Starting phenix.real_space_refine on Tue May 13 00:26:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yu7_39573/05_2025/8yu7_39573.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yu7_39573/05_2025/8yu7_39573.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yu7_39573/05_2025/8yu7_39573.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yu7_39573/05_2025/8yu7_39573.map" model { file = "/net/cci-nas-00/data/ceres_data/8yu7_39573/05_2025/8yu7_39573.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yu7_39573/05_2025/8yu7_39573.cif" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.103 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 48 5.16 5 C 6612 2.51 5 N 1436 2.21 5 O 1520 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 9616 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2264 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 269} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "B" Number of atoms: 2264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2264 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 269} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "C" Number of atoms: 2264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2264 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 269} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "D" Number of atoms: 2264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2264 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 269} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 168 Unusual residues: {'CLR': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 140 Unusual residues: {'CLR': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 112 Unusual residues: {'CLR': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 140 Unusual residues: {'CLR': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 6.27, per 1000 atoms: 0.65 Number of scatterers: 9616 At special positions: 0 Unit cell: (94.35, 94.35, 79.9, 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 48 16.00 O 1520 8.00 N 1436 7.00 C 6612 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 28 " - pdb=" SG CYS A 274 " distance=2.03 Simple disulfide: pdb=" SG CYS A 109 " - pdb=" SG CYS A 186 " distance=2.03 Simple disulfide: pdb=" SG CYS B 28 " - pdb=" SG CYS B 274 " distance=2.03 Simple disulfide: pdb=" SG CYS B 109 " - pdb=" SG CYS B 186 " distance=2.03 Simple disulfide: pdb=" SG CYS C 28 " - pdb=" SG CYS C 274 " distance=2.03 Simple disulfide: pdb=" SG CYS C 109 " - pdb=" SG CYS C 186 " distance=2.03 Simple disulfide: pdb=" SG CYS D 28 " - pdb=" SG CYS D 274 " distance=2.03 Simple disulfide: pdb=" SG CYS D 109 " - pdb=" SG CYS D 186 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.60 Conformation dependent library (CDL) restraints added in 1.0 seconds 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2152 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 4 sheets defined 81.4% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 36 through 64 Proline residue: A 42 - end of helix Processing helix chain 'A' and resid 72 through 100 removed outlier: 4.173A pdb=" N TYR A 76 " --> pdb=" O MET A 72 " (cutoff:3.500A) Proline residue: A 92 - end of helix removed outlier: 3.790A pdb=" N VAL A 99 " --> pdb=" O ALA A 95 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA A 100 " --> pdb=" O VAL A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 140 removed outlier: 3.574A pdb=" N LYS A 110 " --> pdb=" O ASN A 106 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N VAL A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LEU A 125 " --> pdb=" O TYR A 121 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N HIS A 140 " --> pdb=" O LEU A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 175 Proline residue: A 163 - end of helix Proline residue: A 170 - end of helix removed outlier: 3.694A pdb=" N ILE A 173 " --> pdb=" O ILE A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 208 removed outlier: 3.805A pdb=" N VAL A 196 " --> pdb=" O ASN A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 226 removed outlier: 3.742A pdb=" N VAL A 214 " --> pdb=" O LEU A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 237 Processing helix chain 'A' and resid 238 through 251 Processing helix chain 'A' and resid 252 through 267 Processing helix chain 'A' and resid 274 through 305 removed outlier: 4.147A pdb=" N ASN A 278 " --> pdb=" O CYS A 274 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N THR A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Proline residue: A 299 - end of helix removed outlier: 3.959A pdb=" N LEU A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 64 Proline residue: B 42 - end of helix Processing helix chain 'B' and resid 72 through 100 removed outlier: 4.173A pdb=" N TYR B 76 " --> pdb=" O MET B 72 " (cutoff:3.500A) Proline residue: B 92 - end of helix removed outlier: 3.790A pdb=" N VAL B 99 " --> pdb=" O ALA B 95 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA B 100 " --> pdb=" O VAL B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 140 removed outlier: 3.574A pdb=" N LYS B 110 " --> pdb=" O ASN B 106 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N VAL B 124 " --> pdb=" O LEU B 120 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LEU B 125 " --> pdb=" O TYR B 121 