Starting phenix.real_space_refine on Thu Sep 18 10:19:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o48_70089/09_2025/9o48_70089_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o48_70089/09_2025/9o48_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_70089/09_2025/9o48_70089.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o48_70089/09_2025/9o48_70089.map" model { file = "/net/cci-nas-00/data/ceres_data/9o48_70089/09_2025/9o48_70089_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o48_70089/09_2025/9o48_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-2.0-5805/lib/python3.9/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, 2 Unusual residues: {' K': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "H" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 3.49, per 1000 atoms: 0.22 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: 1.34 Conformation dependent library (CDL) restraints added in 630.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.27 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: 2.82 Time building geometry restraints manager: 1.79 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 2.510 nonbonded pdb=" OE1 GLU G 32 " pdb="CA CA G 501 " model vdw 2.309 2.510 nonbonded pdb=" OE1 GLU F 32 " pdb="CA CA F 501 " model vdw 2.309 2.510 nonbonded pdb=" OE1 GLU E 32 " pdb="CA CA E 501 " model vdw 2.312 2.510 nonbonded pdb=" OD1 ASP G 59 " pdb="CA CA G 502 " model vdw 2.333 2.510 ... (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: 3.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 15.040 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 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 aren 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 covalent geometry : bond 0.00201 (16368) covalent geometry : angle 0.35396 (22136) SS BOND : bond 0.00125 ( 4) SS BOND : angle 0.34011 ( 8) hydrogen bonds : bond 0.18944 ( 1233) hydrogen bonds : angle 6.27036 ( 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 : 0.535 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: 0.7480 (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: 0.7726 (ttt90) cc_final: 0.7303 (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: 0.7882 (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: 0.6996 (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: 0.9025 (mmm) cc_final: 0.8810 (mmm) REVERT: D 377 LEU cc_start: 0.8330 (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: 0.7437 (mt-10) cc_final: 0.7013 (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: 0.7023 (mt-10) REVERT: F 72 MET cc_start: 0.7849 (tpt) cc_final: 0.7575 (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: 0.6962 (t) cc_final: 0.6760 (p) REVERT: G 12 GLU cc_start: 0.7215 (pt0) cc_final: 0.6474 (tp30) REVERT: G 48 GLU cc_start: 0.7736 (mt-10) cc_final: 0.6947 (mp0) REVERT: G 68 GLU cc_start: 0.7467 (mt-10) cc_final: 0.7023 (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: 0.5831 (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: 0.6987 (mt-10) REVERT: H 72 MET cc_start: 0.7857 (tpt) cc_final: 0.7578 (tpp) REVERT: H 101 ILE cc_start: 0.6221 (pt) cc_final: 0.5854 (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: 0.1575 time to fit residues: 98.3061 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 : 0.378 ------------------------------------------------------------------------------- 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: 0.9980 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... