Starting phenix.real_space_refine on Fri Jul 3 20:08:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o48_70089/07_2026/9o48_70089_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o48_70089/07_2026/9o48_70089.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9o48_70089/07_2026/9o48_70089.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o48_70089/07_2026/9o48_70089.map" model { file = "/net/cci-nas-00/data/ceres_data/9o48_70089/07_2026/9o48_70089_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o48_70089/07_2026/9o48_70089_neut.cif" } resolution = 3.1 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= 0.078 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: 6 Type Number sf(0) Gaussians Ca 16 9.91 5 K 2 8.98 5 S 128 5.16 5 C 10280 2.51 5 N 2716 2.21 5 O 2952 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16094 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2967 Classifications: {'peptide': 373} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 6, 'TRANS': 366} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 2967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2967 Classifications: {'peptide': 373} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 6, 'TRANS': 366} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 2967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2967 Classifications: {'peptide': 373} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 6, 'TRANS': 366} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 2967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2967 Classifications: {'peptide': 373} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 6, 'TRANS': 366} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "E" Number of atoms: 1052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1052 Classifications: {'peptide': 138} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 2, 'TRANS': 135} Chain breaks: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 25 Chain: "F" Number of atoms: 1052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1052 Classifications: {'peptide': 138} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 2, 'TRANS': 135} Chain breaks: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 25 Chain: "G" Number of atoms: 1052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1052 Classifications: {'peptide': 138} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 2, 'TRANS': 135} Chain breaks: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 25 Chain: "H" Number of atoms: 1052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1052 Classifications: {'peptide': 138} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 2, 'TRANS': 135} Chain breaks: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 25 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' K': 2} Chain breaks: 2 Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 0 Ad-hoc single atom residues: {' CA': 4} Chain breaks: 4 Chain: "F" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 0 Ad-hoc single atom residues: {' CA': 4} Chain breaks: 4 Chain: "G" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 0 Ad-hoc single atom residues: {' CA': 4} Chain breaks: 4 Chain: "H" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 0 Ad-hoc single atom residues: {' CA': 4} Chain breaks: 4 Time building chain proxies: 2.96, per 1000 atoms: 0.18 Number of scatterers: 16094 At special positions: 0 Unit cell: (120.835, 120.835, 99.71, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 16 19.99 K 2 19.00 S 128 16.00 O 2952 8.00 N 2716 7.00 C 10280 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 332 " - pdb=" SG CYS A 370 " distance=2.03 Simple disulfide: pdb=" SG CYS B 332 " - pdb=" SG CYS B 370 " distance=2.03 Simple disulfide: pdb=" SG CYS C 332 " - pdb=" SG CYS C 370 " distance=2.03 Simple disulfide: pdb=" SG CYS D 332 " - pdb=" SG CYS D 370 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.17 Conformation dependent library (CDL) restraints added in 590.0 milliseconds 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3872 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 4 sheets defined 78.1% alpha, 2.3% 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 118 through 159 removed outlier: 3.716A pdb=" N TRP A 157 " --> pdb=" O THR A 153 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLY A 158 " --> pdb=" O GLU A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 201 Processing helix chain 'A' and resid 204 through 209 Processing helix chain 'A' and resid 210 through 225 Processing helix chain 'A' and resid 255 through 260 removed outlier: 3.583A pdb=" N ILE A 260 " --> pdb=" O ILE A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 265 Processing helix chain 'A' and resid 266 through 276 removed outlier: 4.022A pdb=" N ALA A 270 " --> pdb=" O LEU A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 292 Processing helix chain 'A' and resid 297 through 309 Processing helix chain 'A' and resid 309 through 333 Processing helix chain 'A' and resid 344 through 357 removed outlier: 3.589A pdb=" N TRP A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 397 removed outlier: 3.670A pdb=" N GLY A 384 " --> pdb=" O ILE A 380 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 439 Processing helix chain 'A' and resid 442 through 477 Processing helix chain 'A' and resid 478 through 490 Processing helix chain 'B' and resid 119 through 159 removed outlier: 3.716A pdb=" N TRP B 157 " --> pdb=" O THR B 153 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLY B 158 " --> pdb=" O GLU B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 201 Processing helix chain 'B' and resid 204 through 209 Processing helix chain 'B' and resid 210 through 225 Processing helix chain 'B' and resid 255 through 260 removed outlier: 3.583A pdb=" N ILE B 260 " --> pdb=" O ILE B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 265 Processing helix chain 'B' and resid 266 through 276 removed outlier: 4.022A pdb=" N ALA B 270 " --> pdb=" O LEU B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 292 Processing helix chain 'B' and resid 297 through 309 Processing helix chain 'B' and resid 309 through 333 Processing helix chain 'B' and resid 344 through 357 removed outlier: 3.589A pdb=" N TRP B 350 " --> pdb=" O LEU B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 397 removed outlier: 3.670A pdb=" N GLY B 384 " --> pdb=" O ILE B 380 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA B 387 " --> pdb=" O ALA B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 439 Processing helix chain 'B' and resid 442 through 477 Processing helix chain 'B' and resid 478 through 490 Processing helix chain 'C' and resid 119 through 159 removed outlier: 3.716A pdb=" N TRP C 157 " --> pdb=" O THR C 153 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLY C 158 " --> pdb=" O GLU C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 201 Processing helix chain 'C' and resid 204 through 209 Processing helix chain 'C' and resid 210 through 225 Processing helix chain 'C' and resid 255 through 260 removed outlier: 3.583A pdb=" N ILE C 260 " --> pdb=" O ILE C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 265 Processing helix chain 'C' and resid 266 through 276 removed outlier: 4.022A pdb=" N ALA C 270 " --> pdb=" O LEU C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 292 Processing helix chain 'C' and resid 297 through 309 Processing helix chain 'C' and resid 309 through 333 Processing helix chain 'C' and resid 344 through 357 removed outlier: 3.589A pdb=" N TRP C 350 " --> pdb=" O LEU C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 