Starting phenix.real_space_refine on Wed Sep 17 20:01:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9neg_49308/09_2025/9neg_49308.cif Found real_map, /net/cci-nas-00/data/ceres_data/9neg_49308/09_2025/9neg_49308.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9neg_49308/09_2025/9neg_49308.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9neg_49308/09_2025/9neg_49308.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9neg_49308/09_2025/9neg_49308.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9neg_49308/09_2025/9neg_49308.map" } resolution = 3.17 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.018 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 K 2 8.98 5 S 32 5.16 5 C 7121 2.51 5 N 1661 2.21 5 O 1780 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10596 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2530 Classifications: {'peptide': 314} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 16, 'TRANS': 297} Chain breaks: 5 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 27 Chain: "B" Number of atoms: 2526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2526 Classifications: {'peptide': 314} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 16, 'TRANS': 297} Chain breaks: 5 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 31 Chain: "C" Number of atoms: 2524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2524 Classifications: {'peptide': 314} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 16, 'TRANS': 297} Chain breaks: 5 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 3, 'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 32 Chain: "D" Number of atoms: 2525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2525 Classifications: {'peptide': 313} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 16, 'TRANS': 296} Chain breaks: 5 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'ARG:plan': 2, 'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 27 Chain: "J" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 62 Unusual residues: {'ACE': 1} Classifications: {'peptide': 10, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 9} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 74 Unusual residues: {'ACE': 1} Classifications: {'peptide': 11, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 10} Chain: "A" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 102 Unusual residues: {' K': 1, 'POV': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 367 Unresolved non-hydrogen angles: 442 Unresolved non-hydrogen dihedrals: 327 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'POV:plan-1': 7, 'POV:plan-2': 6, 'POV:plan-3': 7} Unresolved non-hydrogen planarities: 71 Chain: "B" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 87 Unusual residues: {' K': 1, 'POV': 8} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 330 Unresolved non-hydrogen angles: 397 Unresolved non-hydrogen dihedrals: 294 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'POV:plan-1': 8, 'POV:plan-2': 7, 'POV:plan-3': 5} Unresolved non-hydrogen planarities: 71 Chain: "C" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 77 Unusual residues: {'POV': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 287 Unresolved non-hydrogen angles: 346 Unresolved non-hydrogen dihedrals: 255 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'POV:plan-1': 6, 'POV:plan-2': 5, 'POV:plan-3': 6} Unresolved non-hydrogen planarities: 59 Chain: "D" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 88 Unusual residues: {'POV': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 328 Unresolved non-hydrogen angles: 395 Unresolved non-hydrogen dihedrals: 292 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'POV:plan-1': 7, 'POV:plan-2': 6, 'POV:plan-3': 6} Unresolved non-hydrogen planarities: 67 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 2.80, per 1000 atoms: 0.26 Number of scatterers: 10596 At special positions: 0 Unit cell: (107.07, 107.07, 113.71, 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) K 2 19.00 S 32 16.00 O 1780 8.00 N 1661 7.00 C 7121 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 0.99 Conformation dependent library (CDL) restraints added in 369.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2412 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 4 sheets defined 69.7% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 112 through 117 Processing helix chain 'A' and resid 125 through 129 removed outlier: 3.571A pdb=" N ARG A 128 " --> pdb=" O ASP A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 159 removed outlier: 3.982A pdb=" N ILE A 152 " --> pdb=" O SER A 148 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TYR A 156 " --> pdb=" O ILE A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 181 removed outlier: 3.622A pdb=" N PHE A 173 " --> pdb=" O PRO A 169 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 194 removed outlier: 3.548A pdb=" N ASN A 188 " --> pdb=" O ASP A 184 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS A 189 " --> pdb=" O GLN A 185 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU A 192 " --> pdb=" O ASN A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 248 removed outlier: 4.324A pdb=" N VAL A 229 " --> pdb=" O ALA A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 298 Processing helix chain 'A' and resid 311 through 319 Processing helix chain 'A' and resid 320 through 326 Processing helix chain 'A' and resid 358 through 368 Processing helix chain 'A' and resid 