Starting phenix.real_space_refine on Sun Apr 7 12:14:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vdc_31913/04_2024/7vdc_31913.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vdc_31913/04_2024/7vdc_31913.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vdc_31913/04_2024/7vdc_31913.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vdc_31913/04_2024/7vdc_31913.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vdc_31913/04_2024/7vdc_31913.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vdc_31913/04_2024/7vdc_31913.pdb" } resolution = 3.28 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= 0.003 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 44 5.16 5 C 6588 2.51 5 N 1860 2.21 5 O 1980 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 109": "OD1" <-> "OD2" Residue "A ASP 140": "OD1" <-> "OD2" Residue "A ASP 197": "OD1" <-> "OD2" Residue "A TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 325": "OE1" <-> "OE2" Residue "B ASP 66": "OD1" <-> "OD2" Residue "B ASP 109": "OD1" <-> "OD2" Residue "B ASP 197": "OD1" <-> "OD2" Residue "B TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 66": "OD1" <-> "OD2" Residue "C TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 10472 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2618 Classifications: {'peptide': 343} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 324} Chain: "B" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2618 Classifications: {'peptide': 343} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 324} Chain: "C" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2618 Classifications: {'peptide': 343} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 324} Chain: "D" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2618 Classifications: {'peptide': 343} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 324} Time building chain proxies: 5.96, per 1000 atoms: 0.57 Number of scatterers: 10472 At special positions: 0 Unit cell: (97.5, 81.25, 107.25, 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 44 16.00 O 1980 8.00 N 1860 7.00 C 6588 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: 4.31 Conformation dependent library (CDL) restraints added in 1.9 seconds 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2520 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 10 sheets defined 54.7% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 8 through 23 Processing helix chain 'A' and resid 37 through 47 removed outlier: 3.956A pdb=" N ILE A 46 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 64 Processing helix chain 'A' and resid 66 through 70 removed outlier: 3.829A pdb=" N VAL A 69 " --> pdb=" O ASP A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 84 removed outlier: 3.635A pdb=" N LEU A 83 " --> pdb=" O PHE A 79 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N TYR A 84 " --> pdb=" O HIS A 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 79 through 84' Processing helix chain 'A' and resid 92 through 101 Processing helix chain 'A' and resid 129 through 141 removed outlier: 3.937A pdb=" N ARG A 133 " --> pdb=" O GLY A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 181 Processing helix chain 'A' and resid 197 through 219 removed outlier: 3.657A pdb=" N CYS A 201 " --> pdb=" O ASP A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 225 Processing helix chain 'A' and resid 244 through 260 removed outlier: 3.816A pdb=" N THR A 259 " --> pdb=" O ALA A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 287 Processing helix chain 'A' and resid 306 through 314 Processing helix chain 'A' and resid 319 through 339 removed outlier: 3.728A pdb=" N ALA A 323 " --> pdb=" O ASN A 319 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLN A 339 " --> pdb=" O SER A 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 23 Processing helix chain 'B' and resid 37 through 46 removed outlier: 4.056A pdb=" N LYS B 41 " --> pdb=" O GLY B 37 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ARG B 42 " --> pdb=" O SER B 38 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE B 46 " --> pdb=" O ARG B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 64 Processing helix chain 'B' and resid 66 through 73 Proline residue: B 71 - end of helix Processing helix chain 'B' and resid 79 through 84 removed outlier: 3.584A pdb=" N LEU B 83 " --> pdb=" O PHE B 79 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N TYR B 84 " --> pdb=" O HIS B 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 79 through 84' Processing helix chain 'B' and resid 92 through 101 Processing helix chain 'B' and resid 129 through 141 removed outlier: 3.803A pdb=" N ARG B 133 " --> pdb=" O GLY