Starting phenix.real_space_refine on Sun Dec 29 05:43:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g16_29663/12_2024/8g16_29663.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g16_29663/12_2024/8g16_29663.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g16_29663/12_2024/8g16_29663.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g16_29663/12_2024/8g16_29663.map" model { file = "/net/cci-nas-00/data/ceres_data/8g16_29663/12_2024/8g16_29663.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g16_29663/12_2024/8g16_29663.cif" } resolution = 2.07 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 48 5.16 5 C 6388 2.51 5 N 1756 2.21 5 O 1912 1.98 5 H 4 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 10108 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2527 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 321} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2527 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 321} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 2527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2527 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 321} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 2527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2527 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 321} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.34, per 1000 atoms: 0.63 Number of scatterers: 10108 At special positions: 0 Unit cell: (99.365, 102.705, 91.015, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 48 16.00 O 1912 8.00 N 1756 7.00 C 6388 6.00 H 4 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.77 Conformation dependent library (CDL) restraints added in 1.4 seconds 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2408 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 9 sheets defined 36.8% alpha, 24.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.34 Creating SS restraints... Processing helix chain 'A' and resid 12 through 26 Processing helix chain 'A' and resid 39 through 49 Processing helix chain 'A' and resid 81 through 85 removed outlier: 3.548A pdb=" N ILE A 85 " --> pdb=" O PRO A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 109 Processing helix chain 'A' and resid 110 through 113 Processing helix chain 'A' and resid 136 through 140 removed outlier: 3.553A pdb=" N TYR A 140 " --> pdb=" O HIS A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 169 Proline residue: A 159 - end of helix Processing helix chain 'A' and resid 196 through 200 Processing helix chain 'A' and resid 212 through 221 removed outlier: 4.038A pdb=" N GLY A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS A 219 " --> pdb=" O LYS A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 225 Processing helix chain 'A' and resid 254 through 268 Processing helix chain 'A' and resid 282 through 287 removed outlier: 3.504A pdb=" N ASN A 287 " --> pdb=" O SER A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 334 Processing helix chain 'B' and resid 12 through 26 Processing helix chain 'B' and resid 39 through 49 Processing helix chain 'B' and resid 81 through 85 removed outlier: 3.562A pdb=" N ILE B 85 " --> pdb=" O PRO B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 109 Processing helix chain 'B' and resid 110 through 113 Processing helix chain 'B' and resid 136 through 140 removed outlier: 3.553A pdb=" N TYR B 140 " --> pdb=" O HIS B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 169 Proline residue: B 159 - end of helix Processing helix chain 'B' and resid 196 through 200 Processing helix chain 'B' and resid 212 through 221 removed outlier: 4.022A pdb=" N GLY B 218 " --> pdb=" O ALA B 214 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS B 219 " --> pdb=" O LYS B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 225 Processing helix chain 'B' and resid 254 through 268 Processing helix chain 'B' and resid 282 through 287 removed outlier: 3.504A pdb=" N ASN B 287 " --> pdb=" O SER B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 334 Processing helix chain 'C' and resid 12 through 26 Processing helix chain 'C' and resid 39 through 49 Processing helix chain 'C' and resid 81 through 85 removed outlier: 3.549A pdb=" N ILE C 85 " --> pdb=" O PRO C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 109 Processing helix chain 'C' and resid 110 through 113 Processing helix chain 'C' and resid 136 through 140 removed outlier: 3.553A pdb=" N TYR C 140 " --> pdb=" O HIS C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 169 Proline