369 through 377 removed outlier: 3.551A pdb=" N LEU A 375 " --> pdb=" O ILE A 372 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG A 377 " --> pdb=" O LYS A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 392 removed outlier: 3.732A pdb=" N GLN A 383 " --> pdb=" O SER A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 419 Processing helix chain 'A' and resid 429 through 431 No H-bonds generated for 'chain 'A' and resid 429 through 431' Processing helix chain 'A' and resid 432 through 441 Processing helix chain 'A' and resid 452 through 472 Processing helix chain 'A' and resid 473 through 489 removed outlier: 3.996A pdb=" N ILE A 477 " --> pdb=" O PRO A 473 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N SER A 479 " --> pdb=" O PRO A 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 117 Processing helix chain 'B' and resid 145 through 147 No H-bonds generated for 'chain 'B' and resid 145 through 147' Processing helix chain 'B' and resid 148 through 159 removed outlier: 3.580A pdb=" N ILE B 152 " --> pdb=" O SER B 148 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TYR B 156 " --> pdb=" O ILE B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 181 removed outlier: 3.621A pdb=" N PHE B 173 " --> pdb=" O PRO B 169 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS B 178 " --> pdb=" O SER B 174 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE B 179 " --> pdb=" O GLU B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 194 Processing helix chain 'B' and resid 226 through 248 removed outlier: 3.749A pdb=" N ALA B 230 " --> pdb=" O ALA B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 298 Processing helix chain 'B' and resid 311 through 319 Processing helix chain 'B' and resid 320 through 326 Processing helix chain 'B' and resid 358 through 368 Processing helix chain 'B' and resid 369 through 377 removed outlier: 3.524A pdb=" N LEU B 375 " --> pdb=" O ILE B 372 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG B 377 " --> pdb=" O LYS B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 392 removed outlier: 3.754A pdb=" N GLN B 383 " --> pdb=" O SER B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 419 Processing helix chain 'B' and resid 429 through 431 No H-bonds generated for 'chain 'B' and resid 429 through 431' Processing helix chain 'B' and resid 432 through 441 Processing helix chain 'B' and resid 452 through 472 Processing helix chain 'B' and resid 473 through 489 removed outlier: 3.931A pdb=" N ILE B 477 " --> pdb=" O PRO B 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 117 Processing helix chain 'C' and resid 120 through 125 removed outlier: 4.253A pdb=" N ASP C 125 " --> pdb=" O THR C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 129 removed outlier: 3.513A pdb=" N ARG C 129 " --> pdb=" O PRO C 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 126 through 129' Processing helix chain 'C' and resid 148 through 159 removed outlier: 3.839A pdb=" N ILE C 152 " --> pdb=" O SER C 148 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TYR C 156 " --> pdb=" O ILE C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 181 removed outlier: 3.568A pdb=" N TYR C 180 " --> pdb=" O GLU C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 194 Processing helix chain 'C' and resid 226 through 248 Processing helix chain 'C' and resid 279 through 298 Processing helix chain 'C' and resid 311 through 319 Processing helix chain 'C' and resid 320 through 326 Processing helix chain 'C' and resid 358 through 368 Processing helix chain 'C' and resid 369 through 378 Processing helix chain 'C' and resid 379 through 392 removed outlier: 3.871A pdb=" N GLN C 383 " --> pdb=" O SER C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 419 Processing helix chain 'C' and resid 429 through 431 No H-bonds generated for 'chain 'C' and resid 429 through 431' Processing helix chain 'C' and resid 432 through 441 Processing helix chain 'C' and resid 452 through 472 Processing helix chain 'C' and resid 473 through 489 removed outlier: 3.766A pdb=" N ILE C 477 " --> pdb=" O PRO C 473 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N SER C 479 " --> pdb=" O PRO C 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 117 Processing helix chain 'D' and resid 120 through 125 removed outlier: 4.254A pdb=" N ASP D 125 " --> pdb=" O THR D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 129 Processing helix chain 'D' and resid 148 through 159 removed outlier: 3.555A pdb=" N ILE D 152 " --> pdb=" O SER D 148 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TYR D 156 " --> pdb=" O ILE D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 181 Processing helix chain 'D' and resid 183 through 188 Processing helix chain 'D' and resid 189 through 194 removed outlier: 4.240A pdb=" N GLU D 192 " --> pdb=" O LYS D 189 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLU D 194 " --> pdb=" O ARG D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 248 Processing helix chain 'D' and resid 279 through 298 Processing helix chain 'D' and resid 311 through 319 Processing helix chain 'D' and resid 320 through 326 Processing helix chain 'D' and resid 358 through 368 Processing helix chain 'D' and resid 369 through 377 removed outlier: 3.535A pdb=" N LEU D 375 " --> pdb=" O ILE D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 392 removed outlier: 3.690A pdb=" N GLN D 383 " --> pdb=" O SER D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 419 Processing helix chain 'D' and resid 429 through 