Starting phenix.real_space_refine on Mon Apr 8 01:42:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x82_38133/04_2024/8x82_38133_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x82_38133/04_2024/8x82_38133.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x82_38133/04_2024/8x82_38133.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x82_38133/04_2024/8x82_38133.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x82_38133/04_2024/8x82_38133_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8x82_38133/04_2024/8x82_38133_neut.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 7796 2.51 5 N 2048 2.21 5 O 2088 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 2": "OE1" <-> "OE2" Residue "A GLU 33": "OE1" <-> "OE2" Residue "A GLU 107": "OE1" <-> "OE2" Residue "A GLU 346": "OE1" <-> "OE2" Residue "B GLU 2": "OE1" <-> "OE2" Residue "B GLU 33": "OE1" <-> "OE2" Residue "B GLU 107": "OE1" <-> "OE2" Residue "B GLU 346": "OE1" <-> "OE2" Residue "C GLU 2": "OE1" <-> "OE2" Residue "C GLU 33": "OE1" <-> "OE2" Residue "C GLU 107": "OE1" <-> "OE2" Residue "C GLU 346": "OE1" <-> "OE2" Residue "D GLU 2": "OE1" <-> "OE2" Residue "D GLU 33": "OE1" <-> "OE2" Residue "D GLU 107": "OE1" <-> "OE2" Residue "D GLU 346": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 12004 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3001 Classifications: {'peptide': 380} Link IDs: {'PTRANS': 6, 'TRANS': 373} Chain breaks: 1 Chain: "B" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3001 Classifications: {'peptide': 380} Link IDs: {'PTRANS': 6, 'TRANS': 373} Chain breaks: 1 Chain: "C" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3001 Classifications: {'peptide': 380} Link IDs: {'PTRANS': 6, 'TRANS': 373} Chain breaks: 1 Chain: "D" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3001 Classifications: {'peptide': 380} Link IDs: {'PTRANS': 6, 'TRANS': 373} Chain breaks: 1 Time building chain proxies: 6.24, per 1000 atoms: 0.52 Number of scatterers: 12004 At special positions: 0 Unit cell: (108.81, 108.81, 105.09, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 2088 8.00 N 2048 7.00 C 7796 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: 5.19 Conformation dependent library (CDL) restraints added in 2.4 seconds 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2896 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 8 sheets defined 85.3% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 7 through 17 Processing helix chain 'A' and resid 37 through 64 Processing helix chain 'A' and resid 73 through 100 removed outlier: 3.603A pdb=" N VAL A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 119 Processing helix chain 'A' and resid 120 through 123 removed outlier: 3.539A pdb=" N ASN A 123 " --> pdb=" O ASN A 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 120 through 123' Processing helix chain 'A' and resid 124 through 162 Processing helix chain 'A' and resid 168 through 174 removed outlier: 3.534A pdb=" N VAL A 172 " --> pdb=" O THR A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 215 Processing helix chain 'A' and resid 263 through 321 removed outlier: 6.049A pdb=" N ILE A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ALA A 295 " --> pdb=" O SER A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 357 Proline residue: A 347 - end of helix Processing helix chain 'A' and resid 357 through 369 Processing helix chain 'A' and resid 371 through 387 removed outlier: 4.207A pdb=" N VAL A 387 " --> pdb=" O GLN A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 425 removed outlier: 3.651A pdb=" N THR A 406 " --> pdb=" O ARG A 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 17 Processing helix chain 'B' and resid 37 through 64 Processing helix chain 'B' and resid 73 through 100 removed outlier: 3.603A pdb=" N VAL B 87 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 119 Processing helix chain 'B' and resid 120 through 123 removed outlier: 3.539A pdb=" N ASN B 123 " --> pdb=" O ASN B 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 120 through 123' Processing helix chain 'B' and resid 124 through 162 Processing helix chain 'B' and resid 168 through 174 removed outlier: 3.534A pdb=" N VAL B 172 " --> pdb=" O THR B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 215 Processing helix chain 'B' and resid 263 through 321 removed outlier: 6.049A pdb=" N ILE B 294 " --> pdb=" O ASN B 290 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ALA B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 357 Proline residue: B 347 - end of helix Processing helix chain 'B' and resid 357 through 369 Processing helix chain 'B' and resid 371 through 387 removed outlier: 4.207A pdb=" N VAL B 387 " --> pdb=" O GLN B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 425 removed outlier: 3.652A pdb=" N THR B 406 " --> pdb=" O ARG B 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 17 Processing helix chain 'C' and resid 37 through 64 Processing helix chain 'C' and resid 73 through 100 removed outlier: 3.603A pdb=" N VAL C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 119 Processing helix chain 'C' and resid 120 through 123 removed outlier: 3.539A pdb=" N ASN C 123 " --> pdb=" O ASN C 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 120 through 123' Processing helix chain 'C' and resid 124 through 162 Processing helix chain 'C' and resid 168 through 174 removed outlier: 3.534A pdb=" N VAL C 172 " --> pdb=" O THR C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 215 Processing helix chain 'C' and resid 263 through 321 removed outlier: 6.049A pdb=" N ILE C 294 " --> pdb=" O ASN C 290 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ALA C 295 " --> pdb=" O SER C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 357 Proline residue: C 347 - end of helix Processing helix chain 'C' and resid 357 through 369 Processing helix chain 'C' and resid 371 through 387 removed outlier: 4.207A pdb=" N VAL C 387 " --> pdb=" O GLN C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 425 removed outlier: 3.651A pdb=" N THR C 406 " --> pdb=" O ARG C 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 17 Processing helix chain 'D' and resid 37 through 64 Processing helix chain 'D' and resid 73 through 100 removed outlier: 3.603A pdb=" N VAL D 87 " --> pdb=" O ASP D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 119 Processing helix chain 'D' and resid 120 through 123 removed outlier: 3.539A pdb=" N ASN D 123 " --> pdb=" O ASN D 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 120 through 123' Processing helix chain 'D' and resid 124 through 162 Processing helix chain 'D' and resid 168 through 174 removed outlier: 3.534A pdb=" N VAL D 172 " --> pdb=" O THR D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 215 Processing helix chain 'D' and resid 263 through 321 removed outlier: 6.049A pdb=" N ILE D 294 " --> pdb=" O ASN D 290 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ALA D 295 " --> pdb=" O SER D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 357 Proline residue: D 347 - end of helix Processing helix chain 'D' and resid 357 through 369 Processing helix chain 'D' and resid 371 through 387 removed outlier: 4.207A pdb=" N VAL D 387 " --> pdb=" O GLN D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 425 removed outlier: 3.651A pdb=" N THR D 406 " --> pdb=" O ARG D 402 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 22 through 26 removed outlier: 3.527A pdb=" N VAL A 25 " --> pdb=" O GLU A 33 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 392 through 393 removed outlier: 4.511A pdb=" N PHE A 392 " --> pdb=" O VAL A 400 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 22 through 26 removed outlier: 3.527A pdb=" N VAL B 25 " --> pdb=" O GLU B 33 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 392 through 393 removed outlier: 4.511A pdb=" N PHE B 392 " --> pdb=" O VAL B 400 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 22 through 26 removed outlier: 3.527A pdb=" N VAL C 25 " --> pdb=" O GLU C 33 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 392 through 393 removed outlier: 4.511A pdb=" N PHE C 392 " --> pdb=" O VAL C 400 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 22 through 26 removed outlier: 3.527A pdb=" N VAL D 25 " --> pdb=" O GLU D 33 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 392 through 393 removed outlier: 4.511A pdb=" N PHE D 392 " --> pdb=" O VAL D 400 " (cutoff:3.500A) 1068 hydrogen bonds defined for protein. 