residue: C 159 - end of helix Processing helix chain 'C' and resid 196 through 200 Processing helix chain 'C' and resid 212 through 221 removed outlier: 3.924A pdb=" N GLY C 218 " --> pdb=" O ALA C 214 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS C 219 " --> pdb=" O LYS C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 225 Processing helix chain 'C' and resid 254 through 268 Processing helix chain 'C' and resid 282 through 287 removed outlier: 3.504A pdb=" N ASN C 287 " --> pdb=" O SER C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 334 Processing helix chain 'D' and resid 12 through 26 Processing helix chain 'D' and resid 39 through 49 Processing helix chain 'D' and resid 81 through 85 removed outlier: 3.562A pdb=" N ILE D 85 " --> pdb=" O PRO D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 109 Processing helix chain 'D' and resid 110 through 113 Processing helix chain 'D' and resid 136 through 140 removed outlier: 3.553A pdb=" N TYR D 140 " --> pdb=" O HIS D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 169 Proline residue: D 159 - end of helix Processing helix chain 'D' and resid 196 through 200 Processing helix chain 'D' and resid 212 through 221 removed outlier: 4.033A pdb=" N GLY D 218 " --> pdb=" O ALA D 214 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS D 219 " --> pdb=" O LYS D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 225 Processing helix chain 'D' and resid 254 through 268 Processing helix chain 'D' and resid 282 through 287 removed outlier: 3.504A pdb=" N ASN D 287 " --> pdb=" O SER D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 334 Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 63 removed outlier: 10.263A pdb=" N ASP A 29 " --> pdb=" O PRO A 73 " (cutoff:3.500A) removed outlier: 9.947A pdb=" N THR A 75 " --> pdb=" O ASP A 29 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL A 31 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N PHE A 77 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ILE A 33 " --> pdb=" O PHE A 77 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N VAL A 8 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ILE A 33 " --> pdb=" O VAL A 8 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL A 95 " --> pdb=" O ILE A 120 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 208 through 210 removed outlier: 3.629A pdb=" N THR A 229 " --> pdb=" O GLY A 173 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU A 172 " --> pdb=" O ARG A 248 " (cutoff:3.500A) removed outlier: 12.311A pdb=" N PHE A 307 " --> pdb=" O GLY A 300 " (cutoff:3.500A) removed outlier: 11.141A pdb=" N GLY A 300 " --> pdb=" O PHE A 307 " (cutoff:3.500A) removed outlier: 10.874A pdb=" N LYS A 309 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 8.936A pdb=" N GLY A 298 " --> pdb=" O LYS A 309 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ILE A 311 " --> pdb=" O ASP A 296 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 60 through 63 removed outlier: 10.262A pdb=" N ASP B 29 " --> pdb=" O PRO B 73 " (cutoff:3.500A) removed outlier: 9.940A pdb=" N THR B 75 " --> pdb=" O ASP B 29 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL B 31 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N PHE B 77 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE B 33 " --> pdb=" O PHE B 77 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N VAL B 8 " --> pdb=" O VAL B 31 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ILE B 33 " --> pdb=" O VAL B 8 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N VAL B 95 " --> pdb=" O ILE B 120 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 208 through 210 removed outlier: 3.701A pdb=" N THR B 229 " --> pdb=" O GLY B 173 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU B 172 " --> pdb=" O ARG B 248 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ILE B 311 " --> pdb=" O ASP B 296 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 208 through 210 removed outlier: 3.701A pdb=" N THR B 229 " --> pdb=" O GLY B 173 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU B 172 " --> pdb=" O ARG B 248 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N PHE B 307 " --> pdb=" O LEU B 303 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 60 through 63 removed outlier: 10.262A pdb=" N ASP C 29 " --> pdb=" O PRO C 73 " (cutoff:3.500A) removed outlier: 9.943A pdb=" N THR C 75 " --> pdb=" O ASP C 29 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL C 31 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N PHE C 77 