431 No H-bonds generated for 'chain 'D' and resid 429 through 431' Processing helix chain 'D' and resid 432 through 441 Processing helix chain 'D' and resid 452 through 472 Processing helix chain 'D' and resid 473 through 488 removed outlier: 4.247A pdb=" N ILE D 477 " --> pdb=" O PRO D 473 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N SER D 479 " --> pdb=" O PRO D 475 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 106 through 111 Processing sheet with id=AA2, first strand: chain 'B' and resid 106 through 111 removed outlier: 3.657A pdb=" N GLU B 139 " --> pdb=" O ASP B 134 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 106 through 111 Processing sheet with id=AA4, first strand: chain 'D' and resid 106 through 111 removed outlier: 3.670A pdb=" N GLU D 139 " --> pdb=" O ASP D 134 " (cutoff:3.500A) 615 hydrogen bonds defined for protein. 1758 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: 1.76 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1577 1.31 - 1.44: 3030 1.44 - 1.56: 6085 1.56 - 1.68: 81 1.68 - 1.81: 48 Bond restraints: 10821 Sorted by residual: bond pdb=" C31 POV A 701 " pdb=" O31 POV A 701 " ideal model delta sigma weight residual 1.327 1.442 -0.115 2.00e-02 2.50e+03 3.32e+01 bond pdb=" C31 POV C 701 " pdb=" O31 POV C 701 " ideal model delta sigma weight residual 1.327 1.442 -0.115 2.00e-02 2.50e+03 3.31e+01 bond pdb=" C31 POV D 703 " pdb=" O31 POV D 703 " ideal model delta sigma weight residual 1.327 1.441 -0.114 2.00e-02 2.50e+03 3.27e+01 bond pdb=" C31 POV D 704 " pdb=" O31 POV D 704 " ideal model delta sigma weight residual 1.327 1.441 -0.114 2.00e-02 2.50e+03 3.27e+01 bond pdb=" C31 POV B 705 " pdb=" O31 POV B 705 " ideal model delta sigma weight residual 1.327 1.441 -0.114 2.00e-02 2.50e+03 3.25e+01 ... (remaining 10816 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 14004 1.93 - 3.87: 347 3.87 - 5.80: 170 5.80 - 7.73: 24 7.73 - 9.66: 17 Bond angle restraints: 14562 Sorted by residual: angle pdb=" N GLU A 218 " pdb=" CA GLU A 218 " pdb=" C GLU A 218 " ideal model delta sigma weight residual 113.16 108.52 4.64 1.24e+00 6.50e-01 1.40e+01 angle pdb=" N VAL D 311 " pdb=" CA VAL D 311 " pdb=" C VAL D 311 " ideal model delta sigma weight residual 112.96 109.32 3.64 1.00e+00 1.00e+00 1.33e+01 angle pdb=" CA SER B 222 " pdb=" C SER B 222 " pdb=" O SER B 222 " ideal model delta sigma weight residual 122.13 118.04 4.09 1.13e+00 7.83e-01 1.31e+01 angle pdb=" N ALA B 226 " pdb=" CA ALA B 226 " pdb=" C ALA B 226 " ideal model delta sigma weight residual 113.16 108.76 4.40 1.24e+00 6.50e-01 1.26e+01 angle pdb=" N PHE A 217 " pdb=" CA PHE A 217 " pdb=" C PHE A 217 " ideal model delta sigma weight residual 111.90 107.31 4.59 1.32e+00 5.74e-01 1.21e+01 ... (remaining 14557 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.84: 6190 35.84 - 71.67: 160 71.67 - 107.50: 9 107.50 - 143.34: 4 143.34 - 179.17: 1 Dihedral angle restraints: 6364 sinusoidal: 2652 harmonic: 3712 Sorted by residual: dihedral pdb=" CH3 ACE I 1 " pdb=" C ACE I 1 " pdb=" N ALA I 2 " pdb=" CA ALA I 2 " ideal model delta sinusoidal sigma weight residual 180.00 0.83 179.17 1 5.00e+00 4.00e-02 7.68e+02 dihedral pdb=" CA PRO D 475 " pdb=" C PRO D 475 " pdb=" N VAL D 476 " pdb=" CA VAL D 476 " ideal model delta harmonic sigma weight residual 180.00 159.59 20.41 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA PRO A 475 " pdb=" C PRO A 475 " pdb=" N VAL A 476 " pdb=" CA VAL A 476 " ideal model delta harmonic sigma weight residual 180.00 160.42 19.58 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 6361 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1225 0.044 - 0.088: 332 0.088 - 0.132: 82 0.132 - 0.176: 5 0.176 - 0.220: 3 Chirality restraints: 1647 Sorted by residual: chirality pdb=" CA TYR I 8 " pdb=" N TYR I 8 " pdb=" C TYR I 8 " pdb=" CB TYR I 8 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA GLU D 218 " pdb=" N GLU D 218 " pdb=" C GLU D 218 " pdb=" CB GLU D 218 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA GLU A 218 " pdb=" N GLU A 218 " pdb=" C GLU A 218 " pdb=" CB GLU A 218 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 1644 not shown) Planarity restraints: 1788 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG D 164 " 0.042 5.00e-02 4.00e+02 6.28e-02 6.31e+00 pdb=" N PRO D 165 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO D 165 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 165 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 224 " 0.012 2.00e-02 2.50e+03 2.44e-02 5.94e+00 pdb=" C GLN A 224 " -0.042 2.00e-02 2.50e+03 pdb=" O GLN A 224 " 0.016 2.00e-02 2.50e+03 pdb=" N ALA A 225 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 474 " -0.035 5.00e-02 4.00e+02 5.35e-02 4.58e+00 pdb=" N PRO B 475 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 475 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 475 " -0.030 5.00e-02 4.00e+02 ... (remaining 1785 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.79: 2511 2.79 - 3.38: 12151 3.38 - 3.96: 19385 3.96 - 4.55: 27366 4.55 - 5.14: 39840 Nonbonded interactions: 101253 Sorted by model distance: nonbonded pdb=" NE ARG C 297 " pdb=" NH1 ARG C 377 " model vdw 2.202 3.200 nonbonded pdb=" NH2 ARG A 164 " pdb=" O VAL A 168 " model vdw 2.216 3.120 nonbonded pdb=" O SER B 104 " pdb=" NH2 ARG B 146 " model vdw 2.222 3.120 nonbonded pdb=" OD2 ASP B 316 " pdb=" NH2 ARG B 377 " model vdw 2.247 3.120 nonbonded pdb=" OE2 GLU D 418 " pdb=" N GLY D 452 " model vdw 2.252 3.120 ... (remaining 101248 