3204 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: 4.07 Time building geometry restraints manager: 5.50 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: 3790 1.34 - 1.46: 2718 1.46 - 1.58: 5616 1.58 - 1.69: 0 1.69 - 1.81: 112 Bond restraints: 12236 Sorted by residual: bond pdb=" CA ILE A 176 " pdb=" C ILE A 176 " ideal model delta sigma weight residual 1.520 1.528 -0.009 8.80e-03 1.29e+04 9.99e-01 bond pdb=" CA ILE B 176 " pdb=" C ILE B 176 " ideal model delta sigma weight residual 1.520 1.528 -0.009 8.80e-03 1.29e+04 9.99e-01 bond pdb=" C ILE B 67 " pdb=" O ILE B 67 " ideal model delta sigma weight residual 1.232 1.240 -0.009 1.01e-02 9.80e+03 7.92e-01 bond pdb=" C ILE D 67 " pdb=" O ILE D 67 " ideal model delta sigma weight residual 1.232 1.240 -0.009 1.01e-02 9.80e+03 7.92e-01 bond pdb=" C ILE D 176 " pdb=" N PRO D 177 " ideal model delta sigma weight residual 1.335 1.345 -0.010 1.28e-02 6.10e+03 6.36e-01 ... (remaining 12231 not shown) Histogram of bond angle deviations from ideal: 100.51 - 107.22: 239 107.22 - 113.92: 7196 113.92 - 120.63: 5342 120.63 - 127.34: 3715 127.34 - 134.04: 104 Bond angle restraints: 16596 Sorted by residual: angle pdb=" C TYR B 175 " pdb=" N ILE B 176 " pdb=" CA ILE B 176 " ideal model delta sigma weight residual 120.24 123.00 -2.76 6.30e-01 2.52e+00 1.91e+01 angle pdb=" C TYR A 175 " pdb=" N ILE A 176 " pdb=" CA ILE A 176 " ideal model delta sigma weight residual 120.24 123.00 -2.76 6.30e-01 2.52e+00 1.91e+01 angle pdb=" C TYR C 175 " pdb=" N ILE C 176 " pdb=" CA ILE C 176 " ideal model delta sigma weight residual 120.33 123.03 -2.70 8.00e-01 1.56e+00 1.14e+01 angle pdb=" C TYR D 175 " pdb=" N ILE D 176 " pdb=" CA ILE D 176 " ideal model delta sigma weight residual 120.33 123.03 -2.70 8.00e-01 1.56e+00 1.14e+01 angle pdb=" C VAL D 345 " pdb=" N GLU D 346 " pdb=" CA GLU D 346 " ideal model delta sigma weight residual 120.26 124.12 -3.86 1.34e+00 5.57e-01 8.31e+00 ... (remaining 16591 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.10: 6284 17.10 - 34.21: 712 34.21 - 51.31: 200 51.31 - 68.42: 32 68.42 - 85.52: 24 Dihedral angle restraints: 7252 sinusoidal: 2792 harmonic: 4460 Sorted by residual: dihedral pdb=" CA ASP B 276 " pdb=" CB ASP B 276 " pdb=" CG ASP B 276 " pdb=" OD1 ASP B 276 " ideal model delta sinusoidal sigma weight residual -30.00 -88.04 58.04 1 2.00e+01 2.50e-03 1.13e+01 dihedral pdb=" CA ASP D 276 " pdb=" CB ASP D 276 " pdb=" CG ASP D 276 " pdb=" OD1 ASP D 276 " ideal model delta sinusoidal sigma weight residual -30.00 -87.99 57.99 1 2.00e+01 2.50e-03 1.13e+01 dihedral pdb=" CA ASP A 276 " pdb=" CB ASP A 276 " pdb=" CG ASP A 276 " pdb=" OD1 ASP A 276 " ideal model delta sinusoidal sigma weight residual -30.00 -87.99 57.99 1 2.00e+01 2.50e-03 1.13e+01 ... (remaining 7249 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 1210 0.024 - 0.047: 470 0.047 - 0.071: 244 0.071 - 0.095: 37 0.095 - 0.119: 27 Chirality restraints: 1988 Sorted by residual: chirality pdb=" CA ILE A 163 " pdb=" N ILE A 163 " pdb=" C ILE A 163 " pdb=" CB ILE A 163 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.51e-01 chirality pdb=" CA ILE C 163 " pdb=" N ILE C 163 " pdb=" C ILE C 163 " pdb=" CB ILE C 163 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.50e-01 chirality pdb=" CA ILE D 163 " pdb=" N ILE D 163 " pdb=" C ILE D 163 " pdb=" CB ILE D 163 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.42e-01 ... (remaining 1985 not shown) Planarity restraints: 2032 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 176 " 0.017 5.00e-02 4.00e+02 2.52e-02 1.01e+00 pdb=" N PRO B 177 " -0.044 5.00e-02 4.00e+02 pdb=" CA PRO B 177 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO B 177 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 176 " 0.017 5.00e-02 4.00e+02 2.52e-02 1.01e+00 pdb=" N PRO A 177 " -0.043 5.00e-02 4.00e+02 pdb=" CA PRO A 177 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 177 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 176 " -0.017 5.00e-02 4.00e+02 2.50e-02 1.00e+00 pdb=" N PRO C 177 " 0.043 5.00e-02 4.00e+02 pdb=" CA PRO C 177 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO C 177 " -0.014 5.00e-02 4.00e+02 ... (remaining 2029 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 284 2.72 - 3.27: 12504 3.27 - 3.81: 21460 3.81 - 4.36: 23941 4.36 - 4.90: 42851 Nonbonded interactions: 101040 Sorted by model distance: nonbonded pdb=" O ALA D 81 " pdb=" OG SER D 85 " model vdw 2.181 2.440 nonbonded pdb=" O ALA A 81 " pdb=" OG SER A 85 " model vdw 2.181 2.440 nonbonded pdb=" O ALA C 81 " pdb=" OG SER C 85 " model vdw 2.181 2.440 nonbonded pdb=" O ALA B 81 " pdb=" OG SER B 85 " model vdw 2.181 2.440 nonbonded pdb=" OD1 ASN A 207 " pdb=" OG1 THR A 358 " model vdw 2.244 2.440 ... (remaining 101035 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' 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: 1.130 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: 3.740 Check model and map are aligned: 0.180 Set scattering table: 0.120 Process input model: 34.480 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.070 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:14.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 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 : 0.002 0.025 12236 Z= 0.134 Angle : 0.408 5.012 16596 Z= 0.260 Chirality : 0.033 0.119 1988 Planarity : 0.002 0.025 2032 Dihedral : 16.428 85.523 4356 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 0.84 % Allowed : 18.12 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.68 (0.21), residues: 1504 helix: 3.02 (0.13), residues: 1248 sheet: 1.67 (0.77), residues: 48 loop : -1.49 (0.41), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 154 HIS 0.002 0.001 HIS A 306 PHE 0.007 0.001 PHE B 178 TYR 0.005 0.001 TYR B 415 ARG 0.002 0.000 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 180 time to evaluate : 1.539 Fit side-chains REVERT: A 126 ARG cc_start: 0.6565 (mmm160) cc_final: 0.5840 (mtm110) REVERT: A 129 ARG cc_start: 0.7396 (ttm-80) cc_final: 0.7061 (ttm170) REVERT: A 131 ARG cc_start: 0.6936 (mpt-90) cc_final: 0.5478 (tmt-80) REVERT: A 272 LYS cc_start: 0.6744 (tppp) cc_final: 0.5990 (ttpp) REVERT: A 279 GLU cc_start: 0.8121 (tt0) cc_final: 0.7790 (tt0) REVERT: A 367 ARG cc_start: 0.6379 (mtm-85) cc_final: 0.6145 (mtm-85) REVERT: A 399 ARG cc_start: 0.7766 (mtm180) cc_final: 0.7120 (tpt170) REVERT: B 126 ARG cc_start: 0.6536 (mmm160) cc_final: 0.5802 (mtm110) REVERT: B 129 ARG cc_start: 0.7396 (ttm-80) cc_final: 0.7064 (ttm170) REVERT: B 131 ARG cc_start: 0.6936 (mpt-90) cc_final: 0.5481 (tmt-80) REVERT: B 272 LYS cc_start: 0.6761 (tppp) cc_final: 0.5993 (ttpp) REVERT: B 279 GLU cc_start: 0.8120 (tt0) cc_final: 0.7791 (tt0) REVERT: B 399 ARG cc_start: 0.7769 (mtm180) cc_final: 0.7140 (tpt170) REVERT: C 126 ARG cc_start: 0.6535 (mmm160) cc_final: 0.5800 (mtm110) REVERT: C 129 ARG cc_start: 0.7396 (ttm-80) cc_final: 0.7064 (ttm170) REVERT: C 131 ARG cc_start: 0.6938 (mpt-90) cc_final: 0.5478 (tmt-80) REVERT: C 272 LYS cc_start: 0.6743 (tppp) cc_final: 0.5988 (ttpp) REVERT: C 279 GLU cc_start: 0.8120 (tt0) cc_final: 0.7791 (tt0) REVERT: C 399 ARG cc_start: 0.7767 (mtm180) cc_final: 0.7175 (tpt170) REVERT: D 126 ARG cc_start: 0.6563 (mmm160) cc_final: 0.5840 (mtm110) REVERT: D 129 ARG cc_start: 0.7395 (ttm-80) cc_final: 0.7061 (ttm170) REVERT: D 131 ARG cc_start: 0.6938 (mpt-90) cc_final: 0.5478 (tmt-80) REVERT: D 272 LYS cc_start: 0.6744 (tppp) cc_final: 0.5985 (ttpp) REVERT: D 279 GLU cc_start: 0.8120 (tt0) cc_final: 0.7716 (tt0) REVERT: D 399 ARG cc_start: 0.7766 (mtm180) cc_final: 0.7137 (tpt170) outliers start: 11 outliers final: 0 residues processed: 191 average time/residue: 1.5220 time to fit residues: 