B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 181 Processing helix chain 'B' and resid 197 through 219 removed outlier: 3.582A pdb=" N CYS B 201 " --> pdb=" O ASP B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 225 Processing helix chain 'B' and resid 244 through 260 removed outlier: 3.784A pdb=" N THR B 259 " --> pdb=" O ALA B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 287 Processing helix chain 'B' and resid 302 through 314 removed outlier: 6.498A pdb=" N SER B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N ALA B 309 " --> pdb=" O LEU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 338 Processing helix chain 'C' and resid 8 through 23 Processing helix chain 'C' and resid 37 through 47 removed outlier: 4.077A pdb=" N LYS C 41 " --> pdb=" O GLY C 37 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG C 42 " --> pdb=" O SER C 38 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ILE C 46 " --> pdb=" O ARG C 42 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLY C 47 " --> pdb=" O LEU C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 63 Processing helix chain 'C' and resid 66 through 73 Proline residue: C 71 - end of helix Processing helix chain 'C' and resid 81 through 85 Processing helix chain 'C' and resid 92 through 101 Processing helix chain 'C' and resid 130 through 141 Processing helix chain 'C' and resid 159 through 181 Processing helix chain 'C' and resid 197 through 219 removed outlier: 3.679A pdb=" N CYS C 201 " --> pdb=" O ASP C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 225 Processing helix chain 'C' and resid 244 through 260 removed outlier: 3.790A pdb=" N THR C 259 " --> pdb=" O ALA C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 287 Processing helix chain 'C' and resid 302 through 314 removed outlier: 3.546A pdb=" N ALA C 307 " --> pdb=" O ARG C 303 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N SER C 308 " --> pdb=" O ALA C 304 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ALA C 309 " --> pdb=" O LEU C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 318 No H-bonds generated for 'chain 'C' and resid 316 through 318' Processing helix chain 'C' and resid 319 through 338 removed outlier: 3.516A pdb=" N ARG C 330 " --> pdb=" O GLU C 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 23 Processing helix chain 'D' and resid 37 through 47 removed outlier: 3.821A pdb=" N LYS D 41 " --> pdb=" O GLY D 37 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG D 42 " --> pdb=" O SER D 38 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE D 46 " --> pdb=" O ARG D 42 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLY D 47 " --> pdb=" O LEU D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 64 Processing helix chain 'D' and resid 66 through 70 removed outlier: 3.514A pdb=" N VAL D 69 " --> pdb=" O ASP D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 84 removed outlier: 4.172A pdb=" N TYR D 84 " --> pdb=" O HIS D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 101 Processing helix chain 'D' and resid 129 through 142 removed outlier: 3.774A pdb=" N ARG D 133 " --> pdb=" O GLY D 129 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA D 142 " --> pdb=" O LYS D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 181 Processing helix chain 'D' and resid 197 through 219 removed outlier: 3.721A pdb=" N CYS D 201 " --> pdb=" O ASP D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 225 Processing helix chain 'D' and resid 244 through 260 removed outlier: 3.792A pdb=" N THR D 259 " --> pdb=" O ALA D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 287 Processing helix chain 'D' and resid 306 through 314 Processing helix chain 'D' and resid 319 through 338 Processing sheet with id=AA1, first strand: chain 'A' and resid 103 through 104 removed outlier: 3.894A pdb=" N TYR A 301 " --> pdb=" O ILE A 29 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA A 31 " --> pdb=" O TYR A 301 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 112 through 114 Processing sheet with id=AA3, first strand: chain 'A' and resid 147 through 152 removed outlier: 7.038A pdb=" N TRP A 147 " --> pdb=" O GLU A 187 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N GLU A 189 " --> pdb=" O TRP A 147 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N CYS A 149 " --> pdb=" O GLU A 189 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LEU A 191 " --> pdb=" O CYS A 149 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N LEU A 151 " --> pdb=" O LEU A 191 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 103 through 106 removed outlier: 6.298A pdb=" N VAL B 76 " --> pdb=" O GLY B 105 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TYR B 301 " --> pdb=" O ILE