397 removed outlier: 3.671A pdb=" N GLY C 384 " --> pdb=" O ILE C 380 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ALA C 387 " --> pdb=" O ALA C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 439 Processing helix chain 'C' and resid 442 through 477 Processing helix chain 'C' and resid 478 through 490 Processing helix chain 'D' and resid 119 through 159 removed outlier: 3.716A pdb=" N TRP D 157 " --> pdb=" O THR D 153 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLY D 158 " --> pdb=" O GLU D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 201 Processing helix chain 'D' and resid 204 through 209 Processing helix chain 'D' and resid 210 through 225 Processing helix chain 'D' and resid 255 through 260 removed outlier: 3.582A pdb=" N ILE D 260 " --> pdb=" O ILE D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 265 Processing helix chain 'D' and resid 266 through 276 removed outlier: 4.022A pdb=" N ALA D 270 " --> pdb=" O LEU D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 292 Processing helix chain 'D' and resid 297 through 309 Processing helix chain 'D' and resid 309 through 333 Processing helix chain 'D' and resid 344 through 357 removed outlier: 3.588A pdb=" N TRP D 350 " --> pdb=" O LEU D 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 397 removed outlier: 3.670A pdb=" N GLY D 384 " --> pdb=" O ILE D 380 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA D 387 " --> pdb=" O ALA D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 439 Processing helix chain 'D' and resid 442 through 477 Processing helix chain 'D' and resid 478 through 490 Processing helix chain 'E' and resid 6 through 21 Processing helix chain 'E' and resid 29 through 40 Processing helix chain 'E' and resid 45 through 54 Processing helix chain 'E' and resid 65 through 77 Processing helix chain 'E' and resid 81 through 94 Processing helix chain 'E' and resid 102 through 109 Processing helix chain 'E' and resid 120 through 130 Processing helix chain 'E' and resid 138 through 147 Processing helix chain 'F' and resid 6 through 21 Processing helix chain 'F' and resid 29 through 40 Processing helix chain 'F' and resid 45 through 54 Processing helix chain 'F' and resid 65 through 77 Processing helix chain 'F' and resid 81 through 94 Processing helix chain 'F' and resid 102 through 109 Processing helix chain 'F' and resid 120 through 130 Processing helix chain 'F' and resid 138 through 147 Processing helix chain 'G' and resid 6 through 21 Processing helix chain 'G' and resid 29 through 40 Processing helix chain 'G' and resid 45 through 54 Processing helix chain 'G' and resid 65 through 77 Processing helix chain 'G' and resid 81 through 94 Processing helix chain 'G' and resid 102 through 109 Processing helix chain 'G' and resid 120 through 130 Processing helix chain 'G' and resid 138 through 147 Processing helix chain 'H' and resid 6 through 21 Processing helix chain 'H' and resid 29 through 40 Processing helix chain 'H' and resid 45 through 54 Processing helix chain 'H' and resid 65 through 77 Processing helix chain 'H' and resid 81 through 94 Processing helix chain 'H' and resid 102 through 109 Processing helix chain 'H' and resid 120 through 130 Processing helix chain 'H' and resid 138 through 147 Processing sheet with id=AA1, first strand: chain 'A' and resid 234 through 240 Processing sheet with id=AA2, first strand: chain 'B' and resid 234 through 240 Processing sheet with id=AA3, first strand: chain 'C' and resid 234 through 240 Processing sheet with id=AA4, first strand: chain 'D' and resid 234 through 240 1233 hydrogen bonds defined for protein. 3639 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.55 Time building geometry restraints manager: 1.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5252 1.34 - 1.46: 3766 1.46 - 1.58: 7126 1.58 - 1.70: 0 1.70 - 1.81: 224 Bond restraints: 16368 Sorted by residual: bond pdb=" N HIS A 336 " pdb=" CA HIS A 336 " ideal model delta sigma weight residual 1.456 1.490 -0.033 1.22e-02 6.72e+03 7.43e+00 bond pdb=" N HIS B 336 " pdb=" CA HIS B 336 " ideal model delta sigma weight residual 1.456 1.490 -0.033 1.22e-02 6.72e+03 7.43e+00 bond pdb=" N HIS D 336 " pdb=" CA HIS D 336 " ideal model delta sigma weight residual 1.456 1.489 -0.032 1.22e-02 6.72e+03 7.04e+00 bond pdb=" N HIS C 336 " pdb=" CA HIS C 336 " ideal model delta sigma weight residual 1.456 1.489 -0.032 1.22e-02 6.72e+03 7.04e+00 bond pdb=" CA SER B 248 " pdb=" CB SER B 248 " ideal model delta sigma weight residual 1.524 1.496 0.029 1.46e-02 4.69e+03 3.93e+00 ... (remaining 16363 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.92: 21554 0.92 - 1.85: 505 1.85 - 2.77: 45 2.77 - 3.69: 24 3.69 - 4.61: 8 Bond angle restraints: 22136 Sorted by residual: angle pdb=" CA SER B 248 " pdb=" C SER B 248 " pdb=" O SER B 248 " ideal model delta sigma weight residual 120.47 117.78 2.69 1.35e+00 5.49e-01 3.97e+00 angle pdb=" CA SER A 248 " pdb=" C SER A 248 " pdb=" O SER A 248 " ideal model delta sigma weight residual 120.47 117.78 2.69 1.35e+00 5.49e-01 3.97e+00 angle pdb=" CA SER D 248 " pdb=" C SER D 248 " pdb=" O SER D 248 " ideal model delta sigma weight residual 120.47 117.82 2.65 1.35e+00 5.49e-01 3.86e+00 angle pdb=" CA SER C 248 " pdb=" C SER C 248 " pdb=" O SER C 248 " ideal model delta sigma weight residual 120.47 117.82 2.65 1.35e+00 5.49e-01 3.85e+00 angle pdb=" N ILE C 359 " pdb=" CA ILE C 359 " pdb=" C ILE C 359 " ideal model delta sigma weight residual 110.42 108.62 1.80 9.40e-01 1.13e+00 3.67e+00 ... (remaining 22131 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.77: 8474 13.77 - 27.54: 994 27.54 - 41.31: 244 41.31 - 55.09: 68 55.09 - 68.86: 8 Dihedral angle restraints: 9788 sinusoidal: 3820 harmonic: 5968 Sorted by residual: dihedral pdb=" CG ARG C 133 " pdb=" CD ARG C 133 " pdb=" NE ARG C 133 " pdb=" CZ ARG C 133 " ideal model delta sinusoidal sigma weight residual 90.00 131.27 -41.27 2 1.50e+01 4.44e-03 9.28e+00 dihedral pdb=" CG ARG A 133 " pdb=" CD ARG A 133 " pdb=" NE ARG A 133 " pdb=" CZ ARG A 133 " ideal model delta sinusoidal sigma weight residual 90.00 131.27 -41.27 2 1.50e+01 4.44e-03 9.28e+00 dihedral pdb=" CG ARG B 133 " pdb=" CD ARG B 133 " pdb=" NE ARG B 133 " pdb=" CZ ARG B 133 " ideal model delta sinusoidal sigma weight residual 90.00 131.27 -41.27 2 1.50e+01 4.44e-03 9.28e+00 ... (remaining 9785 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1598 0.026 - 0.052: 616 0.052 - 0.078: 282 0.078 - 0.104: 56 0.104 - 0.130: 16 Chirality restraints: 2568 Sorted by residual: chirality pdb=" CA ILE B 229 " pdb=" N ILE B 229 " pdb=" C ILE B 229 " pdb=" CB ILE B 229 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.26e-01 chirality pdb=" CA ILE C 229 " pdb=" N ILE C 229 " pdb=" C ILE C 229 " pdb=" CB ILE C 229 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.18e-01 chirality pdb=" CA ILE A 229 " pdb=" N ILE A 229 " pdb=" C ILE A 229 " pdb=" CB ILE A 229 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.15e-01 ... (remaining 2565 not shown) Planarity restraints: 2788 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS C 227 " -0.020 5.00e-02 4.00e+02 3.07e-02 1.50e+00 pdb=" N PRO C 228 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO C 228 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 228 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 227 " 0.020 5.00e-02 4.00e+02 3.05e-02 1.49e+00 pdb=" N PRO A 228 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 228 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 228 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS B 227 " -0.020 5.00e-02 4.00e+02 3.04e-02 1.47e+00 pdb=" N PRO B 228 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO B 228 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 228 " -0.017 5.00e-02 4.00e+02 ... (remaining 2785 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.87: 5908 2.87 - 3.44: 18571 3.44 - 4.01: 30272 4.01 - 4.57: 44954 4.57 - 5.14: 61355 Nonbonded interactions: 161060 Sorted by model distance: nonbonded pdb=" OE1 GLU H 32 " pdb="CA CA H 501 " model vdw 2.308 3.250 nonbonded pdb=" OE1 GLU G 32 " pdb="CA CA G 501 " model vdw 2.309 3.250 nonbonded pdb=" OE1 GLU F 32 " pdb="CA CA F 501 " model vdw 2.309 3.250 nonbonded pdb=" OE1 GLU E 32 " pdb="CA CA E 501 " model vdw 2.312 3.250 nonbonded pdb=" OD1 ASP G 59 " pdb="CA CA G 502 " model vdw 2.333 3.250 ... (remaining 161055 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 118 through 490) selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 3.