312.2203 Evaluate side-chains 136 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.8980 chunk 115 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 119 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 138 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 GLN A 383 GLN ** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 423 GLN B 189 GLN B 383 GLN ** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 GLN C 189 GLN C 383 GLN ** C 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 423 GLN D 189 GLN D 383 GLN ** D 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 423 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.0994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12236 Z= 0.193 Angle : 0.422 4.790 16596 Z= 0.233 Chirality : 0.035 0.131 1988 Planarity : 0.003 0.026 2032 Dihedral : 3.324 11.837 1656 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.14 % Allowed : 16.74 % Favored : 81.12 % 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: 3.57 (0.21), residues: 1504 helix: 2.87 (0.13), residues: 1260 sheet: 1.69 (0.77), residues: 48 loop : -1.23 (0.47), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 38 HIS 0.002 0.001 HIS A 349 PHE 0.009 0.002 PHE A 11 TYR 0.010 0.001 TYR B 175 ARG 0.004 0.000 ARG C 367 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 132 time to evaluate : 1.441 Fit side-chains REVERT: A 126 ARG cc_start: 0.6484 (mtm110) cc_final: 0.5758 (mtm110) REVERT: A 131 ARG cc_start: 0.6996 (mpt-90) cc_final: 0.5540 (tmt-80) REVERT: A 272 LYS cc_start: 0.7030 (tppp) cc_final: 0.6399 (ttpp) REVERT: A 279 GLU cc_start: 0.8072 (tt0) cc_final: 0.7717 (tt0) REVERT: A 399 ARG cc_start: 0.7885 (mtm180) cc_final: 0.7234 (tpt170) REVERT: B 126 ARG cc_start: 0.6486 (mtm110) cc_final: 0.5759 (mtm110) REVERT: B 131 ARG cc_start: 0.6997 (mpt-90) cc_final: 0.5540 (tmt-80) REVERT: B 272 LYS cc_start: 0.7030 (tppp) cc_final: 0.6398 (ttpp) REVERT: B 279 GLU cc_start: 0.8071 (tt0) cc_final: 0.7716 (tt0) REVERT: B 399 ARG cc_start: 0.7890 (mtm180) cc_final: 0.7244 (tpt170) REVERT: C 126 ARG cc_start: 0.6483 (mtm110) cc_final: 0.5761 (mtm110) REVERT: C 131 ARG cc_start: 0.6996 (mpt-90) cc_final: 0.5539 (tmt-80) REVERT: C 272 LYS cc_start: 0.7030 (tppp) cc_final: 0.6399 (ttpp) REVERT: C 279 GLU cc_start: 0.8078 (tt0) cc_final: 0.7721 (tt0) REVERT: C 399 ARG cc_start: 0.7889 (mtm180) cc_final: 0.7243 (tpt170) REVERT: D 126 ARG cc_start: 0.6482 (mtm110) cc_final: 0.5760 (mtm110) REVERT: D 131 ARG cc_start: 0.6998 (mpt-90) cc_final: 0.5540 (tmt-80) REVERT: D 272 LYS cc_start: 0.7027 (tppp) cc_final: 0.6395 (ttpp) REVERT: D 279 GLU cc_start: 0.8048 (tt0) cc_final: 0.7665 (tt0) REVERT: D 399 ARG cc_start: 0.7893 (mtm180) cc_final: 0.7245 (tpt170) outliers start: 28 outliers final: 8 residues processed: 148 average time/residue: 1.3824 time to fit residues: 220.9097 Evaluate side-chains 145 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 137 time to evaluate : 1.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 410 SER Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 410 SER Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 410 SER Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 410 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 6.9990 chunk 42 optimal weight: 0.9980 chunk 114 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 138 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 chunk 123 optimal weight: 0.9990 chunk 137 optimal weight: 0.9980 chunk 47 optimal weight: 0.4980 chunk 110 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 GLN A 383 GLN ** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 GLN B 383 GLN ** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 189 GLN C 383 GLN ** C 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 189 GLN D 383 GLN ** D 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12236 Z= 0.208 Angle : 0.434 5.064 16596 Z= 0.237 Chirality : 0.036 0.130 1988 Planarity : 0.003 0.026 2032 Dihedral : 3.441 12.589 1656 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 3.36 % Allowed : 15.67 % Favored : 80.96 % 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: 3.34 (0.21), residues: 1504 helix: 2.72 (0.13), residues: 1264 sheet: 1.24 (0.76), residues: 48 loop : -1.30 (0.47), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 154 HIS 0.002 0.001 HIS B 349 PHE 0.011 0.002 PHE A 11 TYR 0.014 0.001 TYR B 175 ARG 0.004 0.000 ARG C 424 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 172 time to evaluate : 1.161 Fit side-chains REVERT: A 25 VAL cc_start: 0.7927 (p) cc_final: 0.7678 (m) REVERT: A 33 GLU cc_start: 0.7477 (mt-10) cc_final: 0.7197 (mt-10) REVERT: A 51 MET cc_start: 0.7766 (mmt) cc_final: 0.7525 (tpp) REVERT: A 114 LYS cc_start: 0.7245 (OUTLIER) cc_final: 0.6648 (mtmt) REVERT: A 123 ASN cc_start: 0.7333 (m-40) cc_final: 0.7121 (m-40) REVERT: A 126 ARG cc_start: 0.6409 (mtm110) cc_final: 0.5706 (mtm110) REVERT: A 129 ARG cc_start: 0.7303 (ttm-80) cc_final: 0.6915 (ttm170) REVERT: A 131 ARG cc_start: 0.7004 (OUTLIER) cc_final: 0.5443 (ttt180) REVERT: A 173 HIS cc_start: 0.6227 (OUTLIER) cc_final: 0.5332 (m-70) REVERT: A 272 LYS cc_start: 0.7039 (tppp) cc_final: 0.6493 (ttpp) REVERT: A 279 GLU cc_start: 0.8079 (tt0) cc_final: 0.7657 (tt0) REVERT: A 313 PHE cc_start: 0.6481 (OUTLIER) cc_final: 0.6021 (m-10) REVERT: A 331 MET cc_start: 0.6421 (ttp) cc_final: 0.6148 (ttp) REVERT: A 364 GLU cc_start: 0.6923 (mt-10) cc_final: 0.6720 (mm-30) REVERT: A 380 LYS cc_start: 0.7102 (mmtp) cc_final: 0.6677 (mmmt) REVERT: A 399 ARG cc_start: 0.7952 (mtm180) cc_final: 0.7251 (tpt170) REVERT: B 25 VAL cc_start: 0.7926 (p) cc_final: 0.7678 (m) REVERT: B 33 GLU cc_start: 0.7479 (mt-10) cc_final: 0.7199 (mt-10) REVERT: B 114 LYS cc_start: 0.7245 (OUTLIER) cc_final: 0.6649 (mtmt) REVERT: B 123 ASN cc_start: 0.7378 (m-40) cc_final: 0.7158 (m-40) REVERT: B 126 ARG cc_start: 0.6407 (mtm110) cc_final: 0.5700 (mtm110) REVERT: B 129 ARG cc_start: 0.7301 (ttm-80) cc_final: 0.6914 (ttm170) REVERT: B 131 ARG cc_start: 0.7003 (OUTLIER) cc_final: 0.5442 (ttt180) REVERT: B 173 HIS cc_start: 0.6172 (OUTLIER) cc_final: 0.5267 (m-70) REVERT: B 272 LYS cc_start: 0.7036 (tppp) cc_final: 0.6490 (ttpp) REVERT: B 279 GLU cc_start: 0.8078 (tt0) cc_final: 0.7657 (tt0) REVERT: B 313 PHE cc_start: 0.6481 (OUTLIER) cc_final: 0.6021 (m-10) REVERT: B 331 MET cc_start: 0.6423 (ttp) cc_final: 0.6143 (ttp) REVERT: B 380 LYS cc_start: 0.7103 (mmtp) cc_final: 0.6677 (mmmt) REVERT: B 399 ARG cc_start: 0.7955 (mtm180) cc_final: 0.7260 (tpt170) REVERT: C 25 VAL cc_start: 0.7926 (p) cc_final: 0.7679 (m) REVERT: C 33 GLU cc_start: 0.7477 (mt-10) cc_final: 0.7201 (mt-10) REVERT: C 114 LYS cc_start: 0.7246 (OUTLIER) cc_final: 0.6650 (mtmt) REVERT: C 123 ASN cc_start: 0.7378 (m-40) cc_final: 0.7160 (m-40) REVERT: C 126 ARG cc_start: 0.6405 (mtm110) cc_final: 0.5698 (mtm110) REVERT: C 129 ARG cc_start: 0.7300 (ttm-80) cc_final: 0.6907 (ttm170) REVERT: C 131 ARG cc_start: 0.7003 (OUTLIER) cc_final: 0.5443 (ttt180) REVERT: C 173 HIS cc_start: 0.6169 (OUTLIER) cc_final: 0.5262 (m-70) REVERT: C 272 LYS cc_start: 0.7037 (tppp) cc_final: 0.6495 (ttpp) REVERT: C 279 GLU cc_start: 0.8079 (tt0) cc_final: 0.7658 (tt0) REVERT: C 313 PHE cc_start: 0.6479 (OUTLIER) cc_final: 0.6020 (m-10) REVERT: C 331 MET cc_start: 0.6422 (ttp) cc_final: 0.6141 (ttp) REVERT: C 364 GLU cc_start: 0.6934 (mt-10) cc_final: 0.6725 (mm-30) REVERT: C 380 LYS cc_start: 0.7110 (mmtp) cc_final: 0.6684 (mmmt) REVERT: C 399 ARG cc_start: 0.7956 (mtm180) cc_final: 0.7259 (tpt170) REVERT: D 25 VAL cc_start: 0.7928 (p) cc_final: 0.7678 (m) REVERT: D 33 GLU cc_start: 0.7500 (mt-10) cc_final: 0.7219 (mt-10) REVERT: D 51 MET cc_start: 0.7767 (mmt) cc_final: 0.7523 (tpp) REVERT: D 114 LYS cc_start: 0.7246 (OUTLIER) cc_final: 0.6650 (mtmt) REVERT: D 123 ASN cc_start: 0.7375 (m-40) cc_final: 0.7159 (m-40) REVERT: D 126 ARG cc_start: 0.6409 (mtm110) cc_final: 0.5704 (mtm110) REVERT: D 129 ARG cc_start: 0.7301 (ttm-80) cc_final: 0.6910 (ttm170) REVERT: D 131 ARG cc_start: 0.7006 (OUTLIER) cc_final: 0.5445 (ttt180) REVERT: D 173 HIS cc_start: 0.6171 (OUTLIER) cc_final: 0.5260 (m-70) REVERT: D 272 LYS cc_start: 0.7036 (tppp) cc_final: 0.6490 (ttpp) REVERT: D 279 GLU cc_start: 0.8059 (tt0) cc_final: 0.7599 (tt0) REVERT: D 313 PHE cc_start: 0.6480 (OUTLIER) cc_final: 0.6022 (m-10) REVERT: D 331 MET cc_start: 0.6424 (ttp) cc_final: 0.6149 (ttp) REVERT: D 364 GLU cc_start: 0.6935 (mt-10) cc_final: 0.6727 (mm-30) REVERT: D 380 LYS cc_start: 0.7100 (mmtp) cc_final: 0.6674 (mmmt) REVERT: D 399 ARG cc_start: 0.7955 (mtm180) cc_final: 0.7257 (tpt170) outliers start: 44 outliers final: 14 residues processed: 200 average time/residue: 1.3847 time to fit residues: 298.3881 Evaluate side-chains 196 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 166 time to evaluate : 1.