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE C 33 " --> pdb=" O PHE C 77 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N VAL C 8 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ILE C 33 " --> pdb=" O VAL C 8 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N VAL C 95 " --> pdb=" O ILE C 120 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 208 through 210 removed outlier: 3.673A pdb=" N THR C 229 " --> pdb=" O GLY C 173 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU C 172 " --> pdb=" O ARG C 248 " (cutoff:3.500A) removed outlier: 12.307A pdb=" N PHE C 307 " --> pdb=" O GLY C 300 " (cutoff:3.500A) removed outlier: 11.136A pdb=" N GLY C 300 " --> pdb=" O PHE C 307 " (cutoff:3.500A) removed outlier: 10.890A pdb=" N LYS C 309 " --> pdb=" O GLY C 298 " (cutoff:3.500A) removed outlier: 8.939A pdb=" N GLY C 298 " --> pdb=" O LYS C 309 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ILE C 311 " --> pdb=" O ASP C 296 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 60 through 63 removed outlier: 10.261A pdb=" N ASP D 29 " --> pdb=" O PRO D 73 " (cutoff:3.500A) removed outlier: 9.943A pdb=" N THR D 75 " --> pdb=" O ASP D 29 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL D 31 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N PHE D 77 " --> pdb=" O VAL D 31 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE D 33 " --> pdb=" O PHE D 77 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N VAL D 8 " --> pdb=" O VAL D 31 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ILE D 33 " --> pdb=" O VAL D 8 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL D 95 " --> pdb=" O ILE D 120 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 208 through 210 removed outlier: 3.683A pdb=" N THR D 229 " --> pdb=" O GLY D 173 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU D 172 " --> pdb=" O ARG D 248 " (cutoff:3.500A) removed outlier: 12.309A pdb=" N PHE D 307 " --> pdb=" O GLY D 300 " (cutoff:3.500A) removed outlier: 11.140A pdb=" N GLY D 300 " --> pdb=" O PHE D 307 " (cutoff:3.500A) removed outlier: 10.873A pdb=" N LYS D 309 " --> pdb=" O GLY D 298 " (cutoff:3.500A) removed outlier: 8.937A pdb=" N GLY D 298 " --> pdb=" O LYS D 309 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N ILE D 311 " --> pdb=" O ASP D 296 " (cutoff:3.500A) 480 hydrogen bonds defined for protein. 1305 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: 5.57 Time building geometry restraints manager: 3.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.97 - 1.14: 4 1.14 - 1.31: 1709 1.31 - 1.47: 3988 1.47 - 1.64: 4523 1.64 - 1.81: 84 Bond restraints: 10308 Sorted by residual: bond pdb=" N VAL D 188 " pdb=" CA VAL D 188 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.23e-02 6.61e+03 9.97e+00 bond pdb=" N ASN D 142 " pdb=" CA ASN D 142 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.29e-02 6.01e+03 9.61e+00 bond pdb=" N ASN C 142 " pdb=" CA ASN C 142 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.29e-02 6.01e+03 9.61e+00 bond pdb=" N ASN B 142 " pdb=" CA ASN B 142 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.29e-02 6.01e+03 9.61e+00 bond pdb=" N ASN A 142 " pdb=" CA ASN A 142 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.29e-02 6.01e+03 9.61e+00 ... (remaining 10303 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.96: 13843 2.96 - 5.92: 96 5.92 - 8.88: 9 8.88 - 11.85: 0 11.85 - 14.81: 8 Bond angle restraints: 13956 Sorted by residual: angle pdb=" N ILE B 207 " pdb=" CA ILE B 207 " pdb=" C ILE B 207 " ideal model delta sigma weight residual 108.88 122.74 -13.86 2.16e+00 2.14e-01 4.12e+01 angle pdb=" N ILE D 207 " pdb=" CA ILE D 207 " pdb=" C ILE D 207 " ideal model delta sigma weight residual 108.88 122.70 -13.82 2.16e+00 2.14e-01 4.09e+01 angle pdb=" N ILE A 207 " pdb=" CA ILE A 207 " pdb=" C ILE A 207 " ideal model delta sigma weight residual 108.88 122.70 -13.82 2.16e+00 2.14e-01 4.09e+01 angle pdb=" N ILE C 207 " pdb=" CA ILE C 207 " pdb=" C ILE C 207 " ideal model delta sigma weight residual 108.88 122.69 -13.81 2.16e+00 2.14e-01 4.09e+01 angle pdb=" CA LEU C 203 " pdb=" CB LEU C 203 " pdb=" CG LEU C 203 " ideal model delta sigma weight residual 116.30 131.11 -14.81 3.50e+00 8.16e-02 1.79e+01 ... (remaining 13951 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.31: 5387 17.31 - 34.61: 512 34.61 - 51.92: 160 51.92 - 69.23: 52 69.23 - 86.53: 11 Dihedral angle restraints: 6122 sinusoidal: 2346 harmonic: 3776 Sorted by residual: dihedral pdb=" CA GLN A 204 " pdb=" C GLN A 204 " pdb=" N ASN A 205 " pdb=" CA