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.560 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 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:0.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16372 Z= 0.114 Angle : 0.354 4.613 22144 Z= 0.211 Chirality : 0.034 0.130 2568 Planarity : 0.002 0.031 2788 Dihedral : 12.864 68.857 5904 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % 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 are not related in a simple way. whole: 0.27 (0.18), residues: 2020 helix: 0.32 (0.12), residues: 1540 sheet: 0.91 (0.64), residues: 64 loop : 0.07 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 123 TYR 0.004 0.001 TYR B 267 PHE 0.007 0.001 PHE B 356 TRP 0.003 0.001 TRP C 327 HIS 0.002 0.000 HIS A 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00201 / 0.11 (16368) covalent geometry : angle 0.35396 / 0.21 (22136) SS BOND : bond 0.00125 / 0.06 ( 4) SS BOND : angle 0.34011 / 0.17 ( 8) hydrogen bonds : bond 0.18944 / 12.78 ( 1233) hydrogen bonds : angle 6.27036 / 4.54 ( 3639) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 451 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 THR cc_start: 0.8759 (t) cc_final: 0.8450 (p) REVERT: A 282 ASP cc_start: 0.7826 (t0) cc_final: 0.7481 (t0) REVERT: A 306 MET cc_start: 0.9026 (mmm) cc_final: 0.8814 (mmm) REVERT: A 377 LEU cc_start: 0.8365 (tp) cc_final: 0.7886 (mt) REVERT: A 451 LYS cc_start: 0.8418 (mmmt) cc_final: 0.8119 (mttp) REVERT: A 460 ARG cc_start: 0.7725 (ttt90) cc_final: 0.7302 (ttm-80) REVERT: A 465 LYS cc_start: 0.8770 (ptmt) cc_final: 0.8356 (ptpt) REVERT: A 467 ARG cc_start: 0.7677 (ttt90) cc_final: 0.7024 (ttp80) REVERT: B 250 THR cc_start: 0.8747 (t) cc_final: 0.8436 (p) REVERT: B 282 ASP cc_start: 0.7830 (t0) cc_final: 0.7485 (t0) REVERT: B 306 MET cc_start: 0.9028 (mmm) cc_final: 0.8809 (mmm) REVERT: B 377 LEU cc_start: 0.8368 (tp) cc_final: 0.7891 (mt) REVERT: B 451 LYS cc_start: 0.8399 (mmmt) cc_final: 0.8088 (mttp) REVERT: B 465 LYS cc_start: 0.8768 (ptmt) cc_final: 0.8351 (ptpt) REVERT: B 467 ARG cc_start: 0.7675 (ttt90) cc_final: 0.7019 (ttp80) REVERT: C 250 THR cc_start: 0.8751 (t) cc_final: 0.8450 (p) REVERT: C 282 ASP cc_start: 0.7829 (t0) cc_final: 0.7478 (t0) REVERT: C 306 MET cc_start: 0.9029 (mmm) cc_final: 0.8813 (mmm) REVERT: C 377 LEU cc_start: 0.8331 (tp) cc_final: 0.7881 (mt) REVERT: C 451 LYS cc_start: 0.8405 (mmmt) cc_final: 0.8098 (mttp) REVERT: C 465 LYS cc_start: 0.8773 (ptmt) cc_final: 0.8361 (ptpt) REVERT: C 467 ARG cc_start: 0.7667 (ttt90) cc_final: 0.6997 (ttp80) REVERT: D 250 THR cc_start: 0.8753 (t) cc_final: 0.8448 (p) REVERT: D 282 ASP cc_start: 0.7826 (t0) cc_final: 0.7485 (t0) REVERT: D 306 MET cc_start: 0.9024 (mmm) cc_final: 0.8810 (mmm) REVERT: D 377 LEU cc_start: 0.8329 (tp) cc_final: 0.7881 (mt) REVERT: D 451 LYS cc_start: 0.8405 (mmmt) cc_final: 0.8098 (mttp) REVERT: D 465 LYS cc_start: 0.8774 (ptmt) cc_final: 0.8361 (ptpt) REVERT: D 467 ARG cc_start: 0.7667 (ttt90) cc_final: 0.6996 (ttp80) REVERT: E 12 GLU cc_start: 0.7233 (pt0) cc_final: 0.6478 (tp30) REVERT: E 48 GLU cc_start: 0.7684 (mt-10) cc_final: 0.6940 (mp0) REVERT: E 68 GLU cc_start: 0.7436 (mt-10) cc_final: 0.7020 (mt-10) REVERT: E 72 MET cc_start: 0.7826 (tpt) cc_final: 0.7550 (tpp) REVERT: E 101 ILE cc_start: 0.6233 (pt) cc_final: 0.5865 (pt) REVERT: F 12 GLU cc_start: 0.7190 (pt0) cc_final: 0.6448 (tp30) REVERT: F 48 GLU cc_start: 0.7721 (mt-10) cc_final: 0.6943 (mp0) REVERT: F 68 GLU cc_start: 0.7468 (mt-10) cc_final: 0.7031 (mt-10) REVERT: F 72 MET cc_start: 0.7849 (tpt) cc_final: 0.7576 (tpp) REVERT: F 101 ILE cc_start: 0.6189 (pt) cc_final: 0.5823 (pt) REVERT: F 123 ASP cc_start: 0.4833 (m-30) cc_final: 0.4594 (m-30) REVERT: F 137 VAL cc_start: 0.6961 (t) cc_final: 0.6759 (p) REVERT: G 12 GLU cc_start: 0.7214 (pt0) cc_final: 0.6473 (tp30) REVERT: G 48 GLU cc_start: 0.7737 (mt-10) cc_final: 0.6947 (mp0) REVERT: G 68 GLU cc_start: 0.7467 (mt-10) cc_final: 0.7029 (mt-10) REVERT: G 72 MET cc_start: 0.7834 (tpt) cc_final: 0.7557 (tpp) REVERT: G 101 ILE cc_start: 0.6201 (pt) cc_final: 0.5830 (pt) REVERT: G 123 ASP cc_start: 0.4884 (m-30) cc_final: 0.4638 (m-30) REVERT: H 12 GLU cc_start: 0.7195 (pt0) cc_final: 0.6470 (tp30) REVERT: H 48 GLU cc_start: 0.7711 (mt-10) cc_final: 0.6930 (mp0) REVERT: H 68 GLU cc_start: 0.7438 (mt-10) cc_final: 0.6994 (mt-10) REVERT: H 72 MET cc_start: 0.7857 (tpt) cc_final: 0.7579 (tpp) REVERT: H 101 ILE cc_start: 0.6221 (pt) cc_final: 0.5853 (pt) REVERT: H 123 ASP cc_start: 0.4879 (m-30) cc_final: 0.4632 (m-30) outliers start: 0 outliers final: 0 residues processed: 451 average time/residue: 0.1321 time to fit residues: 84.1554 Evaluate side-chains 320 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 320 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.0870 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.171731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.122567 restraints weight = 15756.822| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.76 r_work: 0.3169 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16372 Z= 0.132 Angle : 0.469 7.928 22144 Z= 0.257 Chirality : 0.037 0.179 2568 Planarity : 0.004 0.032 2788 Dihedral : 3.433 11.372 2212 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.88 % Allowed : 9.32 % Favored : 89.80 % 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 are not related in a simple way. whole: 2.37 (0.18), residues: 2020 helix: 2.02 (0.13), residues: 1524 sheet: 0.91 (0.65), residues: 64 loop : 0.15 (0.33), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 124 TYR 0.007 0.001 TYR G 100 PHE 0.007 0.001 PHE C 409 TRP 0.006 0.001 TRP C 327 HIS 0.003 0.001 HIS B 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (16368) covalent geometry : angle 0.46932 / 0.26 (22136) SS BOND : bond 0.00004 / 0.00 ( 4) SS BOND : angle 0.57676 / 0.26 ( 8) hydrogen bonds : bond 0.04700 / 3.22 ( 1233) hydrogen bonds : angle 3.53908 / 2.55 ( 3639) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 315 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 THR cc_start: 0.8886 (t) cc_final: 0.8586 (p) REVERT: A 377 LEU cc_start: 0.8343 (tp) cc_final: 0.7859 (mt) REVERT: A 451 LYS cc_start: 0.8437 (mmmt) cc_final: 0.8088 (mttp) REVERT: A 460 ARG cc_start: 0.7796 (ttt90) cc_final: 0.7416 (ttm-80) REVERT: A 467 ARG cc_start: 0.7731 (ttt90) cc_final: 0.7067 (ttp80) REVERT: B 250 THR cc_start: 0.8885 (t) cc_final: 0.8587 (p) REVERT: B 377 LEU cc_start: 0.8343 (tp) cc_final: 0.7860 (mt) REVERT: B 451 LYS cc_start: 0.8413 (mmmt) cc_final: 0.8044 (mttp) REVERT: B 460 ARG cc_start: 0.7791 (ttt90) cc_final: 0.7421 (ttm-80) REVERT: B 467 ARG cc_start: 0.7733 (ttt90) cc_final: 0.7089 (ttp80) REVERT: C 250 THR cc_start: 0.8885 (t) cc_final: 0.8586 (p) REVERT: C 377 LEU cc_start: 