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS B 140 " --> pdb=" O LEU B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 175 Proline residue: B 163 - end of helix Proline residue: B 170 - end of helix removed outlier: 3.693A pdb=" N ILE B 173 " --> pdb=" O ILE B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 208 removed outlier: 3.805A pdb=" N VAL B 196 " --> pdb=" O ASN B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 226 removed outlier: 3.742A pdb=" N VAL B 214 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 237 Processing helix chain 'B' and resid 238 through 251 Processing helix chain 'B' and resid 252 through 267 Processing helix chain 'B' and resid 274 through 305 removed outlier: 4.148A pdb=" N ASN B 278 " --> pdb=" O CYS B 274 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N THR B 279 " --> pdb=" O GLU B 275 " (cutoff:3.500A) Proline residue: B 299 - end of helix removed outlier: 3.960A pdb=" N LEU B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 64 Proline residue: C 42 - end of helix Processing helix chain 'C' and resid 72 through 100 removed outlier: 4.173A pdb=" N TYR C 76 " --> pdb=" O MET C 72 " (cutoff:3.500A) Proline residue: C 92 - end of helix removed outlier: 3.789A pdb=" N VAL C 99 " --> pdb=" O ALA C 95 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA C 100 " --> pdb=" O VAL C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 140 removed outlier: 3.573A pdb=" N LYS C 110 " --> pdb=" O ASN C 106 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N VAL C 124 " --> pdb=" O LEU C 120 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LEU C 125 " --> pdb=" O TYR C 121 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N HIS C 140 " --> pdb=" O LEU C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 175 Proline residue: C 163 - end of helix Proline residue: C 170 - end of helix removed outlier: 3.694A pdb=" N ILE C 173 " --> pdb=" O ILE C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 208 removed outlier: 3.804A pdb=" N VAL C 196 " --> pdb=" O ASN C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 226 removed outlier: 3.742A pdb=" N VAL C 214 " --> pdb=" O LEU C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 237 Processing helix chain 'C' and resid 238 through 251 Processing helix chain 'C' and resid 252 through 267 Processing helix chain 'C' and resid 274 through 305 removed outlier: 4.147A pdb=" N ASN C 278 " --> pdb=" O CYS C 274 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N THR C 279 " --> pdb=" O GLU C 275 " (cutoff:3.500A) Proline residue: C 299 - end of helix removed outlier: 3.959A pdb=" N LEU C 305 " --> pdb=" O LEU C 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 64 Proline residue: D 42 - end of helix Processing helix chain 'D' and resid 72 through 100 removed outlier: 4.173A pdb=" N TYR D 76 " --> pdb=" O MET D 72 " (cutoff:3.500A) Proline residue: D 92 - end of helix removed outlier: 3.789A pdb=" N VAL D 99 " --> pdb=" O ALA D 95 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA D 100 " --> pdb=" O VAL D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 140 removed outlier: 3.573A pdb=" N LYS D 110 " --> pdb=" O ASN D 106 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N VAL D 124 " --> pdb=" O LEU D 120 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LEU D 125 " --> pdb=" O TYR D 121 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N HIS D 140 " --> pdb=" O LEU D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 175 Proline residue: D 163 - end of helix Proline residue: D 170 - end of helix removed outlier: 3.693A pdb=" N ILE D 173 " --> pdb=" O ILE D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 208 removed outlier: 3.805A pdb=" N VAL D 196 " --> pdb=" O ASN D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 226 removed outlier: 3.742A pdb=" N VAL D 214 " --> pdb=" O LEU D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 237 Processing helix chain 'D' and resid 238 through 251 Processing helix chain 'D' and resid 252 through 267 Processing helix chain 'D' and resid 274 through 305 removed outlier: 4.146A pdb=" N ASN D 278 " --> pdb=" O CYS D 274 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N THR D 279 " --> pdb=" O GLU D 275 " (cutoff:3.500A) Proline residue: D 299 - end of helix removed outlier: 3.959A pdb=" N LEU D 305 " --> pdb=" O LEU D 301 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 177 through 178 removed outlier: 3.595A pdb=" N ILE A 185 " --> pdb=" O SER A 178 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 177 through 178 removed outlier: 3.595A pdb=" N ILE B 185 " --> pdb=" O SER B 178 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 177 through 178 removed outlier: 3.595A pdb=" N ILE C 185 " --> pdb=" O SER C 178 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 177 through 178 removed outlier: 3.595A pdb=" N ILE D 185 " --> pdb=" O SER D 178 " (cutoff:3.500A) 644 hydrogen bonds defined for protein. 