ASN A 205 " ideal model delta harmonic sigma weight residual 180.00 -161.98 -18.02 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA GLN D 204 " pdb=" C GLN D 204 " pdb=" N ASN D 205 " pdb=" CA ASN D 205 " ideal model delta harmonic sigma weight residual -180.00 -162.02 -17.98 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA GLN C 204 " pdb=" C GLN C 204 " pdb=" N ASN C 205 " pdb=" CA ASN C 205 " ideal model delta harmonic sigma weight residual -180.00 -162.04 -17.96 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 6119 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1226 0.058 - 0.115: 285 0.115 - 0.173: 57 0.173 - 0.231: 4 0.231 - 0.288: 4 Chirality restraints: 1576 Sorted by residual: chirality pdb=" CA ILE B 207 " pdb=" N ILE B 207 " pdb=" C ILE B 207 " pdb=" CB ILE B 207 " both_signs ideal model delta sigma weight residual False 2.43 2.15 0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" CA ILE A 207 " pdb=" N ILE A 207 " pdb=" C ILE A 207 " pdb=" CB ILE A 207 " both_signs ideal model delta sigma weight residual False 2.43 2.15 0.29 2.00e-01 2.50e+01 2.07e+00 chirality pdb=" CA ILE D 207 " pdb=" N ILE D 207 " pdb=" C ILE D 207 " pdb=" CB ILE D 207 " both_signs ideal model delta sigma weight residual False 2.43 2.15 0.29 2.00e-01 2.50e+01 2.04e+00 ... (remaining 1573 not shown) Planarity restraints: 1804 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE C 318 " 0.019 2.00e-02 2.50e+03 3.91e-02 1.53e+01 pdb=" C PHE C 318 " -0.068 2.00e-02 2.50e+03 pdb=" O PHE C 318 " 0.025 2.00e-02 2.50e+03 pdb=" N GLY C 319 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 318 " -0.019 2.00e-02 2.50e+03 3.91e-02 1.53e+01 pdb=" C PHE A 318 " 0.068 2.00e-02 2.50e+03 pdb=" O PHE A 318 " -0.025 2.00e-02 2.50e+03 pdb=" N GLY A 319 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 318 " -0.019 2.00e-02 2.50e+03 3.91e-02 1.53e+01 pdb=" C PHE B 318 " 0.068 2.00e-02 2.50e+03 pdb=" O PHE B 318 " -0.025 2.00e-02 2.50e+03 pdb=" N GLY B 319 " -0.023 2.00e-02 2.50e+03 ... (remaining 1801 not shown) Histogram of nonbonded interaction distances: 0.80 - 1.56: 15 1.56 - 2.32: 33 2.32 - 3.08: 6414 3.08 - 3.84: 21234 3.84 - 4.60: 33902 Warning: very small nonbonded interaction distances. Nonbonded interactions: 61598 Sorted by model distance: nonbonded pdb=" ND1 HIS A 179 " pdb=" NH1 ARG A 234 " model vdw 0.795 3.100 nonbonded pdb=" ND1 HIS C 179 " pdb=" NH1 ARG C 234 " model vdw 0.802 3.100 nonbonded pdb=" ND1 HIS D 179 " pdb=" NH1 ARG D 234 " model vdw 0.808 3.100 nonbonded pdb=" ND1 HIS B 179 " pdb=" NH1 ARG B 234 " model vdw 0.809 3.100 nonbonded pdb=" CG HIS B 179 " pdb=" NH1 ARG B 234 " model vdw 0.959 3.300 ... (remaining 61593 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.110 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: 0.300 Extract box with map and model: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.200 Process input model: 29.490 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 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 : 0.004 0.041 10304 Z= 0.279 Angle : 0.793 14.807 13944 Z= 0.459 Chirality : 0.053 0.288 1576 Planarity : 0.007 0.081 1804 Dihedral : 16.155 86.532 3714 Min Nonbonded Distance : 0.795 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.21 % Allowed : 17.72 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.22), residues: 1328 helix: -0.98 (0.23), residues: 348 sheet: -0.14 (0.38), residues: 220 loop : -0.91 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 87 HIS 0.002 0.001 HIS B 53 PHE 0.006 0.001 PHE B 11 TYR 0.008 0.001 TYR C 314 ARG 0.002 0.000 ARG C 323 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 9 residues processed: 104 average time/residue: 1.5292 time to fit residues: 169.9329 Evaluate side-chains 85 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 76 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain B residue 57 HIS Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 243 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 20.0000 chunk 100 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 40 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 77 optimal weight: 6.9990 chunk 119 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN B 185 GLN C 185 GLN D 185 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9001 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 10304 Z= 0.357 Angle : 0.599 8.872 13944 Z= 0.332 Chirality : 0.048 0.146 1576 Planarity : 0.006 0.068 1804 Dihedral : 5.327 32.312 1422 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.01 % Favored : 96.69 % Rotamer: Outliers : 2.32 % Allowed : 16.05 % Favored : 81.63 % 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: -0.12 (0.23), residues: 1328 helix: 0.70 (0.26), residues: 364 sheet: 0.08 (0.37), residues: 204 loop : -0.46 (0.24), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 87 HIS 0.007 0.001 HIS C 179 PHE 0.014 0.002 PHE A 318 TYR 0.015 0.002 TYR D 314 ARG 0.008 0.001 ARG A 80 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 74 time to evaluate : 0.949 Fit side-chains REVERT: A 142 ASN cc_start: 0.8584 (OUTLIER) cc_final: 0.8272 (t0) REVERT: B 142 ASN cc_start: 0.8585 (OUTLIER) cc_final: 0.8275 (t0) REVERT: C 142 ASN cc_start: 0.8585 (OUTLIER) cc_final: 0.8275 (t0) REVERT: D 142 ASN cc_start: 0.8576 (OUTLIER) cc_final: 0.8266 (t0) outliers start: 25 outliers final: 8 residues processed: 91 average time/residue: 1.6015 time to fit residues: 155.0218 Evaluate side-chains 76 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 HIS Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain C residue 57 HIS Chi-restraints excluded: chain C residue 142 ASN Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 57 HIS Chi-restraints excluded: chain D residue 142 ASN Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 243 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 66 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 99 optimal weight: 10.0000 chunk 81 optimal weight: 2.9990 chunk 33 optimal weight: 10.0000 chunk 120 optimal weight: 0.9990 chunk 129 optimal weight: 0.3980 chunk 106 optimal weight: 6.9990 chunk 119 optimal weight: 4.9990 chunk 40 optimal weight: 8.9990 chunk 96 optimal weight: 3.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8967 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 : 0.003 0.056 10304 Z= 0.223 Angle : 0.562 13.183 13944 Z= 0.303 Chirality : 0.045 0.138 1576 Planarity : 0.007 0.175 1804 Dihedral : 4.871 29.433 1416 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.13 % Allowed : 16.51 % Favored : 81.35 % 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: 0.27 (0.24), residues: 1328 helix: 1.28 (0.26), residues: 372 sheet: -0.02 (0.34), residues: 240 loop : -0.27 (0.26), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 313 HIS 0.002 0.001 HIS A 179 PHE 0.006 0.001 PHE D 286 TYR 0.011 0.001 TYR D 314 ARG 0.009 0.001 ARG B 80 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 69 time to evaluate : 1.202 Fit side-chains REVERT: A 142 ASN cc_start: 0.8436 (OUTLIER) cc_final: 0.8223 (t0) REVERT: B 142 ASN cc_start: 0.8444 (OUTLIER) cc_final: 0.8223 (t0) REVERT: C 142 ASN cc_start: 0.8440 (OUTLIER) cc_final: 0.8226 (t0) REVERT: D 142 ASN cc_start: 0.8437 (OUTLIER) cc_final: 0.8219 (t0) outliers start: 23 outliers final: 5 residues processed: 79 average time/residue: 1.7659 time to fit residues: 148.0571 Evaluate side-chains 73 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 HIS Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain B residue 57 HIS Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain C residue 57 HIS Chi-restraints excluded: chain C residue 142 ASN Chi-restraints excluded: chain D residue 57 HIS Chi-restraints excluded: chain D residue 142 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 9.9990 chunk 90 optimal weight: 30.0000 chunk 62 optimal weight: 9.9990 chunk 13 optimal weight: 4.9990 chunk 57 optimal weight: 0.0020 chunk 80 optimal weight: 7.9990 chunk 120 optimal weight: 0.2980 chunk 127 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 overall best weight: 2.2594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 264 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8965 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 10304 Z= 0.244 Angle : 0.640 15.150 13944 Z= 0.337 Chirality : 0.046 0.221 1576 Planarity : 0.008 0.155 1804 Dihedral : 6.454 166.889 1413 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.34 % Allowed : 15.21 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.24), residues: 1328 helix: 1.47 (0.26), residues: 372 sheet: -0.01 (0.34), residues: 240 loop : -0.20 (0.26), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 313 HIS 0.002 0.000 HIS B 53 PHE 0.008 0.001 PHE C 233 TYR 0.010 0.001 TYR C 314 ARG 0.021 0.002 ARG A 234 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 70 time to evaluate : 1.288 Fit side-chains REVERT: A 142 ASN cc_start: 0.8604 (OUTLIER) cc_final: 0.8340 (t0) REVERT: B 142 ASN cc_start: 0.8606 (OUTLIER) cc_final: 0.8345 (t0) REVERT: C 142 ASN cc_start: 0.8606 (OUTLIER) cc_final: 