0.8344 (tp) cc_final: 0.7861 (mt) REVERT: C 451 LYS cc_start: 0.8426 (mmmt) cc_final: 0.8061 (mttp) REVERT: C 460 ARG cc_start: 0.7794 (ttt90) cc_final: 0.7417 (ttm-80) REVERT: C 467 ARG cc_start: 0.7721 (ttt90) cc_final: 0.7058 (ttp80) REVERT: D 250 THR cc_start: 0.8884 (t) cc_final: 0.8584 (p) REVERT: D 377 LEU cc_start: 0.8337 (tp) cc_final: 0.7853 (mt) REVERT: D 451 LYS cc_start: 0.8436 (mmmt) cc_final: 0.8076 (mttp) REVERT: D 460 ARG cc_start: 0.7801 (ttt90) cc_final: 0.7428 (ttm-80) REVERT: D 467 ARG cc_start: 0.7707 (ttt90) cc_final: 0.7051 (ttp80) REVERT: E 12 GLU cc_start: 0.7218 (pt0) cc_final: 0.6488 (tp30) REVERT: E 68 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7736 (mt-10) REVERT: E 72 MET cc_start: 0.7869 (tpt) cc_final: 0.7583 (tpp) REVERT: E 141 GLU cc_start: 0.7882 (mp0) cc_final: 0.7510 (mp0) REVERT: F 12 GLU cc_start: 0.7218 (pt0) cc_final: 0.6501 (tp30) REVERT: F 68 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7735 (mt-10) REVERT: F 72 MET cc_start: 0.7878 (tpt) cc_final: 0.7579 (tpp) REVERT: F 123 ASP cc_start: 0.4858 (m-30) cc_final: 0.4614 (m-30) REVERT: F 137 VAL cc_start: 0.7311 (t) cc_final: 0.6922 (p) REVERT: G 12 GLU cc_start: 0.7226 (pt0) cc_final: 0.6515 (tp30) REVERT: G 68 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7747 (mt-10) REVERT: G 72 MET cc_start: 0.7876 (tpt) cc_final: 0.7580 (tpp) REVERT: G 123 ASP cc_start: 0.4874 (m-30) cc_final: 0.4614 (m-30) REVERT: H 12 GLU cc_start: 0.7192 (pt0) cc_final: 0.6482 (tp30) REVERT: H 68 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7727 (mt-10) REVERT: H 72 MET cc_start: 0.7887 (tpt) cc_final: 0.7590 (tpp) REVERT: H 123 ASP cc_start: 0.4829 (m-30) cc_final: 0.4590 (m-30) REVERT: H 137 VAL cc_start: 0.6914 (OUTLIER) cc_final: 0.6668 (p) REVERT: H 141 GLU cc_start: 0.7911 (mp0) cc_final: 0.7538 (mp0) outliers start: 15 outliers final: 8 residues processed: 320 average time/residue: 0.1452 time to fit residues: 66.7212 Evaluate side-chains 302 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 293 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 340 ASP Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 340 ASP Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 340 ASP Chi-restraints excluded: chain H residue 137 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 160 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 75 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 12 optimal weight: 0.4980 chunk 158 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 185 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 116 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 367 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.171297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.122263 restraints weight = 15942.927| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.75 r_work: 0.3204 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16372 Z= 0.122 Angle : 0.424 7.778 22144 Z= 0.231 Chirality : 0.036 0.149 2568 Planarity : 0.003 0.033 2788 Dihedral : 3.383 11.328 2212 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.12 % Allowed : 10.67 % Favored : 88.21 % 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 are not related in a simple way. whole: 3.13 (0.19), residues: 2020 helix: 2.62 (0.13), residues: 1528 sheet: 0.87 (0.69), residues: 64 loop : 0.22 (0.33), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 124 TYR 0.006 0.001 TYR B 369 PHE 0.009 0.001 PHE D 356 TRP 0.005 0.001 TRP C 327 HIS 0.003 0.001 HIS C 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (16368) covalent geometry : angle 0.42381 / 0.23 (22136) SS BOND : bond 0.00055 / 0.03 ( 4) SS BOND : angle 0.45010 / 0.21 ( 8) hydrogen bonds : bond 0.04009 / 2.73 ( 1233) hydrogen bonds : angle 3.29617 / 2.37 ( 3639) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 323 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 THR cc_start: 0.8911 (t) cc_final: 0.8562 (p) REVERT: A 377 LEU cc_start: 0.8294 (tp) cc_final: 0.7838 (mt) REVERT: A 451 LYS cc_start: 0.8462 (mmmt) cc_final: 0.8080 (mttp) REVERT: A 460 ARG cc_start: 0.7838 (ttt90) cc_final: 0.7466 (ttm-80) REVERT: A 467 ARG cc_start: 0.7693 (ttt90) cc_final: 0.6990 (ttp80) REVERT: B 250 THR cc_start: 0.8909 (t) cc_final: 0.8560 (p) REVERT: B 377 LEU cc_start: 0.8294 (tp) cc_final: 0.7844 (mt) REVERT: B 451 LYS cc_start: 0.8481 (mmmt) cc_final: 0.8090 (mttp) REVERT: B 460 ARG cc_start: 0.7824 (ttt90) cc_final: 0.7456 (ttm-80) REVERT: B 467 ARG cc_start: 0.7689 (ttt90) cc_final: 0.6965 (ttp80) REVERT: C 250 THR cc_start: 0.8906 (t) cc_final: 0.8564 (p) REVERT: C 377 LEU cc_start: 0.8301 (tp) cc_final: 0.7846 (mt) REVERT: C 451 LYS cc_start: 0.8461 (mmmt) cc_final: 0.8072 (mttp) REVERT: C 460 ARG cc_start: 0.7840 (ttt90) cc_final: 0.7457 (ttm-80) REVERT: C 467 ARG cc_start: 0.7701 (ttt90) cc_final: 0.6972 (ttp80) REVERT: D 250 THR cc_start: 0.8904 (t) cc_final: 0.8564 (p) REVERT: D 377 LEU cc_start: 0.8290 (tp) cc_final: 0.7835 (mt) REVERT: D 451 LYS cc_start: 0.8463 (mmmt) cc_final: 0.8075 (mttp) REVERT: D 460 ARG cc_start: 0.7835 (ttt90) cc_final: 0.7461 (ttm-80) REVERT: D 467 ARG cc_start: 0.7672 (ttt90) cc_final: 0.6952 (ttp80) REVERT: E 12 GLU cc_start: 0.7210 (pt0) cc_final: 0.6517 (tp30) REVERT: E 68 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7767 (mt-10) REVERT: E 72 MET cc_start: 0.7958 (tpt) cc_final: 0.7680 (tpp) REVERT: E 141 GLU cc_start: 0.7818 (mp0) cc_final: 0.7454 (mp0) REVERT: F 12 GLU cc_start: 0.7192 (pt0) cc_final: 0.6513 (tp30) REVERT: F 68 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7767 (mt-10) REVERT: F 72 MET cc_start: 0.7955 (tpt) cc_final: 0.7673 (tpp) REVERT: F 123 ASP cc_start: 0.4910 (m-30) cc_final: 0.4644 (m-30) REVERT: F 137 VAL cc_start: 0.7324 (t) cc_final: 0.6954 (p) REVERT: G 12 GLU cc_start: 0.7207 (pt0) cc_final: 0.6518 (tp30) REVERT: G 68 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7787 (mt-10) REVERT: G 72 MET cc_start: 0.7963 (tpt) cc_final: 0.7686 (tpp) REVERT: G 123 ASP cc_start: 0.4884 (m-30) cc_final: 0.4583 (m-30) REVERT: H 12 GLU cc_start: 0.7196 (pt0) cc_final: 0.6510 (tp30) REVERT: H 68 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7764 (mt-10) REVERT: H 72 MET cc_start: 0.7948 (tpt) cc_final: 0.7668 (tpp) REVERT: H 123 ASP cc_start: 0.4840 (m-30) cc_final: 0.4557 (m-30) REVERT: H 137 VAL cc_start: 0.6672 (OUTLIER) cc_final: 0.6452 (p) outliers start: 19 outliers final: 10 residues processed: 330 average time/residue: 0.1518 time to fit residues: 71.1291 Evaluate side-chains 318 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 307 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain D residue 342 THR Chi-restraints excluded: chain H residue 137 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 152 optimal weight: 4.9990 chunk 150 optimal weight: 0.0040 chunk 72 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 119 optimal weight: 0.7980 chunk 28 optimal weight: 0.0980 chunk 124 optimal weight: 0.0060 chunk 181 optimal weight: 0.5980 chunk 97 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 177 optimal weight: 0.6980 overall best weight: 0.2808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 367 ASN A 436 HIS B 436 HIS C 367 ASN C 436 HIS D 367 ASN D 436 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.174637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.125380 restraints weight = 15839.570| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.82 r_work: 0.3227 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 16372 Z= 0.091 Angle : 0.391 7.133 22144 Z= 0.211 Chirality : 0.034 0.131 2568 Planarity : 0.003 0.031 2788 Dihedral : 3.226 