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain A residue 173 HIS Chi-restraints excluded: chain A residue 313 PHE Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 410 SER Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 114 LYS Chi-restraints excluded: chain B residue 131 ARG Chi-restraints excluded: chain B residue 173 HIS Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 410 SER Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 114 LYS Chi-restraints excluded: chain C residue 131 ARG Chi-restraints excluded: chain C residue 173 HIS Chi-restraints excluded: chain C residue 313 PHE Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 410 SER Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 114 LYS Chi-restraints excluded: chain D residue 131 ARG Chi-restraints excluded: chain D residue 173 HIS Chi-restraints excluded: chain D residue 313 PHE Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 410 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 71 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 92 optimal weight: 20.0000 chunk 138 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 131 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 ASN A 383 GLN ** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 ASN B 383 GLN ** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 ASN C 383 GLN ** C 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 ASN D 383 GLN ** D 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 12236 Z= 0.298 Angle : 0.488 5.382 16596 Z= 0.265 Chirality : 0.038 0.130 1988 Planarity : 0.003 0.025 2032 Dihedral : 3.605 12.693 1656 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 3.13 % Allowed : 16.36 % Favored : 80.50 % 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: 2.90 (0.20), residues: 1504 helix: 2.44 (0.13), residues: 1264 sheet: 1.03 (0.71), residues: 48 loop : -1.60 (0.44), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 174 HIS 0.004 0.001 HIS C 337 PHE 0.012 0.002 PHE A 422 TYR 0.013 0.002 TYR B 175 ARG 0.005 0.001 ARG A 424 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 147 time to evaluate : 1.419 Fit side-chains REVERT: A 25 VAL cc_start: 0.7806 (OUTLIER) cc_final: 0.7583 (m) REVERT: A 33 GLU cc_start: 0.7487 (mt-10) cc_final: 0.7252 (mt-10) REVERT: A 51 MET cc_start: 0.7880 (mmt) cc_final: 0.7618 (tpp) REVERT: A 71 MET cc_start: 0.6591 (mmm) cc_final: 0.5761 (mmm) REVERT: A 114 LYS cc_start: 0.7215 (OUTLIER) cc_final: 0.6696 (mtmt) REVERT: A 126 ARG cc_start: 0.6458 (mtm110) cc_final: 0.5737 (mtm110) REVERT: A 131 ARG cc_start: 0.7054 (mpt-90) cc_final: 0.5477 (ttt180) REVERT: A 155 MET cc_start: 0.6171 (OUTLIER) cc_final: 0.5970 (mtp) REVERT: A 272 LYS cc_start: 0.7043 (tppp) cc_final: 0.6463 (ttpp) REVERT: A 279 GLU cc_start: 0.8128 (tt0) cc_final: 0.7771 (tt0) REVERT: A 313 PHE cc_start: 0.6511 (OUTLIER) cc_final: 0.6031 (m-10) REVERT: A 331 MET cc_start: 0.6377 (ttp) cc_final: 0.6105 (ttp) REVERT: A 399 ARG cc_start: 0.8077 (mtm180) cc_final: 0.7251 (tpt170) REVERT: A 410 SER cc_start: 0.9006 (OUTLIER) cc_final: 0.8511 (m) REVERT: B 25 VAL cc_start: 0.7806 (OUTLIER) cc_final: 0.7583 (m) REVERT: B 33 GLU cc_start: 0.7488 (mt-10) cc_final: 0.7251 (mt-10) REVERT: B 71 MET cc_start: 0.6587 (mmm) cc_final: 0.5754 (mmm) REVERT: B 114 LYS cc_start: 0.7213 (OUTLIER) cc_final: 0.6694 (mtmt) REVERT: B 126 ARG cc_start: 0.6459 (mtm110) cc_final: 0.5737 (mtm110) REVERT: B 131 ARG cc_start: 0.7045 (mpt-90) cc_final: 0.5481 (ttt180) REVERT: B 155 MET cc_start: 0.6167 (OUTLIER) cc_final: 0.5960 (mtp) REVERT: B 272 LYS cc_start: 0.7039 (tppp) cc_final: 0.6459 (ttpp) REVERT: B 279 GLU cc_start: 0.8132 (tt0) cc_final: 0.7753 (tt0) REVERT: B 313 PHE cc_start: 0.6511 (OUTLIER) cc_final: 0.6034 (m-10) REVERT: B 331 MET cc_start: 0.6380 (ttp) cc_final: 0.6103 (ttp) REVERT: B 399 ARG cc_start: 0.8078 (mtm180) cc_final: 0.7257 (tpt170) REVERT: C 25 VAL cc_start: 0.7808 (OUTLIER) cc_final: 0.7584 (m) REVERT: C 33 GLU cc_start: 0.7486 (mt-10) cc_final: 0.7257 (mt-10) REVERT: C 71 MET cc_start: 0.6587 (mmm) cc_final: 0.5750 (mmm) REVERT: C 114 LYS cc_start: 0.7215 (OUTLIER) cc_final: 0.6696 (mtmt) REVERT: C 126 ARG cc_start: 0.6459 (mtm110) cc_final: 0.5738 (mtm110) REVERT: C 131 ARG cc_start: 0.7054 (mpt-90) cc_final: 0.5477 (ttt180) REVERT: C 272 LYS cc_start: 0.7057 (tppp) cc_final: 0.6464 (ttpp) REVERT: C 279 GLU cc_start: 0.8133 (tt0) cc_final: 0.7752 (tt0) REVERT: C 313 PHE cc_start: 0.6510 (OUTLIER) cc_final: 0.6034 (m-10) REVERT: C 331 MET cc_start: 0.6376 (ttp) cc_final: 0.6099 (ttp) REVERT: C 380 LYS cc_start: 0.7051 (mmtp) cc_final: 0.6588 (mmmt) REVERT: C 399 ARG cc_start: 0.8079 (mtm180) cc_final: 0.7257 (tpt170) REVERT: D 25 VAL cc_start: 0.7807 (OUTLIER) cc_final: 0.7584 (m) REVERT: D 33 GLU cc_start: 0.7485 (mt-10) cc_final: 0.7249 (mt-10) REVERT: D 51 MET cc_start: 0.7881 (mmt) cc_final: 0.7619 (tpp) REVERT: D 71 MET cc_start: 0.6591 (mmm) cc_final: 0.5759 (mmm) REVERT: D 114 LYS cc_start: 0.7214 (OUTLIER) cc_final: 0.6695 (mtmt) REVERT: D 126 ARG cc_start: 0.6459 (mtm110) cc_final: 0.5739 (mtm110) REVERT: D 131 ARG cc_start: 0.7056 (mpt-90) cc_final: 0.5477 (ttt180) REVERT: D 155 MET cc_start: 0.6167 (OUTLIER) cc_final: 0.5959 (mtp) REVERT: D 272 LYS cc_start: 0.7040 (tppp) cc_final: 0.6458 (ttpp) REVERT: D 279 GLU cc_start: 0.8117 (tt0) cc_final: 0.7717 (tt0) REVERT: D 313 PHE cc_start: 0.6510 (OUTLIER) cc_final: 0.6033 (m-10) REVERT: D 331 MET cc_start: 0.6379 (ttp) cc_final: 0.6101 (ttp) REVERT: D 399 ARG cc_start: 0.8078 (mtm180) cc_final: 0.7256 (tpt170) outliers start: 41 outliers final: 11 residues processed: 172 average time/residue: 1.3384 time to fit residues: 249.4351 Evaluate side-chains 172 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 145 time to evaluate : 1.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 313 PHE Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 410 SER Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 114 LYS Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 114 LYS Chi-restraints excluded: chain C residue 313 PHE Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 114 LYS Chi-restraints excluded: chain D residue 155 MET Chi-restraints excluded: chain D residue 313 PHE Chi-restraints excluded: chain D residue 404 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 7.9990 chunk 83 optimal weight: 9.9990 chunk 2 optimal weight: 6.9990 chunk 109 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 101 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 75 optimal weight: 0.8980 chunk 131 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 GLN ** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 383 GLN ** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 383 GLN ** C 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 383 GLN ** D 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12236 Z= 0.202 Angle : 0.426 5.103 16596 Z= 0.234 Chirality : 0.035 0.130 1988 Planarity : 0.003 0.025 2032 Dihedral : 3.499 13.148 1656 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.68 % Allowed : 17.58 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.14 (0.21), residues: 1504 helix: 2.61 (0.13), residues: 1264 sheet: 0.81 (0.73), residues: 48 loop : -1.49 (0.44), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 154 HIS 0.002 0.000 HIS A 349 PHE 0.011 0.002 PHE D 11 TYR 0.008 0.001 TYR D 175 ARG 0.002 0.000 ARG B 402 