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 83 through 110 or (resid 111 and (name N or name CA or nam \ e C or name O or name CB )) or resid 112 through 162 or (resid 163 and (name N o \ r name CA or name C or name O or name CB )) or resid 164 through 488 or (resid 7 \ 03 and (name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or \ name C39)) or (resid 704 and (name C31 or name C32 or name C33 or name C34 or na \ me C35 or name C36 or name C37)) or (resid 707 and (name C32 or name C33 or name \ C34 or name C35 or name C36)))) selection = (chain 'B' and (resid 83 through 162 or (resid 163 and (name N or name CA or nam \ e C or name O or name CB )) or resid 164 through 488 or (resid 703 and (name C33 \ or name C34 or name C35 or name C36 or name C37 or name C38 or name C39)) or re \ sid 704 or (resid 707 and (name C32 or name C33 or name C34 or name C35 or name \ C36)))) selection = (chain 'C' and (resid 83 through 110 or (resid 111 and (name N or name CA or nam \ e C or name O or name CB )) or resid 112 through 488 or (resid 703 and (name C33 \ or name C34 or name C35 or name C36 or name C37 or name C38 or name C39)) or (r \ esid 704 and (name C31 or name C32 or name C33 or name C34 or name C35 or name C \ 36 or name C37)) or (resid 707 and (name C32 or name C33 or name C34 or name C35 \ or name C36)))) selection = (chain 'D' and (resid 83 through 110 or (resid 111 and (name N or name CA or nam \ e C or name O or name CB )) or resid 112 through 162 or (resid 163 and (name N o \ r name CA or name C or name O or name CB )) or resid 164 through 488 or (resid 7 \ 01 and (name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or \ name C39)) or resid 702 or (resid 705 and (name C32 or name C33 or name C34 or n \ ame C35 or name C36)))) } ncs_group { reference = (chain 'I' and (resid 1 through 9 or (resid 10 and (name N or name CA or name C \ or name O or name CB )) or resid 11)) selection = chain 'J' } 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: 2.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.450 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.020 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 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 : 0.008 0.115 10821 Z= 0.397 Angle : 0.881 9.664 14562 Z= 0.401 Chirality : 0.042 0.220 1647 Planarity : 0.005 0.063 1788 Dihedral : 15.890 179.174 3952 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.47 (0.25), residues: 1224 helix: 2.33 (0.20), residues: 747 sheet: 1.12 (0.76), residues: 40 loop : -1.58 (0.27), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 377 TYR 0.011 0.001 TYR I 8 PHE 0.013 0.001 PHE B 179 TRP 0.005 0.001 TRP C 434 HIS 0.003 0.001 HIS D 85 Details of bonding type rmsd covalent geometry : bond 0.00756 (10821) covalent geometry : angle 0.88057 (14562) hydrogen bonds : bond 0.14155 ( 615) hydrogen bonds : angle 5.26644 ( 1758) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 PHE cc_start: 0.7727 (p90) cc_final: 0.7486 (p90) REVERT: A 134 ASP cc_start: 0.7570 (t70) cc_final: 0.7025 (t0) REVERT: A 189 LYS cc_start: 0.9157 (ptpp) cc_final: 0.8915 (ptpp) REVERT: B 134 ASP cc_start: 0.8146 (t0) cc_final: 0.7634 (t0) REVERT: B 362 ARG cc_start: 0.7623 (mtp180) cc_final: 0.7100 (ttp-170) REVERT: C 134 ASP cc_start: 0.8066 (t0) cc_final: 0.7709 (t0) REVERT: D 178 LYS cc_start: 0.8798 (mmpt) cc_final: 0.8535 (mmmt) REVERT: D 362 ARG cc_start: 0.7480 (mtt180) cc_final: 0.7000 (ttt180) outliers start: 0 outliers final: 0 residues processed: 196 average time/residue: 0.1169 time to fit residues: 31.9693 Evaluate side-chains 143 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 9.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 7.9990 chunk 123 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.139315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.097017 restraints weight = 19501.591| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.77 r_work: 0.3169 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10821 Z= 0.159 Angle : 0.572 7.563 14562 Z= 0.295 Chirality : 0.041 0.147 1647 Planarity : 0.005 0.057 1788 Dihedral : 12.912 178.101 1623 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.18 % Allowed : 8.26 % Favored : 90.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.65 (0.25), residues: 1224 helix: 2.47 (0.20), residues: 746 sheet: 1.72 (0.81), residues: 40 loop : -1.55 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 191 TYR 0.014 0.001 TYR D 483 PHE 0.020 0.001 PHE C 292 TRP 0.005 0.001 TRP C 454 HIS 0.003 0.001 HIS D 85 Details of bonding type rmsd covalent geometry : bond 0.00370 (10821) covalent geometry : angle 0.57228 (14562) hydrogen bonds : bond 0.04570 ( 615) hydrogen bonds : angle 4.25112 ( 1758) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 163 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 PHE cc_start: 0.7756 (p90) cc_final: 0.7506 (p90) REVERT: A 134 ASP cc_start: 0.7189 (t70) cc_final: 0.6644 (t0) REVERT: B 178 LYS cc_start: 0.8994 (mppt) cc_final: 0.8528 (mmtt) REVERT: B 293 GLU cc_start: 0.8348 (tm-30) cc_final: 0.8135 (tm-30) REVERT: B 362 ARG cc_start: 0.7530 (mtp180) cc_final: 0.6613 (ttt180) REVERT: C 134 ASP cc_start: 0.8150 (t0) cc_final: 0.7715 (t0) REVERT: C 293 GLU cc_start: 0.8704 (tt0) cc_final: 0.8494 (tm-30) REVERT: C 427 LYS cc_start: 0.9247 (mmtt) cc_final: 0.9021 (mmtt) REVERT: D 178 LYS cc_start: 0.8686 (mmpt) cc_final: 0.8470 (mmmt) REVERT: D 362 ARG cc_start: 0.7638 (mtt180) cc_final: 0.6772 (ttp-170) outliers start: 13 outliers final: 10 residues processed: 