11.416 2212 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.94 % Allowed : 11.62 % Favored : 87.44 % 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 are not related in a simple way. whole: 3.56 (0.19), residues: 2020 helix: 2.98 (0.13), residues: 1524 sheet: 0.88 (0.71), residues: 64 loop : 0.24 (0.33), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 87 TYR 0.005 0.001 TYR A 188 PHE 0.008 0.001 PHE D 356 TRP 0.007 0.001 TRP B 327 HIS 0.001 0.000 HIS A 436 Details of bonding type rmsd/Z covalent geometry : bond 0.00183 / 0.09 (16368) covalent geometry : angle 0.39081 / 0.21 (22136) SS BOND : bond 0.00038 / 0.02 ( 4) SS BOND : angle 0.49193 / 0.23 ( 8) hydrogen bonds : bond 0.03344 / 2.28 ( 1233) hydrogen bonds : angle 3.13939 / 2.26 ( 3639) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 317 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 THR cc_start: 0.8844 (t) cc_final: 0.8565 (p) REVERT: A 377 LEU cc_start: 0.8210 (tp) cc_final: 0.7701 (mt) REVERT: A 451 LYS cc_start: 0.8273 (mmmt) cc_final: 0.7869 (mttp) REVERT: A 460 ARG cc_start: 0.7700 (ttt90) cc_final: 0.7481 (ttm-80) REVERT: A 467 ARG cc_start: 0.7521 (ttt90) cc_final: 0.6750 (ttp80) REVERT: B 250 THR cc_start: 0.8843 (t) cc_final: 0.8562 (p) REVERT: B 377 LEU cc_start: 0.8230 (tp) cc_final: 0.7707 (mt) REVERT: B 451 LYS cc_start: 0.8278 (mmmt) cc_final: 0.7877 (mttp) REVERT: B 460 ARG cc_start: 0.7687 (ttt90) cc_final: 0.7472 (ttm-80) REVERT: B 467 ARG cc_start: 0.7556 (ttt90) cc_final: 0.6814 (ttp80) REVERT: C 250 THR cc_start: 0.8841 (t) cc_final: 0.8573 (p) REVERT: C 377 LEU cc_start: 0.8226 (tp) cc_final: 0.7703 (mt) REVERT: C 451 LYS cc_start: 0.8277 (mmmt) cc_final: 0.7875 (mttp) REVERT: C 460 ARG cc_start: 0.7707 (ttt90) cc_final: 0.7501 (ttm-80) REVERT: C 467 ARG cc_start: 0.7557 (ttt90) cc_final: 0.6803 (ttp80) REVERT: D 250 THR cc_start: 0.8824 (t) cc_final: 0.8550 (p) REVERT: D 377 LEU cc_start: 0.8192 (tp) cc_final: 0.7684 (mt) REVERT: D 451 LYS cc_start: 0.8275 (mmmt) cc_final: 0.7875 (mttp) REVERT: D 460 ARG cc_start: 0.7694 (ttt90) cc_final: 0.7478 (ttm-80) REVERT: D 467 ARG cc_start: 0.7553 (ttt90) cc_final: 0.6812 (ttp80) REVERT: E 12 GLU cc_start: 0.6975 (pt0) cc_final: 0.6320 (tp30) REVERT: E 65 ASP cc_start: 0.7179 (p0) cc_final: 0.6356 (p0) REVERT: E 68 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7446 (mt-10) REVERT: E 72 MET cc_start: 0.7783 (tpt) cc_final: 0.7500 (tpp) REVERT: F 12 GLU cc_start: 0.6959 (pt0) cc_final: 0.6302 (tp30) REVERT: F 65 ASP cc_start: 0.7149 (p0) cc_final: 0.6320 (p0) REVERT: F 68 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7492 (mt-10) REVERT: F 72 MET cc_start: 0.7776 (tpt) cc_final: 0.7490 (tpp) REVERT: F 123 ASP cc_start: 0.4827 (m-30) cc_final: 0.4524 (m-30) REVERT: F 137 VAL cc_start: 0.7085 (t) cc_final: 0.6704 (p) REVERT: G 12 GLU cc_start: 0.6957 (pt0) cc_final: 0.6316 (tp30) REVERT: G 65 ASP cc_start: 0.7177 (p0) cc_final: 0.6343 (p0) REVERT: G 68 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7516 (mt-10) REVERT: G 72 MET cc_start: 0.7793 (tpt) cc_final: 0.7512 (tpp) REVERT: G 123 ASP cc_start: 0.4864 (m-30) cc_final: 0.4566 (m-30) REVERT: H 12 GLU cc_start: 0.6935 (pt0) cc_final: 0.6292 (tp30) REVERT: H 65 ASP cc_start: 0.7149 (p0) cc_final: 0.6312 (p0) REVERT: H 68 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7480 (mt-10) REVERT: H 72 MET cc_start: 0.7788 (tpt) cc_final: 0.7502 (tpp) REVERT: H 123 ASP cc_start: 0.4830 (m-30) cc_final: 0.4523 (m-30) outliers start: 16 outliers final: 9 residues processed: 324 average time/residue: 0.1465 time to fit residues: 67.5953 Evaluate side-chains 307 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 298 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 340 ASP Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain C residue 340 ASP Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 298 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 180 optimal weight: 0.9980 chunk 122 optimal weight: 0.5980 chunk 176 optimal weight: 2.9990 chunk 177 optimal weight: 0.6980 chunk 181 optimal weight: 0.8980 chunk 197 optimal weight: 0.9990 chunk 188 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 44 optimal weight: 0.5980 chunk 58 optimal weight: 0.9990 chunk 125 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.181320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.134532 restraints weight = 15722.407| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.65 r_work: 0.3269 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 16372 Z= 0.110 Angle : 0.404 6.979 22144 Z= 0.219 Chirality : 0.035 0.141 2568 Planarity : 0.003 0.031 2788 Dihedral : 3.242 11.873 2212 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.00 % Allowed : 9.91 % Favored : 88.09 % 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 are not related in a simple way. whole: 3.61 (0.19), residues: 2020 helix: 2.99 (0.13), residues: 1528 sheet: 0.96 (0.72), residues: 64 loop : 0.29 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 395 TYR 0.005 0.001 TYR B 369 PHE 0.009 0.001 PHE C 356 TRP 0.005 0.001 TRP C 327 HIS 0.003 0.001 HIS B 448 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (16368) covalent geometry : angle 0.40438 / 0.22 (22136) SS BOND : bond 0.00082 / 0.04 ( 4) SS BOND : angle 0.26896 / 0.13 ( 8) hydrogen bonds : bond 0.03511 / 2.39 ( 1233) hydrogen bonds : angle 3.10404 / 2.23 ( 3639) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 310 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 THR cc_start: 0.8922 (t) cc_final: 0.8617 (p) REVERT: A 377 LEU cc_start: 0.8353 (tp) cc_final: 0.7874 (mt) REVERT: A 451 LYS cc_start: 0.8485 (mmmt) cc_final: 0.8114 (mttp) REVERT: A 460 ARG cc_start: 0.7881 (ttt90) cc_final: 0.7676 (ttm-80) REVERT: A 467 ARG cc_start: 0.7744 (ttt90) cc_final: 0.7055 (ttp80) REVERT: B 250 THR cc_start: 0.8914 (t) cc_final: 0.8610 (p) REVERT: B 377 LEU cc_start: 0.8353 (tp) cc_final: 0.7874 (mt) REVERT: B 451 LYS cc_start: 0.8487 (mmmt) cc_final: 0.8113 (mttp) REVERT: B 460 ARG cc_start: 0.7855 (ttt90) cc_final: 0.7652 (ttm-80) REVERT: B 467 ARG cc_start: 0.7746 (ttt90) cc_final: 0.7046 (ttp80) REVERT: C 250 THR cc_start: 0.8914 (t) cc_final: 0.8613 (p) REVERT: C 377 LEU cc_start: 0.8336 (tp) cc_final: 0.7856 (mt) REVERT: C 451 LYS cc_start: 0.8492 (mmmt) cc_final: 0.8120 (mttp) REVERT: C 460 ARG cc_start: 0.7869 (ttt90) cc_final: 0.7665 (ttm-80) REVERT: C 467 ARG cc_start: 0.7744 (ttt90) cc_final: 0.7044 (ttp80) REVERT: D 250 THR cc_start: 0.8914 (t) cc_final: 0.8609 (p) REVERT: D 377 LEU cc_start: 0.8335 (tp) cc_final: 0.7856 (mt) REVERT: D 451 LYS cc_start: 0.8493 (mmmt) cc_final: 0.8122 (mttp) REVERT: D 460 ARG cc_start: 0.7886 (ttt90) cc_final: 0.7683 (ttm-80) REVERT: D 467 ARG cc_start: 0.7753 (ttt90) cc_final: 0.7046 (ttp80) REVERT: E 12 GLU cc_start: 0.7225 (pt0) cc_final: 0.6604 (tp30) REVERT: E 65 ASP cc_start: 0.7352 (p0) cc_final: 0.6554 (p0) REVERT: E 68 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7685 (mt-10) REVERT: E 72 MET cc_start: 0.7981 (tpt) cc_final: 0.7720 (tpp) REVERT: F 12 GLU cc_start: 0.7232 (pt0) cc_final: 0.6624 (tp30) REVERT: F 65 ASP cc_start: 0.7328 (p0) cc_final: 0.6520 (p0) REVERT: F 68 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7680 (mt-10) REVERT: F 72 MET cc_start: 0.7974 (tpt) cc_final: 0.7709 (tpp) REVERT: F 123 ASP cc_start: 0.4987 (m-30) cc_final: 0.4662 (m-30) REVERT: F 137 VAL cc_start: 0.7309 (t) cc_final: 0.6913 (p) REVERT: G 12 GLU cc_start: 0.7207 (pt0) cc_final: 0.6607 (tp30) REVERT: G 65 ASP cc_start: 0.7335 (p0) cc_final: 0.6533 (p0) REVERT: G 68 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7680 (mt-10) REVERT: G 72 MET cc_start: 0.7968 (tpt) cc_final: 0.7703 (tpp) REVERT: G 123 ASP cc_start: 0.5044 (m-30) cc_final: 0.4713 (m-30) REVERT: H 12 GLU cc_start: 0.7222 (pt0) cc_final: 0.6611 (tp30) REVERT: H 65 ASP cc_start: 0.7346 (p0) cc_final: 0.6536 (p0) REVERT: H 68 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7679 (mt-10) REVERT: H 72 MET cc_start: 0.7979 (tpt) cc_final: 0.7720 (tpp) REVERT: H 123 ASP cc_start: 0.5047 (m-30) cc_final: 0.4722 (m-30) outliers start: 34 outliers final: 13 residues processed: 321 average time/residue: 0.1442 time to fit residues: 66.9623 Evaluate side-chains 304 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 291 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain D residue 342 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 67 optimal weight: 0.9980 chunk 117 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 158 optimal weight: 6.9990 chunk 169 optimal weight: 0.9980 chunk 193 optimal weight: 0.6980 chunk 87 optimal weight: 0.6980 chunk 16 optimal weight: 5.9990 chunk 195 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 181 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.180222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.133234 restraints weight = 15666.201| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.65 r_work: 0.3325 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16372 Z= 0.130 Angle : 0.431 6.953 22144 Z= 0.231 Chirality : 0.036 0.148 2568 Planarity : 0.003 0.033 2788 Dihedral : 3.287 11.763 2212 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.06 % Allowed : 11.67 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.58 (0.19), residues: 2020 helix: 2.94 (0.13), residues: 1532 sheet: 0.99 (0.71), residues: 64 loop : 0.36 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 395 TYR 0.006 0.001 TYR C 369 PHE 0.009 0.001 PHE D 356 TRP 0.004 0.001 TRP A 327 HIS 0.003 0.001 HIS D 448 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (16368) covalent geometry : angle 0.43090 / 0.23 (22136) SS BOND : bond 0.00167 / 0.08 ( 4) SS BOND : angle 0.18705 / 0.08 ( 8) hydrogen bonds : bond 0.03689 / 2.50 ( 1233) hydrogen bonds : angle 3.11906 / 2.24 ( 3639) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 298 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 THR cc_start: 0.8926 (t) cc_final: 0.8565 (p) REVERT: A 377 LEU cc_start: 0.8309 (tp) cc_final: 0.7843 (mt) REVERT: A 451 LYS cc_start: 0.8435 (mmmt) cc_final: 0.8031 (mttp) REVERT: A 460 ARG cc_start: 0.7756 (ttt90) cc_final: 0.7544 (ttm-80) REVERT: A 467 ARG cc_start: 0.7659 (ttt90) cc_final: 0.6846 (ttp80) REVERT: B 250 THR cc_start: 0.8922 (t) cc_final: 0.8565 (p) REVERT: B 377 LEU cc_start: 0.8309 (tp) cc_final: 0.7842 (mt) REVERT: B 451 LYS cc_start: 0.8429 (mmmt) cc_final: 0.8023 (mttp) REVERT: B 460 ARG cc_start: 0.7742 (ttt90) cc_final: 0.6809 (ttp80) REVERT: B 467 ARG cc_start: 0.7652 (ttt90) cc_final: 0.6847 (ttp80) REVERT: C 250 THR cc_start: 0.8921 (t) cc_final: 0.8562 (p) REVERT: C 377 LEU cc_start: 0.8303 (tp) cc_final: 0.7836 (mt) REVERT: C 451 LYS cc_start: 0.8429 (mmmt) cc_final: 0.8024 (mttp) REVERT: C 460 ARG cc_start: 0.7734 (ttt90) cc_final: 0.7525 (ttm-80) REVERT: C 467 ARG cc_start: 0.7642 (ttt90) cc_final: 0.6826 (ttp80) REVERT: D 250 THR cc_start: 0.8915 (t) cc_final: 0.8559 (p) REVERT: D 377 LEU cc_start: 0.8304 (tp) cc_final: 0.7835 (mt) REVERT: D 451 LYS cc_start: 0.8434 (mmmt) cc_final: 0.8031 (mttp) REVERT: D 460 ARG cc_start: 0.7762 (ttt90) cc_final: 0.6833 (ttp80) REVERT: D 467 ARG cc_start: 0.7653 (ttt90) cc_final: 0.6836 (ttp80) REVERT: E 12 GLU cc_start: 0.7168 (pt0) cc_final: 0.6529 (tp30) REVERT: E 68 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7769 (mt-10) REVERT: E 72 MET cc_start: 0.7917 (tpt) cc_final: 0.7644 (tpp) REVERT: F 12 GLU cc_start: 0.7191 (pt0) cc_final: 0.6561 (tp30) REVERT: F 68 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7809 (mt-10) REVERT: F 72 MET cc_start: 0.7905 (tpt) cc_final: 0.7626 (tpp) REVERT: F 123 ASP cc_start: 0.5089 (m-30) cc_final: 0.4772 (m-30) REVERT: F 137 VAL cc_start: 0.7234 (t) cc_final: 0.6828 (p) REVERT: G 12 GLU cc_start: 0.7167 (pt0) cc_final: 0.6556 (tp30) REVERT: G 68 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7801 (mt-10) REVERT: G 72 MET cc_start: 0.7894 (tpt) cc_final: 0.7625 (tpp) REVERT: G 123 ASP cc_start: 0.5109 (m-30) cc_final: 0.4767 (m-30) REVERT: H 12 GLU cc_start: 0.7168 (pt0) cc_final: 0.6549 (tp30) REVERT: H 68 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7810 (mt-10) REVERT: H 72 MET cc_start: 0.7915 (tpt) cc_final: 0.7639 (tpp) REVERT: H 123 ASP cc_start: 0.5102 (m-30) cc_final: 0.4760 (m-30) outliers start: 18 outliers final: 10 residues processed: 312 average time/residue: 0.1450 time to fit residues: 64.4093 Evaluate side-chains 298 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 288 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 342 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 184 optimal weight: 6.9990 chunk 61 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 151 optimal weight: 0.9980 chunk 100 optimal weight: 0.6980 chunk 119 optimal weight: 0.0270 chunk 76 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 164 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 483 HIS D 483 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.175296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.126587 restraints weight = 15783.343| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.70 r_work: 0.3296 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16372 Z= 0.112 Angle : 0.413 6.787 22144 Z= 0.223 Chirality : 0.036 0.133 2568 Planarity : 0.003 0.032 2788 Dihedral : 3.239 11.976 2212 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.00 % Allowed : 11.38 % Favored : 87.62 % 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 are not related in a simple way. whole: 3.66 (0.19), residues: 2020 helix: 3.00 (0.13), residues: 1532 sheet: 0.97 (0.70), residues: 64 loop : 0.40 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 395 TYR 0.006 0.001 TYR C 369 PHE 0.009 0.001 PHE C 356 TRP 0.006 0.001 TRP B 327 HIS 0.002 0.001 HIS A 189 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (16368) covalent geometry : angle 0.41311 / 0.22 (22136) SS BOND : bond 0.00086 / 0.04 ( 4) SS BOND : angle 0.20545 / 0.10 ( 8) hydrogen bonds : bond 0.03519 / 2.39 ( 1233) hydrogen bonds : angle 3.07966 / 2.21 ( 3639) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 295 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 THR cc_start: 0.8945 (t) cc_final: 0.8608 (p) REVERT: A 377 LEU cc_start: 0.8339 (tp) cc_final: 0.7849 (mt) REVERT: A 451 LYS cc_start: 0.8491 (mmmt) cc_final: 0.8112 (mttp) REVERT: A 460 ARG cc_start: 0.7844 (ttt90) cc_final: 0.6939 (ttp80) REVERT: A 467 ARG cc_start: 0.7751 (ttt90) cc_final: 0.6931 (ttp80) REVERT: B 250 THR cc_start: 0.8938 (t) cc_final: 0.8609 (p) REVERT: B 377 LEU cc_start: 0.8334 (tp) cc_final: 0.7886 (mt) REVERT: B 451 LYS cc_start: 0.8486 (mmmt) cc_final: 0.8107 (mttp) REVERT: B 467 ARG cc_start: 0.7765 (ttt90) cc_final: 0.6946 (ttp80) REVERT: C 250 THR cc_start: 0.8942 (t) cc_final: 0.8613 (p) REVERT: C 377 LEU cc_start: 0.8331 (tp) cc_final: 0.7882 (mt) REVERT: C 451 LYS cc_start: 0.8484 (mmmt) cc_final: 0.8105 (mttp) REVERT: C 467 ARG cc_start: 0.7760 (ttt90) cc_final: 0.6936 (ttp80) REVERT: D 250 THR cc_start: 0.8937 (t) cc_final: 0.8609 (p) REVERT: D 377 LEU cc_start: 0.8330 (tp) cc_final: 0.7882 (mt) REVERT: D 451 LYS cc_start: 0.8492 (mmmt) cc_final: 0.8118 (mttp) REVERT: D 467 ARG cc_start: 0.7752 (ttt90) cc_final: 0.6932 (ttp80) REVERT: E 12 GLU cc_start: 0.7219 (pt0) cc_final: 0.6608 (tp30) REVERT: E 39 SER cc_start: 0.8683 (t) cc_final: 0.8308 (p) REVERT: E 68 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7898 (mt-10) REVERT: E 72 MET cc_start: 0.7960 (tpt) cc_final: 0.7683 (tpp) REVERT: F 12 GLU cc_start: 0.7206 (pt0) cc_final: 0.6599 (tp30) REVERT: F 68 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7900 (mt-10) REVERT: F 72 MET cc_start: 0.7966 (tpt) cc_final: 0.7688 (tpp) REVERT: F 123 ASP cc_start: 0.5095 (m-30) cc_final: 0.4782 (m-30) REVERT: F 137 VAL cc_start: 0.7231 (t) cc_final: 0.6805 (p) REVERT: G 12 GLU cc_start: 0.7229 (pt0) cc_final: 0.6647 (tp30) REVERT: G 68 GLU cc_start: 0.8201 (mt-10) cc_final: 0.7913 (mt-10) REVERT: G 72 MET cc_start: 0.7940 (tpt) cc_final: 0.7664 (tpp) REVERT: G 123 ASP cc_start: 0.5098 (m-30) cc_final: 0.4772 (m-30) REVERT: H 12 GLU cc_start: 0.7224 (pt0) cc_final: 0.6639 (tp30) REVERT: H 68 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7902 (mt-10) REVERT: H 72 MET cc_start: 0.7969 (tpt) cc_final: 0.7695 (tpp) REVERT: H 123 ASP cc_start: 0.5101 (m-30) cc_final: 0.4763 (m-30) outliers start: 17 outliers final: 10 residues processed: 307 average time/residue: 0.1296 time to fit residues: 57.1724 Evaluate side-chains 295 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 285 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 342 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 138 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 28 optimal weight: 0.0370 chunk 195 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 178 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 142 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 187 optimal weight: 0.9980 chunk 117 optimal weight: 0.5980 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.174770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.125669 restraints weight = 15936.259| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 1.73 r_work: 0.3305 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16372 Z= 0.117 Angle : 0.419 6.779 22144 Z= 0.224 Chirality : 0.036 0.133 2568 Planarity : 0.003 0.033 2788 Dihedral : 3.248 13.161 2212 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.00 % Allowed : 11.38 % Favored : 87.62 % 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 are not related in a simple way. whole: 3.66 (0.19), residues: 2020 helix: 2.94 (0.13), residues: 1552 sheet: 0.93 (0.70), residues: 64 loop : 0.55 (0.33), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 395 TYR 0.006 0.001 TYR A 335 PHE 0.009 0.001 PHE C 356 TRP 0.005 0.001 TRP B 327 HIS 0.003 0.001 HIS A 448 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (16368) covalent geometry : angle 0.41921 / 0.22 (22136) SS BOND : bond 0.00096 / 0.05 ( 4) SS BOND : angle 0.20539 / 0.10 ( 8) hydrogen bonds : bond 0.03560 / 2.41 ( 1233) hydrogen bonds : angle 3.10370 / 2.23 ( 3639) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 285 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 THR cc_start: 0.8934 (t) cc_final: 0.8569 (p) REVERT: A 377 LEU cc_start: 0.8294 (tp) cc_final: 0.7828 (mt) REVERT: A 451 LYS cc_start: 0.8407 (mmmt) cc_final: 0.8005 (mttp) REVERT: A 460 ARG cc_start: 0.7734 (ttt90) cc_final: 0.6809 (ttp80) REVERT: A 467 ARG cc_start: 0.7643 (ttt90) cc_final: 0.6791 (ttp80) REVERT: B 250 THR cc_start: 0.8929 (t) cc_final: 0.8572 (p) REVERT: B 377 LEU cc_start: 0.8299 (tp) cc_final: 0.7834 (mt) REVERT: B 451 LYS cc_start: 0.8409 (mmmt) cc_final: 0.8005 (mttp) REVERT: B 467 ARG cc_start: 0.7664 (ttt90) cc_final: 0.6808 (ttp80) REVERT: C 250 THR cc_start: 0.8931 (t) cc_final: 0.8576 (p) REVERT: C 377 LEU cc_start: 0.8298 (tp) cc_final: 0.7831 (mt) REVERT: C 451 LYS cc_start: 0.8410 (mmmt) cc_final: 0.8005 (mttp) REVERT: C 467 ARG cc_start: 0.7651 (ttt90) cc_final: 0.6794 (ttp80) REVERT: D 250 THR cc_start: 0.8927 (t) cc_final: 0.8574 (p) REVERT: D 377 LEU cc_start: 0.8292 (tp) cc_final: 0.7824 (mt) REVERT: D 451 LYS cc_start: 0.8412 (mmmt) cc_final: 0.8013 (mttp) REVERT: D 467 ARG cc_start: 0.7653 (ttt90) cc_final: 0.6794 (ttp80) REVERT: E 12 GLU cc_start: 0.7139 (pt0) cc_final: 0.6503 (tp30) REVERT: E 35 THR cc_start: 0.8341 (t) cc_final: 0.8044 (p) REVERT: E 39 SER cc_start: 0.8639 (t) cc_final: 0.8272 (p) REVERT: E 68 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7815 (mt-10) REVERT: E 72 MET cc_start: 0.7852 (tpt) cc_final: 0.7569 (tpp) REVERT: F 12 GLU cc_start: 0.7178 (pt0) cc_final: 0.6555 (tp30) REVERT: F 35 THR cc_start: 0.8344 (t) cc_final: 0.8055 (p) REVERT: F 68 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7803 (mt-10) REVERT: F 72 MET cc_start: 0.7856 (tpt) cc_final: 0.7576 (tpp) REVERT: F 123 ASP cc_start: 0.5059 (m-30) cc_final: 0.4742 (m-30) REVERT: F 137 VAL cc_start: 0.7254 (t) cc_final: 0.6783 (p) REVERT: G 12 GLU cc_start: 0.7141 (pt0) cc_final: 0.6553 (tp30) REVERT: G 35 THR cc_start: 0.8343 (t) cc_final: 0.8050 (p) REVERT: G 68 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7815 (mt-10) REVERT: G 72 MET cc_start: 0.7891 (tpt) cc_final: 0.7595 (tpp) REVERT: G 123 ASP cc_start: 0.5078 (m-30) cc_final: 0.4742 (m-30) REVERT: H 12 GLU cc_start: 0.7161 (pt0) cc_final: 0.6562 (tp30) REVERT: H 68 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7795 (mt-10) REVERT: H 72 MET cc_start: 0.7866 (tpt) cc_final: 0.7587 (tpp) REVERT: H 123 ASP cc_start: 0.5075 (m-30) cc_final: 0.4741 (m-30) outliers start: 17 outliers final: 13 residues processed: 299 average time/residue: 0.1256 time to fit residues: 54.1823 Evaluate side-chains 297 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 284 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain D residue 342 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 150 optimal weight: 0.9980 chunk 174 optimal weight: 2.9990 chunk 176 optimal weight: 2.9990 chunk 95 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 163 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 179 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 118 optimal weight: 0.3980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.175251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.125926 restraints weight = 15753.428| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.75 r_work: 0.3327 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 16372 Z= 0.120 Angle : 0.431 7.423 22144 Z= 0.228 Chirality : 0.036 0.134 2568 Planarity : 0.003 0.033 2788 Dihedral : 3.271 13.143 2212 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.94 % Allowed : 11.62 % Favored : 87.44 % 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 are not related in a simple way. whole: 3.65 (0.19), residues: 2020 helix: 2.92 (0.13), residues: 1552 sheet: 0.94 (0.70), residues: 64 loop : 0.64 (0.33), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 38 TYR 0.006 0.001 TYR B 369 PHE 0.010 0.001 PHE C 356 TRP 0.005 0.001 TRP C 327 HIS 0.003 0.001 HIS A 448 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (16368) covalent geometry : angle 0.43070 / 0.23 (22136) SS BOND : bond 0.00131 / 0.07 ( 4) SS BOND : angle 0.13589 / 0.07 ( 8) hydrogen bonds : bond 0.03566 / 2.42 ( 1233) hydrogen bonds : angle 3.10190 / 2.23 ( 3639) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 295 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 THR cc_start: 0.8936 (t) cc_final: 0.8560 (p) REVERT: A 377 LEU cc_start: 0.8284 (tp) cc_final: 0.7813 (mt) REVERT: A 451 LYS cc_start: 0.8406 (mmmt) cc_final: 0.7992 (mttp) REVERT: A 460 ARG cc_start: 0.7693 (ttt90) cc_final: 0.6763 (ttp80) REVERT: A 467 ARG cc_start: 0.7614 (ttt90) cc_final: 0.6759 (ttp80) REVERT: B 250 THR cc_start: 0.8935 (t) cc_final: 0.8559 (p) REVERT: B 377 