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.170553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.122067 restraints weight = 15994.334| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.75 r_work: 0.3205 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16372 Z= 0.131 Angle : 0.470 7.943 22144 Z= 0.255 Chirality : 0.037 0.183 2568 Planarity : 0.004 0.032 2788 Dihedral : 3.423 11.515 2212 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.88 % Allowed : 9.61 % Favored : 89.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.40 (0.18), residues: 2020 helix: 2.02 (0.13), residues: 1520 sheet: 0.90 (0.65), residues: 64 loop : 0.27 (0.33), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 124 TYR 0.005 0.001 TYR E 139 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 covalent geometry : bond 0.00289 (16368) covalent geometry : angle 0.46965 (22136) SS BOND : bond 0.00017 ( 4) SS BOND : angle 0.64152 ( 8) hydrogen bonds : bond 0.04595 ( 1233) hydrogen bonds : angle 3.51680 ( 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 331 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 316 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 THR cc_start: 0.8854 (t) cc_final: 0.8551 (p) REVERT: A 377 LEU cc_start: 0.8317 (tp) cc_final: 0.7832 (mt) REVERT: A 451 LYS cc_start: 0.8418 (mmmt) cc_final: 0.8059 (mttp) REVERT: A 460 ARG cc_start: 0.7743 (ttt90) cc_final: 0.7359 (ttm-80) REVERT: A 467 ARG cc_start: 0.7687 (ttt90) cc_final: 0.7000 (ttp80) REVERT: B 250 THR cc_start: 0.8854 (t) cc_final: 0.8550 (p) REVERT: B 377 LEU cc_start: 0.8313 (tp) cc_final: 0.7829 (mt) REVERT: B 451 LYS cc_start: 0.8384 (mmmt) cc_final: 0.8010 (mttp) REVERT: B 460 ARG cc_start: 0.7727 (ttt90) cc_final: 0.7351 (ttm-80) REVERT: B 467 ARG cc_start: 0.7690 (ttt90) cc_final: 0.7027 (ttp80) REVERT: C 250 THR cc_start: 0.8841 (t) cc_final: 0.8544 (p) REVERT: C 377 LEU cc_start: 0.8315 (tp) cc_final: 0.7830 (mt) REVERT: C 451 LYS cc_start: 0.8378 (mmmt) cc_final: 0.8004 (mttp) REVERT: C 460 ARG cc_start: 0.7749 (ttt90) cc_final: 0.7365 (ttm-80) REVERT: C 467 ARG cc_start: 0.7699 (ttt90) cc_final: 0.7030 (ttp80) REVERT: D 250 THR cc_start: 0.8844 (t) cc_final: 0.8544 (p) REVERT: D 377 LEU cc_start: 0.8310 (tp) cc_final: 0.7826 (mt) REVERT: D 451 LYS cc_start: 0.8385 (mmmt) cc_final: 0.8014 (mttp) REVERT: D 460 ARG cc_start: 0.7754 (ttt90) cc_final: 0.7384 (ttm-80) REVERT: D 467 ARG cc_start: 0.7717 (ttt90) cc_final: 0.7052 (ttp80) REVERT: E 12 GLU cc_start: 0.7156 (pt0) cc_final: 0.6439 (tp30) REVERT: E 72 MET cc_start: 0.7894 (tpt) cc_final: 0.7588 (tpp) REVERT: F 12 GLU cc_start: 0.7141 (pt0) cc_final: 0.6428 (tp30) REVERT: F 72 MET cc_start: 0.7884 (tpt) cc_final: 0.7581 (tpp) REVERT: F 123 ASP cc_start: 0.4846 (m-30) cc_final: 0.4601 (m-30) REVERT: F 137 VAL cc_start: 0.7237 (t) cc_final: 0.6860 (p) REVERT: G 12 GLU cc_start: 0.7155 (pt0) cc_final: 0.6453 (tp30) REVERT: G 72 MET cc_start: 0.7906 (tpt) cc_final: 0.7605 (tpp) REVERT: G 123 ASP cc_start: 0.4856 (m-30) cc_final: 0.4602 (m-30) REVERT: H 12 GLU cc_start: 0.7133 (pt0) cc_final: 0.6430 (tp30) REVERT: H 72 MET cc_start: 0.7896 (tpt) cc_final: 0.7592 (tpp) REVERT: H 123 ASP cc_start: 0.4818 (m-30) cc_final: 0.4576 (m-30) outliers start: 15 outliers final: 8 residues processed: 