170 average time/residue: 0.1126 time to fit residues: 27.1998 Evaluate side-chains 153 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 143 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain D residue 470 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 124 optimal weight: 0.0370 chunk 78 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 101 optimal weight: 10.0000 chunk 107 optimal weight: 4.9990 chunk 73 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 overall best weight: 1.5464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 157 GLN C 138 ASN D 85 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.137782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.095015 restraints weight = 19594.683| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.78 r_work: 0.3146 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10821 Z= 0.154 Angle : 0.551 7.040 14562 Z= 0.285 Chirality : 0.041 0.146 1647 Planarity : 0.005 0.057 1788 Dihedral : 11.223 179.281 1623 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.76 % Favored : 96.16 % Rotamer: Outliers : 1.81 % Allowed : 10.71 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.67 (0.25), residues: 1224 helix: 2.42 (0.19), residues: 755 sheet: 1.67 (0.84), residues: 40 loop : -1.46 (0.28), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 146 TYR 0.012 0.001 TYR D 483 PHE 0.015 0.001 PHE C 244 TRP 0.005 0.001 TRP C 289 HIS 0.006 0.001 HIS D 85 Details of bonding type rmsd covalent geometry : bond 0.00360 (10821) covalent geometry : angle 0.55118 (14562) hydrogen bonds : bond 0.04255 ( 615) hydrogen bonds : angle 4.05435 ( 1758) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 153 time to evaluate : 0.407 Fit side-chains revert: symmetry clash REVERT: A 86 PHE cc_start: 0.7767 (p90) cc_final: 0.7529 (p90) REVERT: A 134 ASP cc_start: 0.7191 (t70) cc_final: 0.6600 (t0) REVERT: B 178 LYS cc_start: 0.9022 (mppt) cc_final: 0.8759 (mmmm) REVERT: B 293 GLU cc_start: 0.8411 (tm-30) cc_final: 0.8083 (tm-30) REVERT: B 362 ARG cc_start: 0.7555 (mtp180) cc_final: 0.6662 (ttp-170) REVERT: C 134 ASP cc_start: 0.8115 (t0) cc_final: 0.7630 (t0) REVERT: C 189 LYS cc_start: 0.9361 (tptm) cc_final: 0.9105 (tppt) REVERT: C 293 GLU cc_start: 0.8737 (tt0) cc_final: 0.8471 (tm-30) REVERT: C 427 LYS cc_start: 0.9255 (mmtt) cc_final: 0.9038 (mmtt) REVERT: D 178 LYS cc_start: 0.8710 (mmpt) cc_final: 0.8490 (mmmt) REVERT: D 362 ARG cc_start: 0.7697 (mtt180) cc_final: 0.6800 (ttp-170) outliers start: 20 outliers final: 17 residues processed: 165 average time/residue: 0.1072 time to fit residues: 25.2315 Evaluate side-chains 152 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 135 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 470 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 49 optimal weight: 7.9990 chunk 22 optimal weight: 0.6980 chunk 2 optimal weight: 6.9990 chunk 83 optimal weight: 6.9990 chunk 91 optimal weight: 0.7980 chunk 31 optimal weight: 30.0000 chunk 52 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 40 optimal weight: 9.9990 chunk 98 optimal weight: 9.9990 chunk 121 optimal weight: 4.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN B 157 GLN D 85 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.133836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.088902 restraints weight = 19965.932| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.91 r_work: 0.3078 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 10821 Z= 0.272 Angle : 0.651 8.188 14562 Z= 0.336 Chirality : 0.044 0.152 1647 Planarity : 0.005 0.057 1788 Dihedral : 10.649 179.115 1623 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.33 % Favored : 95.59 % Rotamer: Outliers : 2.36 % Allowed : 13.25 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.49 (0.24), residues: 1224 helix: 2.19 (0.19), residues: 762 sheet: 1.42 (0.83), residues: 40 loop : -1.42 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 146 TYR 0.010 0.002 TYR B 415 PHE 0.023 0.002 PHE C 292 TRP 0.007 0.001 TRP C 454 HIS 0.003 0.001 HIS D 85 Details of bonding type rmsd covalent geometry : bond 0.00650 (10821) covalent geometry : angle 0.65105 (14562) hydrogen bonds : bond 0.05019 ( 615) hydrogen bonds : angle 4.22741 ( 1758) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 140 time to evaluate : 0.402 Fit side-chains REVERT: A 86 PHE cc_start: 0.7798 (p90) cc_final: 0.7560 (p90) REVERT: A 247 GLU cc_start: 0.8856 (pt0) cc_final: 0.8584 (pt0) REVERT: B 116 ASN cc_start: 0.8602 (m-40) cc_final: 0.8161 (m110) REVERT: B 178 LYS cc_start: 0.9027 (mppt) cc_final: 0.8716 (mmmm) REVERT: B 362 ARG cc_start: 0.7677 (mtp180) cc_final: 0.6574 (ttp-170) REVERT: C 134 ASP cc_start: 0.8073 (t0) cc_final: 0.7591 (t0) REVERT: C 189 LYS cc_start: 0.9347 (tptm) cc_final: 0.9127 (tppt) REVERT: C 293 GLU cc_start: 0.8775 (tt0) cc_final: 0.8477 (tm-30) REVERT: D 178 LYS cc_start: 0.8751 (mmpt) cc_final: 0.8503 (mmmt) REVERT: D 181 GLU cc_start: 0.7570 (tm-30) cc_final: 0.7252 (pp20) REVERT: D 380 LYS cc_start: 0.8410 (mptt) cc_final: 0.7964 (mppt) outliers start: 26 outliers final: 22 residues processed: 159 average time/residue: 0.1151 time to fit residues: 25.6076 Evaluate side-chains 149 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 GLN Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 372 ILE Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 470 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 33 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 9 optimal weight: 9.9990 