B 29 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA B 31 " --> pdb=" O TYR B 301 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 112 through 114 Processing sheet with id=AA6, first strand: chain 'B' and resid 147 through 151 Processing sheet with id=AA7, first strand: chain 'C' and resid 296 through 297 removed outlier: 3.528A pdb=" N ILE C 185 " --> pdb=" O ALA C 145 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE C 144 " --> pdb=" O VAL C 104 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N VAL C 76 " --> pdb=" O GLY C 105 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N LYS C 107 " --> pdb=" O VAL C 76 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N LEU C 78 " --> pdb=" O LYS C 107 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N TYR C 301 " --> pdb=" O ILE C 29 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 112 through 114 Processing sheet with id=AA9, first strand: chain 'D' and resid 296 through 297 removed outlier: 3.859A pdb=" N PHE D 144 " --> pdb=" O VAL D 104 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL D 76 " --> pdb=" O GLY D 105 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N LYS D 107 " --> pdb=" O VAL D 76 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N LEU D 78 " --> pdb=" O LYS D 107 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N TYR D 301 " --> pdb=" O ILE D 29 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 112 through 114 537 hydrogen bonds defined for protein. 1569 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: 3.14 Time building geometry restraints manager: 4.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3503 1.34 - 1.46: 1330 1.46 - 1.57: 5782 1.57 - 1.69: 1 1.69 - 1.81: 56 Bond restraints: 10672 Sorted by residual: bond pdb=" C ASN D 70 " pdb=" N PRO D 71 " ideal model delta sigma weight residual 1.331 1.348 -0.017 7.90e-03 1.60e+04 4.44e+00 bond pdb=" CB PRO A 92 " pdb=" CG PRO A 92 " ideal model delta sigma weight residual 1.492 1.579 -0.087 5.00e-02 4.00e+02 3.05e+00 bond pdb=" CG PRO A 158 " pdb=" CD PRO A 158 " ideal model delta sigma weight residual 1.512 1.489 0.023 2.70e-02 1.37e+03 7.52e-01 bond pdb=" CB PRO A 158 " pdb=" CG PRO A 158 " ideal model delta sigma weight residual 1.506 1.473 0.033 3.90e-02 6.57e+02 7.05e-01 bond pdb=" C THR A 343 " pdb=" O THR A 343 " ideal model delta sigma weight residual 1.238 1.248 -0.010 1.28e-02 6.10e+03 6.65e-01 ... (remaining 10667 not shown) Histogram of bond angle deviations from ideal: 99.94 - 106.74: 331 106.74 - 113.55: 6002 113.55 - 120.36: 3797 120.36 - 127.17: 4221 127.17 - 133.98: 113 Bond angle restraints: 14464 Sorted by residual: angle pdb=" CA PRO A 92 " pdb=" N PRO A 92 " pdb=" CD PRO A 92 " ideal model delta sigma weight residual 112.00 108.01 3.99 1.40e+00 5.10e-01 8.11e+00 angle pdb=" N VAL A 260 " pdb=" CA VAL A 260 " pdb=" C VAL A 260 " ideal model delta sigma weight residual 107.76 110.60 -2.84 1.01e+00 9.80e-01 7.90e+00 angle pdb=" N GLY A 47 " pdb=" CA GLY A 47 " pdb=" C GLY A 47 " ideal model delta sigma weight residual 114.85 111.86 2.99 1.35e+00 5.49e-01 4.92e+00 angle pdb=" C THR B 157 " pdb=" N PRO B 158 " pdb=" CD PRO B 158 " ideal model delta sigma weight residual 120.60 115.73 4.87 2.20e+00 2.07e-01 4.91e+00 angle pdb=" C LYS C 138 " pdb=" N LYS C 139 " pdb=" CA LYS C 139 " ideal model delta sigma weight residual 121.58 117.50 4.08 1.95e+00 2.63e-01 4.38e+00 ... (remaining 14459 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.81: 5759 16.81 - 33.61: 580 33.61 - 50.42: 125 50.42 - 67.23: 34 67.23 - 84.03: 6 Dihedral angle restraints: 6504 sinusoidal: 2572 harmonic: 3932 Sorted by residual: dihedral pdb=" CG ARG D 172 " pdb=" CD ARG D 172 " pdb=" NE ARG D 172 " pdb=" CZ ARG D 172 " ideal model delta sinusoidal sigma weight residual 90.00 134.39 -44.39 2 1.50e+01 4.44e-03 1.04e+01 dihedral pdb=" CG ARG C 257 " pdb=" CD ARG C 257 " pdb=" NE ARG C 257 " pdb=" CZ ARG C 257 " ideal model delta sinusoidal sigma weight residual -90.00 -133.53 43.53 2 1.50e+01 4.44e-03 1.01e+01 dihedral pdb=" CG ARG C 172 " pdb=" CD ARG C 172 " pdb=" NE ARG C 172 " pdb=" CZ ARG C 172 " ideal model delta sinusoidal sigma weight residual 180.00 136.86 43.14 2 1.50e+01 4.44e-03 9.98e+00 ... (remaining 6501 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 980 0.027 - 0.054: 378 0.054 - 0.080: 169 0.080 - 0.107: 90 0.107 - 0.134: 27 Chirality restraints: 1644 Sorted by residual: chirality pdb=" CB VAL B 23 " pdb=" CA VAL B 23 " pdb=" CG1 VAL B 23 " pdb=" CG2 VAL B 23 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 4.47e-01 chirality pdb=" CA ILE A 182 " pdb=" N ILE A 182 " pdb=" C ILE A 182 " pdb=" CB ILE A 182 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.13e-01 