LEU cc_start: 0.8282 (tp) cc_final: 0.7812 (mt) REVERT: B 451 LYS cc_start: 0.8403 (mmmt) cc_final: 0.7992 (mttp) REVERT: B 467 ARG cc_start: 0.7636 (ttt90) cc_final: 0.6762 (ttp80) REVERT: C 250 THR cc_start: 0.8934 (t) cc_final: 0.8562 (p) REVERT: C 377 LEU cc_start: 0.8283 (tp) cc_final: 0.7810 (mt) REVERT: C 451 LYS cc_start: 0.8396 (mmmt) cc_final: 0.7983 (mttp) REVERT: C 467 ARG cc_start: 0.7612 (ttt90) cc_final: 0.6755 (ttp80) REVERT: D 250 THR cc_start: 0.8933 (t) cc_final: 0.8559 (p) REVERT: D 377 LEU cc_start: 0.8282 (tp) cc_final: 0.7809 (mt) REVERT: D 451 LYS cc_start: 0.8408 (mmmt) cc_final: 0.8001 (mttp) REVERT: D 467 ARG cc_start: 0.7607 (ttt90) cc_final: 0.6744 (ttp80) REVERT: E 12 GLU cc_start: 0.7095 (pt0) cc_final: 0.6473 (tp30) REVERT: E 39 SER cc_start: 0.8630 (t) cc_final: 0.8257 (p) REVERT: E 68 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7800 (mt-10) REVERT: E 72 MET cc_start: 0.7881 (tpt) cc_final: 0.7581 (tpp) REVERT: F 12 GLU cc_start: 0.7122 (pt0) cc_final: 0.6508 (tp30) REVERT: F 35 THR cc_start: 0.8356 (t) cc_final: 0.8125 (p) REVERT: F 68 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7780 (mt-10) REVERT: F 72 MET cc_start: 0.7872 (tpt) cc_final: 0.7572 (tpp) REVERT: F 123 ASP cc_start: 0.5081 (m-30) cc_final: 0.4740 (m-30) REVERT: F 137 VAL cc_start: 0.7167 (t) cc_final: 0.6773 (p) REVERT: G 12 GLU cc_start: 0.7116 (pt0) cc_final: 0.6519 (tp30) REVERT: G 35 THR cc_start: 0.8356 (t) cc_final: 0.8120 (p) REVERT: G 68 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7780 (mt-10) REVERT: G 72 MET cc_start: 0.7873 (tpt) cc_final: 0.7594 (tpp) REVERT: G 123 ASP cc_start: 0.5098 (m-30) cc_final: 0.4743 (m-30) REVERT: H 12 GLU cc_start: 0.7119 (pt0) cc_final: 0.6519 (tp30) REVERT: H 35 THR cc_start: 0.8360 (t) cc_final: 0.8121 (p) REVERT: H 68 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7774 (mt-10) REVERT: H 72 MET cc_start: 0.7887 (tpt) cc_final: 0.7587 (tpp) REVERT: H 123 ASP cc_start: 0.5107 (m-30) cc_final: 0.4734 (m-30) outliers start: 16 outliers final: 14 residues processed: 309 average time/residue: 0.1251 time to fit residues: 56.0252 Evaluate side-chains 301 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 287 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain D residue 342 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 189 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 100 optimal weight: 0.9990 chunk 158 optimal weight: 7.9990 chunk 163 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 147 optimal weight: 8.9990 chunk 98 optimal weight: 1.9990 chunk 166 optimal weight: 5.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.173011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.124053 restraints weight = 15750.256| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.71 r_work: 0.3274 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16372 Z= 0.136 Angle : 0.439 6.816 22144 Z= 0.233 Chirality : 0.037 0.134 2568 Planarity : 0.003 0.033 2788 Dihedral : 3.335 13.846 2212 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.06 % Allowed : 11.56 % Favored : 87.38 % 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 are not related in a simple way. whole: 3.60 (0.19), residues: 2020 helix: 2.85 (0.13), residues: 1552 sheet: 0.90 (0.69), residues: 64 loop : 0.72 (0.33), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 87 TYR 0.007 0.001 TYR C 369 PHE 0.010 0.001 PHE C 356 TRP 0.004 0.001 TRP C 327 HIS 0.003 0.001 HIS C 448 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (16368) covalent geometry : angle 0.43928 / 0.23 (22136) SS BOND : bond 0.00180 / 0.09 ( 4) SS BOND : angle 0.12238 / 0.06 ( 8) hydrogen bonds : bond 0.03736 / 2.53 ( 1233) hydrogen bonds : angle 3.13992 / 2.25 ( 3639) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 283 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 377 LEU cc_start: 0.8283 (tp) cc_final: 0.7837 (mt) REVERT: A 451 LYS cc_start: 0.8464 (mmmt) cc_final: 0.8061 (mttp) REVERT: A 460 ARG cc_start: 0.7748 (ttt90) cc_final: 0.6835 (ttp80) REVERT: A 467 ARG cc_start: 0.7628 (ttt90) cc_final: 0.6810 (ttp80) REVERT: B 377 LEU cc_start: 0.8291 (tp) cc_final: 0.7845 (mt) REVERT: B 451 LYS cc_start: 0.8461 (mmmt) cc_final: 0.8067 (mttp) REVERT: B 467 ARG cc_start: 0.7652 (ttt90) cc_final: 0.6815 (ttp80) REVERT: C 377 LEU cc_start: 0.8297 (tp) cc_final: 0.7845 (mt) REVERT: C 467 ARG cc_start: 0.7635 (ttt90) cc_final: 0.6803 (ttp80) REVERT: C 476 MET cc_start: 0.7388 (ttp) cc_final: 0.6995 (ttp) REVERT: D 377 LEU cc_start: 0.8297 (tp) cc_final: 0.7846 (mt) REVERT: D 467 ARG cc_start: 0.7637 (ttt90) cc_final: 0.6803 (ttp80) REVERT: D 476 MET cc_start: 0.7372 (ttp) cc_final: 0.6975 (ttp) REVERT: E 12 GLU cc_start: 0.7163 (pt0) cc_final: 0.6530 (tp30) REVERT: E 68 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7857 (mt-10) REVERT: E 72 MET cc_start: 0.7892 (tpt) cc_final: 0.7608 (tpp) REVERT: F 12 GLU cc_start: 0.7192 (pt0) cc_final: 0.6566 (tp30) REVERT: F 35 THR cc_start: 0.8421 (t) cc_final: 0.8186 (p) REVERT: F 68 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7843 (mt-10) REVERT: F 72 MET cc_start: 0.7887 (tpt) cc_final: 0.7602 (tpp) REVERT: F 123 ASP cc_start: 0.5128 (m-30) cc_final: 0.4769 (m-30) REVERT: G 12 GLU cc_start: 0.7180 (pt0) cc_final: 0.6571 (tp30) REVERT: G 35 THR cc_start: 0.8413 (t) cc_final: 0.8170 (p) REVERT: G 68 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7849 (mt-10) REVERT: G 72 MET cc_start: 0.7903 (tpt) cc_final: 0.7621 (tpp) REVERT: H 12 GLU cc_start: 0.7186 (pt0) cc_final: 0.6578 (tp30) REVERT: H 68 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7827 (mt-10) REVERT: H 72 MET cc_start: 0.7896 (tpt) cc_final: 0.7612 (tpp) outliers start: 18 outliers final: 17 residues processed: 297 average time/residue: 0.1293 time to fit residues: 55.7773 Evaluate side-chains 299 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 282 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 304 THR Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain D residue 342 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 33 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 140 optimal weight: 0.5980 chunk 95 optimal weight: 0.6980 chunk 85 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 158 optimal weight: 5.9990 chunk 90 optimal weight: 8.9990 chunk 67 optimal weight: 0.7980 chunk 189 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.173715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.124834 restraints weight = 15669.329| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.71 r_work: 0.3223 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16372 Z= 0.122 Angle : 0.438 6.737 22144 Z= 0.232 Chirality : 0.036 0.176 2568 Planarity : 0.003 0.033 2788 Dihedral : 3.322 13.506 2212 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.00 % Allowed : 11.79 % Favored : 87.21 % 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 are not related in a simple way. whole: 3.68 (0.19), residues: 2020 helix: 2.90 (0.13), residues: 1552 sheet: 0.86 (0.69), residues: 64 loop : 0.81 (0.34), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 38 TYR 0.007 0.001 TYR B 369 PHE 0.010 0.001 PHE A 356 TRP 0.005 0.001 TRP C 327 HIS 0.003 0.001 HIS A 448 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (16368) covalent geometry : angle 0.43823 / 0.23 (22136) SS BOND : bond 0.00122 / 0.06 ( 4) SS BOND : angle 0.14649 / 0.07 ( 8) hydrogen bonds : bond 0.03609 / 2.45 ( 1233) hydrogen bonds : angle 3.13540 / 2.25 ( 3639) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4165.46 seconds wall clock time: 72 minutes 1.37 seconds (4321.37 seconds total)