chunk 29 optimal weight: 0.9980 chunk 95 optimal weight: 8.9990 chunk 125 optimal weight: 0.5980 chunk 0 optimal weight: 20.0000 chunk 56 optimal weight: 0.7980 chunk 115 optimal weight: 0.6980 chunk 123 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 157 GLN C 116 ASN D 85 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.137152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.092819 restraints weight = 19637.891| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.92 r_work: 0.3153 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10821 Z= 0.121 Angle : 0.543 8.179 14562 Z= 0.280 Chirality : 0.041 0.146 1647 Planarity : 0.004 0.057 1788 Dihedral : 9.614 179.066 1623 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.36 % Allowed : 14.34 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.75 (0.25), residues: 1224 helix: 2.40 (0.19), residues: 763 sheet: 1.88 (0.84), residues: 40 loop : -1.35 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 146 TYR 0.010 0.001 TYR B 415 PHE 0.012 0.001 PHE B 190 TRP 0.006 0.001 TRP A 289 HIS 0.002 0.001 HIS D 85 Details of bonding type rmsd covalent geometry : bond 0.00262 (10821) covalent geometry : angle 0.54258 (14562) hydrogen bonds : bond 0.04073 ( 615) hydrogen bonds : angle 3.93000 ( 1758) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 145 time to evaluate : 0.434 Fit side-chains REVERT: A 86 PHE cc_start: 0.7765 (p90) cc_final: 0.7511 (p90) REVERT: A 134 ASP cc_start: 0.6926 (t70) cc_final: 0.6363 (t70) REVERT: A 143 ASP cc_start: 0.9259 (t0) cc_final: 0.8910 (t0) REVERT: A 155 TYR cc_start: 0.7200 (t80) cc_final: 0.6915 (t80) REVERT: A 188 ASN cc_start: 0.9458 (OUTLIER) cc_final: 0.9050 (p0) REVERT: A 366 LEU cc_start: 0.9208 (tp) cc_final: 0.8967 (tt) REVERT: B 362 ARG cc_start: 0.7615 (mtp180) cc_final: 0.6505 (ttp-170) REVERT: C 134 ASP cc_start: 0.8075 (t0) cc_final: 0.7631 (t0) REVERT: C 189 LYS cc_start: 0.9345 (tptm) cc_final: 0.9061 (tppt) REVERT: C 293 GLU cc_start: 0.8738 (tt0) cc_final: 0.8503 (tm-30) REVERT: C 427 LYS cc_start: 0.9270 (mmtt) cc_final: 0.9023 (mmpt) REVERT: D 181 GLU cc_start: 0.7678 (tm-30) cc_final: 0.7379 (pp20) outliers start: 26 outliers final: 20 residues processed: 160 average time/residue: 0.1043 time to fit residues: 24.0314 Evaluate side-chains 150 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 GLN Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 393 MET Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 403 LEU Chi-restraints excluded: chain D residue 470 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 31 optimal weight: 20.0000 chunk 104 optimal weight: 0.0770 chunk 107 optimal weight: 6.9990 chunk 117 optimal weight: 6.9990 chunk 83 optimal weight: 6.9990 chunk 114 optimal weight: 7.9990 chunk 42 optimal weight: 0.0370 chunk 22 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 67 optimal weight: 8.9990 chunk 35 optimal weight: 0.8980 overall best weight: 1.6020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN B 157 GLN B 480 ASN C 116 ASN D 85 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.135955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.091623 restraints weight = 19785.238| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.93 r_work: 0.3119 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10821 Z= 0.157 Angle : 0.563 8.260 14562 Z= 0.287 Chirality : 0.041 0.142 1647 Planarity : 0.005 0.056 1788 Dihedral : 9.328 179.107 1623 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.18 % Allowed : 14.61 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.82 (0.25), residues: 1224 helix: 2.41 (0.19), residues: 772 sheet: 1.95 (0.83), residues: 40 loop : -1.32 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 146 TYR 0.008 0.001 TYR B 415 PHE 0.026 0.001 PHE C 292 TRP 0.005 0.001 TRP C 454 HIS 0.001 0.000 HIS B 378 Details of bonding type rmsd covalent geometry : bond 0.00371 (10821) covalent geometry : angle 0.56256 (14562) hydrogen bonds : bond 0.04206 ( 615) hydrogen bonds : angle 3.90190 ( 1758) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 135 time to evaluate : 0.407 Fit side-chains REVERT: A 86 PHE cc_start: 0.7796 (p90) cc_final: 0.7536 (p90) REVERT: A 134 ASP cc_start: 0.6944 (t70) cc_final: 0.6391 (t70) REVERT: A 143 ASP cc_start: 0.9297 (t0) cc_final: 0.8983 (t0) REVERT: A 155 TYR cc_start: 0.7202 (t80) cc_final: 0.6917 (t80) REVERT: B 178 LYS cc_start: 0.9007 (mmtm) cc_final: 0.8587 (mmmm) REVERT: B 362 ARG cc_start: 0.7572 (mtp180) cc_final: 0.6516 (ttp-170) REVERT: C 134 ASP cc_start: 0.8135 (t0) cc_final: 0.7708 (t0) REVERT: C 189 LYS cc_start: 0.9330 (tptm) cc_final: 0.9048 (tppt) REVERT: C 293 GLU cc_start: 0.8754 (tt0) cc_final: 0.8493 (tm-30) REVERT: D 181 GLU cc_start: 0.7739 (tm-30) cc_final: 0.7412 (pp20) outliers start: 24 outliers final: 23 residues processed: 151 average time/residue: 0.1057 time to fit residues: 23.0550 Evaluate side-chains 152 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 129 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 GLN Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 393 MET Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 403 LEU Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 470 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 31 optimal weight: 20.0000 chunk 87 optimal weight: 2.9990 chunk 118 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 42 optimal weight: 0.4980 chunk 62 optimal weight: 0.5980 chunk 97 optimal weight: 8.9990 chunk 25 optimal weight: 0.0050 chunk 6 optimal weight: 7.9990 overall best weight: 0.