1932 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.88 Time building geometry restraints manager: 3.00 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: 2675 1.34 - 1.46: 2045 1.46 - 1.58: 5152 1.58 - 1.70: 0 1.70 - 1.82: 60 Bond restraints: 9932 Sorted by residual: bond pdb=" C13 CLR B 403 " pdb=" C17 CLR B 403 " ideal model delta sigma weight residual 1.550 1.484 0.066 2.00e-02 2.50e+03 1.08e+01 bond pdb=" C13 CLR A 406 " pdb=" C17 CLR A 406 " ideal model delta sigma weight residual 1.550 1.485 0.065 2.00e-02 2.50e+03 1.06e+01 bond pdb=" C13 CLR A 402 " pdb=" C17 CLR A 402 " ideal model delta sigma weight residual 1.550 1.485 0.065 2.00e-02 2.50e+03 1.06e+01 bond pdb=" C13 CLR D 401 " pdb=" C17 CLR D 401 " ideal model delta sigma weight residual 1.550 1.489 0.061 2.00e-02 2.50e+03 9.24e+00 bond pdb=" C13 CLR A 405 " pdb=" C17 CLR A 405 " ideal model delta sigma weight residual 1.550 1.489 0.061 2.00e-02 2.50e+03 9.24e+00 ... (remaining 9927 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.84: 13230 2.84 - 5.68: 332 5.68 - 8.51: 76 8.51 - 11.35: 17 11.35 - 14.19: 5 Bond angle restraints: 13660 Sorted by residual: angle pdb=" C13 CLR D 402 " pdb=" C14 CLR D 402 " pdb=" C8 CLR D 402 " ideal model delta sigma weight residual 115.50 101.31 14.19 3.00e+00 1.11e-01 2.24e+01 angle pdb=" N GLY B 159 " pdb=" CA GLY B 159 " pdb=" C GLY B 159 " ideal model delta sigma weight residual 113.27 118.88 -5.61 1.33e+00 5.65e-01 1.78e+01 angle pdb=" N GLY D 159 " pdb=" CA GLY D 159 " pdb=" C GLY D 159 " ideal model delta sigma weight residual 113.27 118.88 -5.61 1.33e+00 5.65e-01 1.78e+01 angle pdb=" N GLY A 159 " pdb=" CA GLY A 159 " pdb=" C GLY A 159 " ideal model delta sigma weight residual 113.27 118.88 -5.61 1.33e+00 5.65e-01 1.78e+01 angle pdb=" N GLY C 159 " pdb=" CA GLY C 159 " pdb=" C GLY C 159 " ideal model delta sigma weight residual 113.27 118.85 -5.58 1.33e+00 5.65e-01 1.76e+01 ... (remaining 13655 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.05: 5540 17.05 - 34.10: 924 34.10 - 51.14: 177 51.14 - 68.19: 47 68.19 - 85.24: 20 Dihedral angle restraints: 6708 sinusoidal: 3384 harmonic: 3324 Sorted by residual: dihedral pdb=" CA ILE A 173 " pdb=" C ILE A 173 " pdb=" N PHE A 174 " pdb=" CA PHE A 174 " ideal model delta harmonic sigma weight residual -180.00 -163.15 -16.85 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA ILE C 173 " pdb=" C ILE C 173 " pdb=" N PHE C 174 " pdb=" CA PHE C 174 " ideal model delta harmonic sigma weight residual -180.00 -163.16 -16.84 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA ILE D 173 " pdb=" C ILE D 173 " pdb=" N PHE D 174 " pdb=" CA PHE D 174 " ideal model delta harmonic sigma weight residual -180.00 -163.22 -16.78 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 6705 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 1498 0.088 - 0.175: 101 0.175 - 0.263: 21 0.263 - 0.351: 16 0.351 - 0.438: 16 Chirality restraints: 1652 Sorted by residual: chirality pdb=" C13 CLR D 401 " pdb=" C12 CLR D 401 " pdb=" C14 CLR D 401 " pdb=" C17 CLR D 401 " both_signs ideal model delta sigma weight residual False -2.93 -2.49 -0.44 2.00e-01 2.50e+01 4.81e+00 chirality pdb=" C13 CLR B 401 " pdb=" C12 CLR B 401 " pdb=" C14 CLR B 401 " pdb=" C17 CLR B 401 " both_signs ideal model delta sigma weight residual False -2.93 -2.50 -0.44 2.00e-01 2.50e+01 4.74e+00 chirality pdb=" C13 CLR A 405 " pdb=" C12 CLR A 405 " pdb=" C14 CLR A 405 " pdb=" C17 CLR A 405 " both_signs ideal model delta sigma weight residual False -2.93 -2.50 -0.44 2.00e-01 2.50e+01 4.73e+00 ... (remaining 1649 not shown) Planarity restraints: 1536 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL D 156 " 0.011 2.00e-02 2.50e+03 2.09e-02 4.36e+00 pdb=" C VAL D 156 " -0.036 2.00e-02 2.50e+03 pdb=" O VAL D 156 " 0.014 2.00e-02 2.50e+03 pdb=" N TYR D 157 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 156 " 0.010 2.00e-02 2.50e+03 2.08e-02 4.33e+00 pdb=" C VAL A 156 " -0.036 2.00e-02 2.50e+03 pdb=" O VAL A 156 " 0.014 2.00e-02 2.50e+03 pdb=" N TYR A 157 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 156 " -0.010 2.00e-02 2.50e+03 2.08e-02 4.31e+00 pdb=" C VAL C 156 " 0.036 2.00e-02 2.50e+03 pdb=" O VAL C 156 " -0.013 2.00e-02 2.50e+03 pdb=" N TYR C 157 " -0.012 2.00e-02 2.50e+03 ... (remaining 1533 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 135 2.67 - 3.23: 9214 3.23 - 3.78: 14422 3.78 - 4.34: 18836 4.34 - 4.90: 32234 Nonbonded interactions: 74841 Sorted by model distance: nonbonded pdb=" O ALA B 291 " pdb=" ND1 HIS B 294 " model vdw 2.110 3.120 nonbonded pdb=" O ALA A 291 " pdb=" ND1 HIS A 294 " model vdw 2.110 3.120 nonbonded pdb=" O ALA C 291 " pdb=" ND1 HIS C 294 " model vdw 2.110 3.120 nonbonded pdb=" O ALA D 291 " pdb=" ND1 HIS D 294 " model vdw 2.110 3.120 nonbonded pdb=" OE1 GLN B 272 " pdb=" NZ LYS C 38 " model vdw 2.281 3.120 ... (remaining 74836 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 26 through 305 or resid 401 through 404)) selection = (chain 'B' and (resid 26 through 305 or resid 401 through 404)) selection = chain 'C' selection = (chain 'D' and (resid 26 through 305 or resid 401 through 404)) } 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: 5.