chirality pdb=" CA ILE C 190 " pdb=" N ILE C 190 " pdb=" C ILE C 190 " pdb=" CB ILE C 190 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.50e-01 ... (remaining 1641 not shown) Planarity restraints: 1880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 157 " -0.063 5.00e-02 4.00e+02 9.71e-02 1.51e+01 pdb=" N PRO B 158 " 0.168 5.00e-02 4.00e+02 pdb=" CA PRO B 158 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO B 158 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 187 " -0.049 5.00e-02 4.00e+02 7.43e-02 8.83e+00 pdb=" N PRO D 188 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO D 188 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO D 188 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 91 " -0.044 5.00e-02 4.00e+02 6.46e-02 6.67e+00 pdb=" N PRO A 92 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 92 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 92 " -0.036 5.00e-02 4.00e+02 ... (remaining 1877 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 97 2.63 - 3.20: 9371 3.20 - 3.77: 16904 3.77 - 4.33: 22564 4.33 - 4.90: 37030 Nonbonded interactions: 85966 Sorted by model distance: nonbonded pdb=" O GLU C 224 " pdb=" OG1 THR C 265 " model vdw 2.066 2.440 nonbonded pdb=" O GLU D 224 " pdb=" OG1 THR D 265 " model vdw 2.075 2.440 nonbonded pdb=" O GLU A 224 " pdb=" OG1 THR A 265 " model vdw 2.155 2.440 nonbonded pdb=" O GLU B 224 " pdb=" OG1 THR B 265 " model vdw 2.201 2.440 nonbonded pdb=" OG SER C 275 " pdb=" OE1 GLU C 276 " model vdw 2.209 2.440 ... (remaining 85961 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=0.00 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: 1.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 5.650 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 30.990 Find NCS groups from input model: 0.650 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:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 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 0.087 10672 Z= 0.143 Angle : 0.516 7.148 14464 Z= 0.266 Chirality : 0.040 0.134 1644 Planarity : 0.005 0.097 1880 Dihedral : 14.497 84.033 3984 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.09 % Allowed : 0.27 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.23), residues: 1364 helix: 1.77 (0.19), residues: 672 sheet: -1.80 (0.31), residues: 248 loop : -1.30 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP C 295 HIS 0.002 0.000 HIS D 156 PHE 0.008 0.001 PHE C 144 TYR 0.014 0.002 TYR B 203 ARG 0.006 0.000 ARG A 330 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 281 time to evaluate : 1.155 Fit side-chains REVERT: A 170 LEU cc_start: 0.8677 (mt) cc_final: 0.8449 (mt) REVERT: B 72 CYS cc_start: 0.6881 (m) cc_final: 0.6358 (t) REVERT: B 139 LYS cc_start: 0.7843 (pttt) cc_final: 0.6882 (ttpt) REVERT: C 130 LEU cc_start: 0.7920 (tp) cc_final: 0.7701 (tp) REVERT: C 139 LYS cc_start: 0.7884 (pttt) cc_final: 0.6888 (ttpt) REVERT: C 298 THR cc_start: 0.7512 (m) cc_final: 0.6974 (p) REVERT: D 189 GLU cc_start: 0.7332 (tp30) cc_final: 0.7121 (tp30) outliers start: 1 outliers final: 0 residues processed: 281 average time/residue: 0.2404 time to fit residues: 93.9420 Evaluate side-chains 229 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 229 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 106 optimal weight: 10.0000 chunk 41 optimal weight: 8.9990 chunk 64 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 chunk 123 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 11 GLN B 60 GLN ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 GLN C 54 ASN C 80 HIS ** D 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 HIS D 339 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.1044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10672 Z= 0.234 Angle : 0.551 6.758 14464 Z= 0.280 Chirality : 0.042 0.142 1644 Planarity : 0.005 0.063 1880 Dihedral : 3.757 15.392 1472 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.99 % Allowed : 9.26 % Favored : 89.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.23), residues: 1364 helix: 1.91 (0.19), residues: 676 sheet: -1.97 (0.41), residues: 152 loop : -1.45 (0.25), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 313 HIS 0.009 0.001 HIS C 2 PHE 0.015 0.002 PHE C 144 TYR 0.020 0.002 TYR A 58 ARG 0.003 0.000 ARG D 59 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 242 time to evaluate : 1.075 Fit side-chains revert: symmetry clash REVERT: A 114 PRO cc_start: 0.7879 (Cg_endo) cc_final: 0.7583 (Cg_exo) REVERT: A 139 LYS cc_start: 0.7508 (pttt) cc_final: 0.7187 (ttpt) REVERT: C 130 LEU cc_start: 0.7976 (tp) cc_final: 0.7741 (tp) outliers start: 11 outliers final: 11 residues processed: 247 average