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 157 GLN C 116 ASN D 85 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.137627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.095344 restraints weight = 19357.054| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.75 r_work: 0.3156 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10821 Z= 0.124 Angle : 0.541 8.573 14562 Z= 0.275 Chirality : 0.041 0.140 1647 Planarity : 0.004 0.056 1788 Dihedral : 8.867 179.046 1623 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.54 % Allowed : 14.70 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.90 (0.25), residues: 1224 helix: 2.45 (0.19), residues: 772 sheet: 2.10 (0.82), residues: 40 loop : -1.27 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 146 TYR 0.008 0.001 TYR B 415 PHE 0.012 0.001 PHE D 244 TRP 0.005 0.001 TRP C 289 HIS 0.001 0.000 HIS A 85 Details of bonding type rmsd covalent geometry : bond 0.00282 (10821) covalent geometry : angle 0.54121 (14562) hydrogen bonds : bond 0.03925 ( 615) hydrogen bonds : angle 3.80464 ( 1758) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 141 time to evaluate : 0.402 Fit side-chains revert: symmetry clash REVERT: A 86 PHE cc_start: 0.7794 (p90) cc_final: 0.7516 (p90) REVERT: A 134 ASP cc_start: 0.6947 (t70) cc_final: 0.6418 (t70) REVERT: A 143 ASP cc_start: 0.9299 (t0) cc_final: 0.8999 (t0) REVERT: A 155 TYR cc_start: 0.7214 (t80) cc_final: 0.6934 (t80) REVERT: B 178 LYS cc_start: 0.9013 (mmtm) cc_final: 0.8691 (mmmm) REVERT: B 362 ARG cc_start: 0.7599 (mtp180) cc_final: 0.6514 (ttp-170) REVERT: C 293 GLU cc_start: 0.8763 (tt0) cc_final: 0.8504 (tm-30) REVERT: D 181 GLU cc_start: 0.7759 (tm-30) cc_final: 0.7440 (pp20) outliers start: 28 outliers final: 25 residues processed: 161 average time/residue: 0.1070 time to fit residues: 24.6772 Evaluate side-chains 156 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 GLN Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 393 MET Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 403 LEU Chi-restraints excluded: chain D residue 470 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 26 optimal weight: 3.9990 chunk 98 optimal weight: 0.0070 chunk 0 optimal weight: 20.0000 chunk 118 optimal weight: 0.9980 chunk 115 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 2 optimal weight: 9.9990 chunk 66 optimal weight: 8.9990 chunk 48 optimal weight: 0.5980 chunk 61 optimal weight: 4.9990 chunk 31 optimal weight: 30.0000 overall best weight: 1.7202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 157 GLN C 116 ASN D 85 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.136658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.094746 restraints weight = 19357.308| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.72 r_work: 0.3133 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10821 Z= 0.167 Angle : 0.585 9.953 14562 Z= 0.298 Chirality : 0.042 0.169 1647 Planarity : 0.005 0.056 1788 Dihedral : 8.883 179.089 1623 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.45 % Allowed : 15.25 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.87 (0.25), residues: 1224 helix: 2.44 (0.19), residues: 772 sheet: 2.06 (0.81), residues: 40 loop : -1.30 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 191 TYR 0.008 0.001 TYR B 415 PHE 0.016 0.001 PHE C 244 TRP 0.006 0.001 TRP C 454 HIS 0.001 0.000 HIS B 378 Details of bonding type rmsd covalent geometry : bond 0.00393 (10821) covalent geometry : angle 0.58532 (14562) hydrogen bonds : bond 0.04219 ( 615) hydrogen bonds : angle 3.85620 ( 1758) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 134 time to evaluate : 0.410 Fit side-chains REVERT: A 86 PHE cc_start: 0.7818 (p90) cc_final: 0.7541 (p90) REVERT: A 134 ASP cc_start: 0.6891 (t70) cc_final: 0.6317 (t70) REVERT: A 143 ASP cc_start: 0.9318 (t0) cc_final: 0.9035 (t0) REVERT: A 155 TYR cc_start: 0.7196 (t80) cc_final: 0.6918 (t80) REVERT: B 178 LYS cc_start: 0.9021 (mmtm) cc_final: 0.8681 (mmmm) REVERT: B 362 ARG cc_start: 0.7610 (mtp180) cc_final: 0.6511 (ttp-170) REVERT: C 170 LEU cc_start: 0.9301 (pp) cc_final: 0.9077 (mp) REVERT: C 293 GLU cc_start: 0.8761 (tt0) cc_final: 0.8501 (tm-30) REVERT: D 181 GLU cc_start: 0.7805 (tm-30) cc_final: 0.7545 (tm-30) outliers start: 27 outliers final: 27 residues processed: 153 average time/residue: 0.1046 time to fit residues: 23.0945 Evaluate side-chains 158 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 131 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 GLN Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 393 MET Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 403 LEU Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 470 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 27 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 117 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 111 optimal weight: 7.