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 23.880 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 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 : 0.007 0.066 9940 Z= 0.338 Angle : 1.068 14.191 13676 Z= 0.462 Chirality : 0.069 0.438 1652 Planarity : 0.004 0.038 1536 Dihedral : 16.843 85.240 4532 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 0.81 % Allowed : 30.36 % Favored : 68.83 % 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: 0.96 (0.26), residues: 1112 helix: 1.95 (0.19), residues: 780 sheet: None (None), residues: 0 loop : -2.78 (0.32), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 94 HIS 0.005 0.001 HIS A 294 PHE 0.010 0.001 PHE B 49 TYR 0.007 0.001 TYR C 190 ARG 0.002 0.000 ARG A 77 Details of bonding type rmsd hydrogen bonds : bond 0.11058 ( 644) hydrogen bonds : angle 6.31000 ( 1932) SS BOND : bond 0.00169 ( 8) SS BOND : angle 1.10351 ( 16) covalent geometry : bond 0.00668 ( 9932) covalent geometry : angle 1.06808 (13660) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 104 time to evaluate : 0.924 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 108 average time/residue: 0.1527 time to fit residues: 25.8546 Evaluate side-chains 105 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 100 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain D residue 53 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 4.9990 chunk 84 optimal weight: 20.0000 chunk 47 optimal weight: 2.9990 chunk 28 optimal weight: 20.0000 chunk 57 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.167619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.131695 restraints weight = 10551.000| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 2.59 r_work: 0.3491 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.0884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9940 Z= 0.196 Angle : 0.716 5.869 13676 Z= 0.353 Chirality : 0.046 0.225 1652 Planarity : 0.005 0.031 1536 Dihedral : 10.117 59.177 2518 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 4.45 % Allowed : 24.19 % Favored : 71.36 % 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: 0.68 (0.27), residues: 1112 helix: 1.72 (0.19), residues: 788 sheet: -1.48 (0.89), residues: 48 loop : -3.12 (0.35), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 161 HIS 0.008 0.001 HIS B 294 PHE 0.019 0.002 PHE C 264 TYR 0.011 0.001 TYR C 219 ARG 0.001 0.000 ARG A 77 Details of bonding type rmsd hydrogen bonds : bond 0.07733 ( 644) hydrogen bonds : angle 5.88604 ( 1932) SS BOND : bond 0.00114 ( 8) SS BOND : angle 1.24562 ( 16) covalent geometry : bond 0.00433 ( 9932) covalent geometry : angle 0.71548 (13660) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 135 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.6406 (pm20) REVERT: B 179 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.6407 (pm20) REVERT: C 179 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.6397 (pm20) REVERT: D 179 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.6400 (pm20) outliers start: 44 outliers final: 20 residues processed: 163 average time/residue: 0.1908 time to fit residues: 45.3310 Evaluate side-chains 124 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 100 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 186 CYS Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 294 HIS Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 186 CYS Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 294 HIS Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 186 CYS Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain C residue 294 HIS Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 186 CYS Chi-restraints excluded: chain D residue 293 PHE Chi-restraints excluded: chain D residue 294 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 45 optimal weight: 4.9990 chunk 12 optimal weight: 0.2980 chunk 39 optimal weight: 2.9990 chunk 24 optimal weight: 0.0270 chunk 41 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 106 optimal weight: 0.5980 chunk 109 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 ASN C 106 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.172939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.137285 restraints weight = 10519.311| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 2.66 r_work: 0.3534 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.1098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 9940 Z= 0.157 Angle : 0.619 5.919 13676 Z= 0.318 Chirality : 0.042 0.167 1652 Planarity : 0.005 0.032 1536 Dihedral : 9.352 58.253 2510 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 5.16 % Allowed : 24.09 % Favored : 70.75 % 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: 0.90 (0.27), residues: 1112 helix: 1.83 (0.19), residues: 792 sheet: None (None), residues: 0 loop : -2.77 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 161 HIS 0.004 0.001 HIS D 294 PHE 0.023 0.002 PHE D 49 TYR 0.007 0.001 TYR C 219 ARG 0.001 0.000 ARG A 77 Details of bonding type rmsd hydrogen bonds : bond 0.06526 ( 644) hydrogen bonds : angle 5.57055 ( 1932) SS BOND : bond 0.00125 ( 8) SS BOND : angle 1.16449 ( 16) covalent geometry : bond 0.00322 ( 9932) covalent geometry : angle 0.61790 (13660) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 111 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 TYR cc_start: 0.6764 (m-80) cc_final: 0.6479 (m-80) REVERT: A 179 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6312 (pm20) REVERT: A 253 LEU cc_start: 0.7406 (OUTLIER) cc_final: 0.7059 (mp) REVERT: B 157 TYR cc_start: 0.6760 (m-80) cc_final: 0.6463 (m-80) REVERT: B 179 GLU cc_start: 0.7297 (OUTLIER) cc_final: 0.6308 (pm20) REVERT: B 253 LEU cc_start: 0.7397 (OUTLIER) cc_final: 0.7051 (mp) REVERT: C 