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 156 time to evaluate : 1.336 Fit side-chains REVERT: A 25 VAL cc_start: 0.7867 (p) cc_final: 0.7652 (m) REVERT: A 33 GLU cc_start: 0.7518 (mt-10) cc_final: 0.7283 (mt-10) REVERT: A 51 MET cc_start: 0.7837 (mmt) cc_final: 0.7609 (tpp) REVERT: A 71 MET cc_start: 0.6566 (mmm) cc_final: 0.5768 (mmm) REVERT: A 114 LYS cc_start: 0.7208 (OUTLIER) cc_final: 0.6587 (mtmt) REVERT: A 126 ARG cc_start: 0.6442 (mtm110) cc_final: 0.5756 (mtm110) REVERT: A 131 ARG cc_start: 0.7041 (mpt-90) cc_final: 0.5478 (tmt-80) REVERT: A 173 HIS cc_start: 0.6324 (OUTLIER) cc_final: 0.5338 (m-70) REVERT: A 272 LYS cc_start: 0.7046 (tppp) cc_final: 0.6484 (ttpp) REVERT: A 279 GLU cc_start: 0.8124 (tt0) cc_final: 0.7658 (tt0) REVERT: A 313 PHE cc_start: 0.6506 (OUTLIER) cc_final: 0.6001 (m-10) REVERT: A 331 MET cc_start: 0.6446 (ttp) cc_final: 0.6175 (ttp) REVERT: A 380 LYS cc_start: 0.7011 (mmtp) cc_final: 0.6538 (mmmt) REVERT: A 399 ARG cc_start: 0.7997 (mtm180) cc_final: 0.7256 (tpt170) REVERT: A 410 SER cc_start: 0.8989 (OUTLIER) cc_final: 0.8509 (m) REVERT: B 25 VAL cc_start: 0.7867 (p) cc_final: 0.7653 (m) REVERT: B 33 GLU cc_start: 0.7521 (mt-10) cc_final: 0.7285 (mt-10) REVERT: B 51 MET cc_start: 0.8270 (tpp) cc_final: 0.8007 (mmt) REVERT: B 71 MET cc_start: 0.6560 (mmm) cc_final: 0.5764 (mmm) REVERT: B 114 LYS cc_start: 0.7206 (OUTLIER) cc_final: 0.6587 (mtmt) REVERT: B 126 ARG cc_start: 0.6425 (mtm110) cc_final: 0.5750 (mtm110) REVERT: B 131 ARG cc_start: 0.7035 (mpt-90) cc_final: 0.5484 (tmt-80) REVERT: B 173 HIS cc_start: 0.6322 (OUTLIER) cc_final: 0.5349 (m-70) REVERT: B 272 LYS cc_start: 0.7046 (tppp) cc_final: 0.6483 (ttpp) REVERT: B 279 GLU cc_start: 0.8097 (tt0) cc_final: 0.7713 (tt0) REVERT: B 313 PHE cc_start: 0.6506 (OUTLIER) cc_final: 0.6000 (m-10) REVERT: B 331 MET cc_start: 0.6449 (ttp) cc_final: 0.6176 (ttp) REVERT: B 380 LYS cc_start: 0.7004 (mmtp) cc_final: 0.6535 (mmmt) REVERT: B 399 ARG cc_start: 0.8004 (mtm180) cc_final: 0.7271 (tpt170) REVERT: B 410 SER cc_start: 0.8991 (OUTLIER) cc_final: 0.8507 (m) REVERT: C 25 VAL cc_start: 0.7869 (p) cc_final: 0.7654 (m) REVERT: C 33 GLU cc_start: 0.7521 (mt-10) cc_final: 0.7287 (mt-10) REVERT: C 51 MET cc_start: 0.8271 (tpp) cc_final: 0.8007 (mmt) REVERT: C 71 MET cc_start: 0.6558 (mmm) cc_final: 0.5758 (mmm) REVERT: C 114 LYS cc_start: 0.7206 (OUTLIER) cc_final: 0.6585 (mtmt) REVERT: C 126 ARG cc_start: 0.6423 (mtm110) cc_final: 0.5748 (mtm110) REVERT: C 131 ARG cc_start: 0.7038 (mpt-90) cc_final: 0.5475 (tmt-80) REVERT: C 173 HIS cc_start: 0.6315 (OUTLIER) cc_final: 0.5342 (m-70) REVERT: C 272 LYS cc_start: 0.7045 (tppp) cc_final: 0.6484 (ttpp) REVERT: C 279 GLU cc_start: 0.8100 (tt0) cc_final: 0.7715 (tt0) REVERT: C 313 PHE cc_start: 0.6506 (OUTLIER) cc_final: 0.6001 (m-10) REVERT: C 331 MET cc_start: 0.6450 (ttp) cc_final: 0.6177 (ttp) REVERT: C 380 LYS cc_start: 0.7015 (mmtp) cc_final: 0.6545 (mmmt) REVERT: C 399 ARG cc_start: 0.8004 (mtm180) cc_final: 0.7270 (tpt170) REVERT: C 410 SER cc_start: 0.8992 (OUTLIER) cc_final: 0.8509 (m) REVERT: D 25 VAL cc_start: 0.7869 (p) cc_final: 0.7649 (m) REVERT: D 33 GLU cc_start: 0.7517 (mt-10) cc_final: 0.7263 (mt-10) REVERT: D 51 MET cc_start: 0.7839 (mmt) cc_final: 0.7609 (tpp) REVERT: D 71 MET cc_start: 0.6562 (mmm) cc_final: 0.5767 (mmm) REVERT: D 114 LYS cc_start: 0.7208 (OUTLIER) cc_final: 0.6587 (mtmt) REVERT: D 126 ARG cc_start: 0.6442 (mtm110) cc_final: 0.5754 (mtm110) REVERT: D 131 ARG cc_start: 0.7042 (mpt-90) cc_final: 0.5476 (tmt-80) REVERT: D 173 HIS cc_start: 0.6316 (OUTLIER) cc_final: 0.5331 (m-70) REVERT: D 272 LYS cc_start: 0.7045 (tppp) cc_final: 0.6483 (ttpp) REVERT: D 279 GLU cc_start: 0.8081 (tt0) cc_final: 0.7680 (tt0) REVERT: D 313 PHE cc_start: 0.6505 (OUTLIER) cc_final: 0.6000 (m-10) REVERT: D 331 MET cc_start: 0.6450 (ttp) cc_final: 0.6177 (ttp) REVERT: D 380 LYS cc_start: 0.7006 (mmtp) cc_final: 0.6537 (mmmt) REVERT: D 399 ARG cc_start: 0.8004 (mtm180) cc_final: 0.7269 (tpt170) REVERT: D 410 SER cc_start: 0.8989 (OUTLIER) cc_final: 0.8505 (m) outliers start: 35 outliers final: 7 residues processed: 176 average time/residue: 1.3266 time to fit residues: 252.7384 Evaluate side-chains 175 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 152 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain A residue 173 HIS Chi-restraints excluded: chain A residue 313 PHE Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 410 SER Chi-restraints excluded: chain B residue 114 LYS Chi-restraints excluded: chain B residue 173 HIS Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 410 SER Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 114 LYS Chi-restraints excluded: chain C residue 173 HIS Chi-restraints excluded: chain C residue 313 PHE Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 410 SER Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 114 LYS Chi-restraints excluded: chain D residue 173 HIS Chi-restraints excluded: chain D residue 313 PHE Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 410 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 0.0370 chunk 132 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 36 optimal weight: 0.6980 chunk 147 optimal weight: 5.9990 chunk 122 optimal weight: 0.9980 chunk 68 optimal weight: 0.5980 chunk 12 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.0660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 GLN ** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 383 GLN ** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 383 GLN ** C 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 383 GLN ** D 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12236 Z= 0.180 Angle : 0.408 4.890 16596 Z= 0.225 Chirality : 0.035 0.130 1988 Planarity : 0.003 0.025 2032 Dihedral : 3.426 13.066 1656 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.68 % Allowed : 17.43 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.37 (0.21), residues: 1504 helix: 2.77 (0.13), residues: 1264 sheet: 0.78 (0.70), residues: 48 loop : -1.40 (0.45), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 154 HIS 0.002 0.000 HIS D 349 PHE 0.010 0.001 PHE A 11 TYR 0.008 0.001 TYR A 175 ARG 0.003 0.000 ARG D 424 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 156 time to evaluate : 1.384 Fit side-chains REVERT: A 25 VAL cc_start: 0.7856 (OUTLIER) cc_final: 0.7644 (m) REVERT: A 33 GLU cc_start: 0.7526 (mt-10) cc_final: 0.7287 (mt-10) REVERT: A 71 MET cc_start: 0.6547 (mmm) cc_final: 0.5754 (mmm) REVERT: A 126 ARG cc_start: 0.6361 (mtm110) cc_final: 0.5667 (mtm110) REVERT: A 131 ARG cc_start: 0.7042 (mpt-90) cc_final: 0.5483 (tmt-80) REVERT: A 173 HIS cc_start: 0.6341 (OUTLIER) cc_final: 0.5331 (m-70) REVERT: A 272 LYS cc_start: 0.7042 (tppp) cc_final: 0.6509 (ttpp) REVERT: A 279 GLU cc_start: 0.8140 (tt0) cc_final: 0.7828 (tt0) REVERT: A 331 MET cc_start: 0.6440 (ttp) cc_final: 0.6172 (ttp) REVERT: A 364 GLU cc_start: 0.7001 (mt-10) cc_final: 0.6765 (mm-30) REVERT: A 380 LYS cc_start: 0.7012 (mmtp) cc_final: 0.6542 (mmmt) REVERT: A 399 ARG cc_start: 0.7983 (mtm180) cc_final: 0.7252 (tpt170) REVERT: A 410 SER cc_start: 0.8990 (OUTLIER) cc_final: 0.8499 (m) REVERT: B 25 VAL cc_start: 0.7855 (OUTLIER) cc_final: 0.7644 (m) REVERT: B 33 GLU cc_start: 0.7528 (mt-10) cc_final: 0.7290 (mt-10) REVERT: B 51 MET cc_start: 0.8316 (tpp) cc_final: 0.8060 (mmt) REVERT: B 71 MET cc_start: 0.6544 (mmm) cc_final: 0.5754 (mmm) REVERT: B 126 ARG cc_start: 0.6360 (mtm110) cc_final: 0.5665 (mtm110) REVERT: B 131 ARG cc_start: 0.7045 (mpt-90) cc_final: 0.5482 (tmt-80) REVERT: B 173 HIS cc_start: 0.6340 (OUTLIER) cc_final: 0.5332 (m-70) REVERT: B 272 LYS cc_start: 0.7040 (tppp) cc_final: 0.6504 (ttpp) REVERT: B 279 GLU cc_start: 0.8071 (tt0) cc_final: 0.7599 (tt0) REVERT: B 331 MET cc_start: 0.6440 (ttp) cc_final: 0.6172 (ttp) REVERT: B 380 LYS cc_start: 0.7012 (mmtp) cc_final: 0.6539 (mmmt) REVERT: B 399 ARG cc_start: 0.7992 (mtm180) cc_final: 0.7267 (tpt170) REVERT: B 410 SER cc_start: 0.8991 (OUTLIER) cc_final: 0.8498 (m) REVERT: C 25 VAL cc_start: 0.7855 (OUTLIER) cc_final: 0.7644 (m) REVERT: C 