0.8343 (t0) REVERT: D 142 ASN cc_start: 0.8601 (OUTLIER) cc_final: 0.8337 (t0) outliers start: 36 outliers final: 18 residues processed: 94 average time/residue: 1.5118 time to fit residues: 151.6379 Evaluate side-chains 85 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 63 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 HIS Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain B residue 57 HIS Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain C residue 57 HIS Chi-restraints excluded: chain C residue 142 ASN Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 266 SER Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain D residue 57 HIS Chi-restraints excluded: chain D residue 142 ASN Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 318 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 0.0470 chunk 1 optimal weight: 7.9990 chunk 95 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 65 optimal weight: 0.7980 chunk 114 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 overall best weight: 1.1684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 264 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8911 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10304 Z= 0.158 Angle : 0.541 13.541 13944 Z= 0.293 Chirality : 0.045 0.214 1576 Planarity : 0.006 0.098 1804 Dihedral : 8.928 169.640 1412 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.43 % Allowed : 15.21 % Favored : 81.35 % 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: 0.84 (0.25), residues: 1328 helix: 1.93 (0.26), residues: 372 sheet: -0.01 (0.34), residues: 268 loop : 0.13 (0.27), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 313 HIS 0.003 0.000 HIS B 179 PHE 0.008 0.001 PHE D 233 TYR 0.007 0.001 TYR B 314 ARG 0.011 0.001 ARG C 234 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 78 time to evaluate : 1.184 Fit side-chains REVERT: A 142 ASN cc_start: 0.8394 (OUTLIER) cc_final: 0.8193 (t0) REVERT: B 142 ASN cc_start: 0.8400 (OUTLIER) cc_final: 0.8192 (t0) REVERT: D 142 ASN cc_start: 0.8401 (OUTLIER) cc_final: 0.8191 (t0) outliers start: 37 outliers final: 18 residues processed: 101 average time/residue: 1.5282 time to fit residues: 164.5751 Evaluate side-chains 87 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 66 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 HIS Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain B residue 57 HIS Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 328 MET Chi-restraints excluded: chain C residue 57 HIS Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 266 SER Chi-restraints excluded: chain C residue 333 SER Chi-restraints excluded: chain D residue 57 HIS Chi-restraints excluded: chain D residue 142 ASN Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 328 MET Chi-restraints excluded: chain D residue 333 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 114 optimal weight: 3.9990 chunk 25 optimal weight: 9.9990 chunk 74 optimal weight: 0.8980 chunk 31 optimal weight: 6.9990 chunk 127 optimal weight: 0.9980 chunk 106 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 10 optimal weight: 8.9990 chunk 42 optimal weight: 9.9990 chunk 67 optimal weight: 7.9990 chunk 123 optimal weight: 30.0000 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 HIS B 330 HIS C 264 GLN C 330 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8992 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 10304 Z= 0.329 Angle : 0.679 16.242 13944 Z= 0.363 Chirality : 0.049 0.299 1576 Planarity : 0.007 0.148 1804 Dihedral : 4.836 19.810 1412 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.71 % Allowed : 15.21 % Favored : 81.08 % 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: 0.57 (0.24), residues: 1328 helix: 1.53 (0.26), residues: 372 sheet: 0.01 (0.33), residues: 272 loop : -0.01 (0.26), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 313 HIS 0.003 0.001 HIS B 179 PHE 0.008 0.001 PHE D 286 TYR 0.012 0.002 TYR B 314 ARG 0.012 0.001 ARG D 80 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 72 time to evaluate : 1.229 Fit side-chains outliers start: 40 outliers final: 17 residues processed: 98 average time/residue: 1.6394 time to fit residues: 170.5391 Evaluate side-chains 79 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 62 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 HIS Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain B residue 57 HIS Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain C residue 57 HIS Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 333 SER