Starting phenix.real_space_refine on Sat Nov 16 00:02:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g16_29663/11_2024/8g16_29663.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g16_29663/11_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g16_29663/11_2024/8g16_29663.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g16_29663/11_2024/8g16_29663.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g16_29663/11_2024/8g16_29663.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g16_29663/11_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 6.18, per 1000 atoms: 0.61 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=0, symmetry=0 Time building additional restraints: 2.62 Conformation dependent library (CDL) restraints added in 1.1 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: 1.35 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: 3.43 Time building geometry restraints manager: 3.03 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: 0.77 - 1.53: 23 1.53 - 2.30: 39 2.30 - 3.07: 6163 3.07 - 3.83: 21274 3.83 - 4.60: 34115 Warning: very small nonbonded interaction distances. Nonbonded interactions: 61614 Sorted by model distance: nonbonded pdb=" CB HIS A 179 " pdb=" NH2 ARG A 234 " model vdw 0.766 3.250 nonbonded pdb=" CB HIS C 179 " pdb=" NH2 ARG C 234 " model vdw 0.766 3.250 nonbonded pdb=" CB HIS D 179 " pdb=" NH2 ARG D 234 " model vdw 0.781 3.250 nonbonded pdb=" CB HIS B 179 " pdb=" NH2 ARG B 234 " model vdw 0.783 3.250 nonbonded pdb=" CB HIS B 179 " pdb=" CZ ARG B 234 " model vdw 0.789 3.400 ... (remaining 61609 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: 0.630 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: 0.280 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 25.990 Find NCS groups from input model: 0.340 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:13.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.860 ------------------------------------------------------------------------------- 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= 0.274 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 : 0.766 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 : 1.294 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: 1.5167 time to fit residues: 168.3015 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 : 1.388 ------------------------------------------------------------------------------- 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: 0.8999 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 10304 Z= 0.358 Angle : 0.610 8.964 13944 Z= 0.337 Chirality : 0.048 0.147 1576 Planarity : 0.005 0.055 1804 Dihedral : 5.312 32.432 1422 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.30 % Allowed : 3.01 % Favored : 96.69 % 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: -0.12 (0.23), residues: 1328 helix: 0.71 (0.26), residues: 364 sheet: 0.11 (0.37), residues: 204 loop : -0.48 (0.24), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 87 HIS 0.004 0.001 HIS C 179 PHE 0.014 0.002 PHE A 318 TYR 0.015 0.002 TYR B 314 ARG 0.008 0.001 ARG B 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 97 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 74 time to evaluate : 1.176 Fit side-chains REVERT: A 142 ASN cc_start: 0.8576 (OUTLIER) cc_final: 0.8266 (t0) REVERT: B 142 ASN cc_start: 0.8577 (OUTLIER) cc_final: 0.8269 (t0) REVERT: C 142 ASN cc_start: 0.8577 (OUTLIER) cc_final: 0.8268 (t0) REVERT: D 142 ASN cc_start: 0.8569 (OUTLIER) cc_final: 0.8262 (t0) outliers start: 23 outliers final: 7 residues processed: 90 average time/residue: 1.6037 time to fit residues: 153.5991 Evaluate side-chains 75 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 1.187 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 99 optimal weight: 10.0000 chunk 81 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 chunk 120 optimal weight: 4.9990 chunk 129 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 119 optimal weight: 8.9990 chunk 40 optimal weight: 6.9990 chunk 96 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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: 0.9017 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 10304 Z= 0.373 Angle : 0.611 9.444 13944 Z= 0.337 Chirality : 0.049 0.145 1576 Planarity : 0.005 0.054 1804 Dihedral : 5.226 33.577 1416 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.69 % Allowed : 16.05 % Favored : 81.26 % 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: 0.09 (0.24), residues: 1328 helix: 1.02 (0.26), residues: 364 sheet: 0.06 (0.36), residues: 216 loop : -0.36 (0.24), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 87 HIS 0.003 0.001 HIS D 53 PHE 0.009 0.001 PHE C 286 TYR 0.013 0.002 TYR D 314 ARG 0.008 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 94 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 65 time to evaluate : 1.232 Fit side-chains REVERT: A 142 ASN cc_start: 0.8671 (OUTLIER) cc_final: 0.8361 (t0) REVERT: B 142 ASN cc_start: 0.8673 (OUTLIER) cc_final: 0.8365 (t0) REVERT: C 142 ASN cc_start: 0.8661 (OUTLIER) cc_final: 0.8347 (t0) REVERT: D 142 ASN cc_start: 0.8651 (OUTLIER) cc_final: 0.8343 (t0) outliers start: 29 outliers final: 16 residues processed: 84 average time/residue: 1.5038 time to fit residues: 135.3446 Evaluate side-chains 86 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 66 time to evaluate : 1.346 ------------------------------------------------------------------------------- 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 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 203 LEU Chi-restraints excluded: chain B residue 243 VAL 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 318 PHE 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 Chi-restraints excluded: chain D residue 318 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 0.7980 chunk 90 optimal weight: 3.9990 chunk 62 optimal weight: 8.9990 chunk 13 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 chunk 80 optimal weight: 0.0270 chunk 120 optimal weight: 3.9990 chunk 127 optimal weight: 7.9990 chunk 114 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 overall best weight: 1.5242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 264 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8966 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10304 Z= 0.168 Angle : 0.483 6.797 13944 Z= 0.265 Chirality : 0.044 0.131 1576 Planarity : 0.005 0.051 1804 Dihedral : 4.710 27.894 1416 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.78 % Allowed : 15.31 % Favored : 81.91 % 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 (0.25), residues: 1328 helix: 1.53 (0.26), residues: 372 sheet: -0.20 (0.32), residues: 280 loop : 0.09 (0.27), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 313 HIS 0.002 0.000 HIS D 137 PHE 0.005 0.001 PHE D 286 TYR 0.008 0.001 TYR B 314 ARG 0.009 0.001 ARG C 80 *********************** 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 104 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 74 time to evaluate : 1.213 Fit side-chains REVERT: A 142 ASN cc_start: 0.8496 (OUTLIER) cc_final: 0.8286 (t0) REVERT: B 142 ASN cc_start: 0.8503 (OUTLIER) cc_final: 0.8277 (t0) REVERT: C 142 ASN cc_start: 0.8501 (OUTLIER) cc_final: 0.8292 (t0) REVERT: D 142 ASN cc_start: 0.8511 (OUTLIER) cc_final: 0.8276 (t0) outliers start: 30 outliers final: 11 residues processed: 95 average time/residue: 1.5537 time to fit residues: 157.6286 Evaluate side-chains 78 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 1.149 ------------------------------------------------------------------------------- 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 266 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 C residue 57 HIS Chi-restraints excluded: chain C residue 142 ASN 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 266 SER Chi-restraints excluded: chain D residue 333 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 72 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 95 optimal weight: 7.9990 chunk 52 optimal weight: 10.0000 chunk 108 optimal weight: 6.9990 chunk 88 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 65 optimal weight: 8.9990 chunk 114 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 42 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 330 HIS D 264 GLN D 330 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9035 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.097 10304 Z= 0.492 Angle : 0.662 10.098 13944 Z= 0.366 Chirality : 0.052 0.167 1576 Planarity : 0.006 0.075 1804 Dihedral : 5.042 18.775 1412 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % 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: 0.19 (0.24), residues: 1328 helix: 1.13 (0.26), residues: 364 sheet: -0.10 (0.35), residues: 216 loop : -0.23 (0.25), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 313 HIS 0.003 0.001 HIS D 53 PHE 0.011 0.002 PHE C 286 TYR 0.014 0.002 TYR B 314 ARG 0.010 0.001 ARG D 80 *********************** 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 103 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 67 time to evaluate : 1.288 Fit side-chains outliers start: 36 outliers final: 19 residues processed: 92 average time/residue: 1.5491 time to fit residues: 152.2078 Evaluate side-chains 82 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 63 time to evaluate : 1.253 ------------------------------------------------------------------------------- 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 318 PHE 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 B residue 318 PHE Chi-restraints excluded: chain C residue 57 HIS Chi-restraints excluded: chain C residue 142 ASN Chi-restraints excluded: chain C residue 203 LEU 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 243 VAL Chi-restraints excluded: chain D residue 318 PHE 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: 0.7980 chunk 25 optimal weight: 0.6980 chunk 74 optimal weight: 8.9990 chunk 31 optimal weight: 5.9990 chunk 127 optimal weight: 5.9990 chunk 106 optimal weight: 8.9990 chunk 59 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 123 optimal weight: 3.