157 TYR cc_start: 0.6774 (m-80) cc_final: 0.6477 (m-80) REVERT: C 179 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.6297 (pm20) REVERT: C 253 LEU cc_start: 0.7422 (OUTLIER) cc_final: 0.7076 (mp) REVERT: D 157 TYR cc_start: 0.6792 (m-80) cc_final: 0.6506 (m-80) REVERT: D 179 GLU cc_start: 0.7297 (OUTLIER) cc_final: 0.6306 (pm20) REVERT: D 253 LEU cc_start: 0.7401 (OUTLIER) cc_final: 0.7060 (mp) outliers start: 51 outliers final: 29 residues processed: 149 average time/residue: 0.1345 time to fit residues: 33.0308 Evaluate side-chains 133 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 96 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 186 CYS Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 294 HIS Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 186 CYS Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 294 HIS Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 186 CYS Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain C residue 294 HIS Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 186 CYS Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 293 PHE Chi-restraints excluded: chain D residue 294 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 44 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 87 optimal weight: 0.3980 chunk 52 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.166323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.130311 restraints weight = 10605.437| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.61 r_work: 0.3469 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 9940 Z= 0.209 Angle : 0.695 6.646 13676 Z= 0.355 Chirality : 0.045 0.186 1652 Planarity : 0.005 0.039 1536 Dihedral : 9.368 59.490 2510 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 4.45 % Allowed : 24.60 % Favored : 70.95 % 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: 0.68 (0.26), residues: 1112 helix: 1.66 (0.19), residues: 788 sheet: None (None), residues: 0 loop : -2.75 (0.32), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 161 HIS 0.007 0.001 HIS D 294 PHE 0.025 0.002 PHE B 49 TYR 0.011 0.001 TYR D 190 ARG 0.002 0.000 ARG D 77 Details of bonding type rmsd hydrogen bonds : bond 0.08054 ( 644) hydrogen bonds : angle 5.81467 ( 1932) SS BOND : bond 0.00228 ( 8) SS BOND : angle 1.42316 ( 16) covalent geometry : bond 0.00481 ( 9932) covalent geometry : angle 0.69374 (13660) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 107 time to evaluate : 0.998 Fit side-chains REVERT: A 179 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.6376 (pm20) REVERT: A 253 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.7417 (mp) REVERT: B 179 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.6372 (pm20) REVERT: B 253 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7416 (mp) REVERT: C 179 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.6365 (pm20) REVERT: C 253 LEU cc_start: 0.7732 (OUTLIER) cc_final: 0.7436 (mp) REVERT: D 179 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.6367 (pm20) REVERT: D 253 LEU cc_start: 0.7711 (OUTLIER) cc_final: 0.7420 (mp) outliers start: 44 outliers final: 32 residues processed: 134 average time/residue: 0.1546 time to fit residues: 32.4942 Evaluate side-chains 134 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 94 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 294 HIS Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 294 HIS Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain C residue 294 HIS Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 293 PHE Chi-restraints excluded: chain D residue 294 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 18 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 81 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 84 optimal weight: 20.0000 chunk 13 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.171477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.135566 restraints weight = 10507.595| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 2.62 r_work: 0.3536 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9940 Z= 0.164 Angle : 0.615 5.654 13676 Z= 0.322 Chirality : 0.042 0.154 1652 Planarity : 0.005 0.044 1536 Dihedral : 8.975 57.556 2510 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 4.76 % Allowed : 24.39 % Favored : 70.85 % 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: 0.82 (0.26), residues: 1112 helix: 1.83 (0.19), residues: 788 sheet: None (None), residues: 0 loop : -2.88 (0.32), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 161 HIS 0.004 0.001 HIS B 294 PHE 0.029 0.002 PHE B 49 TYR 0.022 0.001 TYR A 157 ARG 0.000 0.000 ARG A 134 Details of bonding type rmsd hydrogen bonds : bond 0.06999 ( 644) hydrogen bonds : angle 5.55926 ( 1932) SS BOND : bond 0.00162 ( 8) SS BOND : angle 1.26509 ( 16) covalent geometry : bond 0.00336 ( 9932) covalent geometry : angle 0.61428 (13660) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 119 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.6327 (pm20) REVERT: A 253 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.7248 (mp) REVERT: B 179 GLU cc_start: 0.7349 (OUTLIER) cc_final: 0.6321 (pm20) REVERT: B 253 LEU cc_start: 0.7554 (OUTLIER) cc_final: 0.7244 (mp) REVERT: C 179 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.6314 (pm20) REVERT: C 253 