Chi-restraints excluded: chain D residue 57 HIS Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 333 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 0.0870 chunk 72 optimal weight: 0.1980 chunk 93 optimal weight: 3.9990 chunk 107 optimal weight: 7.9990 chunk 71 optimal weight: 6.9990 chunk 127 optimal weight: 7.9990 chunk 79 optimal weight: 0.8980 chunk 77 optimal weight: 6.9990 chunk 58 optimal weight: 0.1980 chunk 78 optimal weight: 0.0030 chunk 50 optimal weight: 10.0000 overall best weight: 0.2768 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 264 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 10304 Z= 0.112 Angle : 0.533 18.198 13944 Z= 0.282 Chirality : 0.044 0.241 1576 Planarity : 0.006 0.139 1804 Dihedral : 6.121 164.965 1412 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.11 % Allowed : 17.72 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.25), residues: 1328 helix: 2.36 (0.27), residues: 372 sheet: -0.30 (0.34), residues: 268 loop : 0.33 (0.27), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 313 HIS 0.004 0.000 HIS D 179 PHE 0.013 0.001 PHE A 233 TYR 0.006 0.001 TYR B 276 ARG 0.019 0.001 ARG B 234 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 1.212 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 80 average time/residue: 1.4596 time to fit residues: 125.2112 Evaluate side-chains 73 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 HIS Chi-restraints excluded: chain B residue 57 HIS Chi-restraints excluded: chain C residue 57 HIS Chi-restraints excluded: chain D residue 57 HIS Chi-restraints excluded: chain D residue 333 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 0.5980 chunk 38 optimal weight: 10.0000 chunk 24 optimal weight: 8.9990 chunk 80 optimal weight: 6.9990 chunk 86 optimal weight: 0.6980 chunk 62 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 121 optimal weight: 0.0870 chunk 111 optimal weight: 6.9990 overall best weight: 1.8762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 264 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 10304 Z= 0.219 Angle : 0.600 21.795 13944 Z= 0.324 Chirality : 0.048 0.296 1576 Planarity : 0.008 0.141 1804 Dihedral : 10.157 168.120 1412 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.50 % Allowed : 16.14 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: 0.93 (0.25), residues: 1328 helix: 2.13 (0.27), residues: 372 sheet: -0.34 (0.34), residues: 268 loop : 0.28 (0.27), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 313 HIS 0.004 0.001 HIS D 179 PHE 0.008 0.001 PHE A 233 TYR 0.011 0.001 TYR B 314 ARG 0.019 0.001 ARG B 234 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 64 time to evaluate : 1.238 Fit side-chains REVERT: A 142 ASN cc_start: 0.8422 (OUTLIER) cc_final: 0.8103 (t0) REVERT: B 142 ASN cc_start: 0.8420 (OUTLIER) cc_final: 0.8104 (t0) REVERT: D 142 ASN cc_start: 0.8428 (OUTLIER) cc_final: 0.8107 (t0) outliers start: 27 outliers final: 10 residues processed: 78 average time/residue: 1.5450 time to fit residues: 128.9658 Evaluate side-chains 73 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 HIS Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain B residue 57 HIS Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain C residue 57 HIS Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 57 HIS Chi-restraints excluded: chain D residue 142 ASN Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 333 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 9.9990 chunk 121 optimal weight: 0.0980 chunk 71 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 chunk 36 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 chunk 112 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 125 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 264 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 10304 Z= 0.196 Angle : 0.622 24.060 13944 Z= 0.330 Chirality : 0.048 0.465 1576 Planarity : 0.013 0.432 1804 Dihedral : 5.824 68.133 1412 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.61 % Favored : 96.16 % Rotamer: Outliers : 2.04 % Allowed : 16.42 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.55 % 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: 0.91 (0.25), residues: 1328 helix: 2.18 (0.27), residues: 372 sheet: -0.39 (0.35), residues: 248 loop : 0.21 (0.27), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 313 HIS 0.003 0.001 HIS B 179 PHE 0.014 0.001 PHE A 233 TYR 0.007 0.001 TYR B 314 ARG 0.026 0.002 ARG C 234 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 68 time to evaluate : 1.312 Fit