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 GLN B 264 GLN C 264 GLN D 264 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8988 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10304 Z= 0.214 Angle : 0.519 7.908 13944 Z= 0.284 Chirality : 0.045 0.132 1576 Planarity : 0.006 0.070 1804 Dihedral : 4.664 18.756 1412 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.69 % Allowed : 16.05 % Favored : 81.26 % 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: 0.39 (0.24), residues: 1328 helix: 1.48 (0.26), residues: 368 sheet: -0.06 (0.35), residues: 216 loop : -0.20 (0.25), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 313 HIS 0.002 0.001 HIS D 137 PHE 0.006 0.001 PHE C 23 TYR 0.010 0.001 TYR B 314 ARG 0.011 0.001 ARG C 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 95 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 66 time to evaluate : 1.137 Fit side-chains REVERT: A 142 ASN cc_start: 0.8579 (OUTLIER) cc_final: 0.8327 (t0) REVERT: B 142 ASN cc_start: 0.8568 (OUTLIER) cc_final: 0.8315 (t0) REVERT: C 142 ASN cc_start: 0.8582 (OUTLIER) cc_final: 0.8332 (t0) REVERT: D 142 ASN cc_start: 0.8578 (OUTLIER) cc_final: 0.8329 (t0) outliers start: 29 outliers final: 19 residues processed: 85 average time/residue: 1.4564 time to fit residues: 132.5536 Evaluate side-chains 86 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 63 time to evaluate : 1.228 ------------------------------------------------------------------------------- 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 195 LEU Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 328 MET 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 195 LEU 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 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 195 LEU Chi-restraints excluded: chain C residue 243 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 0.5980 chunk 72 optimal weight: 0.0670 chunk 93 optimal weight: 1.9990 chunk 107 optimal weight: 7.9990 chunk 71 optimal weight: 6.9990 chunk 127 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 58 optimal weight: 0.0670 chunk 78 optimal weight: 6.9990 chunk 50 optimal weight: 8.9990 overall best weight: 0.7458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 GLN B 264 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8922 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10304 Z= 0.113 Angle : 0.448 6.163 13944 Z= 0.241 Chirality : 0.043 0.129 1576 Planarity : 0.005 0.058 1804 Dihedral : 4.144 18.312 1412 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.58 % Allowed : 17.16 % Favored : 81.26 % 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: 0.91 (0.25), residues: 1328 helix: 2.10 (0.27), residues: 372 sheet: -0.36 (0.33), residues: 288 loop : 0.32 (0.27), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 313 HIS 0.002 0.000 HIS D 137 PHE 0.004 0.001 PHE B 307 TYR 0.005 0.001 TYR B 276 ARG 0.012 0.001 ARG B 80 *********************** 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 83 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 1.274 Fit side-chains outliers start: 17 outliers final: 9 residues processed: 79 average time/residue: 1.4385 time to fit residues: 122.2445 Evaluate side-chains 75 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 HIS Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain B residue 57 HIS Chi-restraints excluded: chain C residue 57 HIS Chi-restraints excluded: chain C residue 243 VAL 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 333 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 75 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 24 optimal weight: 0.0670 chunk 80 optimal weight: 0.0070 chunk 86 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 100 optimal weight: 0.2980 chunk 115 optimal weight: 2.9990 chunk 121 optimal weight: 0.8980 chunk 111 optimal weight: 5.9990 overall best weight: 0.8538 ------------------------------------------------------------------------------- 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: 0.8927 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10304 Z= 0.119 Angle : 0.441 5.368 13944 Z= 0.240 Chirality : 0.043 0.127 1576 Planarity : 0.005 0.072 1804 Dihedral : 4.087 17.571 1412 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.39 % Allowed : 17.25 % 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: 1.09 (0.25), residues: 1328 helix: 2.32 (0.27), residues: 372 sheet: -0.49 (0.32), residues: 296 loop : 0.53 (0.28), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 313 HIS 0.001 0.000 HIS D 137 PHE 0.004 0.001 PHE B 307 TYR 0.007 0.001 TYR B 314 ARG 0.014 0.001 ARG A 80 *********************** 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 80 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 1.178 Fit side-chains outliers start: 15 outliers final: 12 residues processed: 75 average time/residue: 1.4190 time to fit residues: 114.4665 Evaluate side-chains 75 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 1.251 ------------------------------------------------------------------------------- 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 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 333 SER Chi-restraints