time/residue: 0.2783 time to fit residues: 95.0218 Evaluate side-chains 235 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 224 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 286 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 68 optimal weight: 2.9990 chunk 38 optimal weight: 9.9990 chunk 102 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 123 optimal weight: 3.9990 chunk 133 optimal weight: 7.9990 chunk 110 optimal weight: 0.9990 chunk 122 optimal weight: 0.8980 chunk 42 optimal weight: 0.0000 chunk 99 optimal weight: 20.0000 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 60 GLN ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 GLN C 54 ASN C 80 HIS D 2 HIS ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 HIS D 339 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.1153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10672 Z= 0.139 Angle : 0.483 6.722 14464 Z= 0.244 Chirality : 0.040 0.131 1644 Planarity : 0.004 0.043 1880 Dihedral : 3.556 14.878 1472 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.35 % Allowed : 10.88 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.23), residues: 1364 helix: 2.17 (0.19), residues: 676 sheet: -1.75 (0.40), residues: 152 loop : -1.35 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 313 HIS 0.007 0.001 HIS C 2 PHE 0.011 0.001 PHE C 144 TYR 0.021 0.002 TYR A 58 ARG 0.002 0.000 ARG B 55 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 242 time to evaluate : 1.192 Fit side-chains REVERT: A 114 PRO cc_start: 0.7866 (Cg_endo) cc_final: 0.7587 (Cg_exo) REVERT: A 139 LYS cc_start: 0.7508 (pttt) cc_final: 0.7191 (ttpt) REVERT: A 170 LEU cc_start: 0.8710 (mt) cc_final: 0.8503 (mt) REVERT: A 298 THR cc_start: 0.7366 (OUTLIER) cc_final: 0.6907 (p) REVERT: B 72 CYS cc_start: 0.6902 (m) cc_final: 0.6409 (t) REVERT: B 170 LEU cc_start: 0.8597 (mt) cc_final: 0.8339 (mt) REVERT: C 130 LEU cc_start: 0.7995 (tp) cc_final: 0.7749 (tp) REVERT: C 170 LEU cc_start: 0.8645 (mt) cc_final: 0.8442 (mt) REVERT: C 298 THR cc_start: 0.7482 (OUTLIER) cc_final: 0.6918 (p) REVERT: D 139 LYS cc_start: 0.7484 (pttp) cc_final: 0.7194 (pttt) REVERT: D 170 LEU cc_start: 0.8679 (mt) cc_final: 0.8440 (mt) outliers start: 15 outliers final: 11 residues processed: 250 average time/residue: 0.2694 time to fit residues: 93.3645 Evaluate side-chains 239 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 226 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 324 GLN Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 98 LYS Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 286 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 64 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 83 optimal weight: 9.9990 chunk 124 optimal weight: 0.9980 chunk 131 optimal weight: 6.9990 chunk 117 optimal weight: 7.9990 chunk 35 optimal weight: 0.8980 chunk 109 optimal weight: 7.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 80 HIS B 324 GLN C 54 ASN C 80 HIS D 11 GLN ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10672 Z= 0.166 Angle : 0.488 7.091 14464 Z= 0.246 Chirality : 0.040 0.133 1644 Planarity : 0.004 0.055 1880 Dihedral : 3.521 14.727 1472 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.62 % Allowed : 13.04 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.23), residues: 1364 helix: 2.21 (0.19), residues: 676 sheet: -1.51 (0.42), residues: 144 loop : -1.44 (0.25), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 313 HIS 0.008 0.001 HIS C 2 PHE 0.014 0.001 PHE C 144 TYR 0.017 0.002 TYR A 58 ARG 0.002 0.000 ARG A 172 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 231 time to evaluate : 1.045 Fit side-chains REVERT: A 114 PRO cc_start: 0.7847 (Cg_endo) cc_final: 0.7553 (Cg_exo) REVERT: A 298 THR cc_start: 0.7425 (OUTLIER) cc_final: 0.6910 (p) REVERT: B 170 LEU cc_start: 0.8674 (mt) cc_final: 0.8433 (mt) REVERT: C 130 LEU cc_start: 0.8042 (tp) cc_final: 0.7818 (tp) REVERT: C 298 THR cc_start: 0.7500 (OUTLIER) cc_final: 0.6926 (p) REVERT: D 139 LYS cc_start: 0.7490 (pttp) cc_final: 0.7217 (pttt) outliers start: 18 outliers final: 15 residues processed: 241 average time/residue: 0.2529 time to fit residues: 84.3716 Evaluate side-chains 240 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 223 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 98 LYS Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 286 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 97 optimal weight: 7.9990 chunk 54 optimal weight: 0.9980 chunk 112 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 67 optimal weight: 5.9990 chunk 117 optimal weight: 7.9990 chunk 33 optimal weight: 10.0000 chunk 44 optimal weight: 7.