33 GLU cc_start: 0.7527 (mt-10) cc_final: 0.7289 (mt-10) REVERT: C 51 MET cc_start: 0.8317 (tpp) cc_final: 0.8060 (mmt) REVERT: C 71 MET cc_start: 0.6537 (mmm) cc_final: 0.5745 (mmm) REVERT: C 126 ARG cc_start: 0.6362 (mtm110) cc_final: 0.5669 (mtm110) REVERT: C 131 ARG cc_start: 0.7043 (mpt-90) cc_final: 0.5480 (tmt-80) REVERT: C 173 HIS cc_start: 0.6335 (OUTLIER) cc_final: 0.5330 (m-70) REVERT: C 272 LYS cc_start: 0.7021 (tppp) cc_final: 0.6504 (ttpp) REVERT: C 279 GLU cc_start: 0.8073 (tt0) cc_final: 0.7603 (tt0) REVERT: C 331 MET cc_start: 0.6441 (ttp) cc_final: 0.6171 (ttp) REVERT: C 364 GLU cc_start: 0.6994 (mt-10) cc_final: 0.6764 (mm-30) REVERT: C 380 LYS cc_start: 0.7018 (mmtp) cc_final: 0.6546 (mmmt) REVERT: C 399 ARG cc_start: 0.7994 (mtm180) cc_final: 0.7268 (tpt170) REVERT: C 410 SER cc_start: 0.8992 (OUTLIER) cc_final: 0.8499 (m) REVERT: D 25 VAL cc_start: 0.7858 (OUTLIER) cc_final: 0.7646 (m) REVERT: D 33 GLU cc_start: 0.7524 (mt-10) cc_final: 0.7287 (mt-10) REVERT: D 71 MET cc_start: 0.6545 (mmm) cc_final: 0.5755 (mmm) REVERT: D 123 ASN cc_start: 0.7433 (m-40) cc_final: 0.7184 (m-40) REVERT: D 126 ARG cc_start: 0.6362 (mtm110) cc_final: 0.5668 (mtm110) REVERT: D 131 ARG cc_start: 0.7044 (mpt-90) cc_final: 0.5482 (tmt-80) REVERT: D 173 HIS cc_start: 0.6335 (OUTLIER) cc_final: 0.5324 (m-70) REVERT: D 272 LYS cc_start: 0.7037 (tppp) cc_final: 0.6501 (ttpp) REVERT: D 279 GLU cc_start: 0.8057 (tt0) cc_final: 0.7562 (tt0) REVERT: D 331 MET cc_start: 0.6439 (ttp) cc_final: 0.6171 (ttp) REVERT: D 364 GLU cc_start: 0.6997 (mt-10) cc_final: 0.6764 (mm-30) REVERT: D 380 LYS cc_start: 0.7015 (mmtp) cc_final: 0.6543 (mmmt) REVERT: D 399 ARG cc_start: 0.7993 (mtm180) cc_final: 0.7267 (tpt170) REVERT: D 410 SER cc_start: 0.8991 (OUTLIER) cc_final: 0.8498 (m) outliers start: 35 outliers final: 10 residues processed: 179 average time/residue: 1.2784 time to fit residues: 248.2592 Evaluate side-chains 177 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 155 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 173 HIS Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 410 SER Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 173 HIS Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 410 SER Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 173 HIS Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 410 SER Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 173 HIS Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 410 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 1.9990 chunk 16 optimal weight: 0.0170 chunk 83 optimal weight: 9.9990 chunk 107 optimal weight: 2.9990 chunk 123 optimal weight: 0.5980 chunk 82 optimal weight: 0.6980 chunk 146 optimal weight: 7.9990 chunk 91 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 overall best weight: 0.8622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN A 383 GLN ** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 383 GLN ** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 ASN C 383 GLN ** C 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 383 GLN ** D 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12236 Z= 0.158 Angle : 0.399 6.405 16596 Z= 0.218 Chirality : 0.034 0.131 1988 Planarity : 0.003 0.025 2032 Dihedral : 3.357 13.028 1656 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.91 % Allowed : 18.43 % Favored : 79.66 % 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: 3.52 (0.21), residues: 1504 helix: 2.88 (0.13), residues: 1264 sheet: 0.60 (0.67), residues: 48 loop : -1.35 (0.45), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 154 HIS 0.001 0.000 HIS D 349 PHE 0.009 0.001 PHE A 11 TYR 0.006 0.001 TYR C 175 ARG 0.001 0.000 ARG D 367 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 154 time to evaluate : 1.426 Fit side-chains REVERT: A 33 GLU cc_start: 0.7550 (mt-10) cc_final: 0.7289 (mt-10) REVERT: A 71 MET cc_start: 0.6560 (mmm) cc_final: 0.5779 (mmm) REVERT: A 126 ARG cc_start: 0.6415 (mtm110) cc_final: 0.5678 (mtm110) REVERT: A 131 ARG cc_start: 0.7028 (tpt-90) cc_final: 0.5443 (tmt-80) REVERT: A 173 HIS cc_start: 0.6242 (OUTLIER) cc_final: 0.5288 (m-70) REVERT: A 272 LYS cc_start: 0.7018 (tppp) cc_final: 0.6523 (ttpp) REVERT: A 279 GLU cc_start: 0.8057 (tt0) cc_final: 0.7611 (tt0) REVERT: A 331 MET cc_start: 0.6447 (ttp) cc_final: 0.6175 (ttp) REVERT: A 364 GLU cc_start: 0.6983 (mt-10) cc_final: 0.6749 (mm-30) REVERT: A 380 LYS cc_start: 0.6989 (mmtp) cc_final: 0.6530 (mmmt) REVERT: A 399 ARG cc_start: 0.7935 (mtm180) cc_final: 0.7211 (tpt170) REVERT: B 33 GLU cc_start: 0.7506 (mt-10) cc_final: 0.7239 (mt-10) REVERT: B 51 MET cc_start: 0.8301 (tpp) cc_final: 0.8049 (mmt) REVERT: B 71 MET cc_start: 0.6558 (mmm) cc_final: 0.5777 (mmm) REVERT: B 126 ARG cc_start: 0.6415 (mtm110) cc_final: 0.5677 (mtm110) REVERT: B 131 ARG cc_start: 0.7027 (tpt-90) cc_final: 0.5443 (tmt-80) REVERT: B 173 HIS cc_start: 0.6237 (OUTLIER) cc_final: 0.5283 (m-70) REVERT: B 272 LYS cc_start: 0.7018 (tppp) cc_final: 0.6520 (ttpp) REVERT: B 279 GLU cc_start: 0.8056 (tt0) cc_final: 0.7589 (tt0) REVERT: B 331 MET cc_start: 0.6447 (ttp) cc_final: 0.6179 (ttp) REVERT: B 380 LYS cc_start: 0.6986 (mmtp) cc_final: 0.6532 (mmmt) REVERT: B 399 ARG cc_start: 0.7947 (mtm180) cc_final: 0.7244 (tpt170) REVERT: B 410 SER cc_start: 0.9025 (OUTLIER) cc_final: 0.8528 (m) REVERT: C 33 GLU cc_start: 0.7544 (mt-10) cc_final: 0.7279 (mt-10) REVERT: C 51 MET cc_start: 0.8302 (tpp) cc_final: 0.8050 (mmt) REVERT: C 71 MET cc_start: 0.6530 (mmm) cc_final: 0.5734 (mmm) REVERT: C 126 ARG cc_start: 0.6415 (mtm110) cc_final: 0.5663 (mtm110) REVERT: C 131 ARG cc_start: 0.7028 (tpt-90) cc_final: 0.5443 (tmt-80) REVERT: C 173 HIS cc_start: 0.6230 (OUTLIER) cc_final: 0.5278 (m-70) REVERT: C 272 LYS cc_start: 0.7091 (tppp) cc_final: 0.6601 (ttpp) REVERT: C 279 GLU cc_start: 0.8057 (tt0) cc_final: 0.7589 (tt0) REVERT: C 331 MET cc_start: 0.6447 (ttp) cc_final: 0.6178 (ttp) REVERT: C 364 GLU cc_start: 0.6975 (mt-10) cc_final: 0.6747 (mm-30) REVERT: C 380 LYS cc_start: 0.6984 (mmtp) cc_final: 0.6531 (mmmt) REVERT: C 399 ARG cc_start: 0.7948 (mtm180) cc_final: 0.7245 (tpt170) REVERT: C 410 SER cc_start: 0.9025 (OUTLIER) cc_final: 0.8527 (m) REVERT: D 33 GLU cc_start: 0.7506 (mt-10) cc_final: 0.7238 (mt-10) REVERT: D 71 MET cc_start: 0.6559 (mmm) cc_final: 0.5782 (mmm) REVERT: D 126 ARG cc_start: 0.6414 (mtm110) cc_final: 0.5677 (mtm110) REVERT: D 131 ARG cc_start: 0.7028 (tpt-90) cc_final: 0.5443 (tmt-80) REVERT: D 173 HIS cc_start: 0.6230 (OUTLIER) cc_final: 0.5277 (m-70) REVERT: D 272 LYS cc_start: 0.7014 (tppp) cc_final: 0.6518 (ttpp) REVERT: D 279 GLU cc_start: 0.8047 (tt0) cc_final: 0.7560 (tt0) REVERT: D 331 MET cc_start: 0.6447 (ttp) cc_final: 0.6178 (ttp) REVERT: D 364 GLU cc_start: 0.6973 (mt-10) cc_final: 0.6744 (mm-30) REVERT: D 380 LYS cc_start: 0.6987 (mmtp) cc_final: 0.6533 (mmmt) REVERT: D 399 ARG cc_start: 0.7948 (mtm180) cc_final: 0.7245 (tpt170) REVERT: D 410 SER cc_start: 0.9025 (OUTLIER) cc_final: 0.8528 (m) outliers start: 25 outliers final: 8 residues processed: 167 average time/residue: 1.3899 time to fit residues: 251.2303 Evaluate side-chains 171 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 156 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 HIS Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain B residue 173 HIS Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 410 SER Chi-restraints excluded: chain C residue 173 HIS Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 410 SER Chi-restraints excluded: chain D residue 173 HIS Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 410 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 chunk 44 optimal weight: 0.3980 chunk 28 optimal weight: 2.9990 chunk 93 optimal weight: 8.9990 chunk 99 optimal weight: 0.7980 chunk 72 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 133 optimal weight: 0.5980 chunk 140 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 GLN ** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 ASN B 383 GLN ** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 383 GLN ** C 