excluded: chain C residue 57 HIS Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 333 SER Chi-restraints excluded: chain D residue 57 HIS 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: 0.0670 chunk 71 optimal weight: 10.0000 chunk 51 optimal weight: 7.9990 chunk 93 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 overall best weight: 2.6126 ------------------------------------------------------------------------------- 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: 0.8992 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10304 Z= 0.253 Angle : 0.530 7.540 13944 Z= 0.292 Chirality : 0.046 0.132 1576 Planarity : 0.006 0.077 1804 Dihedral : 4.618 19.167 1412 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.32 % Allowed : 16.33 % 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: 0.86 (0.25), residues: 1328 helix: 1.91 (0.26), residues: 372 sheet: 0.07 (0.33), residues: 272 loop : 0.13 (0.27), residues: 684 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 0.009 0.001 PHE B 318 TYR 0.011 0.001 TYR B 314 ARG 0.014 0.001 ARG A 80 *********************** 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 86 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 61 time to evaluate : 1.117 Fit side-chains REVERT: A 142 ASN cc_start: 0.8516 (OUTLIER) cc_final: 0.8312 (t0) REVERT: B 142 ASN cc_start: 0.8515 (OUTLIER) cc_final: 0.8314 (t0) REVERT: D 142 ASN cc_start: 0.8515 (OUTLIER) cc_final: 0.8314 (t0) outliers start: 25 outliers final: 13 residues processed: 78 average time/residue: 1.3825 time to fit residues: 116.2977 Evaluate side-chains 75 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 59 time to evaluate : 1.280 ------------------------------------------------------------------------------- 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 333 SER 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 333 SER Chi-restraints excluded: chain C residue 57 HIS Chi-restraints excluded: chain C residue 243 VAL 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 333 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 7.9990 chunk 87 optimal weight: 5.9990 chunk 131 optimal weight: 0.9980 chunk 121 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 80 optimal weight: 0.0000 chunk 64 optimal weight: 6.9990 chunk 83 optimal weight: 10.0000 chunk 111 optimal weight: 10.0000 chunk 32 optimal weight: 0.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 264 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8958 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10304 Z= 0.159 Angle : 0.482 6.155 13944 Z= 0.262 Chirality : 0.044 0.130 1576 Planarity : 0.006 0.072 1804 Dihedral : 4.357 18.805 1412 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.30 % Allowed : 17.35 % 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: 0.96 (0.25), residues: 1328 helix: 2.10 (0.27), residues: 372 sheet: -0.34 (0.32), residues: 288 loop : 0.37 (0.28), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 313 HIS 0.002 0.000 HIS D 137 PHE 0.005 0.001 PHE A 23 TYR 0.008 0.001 TYR B 314 ARG 0.015 0.001 ARG C 80 ********************** 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 78 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 1.195 Fit side-chains outliers start: 14 outliers final: 14 residues processed: 72 average time/residue: 1.4363 time to fit residues: 111.4707 Evaluate side-chains 75 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 1.154 ------------------------------------------------------------------------------- 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 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 333 SER 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 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: 6.9990 chunk 15 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 104 optimal weight: 5.9990 chunk 43 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 19 optimal weight: 10.0000 chunk 92 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 chunk 75 optimal weight: 0.0970 overall best weight: 1.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 264 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.090074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.075862 restraints weight = 17115.988| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.08 r_work: 0.3084 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8953 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10304 Z= 0.170 Angle : 0.485 6.306 13944 Z= 0.265 Chirality : 0.044 0.130 1576 Planarity : 0.006 0.074 1804 Dihedral : 4.381 18.891 1412 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.30 % Allowed : 17.35 % 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: 0.95 (0.25), residues: 1328 helix: 2.10 (0.27), residues: 372 sheet: -0.36 (0.32), residues: 288 loop : 0.38 (0.27), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 313 HIS 0.002 0.000 HIS D 137 PHE 0.005 0.001 PHE B 23 TYR 0.009 0.001 TYR B 314 ARG 0.015 0.001 ARG D 80 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3524.08 seconds wall clock time: 64 minutes 22.40 seconds (3862.40 seconds total)