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN B 60 GLN ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 80 HIS B 324 GLN C 54 ASN C 80 HIS ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10672 Z= 0.274 Angle : 0.560 6.717 14464 Z= 0.288 Chirality : 0.042 0.147 1644 Planarity : 0.005 0.060 1880 Dihedral : 3.881 15.084 1472 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.61 % Allowed : 14.57 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.23), residues: 1364 helix: 1.99 (0.19), residues: 676 sheet: -1.72 (0.40), residues: 144 loop : -1.60 (0.25), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 147 HIS 0.009 0.001 HIS C 2 PHE 0.017 0.002 PHE D 144 TYR 0.024 0.002 TYR D 213 ARG 0.003 0.000 ARG C 330 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 224 time to evaluate : 1.175 Fit side-chains REVERT: A 114 PRO cc_start: 0.7851 (Cg_endo) cc_final: 0.7563 (Cg_exo) REVERT: B 189 GLU cc_start: 0.7164 (tp30) cc_final: 0.6667 (tp30) REVERT: D 128 ASP cc_start: 0.5004 (OUTLIER) cc_final: 0.4189 (m-30) REVERT: D 158 PRO cc_start: 0.7758 (Cg_endo) cc_final: 0.7547 (Cg_exo) REVERT: D 320 LEU cc_start: 0.6430 (OUTLIER) cc_final: 0.6115 (mp) outliers start: 29 outliers final: 23 residues processed: 239 average time/residue: 0.2563 time to fit residues: 83.4915 Evaluate side-chains 240 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 215 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 156 HIS Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain C residue 295 TRP Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain D residue 295 TRP Chi-restraints excluded: chain D residue 320 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 118 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 131 optimal weight: 5.9990 chunk 109 optimal weight: 9.9990 chunk 60 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 60 GLN ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 80 HIS B 324 GLN C 54 ASN C 80 HIS ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 10672 Z= 0.156 Angle : 0.492 7.495 14464 Z= 0.250 Chirality : 0.040 0.134 1644 Planarity : 0.004 0.052 1880 Dihedral : 3.603 14.285 1472 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.80 % Allowed : 15.74 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.23), residues: 1364 helix: 2.23 (0.19), residues: 676 sheet: -1.77 (0.39), residues: 152 loop : -1.39 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 313 HIS 0.009 0.001 HIS C 2 PHE 0.011 0.001 PHE C 144 TYR 0.022 0.002 TYR A 58 ARG 0.004 0.000 ARG A 330 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 232 time to evaluate : 1.219 Fit side-chains REVERT: A 114 PRO cc_start: 0.7812 (Cg_endo) cc_final: 0.7506 (Cg_exo) REVERT: A 139 LYS cc_start: 0.7837 (pttt) cc_final: 0.6801 (ttpt) REVERT: B 110 LYS cc_start: 0.6950 (mmmt) cc_final: 0.6682 (mmtt) REVERT: B 139 LYS cc_start: 0.7807 (pttt) cc_final: 0.6817 (ttpt) REVERT: B 170 LEU cc_start: 0.8652 (mt) cc_final: 0.8405 (mt) REVERT: B 189 GLU cc_start: 0.7102 (tp30) cc_final: 0.6627 (tp30) REVERT: C 34 GLU cc_start: 0.2994 (OUTLIER) cc_final: 0.2322 (pm20) REVERT: C 330 ARG cc_start: 0.7442 (tpp-160) cc_final: 0.6439 (mmm-85) REVERT: D 53 GLU cc_start: 0.6127 (pm20) cc_final: 0.5888 (pt0) REVERT: D 170 LEU cc_start: 0.8707 (mt) cc_final: 0.8467 (mt) REVERT: D 320 LEU cc_start: 0.6458 (OUTLIER) cc_final: 0.6097 (mp) outliers start: 20 outliers final: 17 residues processed: 244 average time/residue: 0.2461 time to fit residues: 82.1431 Evaluate side-chains 237 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 218 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 324 GLN Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 338 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 14 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 96 optimal weight: 10.0000 chunk 110 optimal weight: 0.0010 chunk 73 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 82 optimal weight: 9.9990 chunk 79 optimal weight: 6.9990 chunk 60 optimal weight: 8.9990 chunk 81 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 overall best weight: 2.