LEU cc_start: 0.7579 (OUTLIER) cc_final: 0.7267 (mp) REVERT: D 179 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.6305 (pm20) REVERT: D 253 LEU cc_start: 0.7558 (OUTLIER) cc_final: 0.7250 (mp) outliers start: 47 outliers final: 32 residues processed: 143 average time/residue: 0.1523 time to fit residues: 34.3024 Evaluate side-chains 138 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 98 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 186 CYS Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 294 HIS Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 186 CYS Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 294 HIS Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 186 CYS Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain C residue 294 HIS Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 186 CYS Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 293 PHE Chi-restraints excluded: chain D residue 294 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 1 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 6 optimal weight: 0.1980 chunk 81 optimal weight: 0.4980 chunk 25 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.170714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.134514 restraints weight = 10709.921| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 2.71 r_work: 0.3499 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 9940 Z= 0.184 Angle : 0.657 6.610 13676 Z= 0.339 Chirality : 0.043 0.164 1652 Planarity : 0.005 0.032 1536 Dihedral : 8.916 58.995 2510 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 4.66 % Allowed : 24.70 % Favored : 70.65 % 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: 0.69 (0.26), residues: 1112 helix: 1.70 (0.19), residues: 788 sheet: None (None), residues: 0 loop : -2.86 (0.32), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 161 HIS 0.006 0.001 HIS D 294 PHE 0.015 0.002 PHE D 49 TYR 0.010 0.001 TYR B 157 ARG 0.002 0.000 ARG A 77 Details of bonding type rmsd hydrogen bonds : bond 0.07410 ( 644) hydrogen bonds : angle 5.67420 ( 1932) SS BOND : bond 0.00211 ( 8) SS BOND : angle 1.27235 ( 16) covalent geometry : bond 0.00410 ( 9932) covalent geometry : angle 0.65563 (13660) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 99 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.6334 (pm20) REVERT: A 253 LEU cc_start: 0.7620 (OUTLIER) cc_final: 0.7317 (mp) REVERT: B 179 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.6339 (pm20) REVERT: B 253 LEU cc_start: 0.7610 (OUTLIER) cc_final: 0.7308 (mp) REVERT: C 179 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.6320 (pm20) REVERT: C 253 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.7318 (mp) REVERT: D 179 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.6325 (pm20) REVERT: D 253 LEU cc_start: 0.7615 (OUTLIER) cc_final: 0.7314 (mp) outliers start: 46 outliers final: 35 residues processed: 129 average time/residue: 0.1523 time to fit residues: 31.1243 Evaluate side-chains 142 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 99 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 186 CYS Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 294 HIS Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 186 CYS Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 294 HIS Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 186 CYS Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain C residue 294 HIS Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 186 CYS Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 293 PHE Chi-restraints excluded: chain D residue 294 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 79 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 39 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.168367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.132347 restraints weight = 10707.881| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 2.64 r_work: 0.3498 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 9940 Z= 0.181 Angle : 0.638 5.231 13676 Z= 0.329 Chirality : 0.043 0.151 1652 Planarity : 0.005 0.039 1536 Dihedral : 8.827 59.969 2510 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 5.06 % Allowed : 23.68 % Favored : 71.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.26), residues: 1112 helix: 1.74 (0.19), residues: 784 sheet: None (None), residues: 0 loop : -2.77 (0.32), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 94 HIS 0.005 0.001 HIS D 294 PHE 0.026 0.002 PHE C 49 TYR 0.008 0.001 TYR D 190 ARG 0.001 0.000 ARG A 77 Details of bonding type rmsd hydrogen bonds : bond 0.07459 ( 644) hydrogen bonds : angle 5.64174 ( 1932) SS BOND : bond 0.00215 ( 8) SS BOND : angle 1.36104 ( 16) covalent geometry : bond 0.00397 ( 9932) covalent geometry : angle 0.63703 (13660) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 108 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.6331 (pm20) REVERT: A 253 LEU cc_start: 0.7616 (OUTLIER) cc_final: 0.7337 (mp) REVERT: B 179 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.6316 (pm20) REVERT: B 253 LEU cc_start: 0.7628 (OUTLIER) cc_final: 0.7349 (mp) REVERT: C 179 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.6313 (pm20) REVERT: C 253 LEU cc_start: 0.7634 (OUTLIER) cc_final: 0.7353 (mp) REVERT: D 49 PHE cc_start: 0.7458 (t80) cc_final: 