side-chains REVERT: A 142 ASN cc_start: 0.8387 (OUTLIER) cc_final: 0.8080 (t0) REVERT: B 142 ASN cc_start: 0.8377 (OUTLIER) cc_final: 0.8074 (t0) REVERT: D 142 ASN cc_start: 0.8396 (OUTLIER) cc_final: 0.8086 (t0) outliers start: 22 outliers final: 15 residues processed: 80 average time/residue: 1.3865 time to fit residues: 119.3845 Evaluate side-chains 85 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 67 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 HIS Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain B residue 57 HIS Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain B residue 328 MET Chi-restraints excluded: chain C residue 57 HIS Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 328 MET Chi-restraints excluded: chain C residue 333 SER Chi-restraints excluded: chain D residue 57 HIS Chi-restraints excluded: chain D residue 142 ASN Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 328 MET Chi-restraints excluded: chain D residue 333 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 131 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 chunk 10 optimal weight: 8.9990 chunk 80 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 111 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 264 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8931 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.101 10304 Z= 0.319 Angle : 0.658 14.896 13944 Z= 0.357 Chirality : 0.052 0.411 1576 Planarity : 0.011 0.214 1804 Dihedral : 6.037 56.528 1412 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.46 % Favored : 96.23 % Rotamer: Outliers : 2.23 % Allowed : 16.42 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.62 % 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 (0.25), residues: 1328 helix: 1.81 (0.26), residues: 372 sheet: -0.43 (0.34), residues: 268 loop : 0.14 (0.27), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 313 HIS 0.004 0.001 HIS B 179 PHE 0.012 0.001 PHE A 233 TYR 0.012 0.002 TYR B 314 ARG 0.025 0.002 ARG B 234 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 62 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 ASN cc_start: 0.8541 (OUTLIER) cc_final: 0.8197 (t0) REVERT: B 142 ASN cc_start: 0.8540 (OUTLIER) cc_final: 0.8201 (t0) REVERT: D 142 ASN cc_start: 0.8548 (OUTLIER) cc_final: 0.8202 (t0) outliers start: 24 outliers final: 17 residues processed: 77 average time/residue: 1.5259 time to fit residues: 125.7658 Evaluate side-chains 77 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 57 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 HIS Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 234 ARG Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain B residue 57 HIS Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 234 ARG Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 244 ASP Chi-restraints excluded: chain C residue 57 HIS Chi-restraints excluded: chain C residue 234 ARG Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 333 SER Chi-restraints excluded: chain D residue 57 HIS Chi-restraints excluded: chain D residue 142 ASN Chi-restraints excluded: chain D residue 234 ARG Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 333 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 43 optimal weight: 7.9990 chunk 107 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 19 optimal weight: 10.0000 chunk 92 optimal weight: 5.9990 chunk 5 optimal weight: 0.7980 chunk 75 optimal weight: 7.9990 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 = 0.3562 r_free = 0.3562 target = 0.095394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.081620 restraints weight = 17111.947| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.09 r_work: 0.3203 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 10304 Z= 0.168 Angle : 0.542 11.012 13944 Z= 0.293 Chirality : 0.047 0.383 1576 Planarity : 0.010 0.168 1804 Dihedral : 5.323 50.612 1412 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.23 % Allowed : 3.77 % Favored : 96.01 % Rotamer: Outliers : 1.86 % Allowed : 16.70 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.55 % 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: 0.85 (0.25), residues: 1328 helix: 2.22 (0.27), residues: 372 sheet: -0.68 (0.34), residues: 260 loop : 0.27 (0.27), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 313 HIS 0.002 0.000 HIS B 137 PHE 0.012 0.001 PHE D 233 TYR 0.006 0.001 TYR A 314 ARG 0.019 0.002 ARG D 234 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3496.59 seconds wall clock time: 63 minutes 59.17 seconds (3839.17 seconds total)