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 11 GLN B 60 GLN ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 GLN C 54 ASN C 80 HIS ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10672 Z= 0.230 Angle : 0.532 7.584 14464 Z= 0.271 Chirality : 0.041 0.141 1644 Planarity : 0.005 0.069 1880 Dihedral : 3.713 14.525 1472 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.16 % Allowed : 16.37 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.23), residues: 1364 helix: 2.08 (0.19), residues: 676 sheet: -1.67 (0.40), residues: 144 loop : -1.54 (0.25), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 147 HIS 0.009 0.001 HIS C 2 PHE 0.015 0.002 PHE D 144 TYR 0.020 0.002 TYR A 58 ARG 0.003 0.000 ARG A 330 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 222 time to evaluate : 1.111 Fit side-chains REVERT: A 114 PRO cc_start: 0.7845 (Cg_endo) cc_final: 0.7539 (Cg_exo) REVERT: A 330 ARG cc_start: 0.7905 (mmm-85) cc_final: 0.7565 (mmm160) REVERT: B 110 LYS cc_start: 0.6969 (mmmt) cc_final: 0.6727 (mmtt) REVERT: B 189 GLU cc_start: 0.7153 (tp30) cc_final: 0.6686 (tp30) REVERT: C 34 GLU cc_start: 0.3021 (OUTLIER) cc_final: 0.2359 (pm20) REVERT: D 53 GLU cc_start: 0.6143 (pm20) cc_final: 0.5904 (pt0) REVERT: D 139 LYS cc_start: 0.7529 (pttp) cc_final: 0.6717 (ttpt) REVERT: D 320 LEU cc_start: 0.6416 (OUTLIER) cc_final: 0.6087 (mp) outliers start: 24 outliers final: 18 residues processed: 237 average time/residue: 0.2587 time to fit residues: 83.2956 Evaluate side-chains 237 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 217 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain B residue 156 HIS Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain D residue 320 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 6.9990 chunk 39 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 12 optimal weight: 9.9990 chunk 103 optimal weight: 6.9990 chunk 119 optimal weight: 4.9990 chunk 125 optimal weight: 6.9990 chunk 114 optimal weight: 3.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 11 GLN B 60 GLN ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 80 HIS B 324 GLN C 54 ASN C 80 HIS ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10672 Z= 0.191 Angle : 0.518 7.889 14464 Z= 0.263 Chirality : 0.041 0.136 1644 Planarity : 0.005 0.057 1880 Dihedral : 3.666 14.337 1472 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.98 % Allowed : 17.00 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.23), residues: 1364 helix: 2.11 (0.19), residues: 676 sheet: -1.83 (0.39), residues: 152 loop : -1.41 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 147 HIS 0.010 0.001 HIS C 2 PHE 0.013 0.002 PHE C 144 TYR 0.021 0.002 TYR A 58 ARG 0.002 0.000 ARG A 172 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 226 time to evaluate : 1.136 Fit side-chains REVERT: A 114 PRO cc_start: 0.7807 (Cg_endo) cc_final: 0.7506 (Cg_exo) REVERT: A 139 LYS cc_start: 0.7862 (pttt) cc_final: 0.6802 (ttpt) REVERT: B 110 LYS cc_start: 0.6970 (mmmt) cc_final: 0.6753 (mmtt) REVERT: B 139 LYS cc_start: 0.7848 (pttt) cc_final: 0.6794 (ttpt) REVERT: B 170 LEU cc_start: 0.8692 (mt) cc_final: 0.8446 (mt) REVERT: B 189 GLU cc_start: 0.7138 (tp30) cc_final: 0.6668 (tp30) REVERT: C 34 GLU cc_start: 0.2991 (OUTLIER) cc_final: 0.2355 (pm20) REVERT: C 139 LYS cc_start: 0.7797 (pttt) cc_final: 0.6779 (ttpt) REVERT: C 330 ARG cc_start: 0.7459 (tpp-160) cc_final: 0.6428 (mmm-85) REVERT: D 53 GLU cc_start: 0.6123 (pm20) cc_final: 0.5897 (pt0) REVERT: D 139 LYS cc_start: 0.7483 (pttp) cc_final: 0.6739 (ttpt) REVERT: D 320 LEU cc_start: 0.6405 (OUTLIER) cc_final: 0.6066 (mp) outliers start: 22 outliers final: 19 residues processed: 240 average time/residue: 0.2510 time to fit residues: 82.1838 Evaluate side-chains 240 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 219 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain B residue 156 HIS Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain D residue 320 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 0.9980 chunk 125 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 95 optimal weight: 5.9990 chunk 37 optimal weight: 20.0000 chunk 110 optimal weight: 20.0000 chunk 115 optimal weight: 3.9990 chunk 121 optimal weight: 8.9990 chunk 80 optimal weight: 8.9990 chunk 129 optimal weight: 0.6980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 11 GLN B 60 GLN ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 GLN C 54 ASN C 80 HIS ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 339 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10672 Z= 0.169 Angle : 0.509 8.078 14464 Z= 0.258 Chirality : 0.040 0.133 1644 Planarity : 0.004 0.052 1880 Dihedral : 3.578 14.127 1472 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.07 % Allowed : 17.45 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.23), residues: 1364 helix: 2.17 (0.19), residues: 676 sheet: -1.57 (0.40), residues: 144 loop : -1.44 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 313 HIS 0.010 0.001 HIS C 2 PHE 0.013 0.002 PHE D 144 TYR 0.021 0.002 TYR A 58 ARG 0.003 0.000 ARG A 330 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 232 time to evaluate : 1.165 Fit side-chains REVERT: A 114 PRO cc_start: 0.7772 (Cg_endo) cc_final: 0.7470 (Cg_exo) REVERT: A 139 LYS cc_start: 0.7881 (pttt) cc_final: 0.6814 (ttpt) REVERT: A 330 ARG cc_start: 0.7850 (mmm-85) cc_final: 0.7550 (mmm160) REVERT: B 110 LYS cc_start: 0.6965 (mmmt) cc_final: 0.6744 (mmtt) REVERT: B 170 LEU cc_start: 0.8668 (mt) cc_final: 0.8410 (mt) REVERT: B 189 GLU cc_start: 0.7127 (tp30) cc_final: 0.6666 (tp30) REVERT: C 34 GLU cc_start: 0.2962 (OUTLIER) cc_final: 0.2290 (pm20) REVERT: D 128 ASP cc_start: 0.4581 (OUTLIER) cc_final: 0.3886 (m-30) REVERT: D 139 LYS cc_start: 0.7484 (pttp) cc_final: 0.6758 (ttpt) REVERT: D 170 LEU cc_start: 0.8710 (mt) cc_final: 0.8488 (mt) REVERT: D 320 LEU cc_start: 0.6435 (OUTLIER) cc_final: 0.6071 (mp) outliers start: 23 outliers final: 19 residues processed: 244 average time/residue: 0.2478 time to fit residues: 82.7525 Evaluate side-chains 244 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 222 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain B residue 156 HIS Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 324 GLN Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain D residue 320 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 7.9990 chunk 61 optimal weight: 20.0000 chunk 89 optimal weight: 5.9990 chunk 135 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 11 optimal weight: 10.0000 chunk 83 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 114 optimal weight: 5.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 11 GLN B 60 GLN ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 GLN C 54 ASN C 80 HIS ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10672 Z= 0.218 Angle : 0.535 8.060 14464 Z= 0.272 Chirality : 0.041 0.139 1644 Planarity : 0.005 0.052 1880 Dihedral : 3.659 14.257 1472 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.89 % Allowed : 17.99 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.23), residues: 1364 helix: 2.11 (0.19), residues: 676 sheet: -1.86 (0.39), residues: 152 loop : -1.39 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 147 HIS 0.010 0.001 HIS C 2 PHE 0.015 0.002 PHE D 144 TYR 0.023 0.002 TYR B 173 ARG 0.002 0.000 ARG A 172 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 220 time to evaluate : 1.237 Fit side-chains REVERT: A 114 PRO cc_start: 0.7822 (Cg_endo) cc_final: 0.7515 (Cg_exo) REVERT: A 330 ARG cc_start: 0.7874 (mmm-85) cc_final: 0.7562 (mmm160) REVERT: B 110 LYS cc_start: 0.6985 (mmmt) cc_final: 0.6780 (mmtt) REVERT: B 139 LYS cc_start: 0.7885 (pttt) cc_final: 0.6801 (ttpt) REVERT: B 170 LEU cc_start: 0.8693 (mt) cc_final: 0.8470 (mt) REVERT: B 189 GLU cc_start: 0.7135 (tp30) cc_final: 0.6663 (tp30) REVERT: C 34 GLU cc_start: 0.2965 (OUTLIER) cc_final: 0.2373 (pm20) REVERT: C 139 LYS cc_start: 0.7791 (pttt) cc_final: 0.6783 (ttpt) REVERT: C 330 ARG cc_start: 0.7502 (tpp-160) cc_final: 0.6457 (mmm-85) REVERT: D 139 LYS cc_start: 0.7503 (pttp) cc_final: 0.6769 (ttpt) REVERT: D 320 LEU cc_start: 0.6446 (OUTLIER) cc_final: 0.6072 (mp) outliers start: 21 outliers final: 19 residues processed: 232 average time/residue: 0.2564 time to fit residues: 81.0540 Evaluate side-chains 237 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 216 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain B residue 156 HIS Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 286 ILE Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 324 GLN Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 286 ILE Chi-restraints excluded: chain D residue 320 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 33 optimal weight: 8.9990 chunk 99 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 110 optimal weight: 20.0000 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 94 optimal weight: 0.0970 chunk 6 optimal weight: 6.9990 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN B 60 GLN ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 80 HIS B 324 GLN C 54 ASN C 80 HIS ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.189032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.149977 restraints weight = 12492.396| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 2.39 r_work: 0.3699 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 10672 Z= 0.303 Angle : 0.597 7.876 14464 Z= 0.307 Chirality : 0.043 0.149 1644 Planarity : 0.005 0.055 1880 Dihedral : 3.947 15.121 1472 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.34 % Allowed : 17.54 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.23), residues: 1364 helix: 1.85 (0.19), residues: 676 sheet: -1.80 (0.40), residues: 144 loop : -1.59 (0.25), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 147 HIS 0.011 0.001 HIS D 156 PHE 0.018 0.002 PHE D 144 TYR 0.025 0.003 TYR D 213 ARG 0.003 0.001 ARG D 59 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2467.72 seconds wall clock time: 45 minutes 53.90 seconds (2753.90 seconds total)