: B 413 TYR cc_start: 0.6955 (t80) cc_final: 0.6610 (t80) REVERT: B 420 ASP cc_start: 0.7916 (m-30) cc_final: 0.7682 (m-30) REVERT: C 183 MET cc_start: 0.5533 (pmm) cc_final: 0.4698 (mtm) REVERT: C 238 MET cc_start: 0.6702 (mmp) cc_final: 0.6493 (mtm) REVERT: D 304 SER cc_start: 0.8346 (p) cc_final: 0.8123 (p) REVERT: D 413 TYR cc_start: 0.6957 (t80) cc_final: 0.6631 (t80) REVERT: D 420 ASP cc_start: 0.7899 (m-30) cc_final: 0.7669 (m-30) outliers start: 4 outliers final: 2 residues processed: 135 average time/residue: 0.1722 time to fit residues: 32.9194 Evaluate side-chains 130 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 128 time to evaluate : 0.810 ------------------------------------------------------------------------------- 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 68 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 61 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 86 optimal weight: 8.9990 chunk 26 optimal weight: 2.9990 chunk 80 optimal weight: 0.0370 chunk 54 optimal weight: 2.9990 overall best weight: 1.1662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2283 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= 0.270 Angle : 0.554 7.348 11124 Z= 0.285 Chirality : 0.040 0.135 1320 Planarity : 0.006 0.069 1360 Dihedral : 3.816 13.261 1148 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.42 % Allowed : 12.91 % Favored : 85.66 % 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: 1.74 (0.18), residues: 788 sheet: None (None), residues: 0 loop : 0.20 (0.42), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 172 HIS 0.003 0.001 HIS C 306 PHE 0.011 0.001 PHE B 257 TYR 0.015 0.001 TYR B 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 152 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 140 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 304 SER cc_start: 0.8331 (p) cc_final: 0.8089 (p) REVERT: B 420 ASP cc_start: 0.7868 (m-30) cc_final: 0.7563 (m-30) REVERT: C 183 MET cc_start: 0.5566 (pmm) cc_final: 0.4784 (mtm) REVERT: C 238 MET cc_start: 0.6679 (mmp) cc_final: 0.6472 (mtm) REVERT: D 304 SER cc_start: 0.8330 (p) cc_final: 0.8095 (p) REVERT: D 420 ASP cc_start: 0.7876 (m-30) cc_final: 0.7569 (m-30) outliers start: 12 outliers final: 5 residues processed: 147 average time/residue: 0.1967 time to fit residues: 39.4253 Evaluate side-chains 137 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 132 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 393 SER 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 1 optimal weight: 0.4980 chunk 71 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 chunk 82 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 86 optimal weight: 0.0980 chunk 24 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 87 optimal weight: 0.0870 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2507 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= 0.173 Angle : 0.522 9.406 11124 Z= 0.267 Chirality : 0.038 0.134 1320 Planarity : 0.006 0.067 1360 Dihedral : 3.658 12.870 1148 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.07 % Allowed : 15.76 % Favored : 83.18 % 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: 2.25 (0.26), residues: 1028 helix: 1.83 (0.18), residues: 804 sheet: None (None), residues: 0 loop : 0.43 (0.45), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 172 HIS 0.004 0.001 HIS A 306 PHE 0.008 0.001 PHE B 257 TYR 0.021 0.001 TYR D 273 ARG 0.004 0.000 ARG A 311 *********************** 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 146 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 137 time to evaluate : 0.836 Fit side-chains revert: symmetry clash REVERT: B 262 MET cc_start: 0.5892 (OUTLIER) cc_final: 0.5519 (mmp) REVERT: B 420 ASP cc_start: 0.7775 (m-30) cc_final: 0.7526 (m-30) REVERT: B 421 LYS cc_start: 0.7752 (tptt) cc_final: 0.7183 (ttpt) REVERT: C 183 MET cc_start: 0.5591 (pmm) cc_final: 0.4782 (mtt) REVERT: D 262 MET cc_start: 0.5756 (OUTLIER) cc_final: 0.5254 (mmp) REVERT: D 420 ASP cc_start: 0.7766 (m-30) cc_final: 0.7525 (m-30) REVERT: D 421 LYS cc_start: 0.7741 (tptt) cc_final: 0.7173 (ttpt) outliers start: 9 outliers final: 6 residues processed: 139 average time/residue: 0.1754 time to fit residues: 34.2917 Evaluate side-chains 143 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 135 time to evaluate : 0.874 ------------------------------------------------------------------------------- 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 393 SER Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain C residue 320 CYS Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain D residue 262 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 23 optimal weight: 0.0870 chunk 96 optimal weight: 0.0270 chunk 80 optimal weight: 0.6980 chunk 44 optimal weight: 0.1980 chunk 8 optimal weight: 0.0170 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 7.9990 chunk 93 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 overall best weight: 0.2054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8188 Z= 0.137 Angle : 0.495 7.767 11124 Z= 0.252 Chirality : 0.036 0.132 1320 Planarity : 0.005 0.066 1360 Dihedral : 3.494 12.134 1148 