0.7237 (t80) REVERT: D 179 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.6326 (pm20) REVERT: D 253 LEU cc_start: 0.7626 (OUTLIER) cc_final: 0.7346 (mp) outliers start: 50 outliers final: 36 residues processed: 140 average time/residue: 0.1460 time to fit residues: 32.3356 Evaluate side-chains 148 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 104 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 186 CYS Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 294 HIS Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 186 CYS Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 294 HIS Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 186 CYS Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain C residue 294 HIS Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 186 CYS Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 293 PHE Chi-restraints excluded: chain D residue 294 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 7.9990 chunk 103 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 90 optimal weight: 0.4980 chunk 25 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 75 optimal weight: 0.5980 chunk 63 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 105 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.170928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.134915 restraints weight = 10638.741| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 2.64 r_work: 0.3527 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9940 Z= 0.167 Angle : 0.624 6.950 13676 Z= 0.327 Chirality : 0.042 0.137 1652 Planarity : 0.005 0.044 1536 Dihedral : 8.597 59.865 2510 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 4.35 % Allowed : 23.79 % Favored : 71.86 % 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: 0.74 (0.26), residues: 1112 helix: 1.75 (0.19), residues: 788 sheet: None (None), residues: 0 loop : -2.88 (0.32), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 94 HIS 0.004 0.001 HIS B 294 PHE 0.028 0.001 PHE A 49 TYR 0.010 0.001 TYR C 157 ARG 0.001 0.000 ARG D 77 Details of bonding type rmsd hydrogen bonds : bond 0.07140 ( 644) hydrogen bonds : angle 5.51474 ( 1932) SS BOND : bond 0.00180 ( 8) SS BOND : angle 1.29122 ( 16) covalent geometry : bond 0.00348 ( 9932) covalent geometry : angle 0.62251 (13660) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 105 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.6305 (pm20) REVERT: A 253 LEU cc_start: 0.7595 (OUTLIER) cc_final: 0.7297 (mp) REVERT: B 179 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.6306 (pm20) REVERT: B 253 LEU cc_start: 0.7583 (OUTLIER) cc_final: 0.7305 (mp) REVERT: C 179 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.6287 (pm20) REVERT: C 253 LEU cc_start: 0.7594 (OUTLIER) cc_final: 0.7315 (mp) REVERT: D 179 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.6297 (pm20) REVERT: D 253 LEU cc_start: 0.7577 (OUTLIER) cc_final: 0.7298 (mp) outliers start: 43 outliers final: 32 residues processed: 133 average time/residue: 0.1457 time to fit residues: 30.5239 Evaluate side-chains 139 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 99 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 186 CYS Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 294 HIS Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 186 CYS Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 294 HIS Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 186 CYS Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain C residue 294 HIS Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 186 CYS Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 293 PHE Chi-restraints excluded: chain D residue 294 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 55 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 79 optimal weight: 0.6980 chunk 92 optimal weight: 0.9980 chunk 99 optimal weight: 5.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.171099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.135159 restraints weight = 10569.299| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 2.62 r_work: 0.3527 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9940 Z= 0.171 Angle : 0.636 6.082 13676 Z= 0.337 Chirality : 0.042 0.141 1652 Planarity : 0.005 0.041 1536 Dihedral : 8.385 59.759 2510 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 4.86 % Allowed : 23.28 % Favored : 71.86 % 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: 0.69 (0.26), residues: 1112 helix: 1.71 (0.19), residues: 788 sheet: None (None), residues: 0 loop : -2.89 (0.32), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 94 HIS 0.005 0.001 HIS C 294 PHE 0.029 0.002 PHE A 49 TYR 0.008 0.001 TYR D 157 ARG 0.001 0.000 ARG A 77 Details of bonding type rmsd hydrogen bonds : bond 0.07143 ( 644) hydrogen bonds : angle 5.56374 ( 1932) SS BOND : bond 0.00187 ( 8) SS BOND : angle 1.18965 ( 16) covalent geometry : bond 0.00364 ( 9932) covalent geometry : angle 0.63460 (13660) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 102 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 PHE cc_start: 0.7427 (t80) cc_final: 0.7200 (t80) REVERT: A 179 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.6289 (pm20) REVERT: A 253 LEU cc_start: 0.7579 (OUTLIER) cc_final: 0.7281 (mp) REVERT: B 179 