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 157 GLN C 116 ASN D 85 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.135219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.092984 restraints weight = 19569.143| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.74 r_work: 0.3126 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10821 Z= 0.197 Angle : 0.611 8.614 14562 Z= 0.313 Chirality : 0.042 0.178 1647 Planarity : 0.005 0.056 1788 Dihedral : 8.997 179.014 1623 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.63 % Allowed : 15.06 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.80 (0.25), residues: 1224 helix: 2.39 (0.19), residues: 772 sheet: 1.89 (0.80), residues: 40 loop : -1.32 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 144 TYR 0.018 0.001 TYR D 154 PHE 0.032 0.001 PHE C 118 TRP 0.008 0.001 TRP C 454 HIS 0.002 0.001 HIS B 378 Details of bonding type rmsd covalent geometry : bond 0.00471 (10821) covalent geometry : angle 0.61121 (14562) hydrogen bonds : bond 0.04469 ( 615) hydrogen bonds : angle 3.92696 ( 1758) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 0.412 Fit side-chains revert: symmetry clash REVERT: A 86 PHE cc_start: 0.7819 (p90) cc_final: 0.7537 (p90) REVERT: A 134 ASP cc_start: 0.6863 (t70) cc_final: 0.6294 (t70) REVERT: A 143 ASP cc_start: 0.9304 (t0) cc_final: 0.9052 (t0) REVERT: A 155 TYR cc_start: 0.7187 (t80) cc_final: 0.6922 (t80) REVERT: B 178 LYS cc_start: 0.9020 (mmtm) cc_final: 0.8674 (mmmm) REVERT: B 362 ARG cc_start: 0.7650 (mtp180) cc_final: 0.6562 (ttp-170) REVERT: D 181 GLU cc_start: 0.7824 (tm-30) cc_final: 0.7563 (tm-30) REVERT: D 380 LYS cc_start: 0.8469 (mptt) cc_final: 0.7989 (mppt) outliers start: 29 outliers final: 27 residues processed: 151 average time/residue: 0.1092 time to fit residues: 23.6093 Evaluate side-chains 156 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 129 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 GLN Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 393 MET Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 372 ILE Chi-restraints excluded: chain D residue 403 LEU Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 470 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 5 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 87 optimal weight: 0.5980 chunk 102 optimal weight: 10.0000 chunk 122 optimal weight: 0.9980 chunk 71 optimal weight: 9.9990 chunk 8 optimal weight: 8.9990 chunk 78 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 124 optimal weight: 8.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 157 GLN C 116 ASN D 85 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.137449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.095590 restraints weight = 19346.768| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.73 r_work: 0.3161 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10821 Z= 0.139 Angle : 0.580 8.802 14562 Z= 0.296 Chirality : 0.041 0.178 1647 Planarity : 0.005 0.056 1788 Dihedral : 8.609 179.107 1623 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.45 % Allowed : 15.25 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.85 (0.25), residues: 1224 helix: 2.42 (0.19), residues: 772 sheet: 1.96 (0.80), residues: 40 loop : -1.29 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 144 TYR 0.016 0.001 TYR D 154 PHE 0.023 0.001 PHE C 118 TRP 0.007 0.001 TRP C 454 HIS 0.001 0.000 HIS C 378 Details of bonding type rmsd covalent geometry : bond 0.00319 (10821) covalent geometry : angle 0.57959 (14562) hydrogen bonds : bond 0.04075 ( 615) hydrogen bonds : angle 3.81689 ( 1758) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 134 time to evaluate : 0.439 Fit side-chains REVERT: A 86 PHE cc_start: 0.7791 (p90) cc_final: 0.7486 (p90) REVERT: A 134 ASP cc_start: 0.6863 (t70) cc_final: 0.6294 (t70) REVERT: A 143 ASP cc_start: 0.9296 (t0) cc_final: 0.9028 (t0) REVERT: A 155 TYR cc_start: 0.7183 (t80) cc_final: 0.6924 (t80) REVERT: B 178 LYS cc_start: 0.9031 (mmtm) cc_final: 0.8676 (mmmm) REVERT: B 362 ARG cc_start: 0.7631 (mtp180) cc_final: 0.6540 (ttp-170) REVERT: D 181 GLU cc_start: 0.7844 (tm-30) cc_final: 0.7575 (tm-30) REVERT: D 224 GLN cc_start: 0.7890 (pm20) cc_final: 0.7606 (pm20) outliers start: 27 outliers final: 25 residues processed: 153 average time/residue: 0.1027 time to fit residues: 22.7565 Evaluate side-chains 157 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 132 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 GLN Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 393 MET Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 403 LEU Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 470 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 125 optimal weight: 7.9990 chunk 92 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 34 optimal weight: 0.0270 chunk 60 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 overall best weight: 1.1842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 85 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.136767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.092686 restraints weight = 19680.117| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.92 r_work: 0.3147 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10821 Z= 0.139 Angle : 0.591 9.791 14562 Z= 0.301 Chirality : 0.041 0.173 1647 Planarity : 0.005 0.056 1788 Dihedral : 8.397 179.101 1623 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.27 % Allowed : 15.70 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.87 (0.25), residues: 1224 helix: 2.43 (0.19), residues: 772 sheet: 2.02 (0.80), residues: 40 loop : -1.26 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 144 TYR 0.015 0.001 TYR D 154 PHE 0.027 0.001 PHE C 292 TRP 0.006 0.001 TRP C 454 HIS 0.001 0.000 HIS C 378 Details of bonding type rmsd covalent geometry : bond 0.00326 (10821) covalent geometry : angle 0.59130 (14562) hydrogen bonds : bond 0.04032 ( 615) hydrogen bonds : angle 3.78495 ( 1758) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2658.24 seconds wall clock time: 46 minutes 23.47 seconds (2783.47 seconds total)