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.30 % Allowed : 17.18 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.70 (0.27), residues: 1028 helix: 2.14 (0.18), residues: 804 sheet: None (None), residues: 0 loop : 0.62 (0.47), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 172 HIS 0.002 0.000 HIS C 306 PHE 0.006 0.001 PHE D 289 TYR 0.024 0.001 TYR B 273 ARG 0.002 0.000 ARG B 247 *********************** 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 153 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 142 time to evaluate : 0.893 Fit side-chains revert: symmetry clash REVERT: B 262 MET cc_start: 0.5876 (OUTLIER) cc_final: 0.5173 (mmp) REVERT: B 414 HIS cc_start: 0.6426 (m90) cc_final: 0.6196 (m90) REVERT: B 420 ASP cc_start: 0.7639 (m-30) cc_final: 0.7391 (m-30) REVERT: B 421 LYS cc_start: 0.7748 (tptt) cc_final: 0.7322 (ttpt) REVERT: C 183 MET cc_start: 0.5538 (pmm) cc_final: 0.4766 (mtt) REVERT: D 262 MET cc_start: 0.5772 (OUTLIER) cc_final: 0.5275 (mmp) REVERT: D 414 HIS cc_start: 0.6434 (m90) cc_final: 0.6216 (m90) REVERT: D 420 ASP cc_start: 0.7635 (m-30) cc_final: 0.7412 (m-30) REVERT: D 421 LYS cc_start: 0.7792 (tptt) cc_final: 0.7352 (ttpt) outliers start: 11 outliers final: 8 residues processed: 146 average time/residue: 0.1758 time to fit residues: 35.9366 Evaluate side-chains 146 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 136 time to evaluate : 0.852 ------------------------------------------------------------------------------- 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 393 SER Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain C residue 320 CYS Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 391 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 96 optimal weight: 0.0870 chunk 60 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8188 Z= 0.185 Angle : 0.509 7.104 11124 Z= 0.263 Chirality : 0.038 0.129 1320 Planarity : 0.005 0.064 1360 Dihedral : 3.531 12.943 1148 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % 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: 2.79 (0.26), residues: 1028 helix: 2.26 (0.18), residues: 788 sheet: None (None), residues: 0 loop : 0.53 (0.44), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 172 HIS 0.002 0.000 HIS C 306 PHE 0.007 0.001 PHE B 257 TYR 0.022 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 151 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 135 time to evaluate : 0.913 Fit side-chains revert: symmetry clash REVERT: B 262 MET cc_start: 0.5806 (OUTLIER) cc_final: 0.5327 (mmp) REVERT: B 414 HIS cc_start: 0.6444 (m90) cc_final: 0.6242 (m90) REVERT: C 183 MET cc_start: 0.5538 (pmm) cc_final: 0.4773 (mtt) REVERT: D 225 TYR cc_start: 0.7724 (m-10) cc_final: 0.7514 (m-80) REVERT: D 262 MET cc_start: 0.5739 (OUTLIER) cc_final: 0.5215 (mmp) REVERT: D 420 ASP cc_start: 0.7680 (m-30) cc_final: 0.7476 (m-30) outliers start: 16 outliers final: 13 residues processed: 142 average time/residue: 0.1738 time to fit residues: 34.7077 Evaluate side-chains 149 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 134 time to evaluate : 0.808 ------------------------------------------------------------------------------- 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 328 LEU Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain C residue 320 CYS Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain D residue 183 MET Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 391 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 61 optimal weight: 8.9990 chunk 65 optimal weight: 8.9990 chunk 47 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 75 optimal weight: 10.0000 chunk 87 optimal weight: 0.9990 chunk 92 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 chunk 89 optimal weight: 7.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 8188 Z= 0.351 Angle : 0.589 6.655 11124 Z= 0.306 Chirality : 0.042 0.138 1320 Planarity : 0.006 0.063 1360 Dihedral : 3.819 14.061 1148 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.13 % Allowed : 17.06 % 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 (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: 2.34 (0.26), residues: 1028 helix: 1.96 (0.18), residues: 784 sheet: None (None), residues: 0 loop : 0.34 (0.43), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 172 HIS 0.003 0.001 HIS C 306 PHE 0.013 0.001 PHE A 257 TYR 0.019 0.002 TYR D 273 ARG 0.003 0.000 ARG A 305 *********************** 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 152 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 134 time to evaluate : 0.902 Fit side-chains REVERT: B 262 MET cc_start: 0.5836 (OUTLIER) cc_final: 0.5310 (mmp) REVERT: B 346 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7614 (mm-30) REVERT: C 346 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7862 (tp30) REVERT: D 262 MET cc_start: 0.5797 (OUTLIER) cc_final: 0.5203 (mmp) outliers start: 18 outliers final: 15 residues processed: 144 average time/residue: 0.1765 time to fit residues: 35.5886 Evaluate side-chains 148 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 131 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 238 MET 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 