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.6297 (pm20) REVERT: B 253 LEU cc_start: 0.7577 (OUTLIER) cc_final: 0.7275 (mp) REVERT: C 179 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.6276 (pm20) REVERT: C 253 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.7287 (mp) REVERT: D 179 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.6283 (pm20) REVERT: D 253 LEU cc_start: 0.7572 (OUTLIER) cc_final: 0.7270 (mp) outliers start: 48 outliers final: 36 residues processed: 132 average time/residue: 0.1460 time to fit residues: 30.6496 Evaluate side-chains 145 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 101 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 186 CYS Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 294 HIS Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 186 CYS Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 294 HIS Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 186 CYS Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain C residue 294 HIS Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 186 CYS Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 293 PHE Chi-restraints excluded: chain D residue 294 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 86 optimal weight: 0.6980 chunk 83 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 84 optimal weight: 10.0000 chunk 51 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.172093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.136129 restraints weight = 10709.476| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 2.65 r_work: 0.3517 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 9940 Z= 0.170 Angle : 0.627 6.023 13676 Z= 0.333 Chirality : 0.042 0.139 1652 Planarity : 0.005 0.042 1536 Dihedral : 8.083 59.101 2510 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 4.55 % Allowed : 23.58 % Favored : 71.86 % 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: 0.68 (0.26), residues: 1112 helix: 1.71 (0.19), residues: 788 sheet: None (None), residues: 0 loop : -2.90 (0.32), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 94 HIS 0.005 0.001 HIS B 294 PHE 0.029 0.001 PHE A 49 TYR 0.007 0.001 TYR D 157 ARG 0.001 0.000 ARG D 77 Details of bonding type rmsd hydrogen bonds : bond 0.07065 ( 644) hydrogen bonds : angle 5.56341 ( 1932) SS BOND : bond 0.00164 ( 8) SS BOND : angle 1.23060 ( 16) covalent geometry : bond 0.00363 ( 9932) covalent geometry : angle 0.62623 (13660) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 103 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.6280 (pm20) REVERT: A 253 LEU cc_start: 0.7508 (OUTLIER) cc_final: 0.7210 (mp) REVERT: B 179 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.6287 (pm20) REVERT: B 253 LEU cc_start: 0.7498 (OUTLIER) cc_final: 0.7196 (mp) REVERT: C 179 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.6261 (pm20) REVERT: C 253 LEU cc_start: 0.7507 (OUTLIER) cc_final: 0.7188 (mp) REVERT: D 179 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.6273 (pm20) REVERT: D 253 LEU cc_start: 0.7499 (OUTLIER) cc_final: 0.7198 (mp) outliers start: 45 outliers final: 36 residues processed: 130 average time/residue: 0.1520 time to fit residues: 31.1434 Evaluate side-chains 142 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 98 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 186 CYS Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 293 PHE Chi-restraints excluded: chain A residue 294 HIS Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 186 CYS Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 294 HIS Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 186 CYS Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 293 PHE Chi-restraints excluded: chain C residue 294 HIS Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 185 ILE Chi-restraints excluded: chain D residue 186 CYS Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 279 THR Chi-restraints excluded: chain D residue 293 PHE Chi-restraints excluded: chain D residue 294 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 82 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 79 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.171879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.135524 restraints weight = 10740.934| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.72 r_work: 0.3512 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 9940 Z= 0.182 Angle : 0.645 6.281 13676 Z= 0.341 Chirality : 0.042 0.141 1652 Planarity : 0.005 0.041 1536 Dihedral : 8.067 59.357 2510 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 4.66 % Allowed : 23.48 % Favored : 71.86 % 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: 0.65 (0.26), residues: 1112 helix: 1.68 (0.19), residues: 788 sheet: None (None), residues: 0 loop : -2.90 (0.32), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 94 HIS 0.005 0.001 HIS C 294 PHE 0.035 0.002 PHE A 49 TYR 0.010 0.001 TYR D 157 ARG 0.001 0.000 ARG B 77 Details of bonding type rmsd hydrogen bonds : bond 0.07404 ( 644) hydrogen bonds : angle 5.61927 ( 1932) SS BOND : bond 0.00201 ( 8) SS BOND : angle 1.30500 ( 16) covalent geometry : bond 0.00404 ( 9932) covalent geometry : angle 0.64353 (13660) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3812.09 seconds wall clock time: 67 minutes 37.77 seconds (4057.77 seconds total)