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 ASN D 383 GLN ** D 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12236 Z= 0.144 Angle : 0.385 4.672 16596 Z= 0.213 Chirality : 0.034 0.131 1988 Planarity : 0.003 0.026 2032 Dihedral : 3.347 12.562 1656 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.83 % Allowed : 18.81 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.57 (0.21), residues: 1504 helix: 2.92 (0.13), residues: 1264 sheet: 0.65 (0.63), residues: 48 loop : -1.36 (0.45), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 154 HIS 0.001 0.000 HIS C 349 PHE 0.008 0.001 PHE A 11 TYR 0.006 0.001 TYR C 96 ARG 0.002 0.000 ARG D 367 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 158 time to evaluate : 1.357 Fit side-chains REVERT: A 33 GLU cc_start: 0.7546 (mt-10) cc_final: 0.7291 (mt-10) REVERT: A 126 ARG cc_start: 0.6394 (mtm110) cc_final: 0.5609 (mtm110) REVERT: A 131 ARG cc_start: 0.7020 (tpt-90) cc_final: 0.5438 (tmt-80) REVERT: A 173 HIS cc_start: 0.6351 (OUTLIER) cc_final: 0.5351 (m-70) REVERT: A 272 LYS cc_start: 0.7085 (tppp) cc_final: 0.6609 (ttpp) REVERT: A 279 GLU cc_start: 0.8108 (tt0) cc_final: 0.7822 (tt0) REVERT: A 331 MET cc_start: 0.6439 (ttp) cc_final: 0.6164 (ttp) REVERT: A 364 GLU cc_start: 0.6980 (mt-10) cc_final: 0.6747 (mm-30) REVERT: A 380 LYS cc_start: 0.6958 (mmtp) cc_final: 0.6518 (mmmt) REVERT: A 399 ARG cc_start: 0.7926 (mtm180) cc_final: 0.7215 (tpt170) REVERT: A 410 SER cc_start: 0.9023 (OUTLIER) cc_final: 0.8515 (m) REVERT: B 33 GLU cc_start: 0.7503 (mt-10) cc_final: 0.7239 (mt-10) REVERT: B 51 MET cc_start: 0.8290 (tpp) cc_final: 0.8051 (mmt) REVERT: B 126 ARG cc_start: 0.6396 (mtm110) cc_final: 0.5611 (mtm110) REVERT: B 131 ARG cc_start: 0.7021 (tpt-90) cc_final: 0.5438 (tmt-80) REVERT: B 173 HIS cc_start: 0.6343 (OUTLIER) cc_final: 0.5348 (m-70) REVERT: B 272 LYS cc_start: 0.7086 (tppp) cc_final: 0.6605 (ttpp) REVERT: B 279 GLU cc_start: 0.8043 (tt0) cc_final: 0.7568 (tt0) REVERT: B 331 MET cc_start: 0.6439 (ttp) cc_final: 0.6164 (ttp) REVERT: B 380 LYS cc_start: 0.6957 (mmtp) cc_final: 0.6516 (mmmt) REVERT: B 399 ARG cc_start: 0.7932 (mtm180) cc_final: 0.7227 (tpt170) REVERT: B 410 SER cc_start: 0.9022 (OUTLIER) cc_final: 0.8513 (m) REVERT: C 33 GLU cc_start: 0.7547 (mt-10) cc_final: 0.7286 (mt-10) REVERT: C 51 MET cc_start: 0.8291 (tpp) cc_final: 0.8024 (mmt) REVERT: C 126 ARG cc_start: 0.6396 (mtm110) cc_final: 0.5619 (mtm110) REVERT: C 131 ARG cc_start: 0.7020 (tpt-90) cc_final: 0.5440 (tmt-80) REVERT: C 173 HIS cc_start: 0.6339 (OUTLIER) cc_final: 0.5345 (m-70) REVERT: C 272 LYS cc_start: 0.7086 (tppp) cc_final: 0.6607 (ttpp) REVERT: C 279 GLU cc_start: 0.8043 (tt0) cc_final: 0.7570 (tt0) REVERT: C 331 MET cc_start: 0.6440 (ttp) cc_final: 0.6166 (ttp) REVERT: C 364 GLU cc_start: 0.6994 (mt-10) cc_final: 0.6774 (mm-30) REVERT: C 380 LYS cc_start: 0.6958 (mmtp) cc_final: 0.6518 (mmmt) REVERT: C 399 ARG cc_start: 0.7934 (mtm180) cc_final: 0.7228 (tpt170) REVERT: C 410 SER cc_start: 0.9023 (OUTLIER) cc_final: 0.8515 (m) REVERT: D 33 GLU cc_start: 0.7502 (mt-10) cc_final: 0.7237 (mt-10) REVERT: D 126 ARG cc_start: 0.6393 (mtm110) cc_final: 0.5609 (mtm110) REVERT: D 131 ARG cc_start: 0.7022 (tpt-90) cc_final: 0.5439 (tmt-80) REVERT: D 173 HIS cc_start: 0.6341 (OUTLIER) cc_final: 0.5340 (m-70) REVERT: D 272 LYS cc_start: 0.7084 (tppp) cc_final: 0.6604 (ttpp) REVERT: D 279 GLU cc_start: 0.8034 (tt0) cc_final: 0.7543 (tt0) REVERT: D 331 MET cc_start: 0.6441 (ttp) cc_final: 0.6165 (ttp) REVERT: D 364 GLU cc_start: 0.6932 (mt-10) cc_final: 0.6712 (mm-30) REVERT: D 380 LYS cc_start: 0.6961 (mmtp) cc_final: 0.6519 (mmmt) REVERT: D 399 ARG cc_start: 0.7936 (mtm180) cc_final: 0.7230 (tpt170) REVERT: D 410 SER cc_start: 0.9022 (OUTLIER) cc_final: 0.8513 (m) outliers start: 24 outliers final: 6 residues processed: 173 average time/residue: 1.3449 time to fit residues: 252.1845 Evaluate side-chains 166 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 152 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 HIS Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 410 SER Chi-restraints excluded: chain B residue 173 HIS Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 410 SER Chi-restraints excluded: chain C residue 173 HIS Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 410 SER Chi-restraints excluded: chain D residue 173 HIS Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 410 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 4.9990 chunk 136 optimal weight: 0.8980 chunk 140 optimal weight: 5.9990 chunk 82 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 123 optimal weight: 0.6980 chunk 129 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 144 optimal weight: 0.6980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 GLN ** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 383 GLN ** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 383 GLN ** C 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 383 GLN ** D 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12236 Z= 0.238 Angle : 0.447 6.542 16596 Z= 0.243 Chirality : 0.036 0.129 1988 Planarity : 0.003 0.025 2032 Dihedral : 3.545 13.285 1656 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.99 % Allowed : 18.73 % Favored : 79.28 % 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: 3.16 (0.20), residues: 1504 helix: 2.66 (0.13), residues: 1264 sheet: 0.15 (0.58), residues: 48 loop : -1.56 (0.44), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 174 HIS 0.003 0.001 HIS D 337 PHE 0.010 0.002 PHE D 392 TYR 0.010 0.001 TYR A 175 ARG 0.003 0.000 ARG D 424 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 149 time to evaluate : 1.399 Fit side-chains REVERT: A 33 GLU cc_start: 0.7513 (mt-10) cc_final: 0.7256 (mt-10) REVERT: A 71 MET cc_start: 0.6499 (mmm) cc_final: 0.5748 (mmm) REVERT: A 126 ARG cc_start: 0.6453 (mtm110) cc_final: 0.5689 (mtm110) REVERT: A 131 ARG cc_start: 0.7039 (tpt-90) cc_final: 0.5489 (tmt-80) REVERT: A 173 HIS cc_start: 0.6238 (OUTLIER) cc_final: 0.5244 (m-70) REVERT: A 272 LYS cc_start: 0.7064 (tppp) cc_final: 0.6545 (ttpp) REVERT: A 279 GLU cc_start: 0.8174 (tt0) cc_final: 0.7738 (tt0) REVERT: A 331 MET cc_start: 0.6503 (ttp) cc_final: 0.6225 (ttp) REVERT: A 380 LYS cc_start: 0.7039 (mmtp) cc_final: 0.6543 (mmmt) REVERT: A 399 ARG cc_start: 0.8003 (mtm180) cc_final: 0.7280 (tpt170) REVERT: A 410 SER cc_start: 0.9002 (OUTLIER) cc_final: 0.8494 (m) REVERT: B 33 GLU cc_start: 0.7514 (mt-10) cc_final: 0.7256 (mt-10) REVERT: B 51 MET cc_start: 0.8348 (tpp) cc_final: 0.8098 (mmt) REVERT: B 71 MET cc_start: 0.6498 (mmm) cc_final: 0.5743 (mmm) REVERT: B 126 ARG cc_start: 0.6450 (mtm110) cc_final: 0.5687 (mtm110) REVERT: B 131 ARG cc_start: 0.7034 (tpt-90) cc_final: 0.5460 (tmt-80) REVERT: B 173 HIS cc_start: 0.6268 (OUTLIER) cc_final: 0.5269 (m-70) REVERT: B 272 LYS cc_start: 0.7062 (tppp) cc_final: 0.6542 (ttpp) REVERT: B 279 GLU cc_start: 0.8079 (tt0) cc_final: 0.7743 (tt0) REVERT: B 331 MET cc_start: 0.6503 (ttp) cc_final: 0.6225 (ttp) REVERT: B 364 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.7098 (mm-30) REVERT: B 380 LYS cc_start: 0.7002 (mmtp) cc_final: 0.6528 (mmmt) REVERT: B 399 ARG cc_start: 0.8010 (mtm180) cc_final: 0.7276 (tpt170) REVERT: B 410 SER cc_start: 0.9005 (OUTLIER) cc_final: 0.8492 (m) REVERT: C 33 GLU cc_start: 0.7460 (mt-10) cc_final: 0.7204 (mt-10) REVERT: C 51 MET cc_start: 0.8347 (tpp) cc_final: 0.8097 (mmt) REVERT: C 71 MET cc_start: 0.6487 (mmm) cc_final: 0.5723 (mmm) REVERT: C 126 ARG cc_start: 0.6449 (mtm110) cc_final: 0.5685 (mtm110) REVERT: C 131 ARG cc_start: 0.7039 (tpt-90) cc_final: 0.5489 (tmt-80) REVERT: C 173 HIS cc_start: 0.6265 (OUTLIER) cc_final: 0.5265 (m-70) REVERT: C 272 LYS cc_start: 0.7062 (tppp) cc_final: 0.6544 (ttpp) REVERT: C 279 GLU cc_start: 0.8086 (tt0) cc_final: 0.7751 (tt0) REVERT: C 331 MET cc_start: 0.6507 (ttp) cc_final: 0.6225 (ttp) REVERT: C 380 LYS cc_start: 0.7001 (mmtp) cc_final: 0.6529 (mmmt) REVERT: C 399 ARG cc_start: 0.8011 (mtm180) cc_final: 0.7276 (tpt170) REVERT: C 410 SER cc_start: 0.9004 (OUTLIER) cc_final: 0.8491 (m) REVERT: D 33 GLU cc_start: 0.7514 (mt-10) cc_final: 0.7257 (mt-10) REVERT: D 71 MET cc_start: 0.6498 (mmm) cc_final: 0.5747 (mmm) REVERT: D 126 ARG cc_start: 0.6452 (mtm110) cc_final: 0.5687 (mtm110) REVERT: D 131 ARG cc_start: 0.7040 (tpt-90) cc_final: 0.5489 (tmt-80) REVERT: D 173 HIS cc_start: 0.6265 (OUTLIER) cc_final: 0.5265 (m-70) REVERT: D 272 LYS cc_start: 0.7059 (tppp) cc_final: 0.6540 (ttpp) REVERT: D 279 GLU cc_start: 0.8077 (tt0) cc_final: 0.7671 (tt0) REVERT: D 331 MET cc_start: 0.6502 (ttp) cc_final: 0.6224 (ttp) REVERT: D 380 LYS cc_start: 0.7003 (mmtp) cc_final: 0.6526 (mmmt) REVERT: D 399 ARG cc_start: 0.8013 (mtm180) cc_final: 0.7275 (tpt170) REVERT: D 410 SER cc_start: 0.9001 (OUTLIER) cc_final: 0.8490 (m) outliers start: 26 outliers final: 8 residues processed: 167 average time/residue: 1.4123 time to fit residues: 254.1840 Evaluate side-chains 166 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 149 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 HIS Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 410 SER Chi-restraints excluded: chain B residue 173 HIS Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 410 SER Chi-restraints excluded: chain C residue 173 HIS Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 410 SER Chi-restraints excluded: chain D residue 173 HIS Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 410 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 6.9990 chunk 68 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 151 optimal weight: 0.6980 chunk 139 optimal weight: 0.8980 chunk 120 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 95 optimal weight: 0.5980 chunk 128 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 GLN ** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 383 GLN ** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 383 GLN ** C 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 383 GLN ** D 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12236 Z= 0.170 Angle : 0.402 4.739 16596 Z= 0.221 Chirality : 0.034 0.129 1988 Planarity : 0.003 0.025 2032 Dihedral : 3.458 14.040 1656 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.76 % Allowed : 19.19 % Favored : 79.05 % 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: 3.33 (0.20), residues: 1504 helix: 2.78 (0.13), residues: 1264 sheet: 0.01 (0.53), residues: 48 loop : -1.45 (0.44), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 154 HIS 0.002 0.000 HIS D 349 PHE 0.008 0.001 PHE D 11 TYR 0.007 0.001 TYR B 175 ARG 0.001 0.000 ARG D 340 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3008 Ramachandran restraints generated. 1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 154 time to evaluate : 1.388 Fit side-chains REVERT: A 33 GLU cc_start: 0.7476 (mt-10) cc_final: 0.7221 (mt-10) REVERT: A 43 TYR cc_start: 0.8498 (t80) cc_final: 0.8274 (t80) REVERT: A 71 MET cc_start: 0.6528 (mmm) cc_final: 0.5785 (mmm) REVERT: A 126 ARG cc_start: 0.6400 (mtm110) cc_final: 0.5613 (mtm110) REVERT: A 131 ARG cc_start: 0.7030 (tpt-90) cc_final: 0.5450 (tmt-80) REVERT: A 173 HIS cc_start: 0.6204 (OUTLIER) cc_final: 0.5178 (m-70) REVERT: A 272 LYS cc_start: 0.7045 (tppp) cc_final: 0.6541 (ttpp) REVERT: A 279 GLU cc_start: 0.8065 (tt0) cc_final: 0.7635 (tt0) REVERT: A 331 MET cc_start: 0.6444 (ttp) cc_final: 0.6176 (ttp) REVERT: A 380 LYS cc_start: 0.6961 (mmtp) cc_final: 0.6503 (mmmt) REVERT: A 399 ARG cc_start: 0.7954 (mtm180) cc_final: 0.7254 (tpt170) REVERT: A 410 SER cc_start: 0.8995 (OUTLIER) cc_final: 0.8499 (m) REVERT: B 33 GLU cc_start: 0.7474 (mt-10) cc_final: 0.7221 (mt-10) REVERT: B 51 MET cc_start: 0.8314 (tpp) cc_final: 0.8087 (mmt) REVERT: B 71 MET cc_start: 0.6525 (mmm) cc_final: 0.5784 (mmm) REVERT: B 126 ARG cc_start: 0.6450 (mtm110) cc_final: 0.5672 (mtm110) REVERT: B 131 ARG cc_start: 0.7028 (tpt-90) cc_final: 0.5449 (tmt-80) REVERT: B 173 HIS cc_start: 0.6196 (OUTLIER) cc_final: 0.5176 (m-70) REVERT: B 272 LYS cc_start: 0.7042 (tppp) cc_final: 0.6538 (ttpp) REVERT: B 279 GLU cc_start: 0.8060 (tt0) cc_final: 0.7729 (tt0) REVERT: B 331 MET cc_start: 0.6443 (ttp) cc_final: 0.6174 (ttp) REVERT: B 364 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.7138 (mm-30) REVERT: B 380 LYS cc_start: 0.6955 (mmtp) cc_final: 0.6503 (mmmt) REVERT: B 399 ARG cc_start: 0.7961 (mtm180) cc_final: 0.7269 (tpt170) REVERT: B 410 SER cc_start: 0.8996 (OUTLIER) cc_final: 0.8494 (m) REVERT: C 33 GLU cc_start: 0.7456 (mt-10) cc_final: 0.7212 (mt-10) REVERT: C 51 MET cc_start: 0.8315 (tpp) cc_final: 0.8087 (mmt) REVERT: C 71 MET cc_start: 0.6473 (mmm) cc_final: 0.5688 (mmm) REVERT: C 126 ARG cc_start: 0.6450 (mtm110) cc_final: 0.5672 (mtm110) REVERT: C 131 ARG cc_start: 0.7028 (tpt-90) cc_final: 0.5449 (tmt-80) REVERT: C 173 HIS cc_start: 0.6192 (OUTLIER) cc_final: 0.5171 (m-70) REVERT: C 272 LYS cc_start: 0.7044 (tppp) cc_final: 0.6539 (ttpp) REVERT: C 279 GLU cc_start: 0.8058 (tt0) cc_final: 0.7644 (tt0) REVERT: C 331 MET cc_start: 0.6443 (ttp) cc_final: 0.6175 (ttp) REVERT: C 380 LYS cc_start: 0.6959 (mmtp) cc_final: 0.6508 (mmmt) REVERT: C 399 ARG cc_start: 0.7963 (mtm180) cc_final: 0.7269 (tpt170) REVERT: C 410 SER cc_start: 0.8997 (OUTLIER) cc_final: 0.8495 (m) REVERT: D 33 GLU cc_start: 0.7476 (mt-10) cc_final: 0.7220 (mt-10) REVERT: D 43 TYR cc_start: 0.8498 (t80) cc_final: 0.8275 (t80) REVERT: D 71 MET cc_start: 0.6528 (mmm) cc_final: 0.5785 (mmm) REVERT: D 126 ARG cc_start: 0.6451 (mtm110) cc_final: 0.5674 (mtm110) REVERT: D 131 ARG cc_start: 0.7031 (tpt-90) cc_final: 0.5450 (tmt-80) REVERT: D 173 HIS cc_start: 0.6195 (OUTLIER) cc_final: 0.5171 (m-70) REVERT: D 272 LYS cc_start: 0.7040 (tppp) cc_final: 0.6537 (ttpp) REVERT: D 279 GLU cc_start: 0.8053 (tt0) cc_final: 0.7646 (tt0) REVERT: D 331 MET cc_start: 0.6442 (ttp) cc_final: 0.6174 (ttp) REVERT: D 364 GLU cc_start: 0.6978 (mt-10) cc_final: 0.6741 (mm-30) REVERT: D 380 LYS cc_start: 0.6956 (mmtp) cc_final: 0.6500 (mmmt) REVERT: D 399 ARG cc_start: 0.7974 (mtm180) cc_final: 0.7257 (tpt170) REVERT: D 410 SER cc_start: 0.8995 (OUTLIER) cc_final: 0.8494 (m) outliers start: 23 outliers final: 8 residues processed: 168 average time/residue: 1.3722 time to fit residues: 249.2742 Evaluate side-chains 171 residues out of total 1308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 154 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 HIS Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 410 SER Chi-restraints excluded: chain B residue 173 HIS Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 410 SER Chi-restraints excluded: chain C residue 173 HIS Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 410 SER Chi-restraints excluded: chain D residue 173 HIS Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 410 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 0.6980 chunk 111 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 15 optimal weight: 0.7980 chunk 22 optimal weight: 0.0000 chunk 106 optimal weight: 0.8980 chunk 6 optimal weight: 0.1980 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 GLN ** A 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 383 GLN ** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 383 GLN ** D 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.160967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.119122 restraints weight = 12004.871| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.51 r_work: 0.3076 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12236 Z= 0.127 Angle : 0.377 4.620 16596 Z= 0.209 Chirality : 0.034 0.131 1988 Planarity : 0.002 0.026 2032 Dihedral : 3.329 13.017 1656 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.38 % Allowed : 19.57 % Favored : 79.05 % 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: 3.58 (0.21), residues: 1504 helix: 2.94 (0.13), residues: 1264 sheet: 0.01 (0.50), residues: 48 loop : -1.30 (0.45), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 154 HIS 0.001 0.000 HIS C 349 PHE 0.007 0.001 PHE C 11 TYR 0.006 0.001 TYR D 96 ARG 0.001 0.000 ARG D 367 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4491.65 seconds wall clock time: 81 minutes 8.11 seconds (4868.11 seconds total)