391 SER Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 391 SER 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 391 SER Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 304 SER Chi-restraints excluded: chain D residue 391 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 0.5980 chunk 54 optimal weight: 0.9980 chunk 39 optimal weight: 9.9990 chunk 70 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 84 optimal weight: 0.0980 chunk 89 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 57 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8188 Z= 0.186 Angle : 0.523 6.755 11124 Z= 0.270 Chirality : 0.038 0.130 1320 Planarity : 0.006 0.064 1360 Dihedral : 3.640 13.965 1148 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.13 % Allowed : 17.65 % 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: 2.49 (0.26), residues: 1028 helix: 1.98 (0.18), residues: 804 sheet: None (None), residues: 0 loop : 0.59 (0.47), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 172 HIS 0.002 0.000 HIS A 306 PHE 0.007 0.001 PHE B 257 TYR 0.020 0.001 TYR B 273 ARG 0.001 0.000 ARG A 254 *********************** 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 149 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 131 time to evaluate : 0.965 Fit side-chains REVERT: B 262 MET cc_start: 0.5753 (OUTLIER) cc_final: 0.5276 (mmp) REVERT: C 183 MET cc_start: 0.5484 (pmm) cc_final: 0.4729 (mtt) REVERT: D 262 MET cc_start: 0.5770 (OUTLIER) cc_final: 0.5224 (mmp) outliers start: 18 outliers final: 13 residues processed: 140 average time/residue: 0.1784 time to fit residues: 35.4225 Evaluate side-chains 146 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 131 time to evaluate : 0.874 ------------------------------------------------------------------------------- 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 391 SER Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 391 SER 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 391 SER Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 391 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.5980 chunk 66 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 79 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 48 optimal weight: 0.0470 chunk 63 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2958 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= 0.190 Angle : 0.521 7.577 11124 Z= 0.270 Chirality : 0.038 0.129 1320 Planarity : 0.006 0.064 1360 Dihedral : 3.626 14.481 1148 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.01 % Allowed : 18.01 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.55 (0.26), residues: 1028 helix: 2.03 (0.18), residues: 804 sheet: None (None), residues: 0 loop : 0.59 (0.47), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 172 HIS 0.002 0.001 HIS A 306 PHE 0.007 0.001 PHE B 257 TYR 0.019 0.001 TYR B 273 ARG 0.001 0.000 ARG A 305 ********************** 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 147 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 130 time to evaluate : 0.934 Fit side-chains REVERT: B 262 MET cc_start: 0.5840 (OUTLIER) cc_final: 0.5339 (mmp) REVERT: B 421 LYS cc_start: 0.7804 (tptt) cc_final: 0.7266 (ttpt) REVERT: C 183 MET cc_start: 0.5513 (pmm) cc_final: 0.4756 (mtt) REVERT: D 262 MET cc_start: 0.5773 (OUTLIER) cc_final: 0.5219 (mmp) outliers start: 17 outliers final: 14 residues processed: 140 average time/residue: 0.1761 time to fit residues: 34.7136 Evaluate side-chains 144 residues out of total 880 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 128 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 VAL 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 A residue 391 SER Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain C residue 320 CYS Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain C residue 393 SER Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 391 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 0.6980 chunk 11 optimal weight: 8.9990 chunk 22 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 33 optimal weight: 0.2980 chunk 81 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 14 optimal weight: 9.9990 chunk 69 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.194072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.142123 restraints weight = 9521.442| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 1.82 r_work: 0.3356 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2991 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= 0.208 Angle : 0.525 7.360 11124 Z= 0.273 Chirality : 0.039 0.127 1320 Planarity : 0.006 0.064 1360 Dihedral : 3.643 14.714 1148 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.01 % Allowed : 17.54 % 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: 2.47 (0.26), residues: 1028 helix: 1.98 (0.18), residues: 804 sheet: None (None), residues: 0 loop : 0.56 (0.47), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 172 HIS 0.002 0.001 HIS A 306 PHE 0.007 0.001 PHE B 257 TYR 0.018 0.001 TYR B 273 ARG 0.001 0.000 ARG A 305 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2016.50 seconds wall clock time: 37 minutes 25.70 seconds (2245.70 seconds total)