323 average time/residue: 0.1514 time to fit residues: 69.0574 Evaluate side-chains 303 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 295 time to evaluate : 0.431 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 160 optimal weight: 0.0040 chunk 5 optimal weight: 0.5980 chunk 75 optimal weight: 0.8980 chunk 45 optimal weight: 0.0770 chunk 12 optimal weight: 0.9980 chunk 158 optimal weight: 0.0970 chunk 57 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 185 optimal weight: 5.9990 chunk 36 optimal weight: 0.4980 chunk 116 optimal weight: 0.6980 overall best weight: 0.2548 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 436 HIS B 436 HIS C 436 HIS D 436 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.181569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.135348 restraints weight = 15947.673| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.68 r_work: 0.3306 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2003 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= 0.096 Angle : 0.400 7.452 22144 Z= 0.216 Chirality : 0.034 0.136 2568 Planarity : 0.003 0.031 2788 Dihedral : 3.222 11.428 2212 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.88 % Allowed : 10.97 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.42 (0.19), residues: 2020 helix: 2.85 (0.13), residues: 1520 sheet: 0.87 (0.68), residues: 64 loop : 0.32 (0.34), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 87 TYR 0.006 0.001 TYR E 139 PHE 0.008 0.001 PHE D 356 TRP 0.006 0.001 TRP A 327 HIS 0.002 0.000 HIS C 189 Details of bonding type rmsd covalent geometry : bond 0.00187 (16368) covalent geometry : angle 0.39959 (22136) SS BOND : bond 0.00077 ( 4) SS BOND : angle 0.58991 ( 8) hydrogen bonds : bond 0.03591 ( 1233) hydrogen bonds : angle 3.21369 ( 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 331 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 316 time to evaluate : 0.613 Fit side-chains revert: symmetry clash REVERT: A 250 THR cc_start: 0.8830 (t) cc_final: 0.8590 (p) REVERT: A 377 LEU cc_start: 0.8358 (tp) cc_final: 0.7852 (mt) REVERT: A 451 LYS cc_start: 0.8426 (mmmt) cc_final: 0.8064 (mttp) REVERT: A 460 ARG cc_start: 0.7842 (ttt90) cc_final: 0.7633 (ttm-80) REVERT: A 467 ARG cc_start: 0.7749 (ttt90) cc_final: 0.7112 (ttp80) REVERT: B 250 THR cc_start: 0.8826 (t) cc_final: 0.8585 (p) REVERT: B 377 LEU cc_start: 0.8355 (tp) cc_final: 0.7849 (mt) REVERT: B 451 LYS cc_start: 0.8452 (mmmt) cc_final: 0.8086 (mttp) REVERT: B 460 ARG cc_start: 0.7850 (ttt90) cc_final: 0.7626 (ttm-80) REVERT: B 467 ARG cc_start: 0.7746 (ttt90) cc_final: 0.7111 (ttp80) REVERT: C 250 THR cc_start: 0.8822 (t) cc_final: 0.8587 (p) REVERT: C 377 LEU cc_start: 0.8365 (tp) cc_final: 0.7856 (mt) REVERT: C 451 LYS cc_start: 0.8445 (mmmt) cc_final: 0.8078 (mttp) REVERT: C 460 ARG cc_start: 0.7869 (ttt90) cc_final: 0.7652 (ttm-80) REVERT: C 467 ARG cc_start: 0.7748 (ttt90) cc_final: 0.7101 (ttp80) REVERT: D 250 THR cc_start: 0.8815 (t) cc_final: 0.8575 (p) REVERT: D 377 LEU cc_start: 0.8354 (tp) cc_final: 0.7848 (mt) REVERT: D 451 LYS cc_start: 0.8448 (mmmt) cc_final: 0.8080 (mttp) REVERT: D 460 ARG cc_start: 0.7873 (ttt90) cc_final: 0.7656 (ttm-80) REVERT: D 467 ARG cc_start: 0.7746 (ttt90) cc_final: 0.7093 (ttp80) REVERT: E 12 GLU cc_start: 0.7173 (pt0) cc_final: 0.6540 (tp30) REVERT: E 72 MET cc_start: 0.8021 (tpt) cc_final: 0.7752 (tpp) REVERT: F 12 GLU cc_start: 0.7151 (pt0) cc_final: 0.6520 (tp30) REVERT: F 72 MET cc_start: 0.8016 (tpt) cc_final: 0.7745 (tpp) REVERT: F 123 ASP cc_start: 0.4897 (m-30) cc_final: 0.4583 (m-30) REVERT: G 12 GLU cc_start: 0.7154 (pt0) cc_final: 0.6525 (tp30) REVERT: G 72 MET cc_start: 0.8033 (tpt) cc_final: 0.7766 (tpp) REVERT: G 123 ASP cc_start: 0.4926 (m-30) cc_final: 0.4618 (m-30) REVERT: H 12 GLU cc_start: 0.7157 (pt0) cc_final: 0.6523 (tp30) REVERT: H 72 MET cc_start: 0.8008 (tpt) cc_final: 0.7738 (tpp) REVERT: H 123 ASP cc_start: 0.4873 (m-30) cc_final: 0.4584 (m-30) outliers start: 15 outliers final: 7 residues processed: 323 average time/residue: 0.1507 time to fit residues: 68.7675 Evaluate side-chains 293 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 286 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain D residue 342 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 152 optimal weight: 6.9990 chunk 150 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 119 optimal weight: 0.3980 chunk 28 optimal weight: 0.4980 chunk 124 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 chunk 97 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 177 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.176135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.128199 restraints weight = 15973.429| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.70 r_work: 0.3166 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16372 Z= 0.155 Angle : 0.445 7.414 22144 Z= 0.239 Chirality : 0.037 0.135 2568 Planarity : 0.003 0.033 2788 Dihedral : 3.375 12.151 2212 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.59 % Allowed : 11.26 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.35 (0.19), residues: 2020 helix: 2.74 (0.13), residues: 1532 sheet: 0.80 (0.70), residues: 64 loop : 0.46 (0.34), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 395 TYR 0.007 0.001 TYR C 369 PHE 0.011 0.001 PHE B 433 TRP 0.004 0.001 TRP A 327 HIS 0.004 0.001 HIS A 448 Details of bonding type rmsd covalent geometry : bond 0.00366 (16368) covalent geometry : angle 0.44463 (22136) SS BOND : bond 0.00232 ( 4) SS BOND : angle 0.16729 ( 8) hydrogen bonds : bond 0.04059 ( 1233) hydrogen bonds : angle 3.27870 ( 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 339 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 312 time to evaluate : 0.612 Fit side-chains revert: symmetry clash REVERT: A 377 LEU cc_start: 0.8306 (tp) cc_final: 0.7873 (mt) REVERT: A 451 LYS cc_start: 0.8509 (mmmt) cc_final: 0.8152 (mttp) REVERT: A 460 ARG cc_start: 0.7882 (ttt90) cc_final: 0.7672 (ttm-80) REVERT: A 467 ARG cc_start: 0.7765 (ttt90) cc_final: 0.7060 (ttp80) REVERT: B 377 LEU cc_start: 0.8306 (tp) cc_final: 0.7875 (mt) REVERT: B 451 LYS cc_start: 0.8520 (mmmt) cc_final: 0.8155 (mttp) REVERT: B 460 ARG cc_start: 0.7872 (ttt90) cc_final: 0.7657 (ttm-80) REVERT: B 467 ARG cc_start: 0.7746 (ttt90) cc_final: 0.7044 (ttp80) REVERT: C 377 LEU cc_start: 0.8312 (tp) cc_final: 0.7877 (mt) REVERT: C 451 LYS cc_start: 0.8538 (mmmt) cc_final: 0.8168 (mttp) REVERT: C 460 ARG cc_start: 0.7854 (ttt90) cc_final: 0.7639 (ttm-80) REVERT: C 467 ARG cc_start: 0.7749 (ttt90) cc_final: 0.7036 (ttp80) REVERT: D 377 LEU cc_start: 0.8314 (tp) cc_final: 0.7877 (mt) REVERT: D 451 LYS cc_start: 0.8524 (mmmt) cc_final: 0.8160 (mttp) REVERT: D 460 ARG cc_start: 0.7886 (ttt90) cc_final: 0.7676 (ttm-80) REVERT: D 467 ARG cc_start: 0.7770 (ttt90) cc_final: 0.7056 (ttp80) REVERT: E 12 GLU cc_start: 0.7278 (pt0) cc_final: 0.6609 (tp30) REVERT: E 72 MET cc_start: 0.7981 (tpt) cc_final: 0.7691 (tpp) REVERT: F 12 GLU cc_start: 0.7282 (pt0) cc_final: 0.6628 (tp30) REVERT: F 48 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7242 (mp0) REVERT: F 72 MET cc_start: 0.7965 (tpt) cc_final: 0.7681 (tpp) REVERT: F 123 ASP cc_start: 0.5058 (m-30) cc_final: 0.4737 (m-30) REVERT: G 12 GLU cc_start: 0.7284 (pt0) cc_final: 0.6641 (tp30) REVERT: G 48 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7263 (mp0) REVERT: G 72 MET cc_start: 0.7974 (tpt) cc_final: 0.7710 (tpp) REVERT: G 123 ASP cc_start: 0.5071 (m-30) cc_final: 0.4739 (m-30) REVERT: H 12 GLU cc_start: 0.7250 (pt0) cc_final: 0.6621 (tp30) REVERT: H 48 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7234 (mp0) REVERT: H 72 MET cc_start: 0.7963 (tpt) cc_final: 0.7680 (tpp) REVERT: H 123 ASP cc_start: 0.5024 (m-30) cc_final: 0.4702 (m-30) outliers start: 27 outliers final: 14 residues processed: 325 average time/residue: 0.1440 time to fit residues: 66.5868 Evaluate side-chains 310 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 296 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 342 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 F residue 106 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 180 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 chunk 176 optimal weight: 0.9990 chunk 177 optimal weight: 0.9990 chunk 181 optimal weight: 3.9990 chunk 197 optimal weight: 2.9990 chunk 188 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 125 optimal weight: 0.0170 overall best weight: 0.7420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.172566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.123750 restraints weight = 16094.401| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.72 r_work: 0.3223 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 16372 Z= 0.119 Angle : 0.412 7.259 22144 Z= 0.223 Chirality : 0.036 0.148 2568 Planarity : 0.003 0.033 2788 Dihedral : 3.283 11.615 2212 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.53 % Allowed : 11.14 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.51 (0.19), residues: 2020 helix: 2.86 (0.13), residues: 1532 sheet: 0.87 (0.70), residues: 64 loop : 0.49 (0.33), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 395 TYR 0.006 0.001 TYR A 369 PHE 0.010 0.001 PHE B 356 TRP 0.006 0.001 TRP A 327 HIS 0.003 0.001 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00268 (16368) covalent geometry : angle 0.41221 (22136) SS BOND : bond 0.00096 ( 4) SS BOND : angle 0.16294 ( 8) hydrogen bonds : bond 0.03672 ( 1233) hydrogen bonds : angle 3.19305 ( 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 320 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 294 time to evaluate : 0.621 Fit side-chains revert: symmetry clash REVERT: A 250 THR cc_start: 0.8951 (t) cc_final: 0.8609 (p) REVERT: A 298 THR cc_start: 0.8428 (OUTLIER) cc_final: 0.8159 (m) REVERT: A 377 LEU cc_start: 0.8324 (tp) cc_final: 0.7869 (mt) REVERT: A 451 LYS cc_start: 0.8504 (mmmt) cc_final: 0.8126 (mttp) REVERT: A 460 ARG cc_start: 0.7856 (ttt90) cc_final: 0.7653 (ttm-80) REVERT: A 467 ARG cc_start: 0.7748 (ttt90) cc_final: 0.7022 (ttp80) REVERT: B 250 THR cc_start: 0.8951 (t) cc_final: 0.8609 (p) REVERT: B 377 LEU cc_start: 0.8320 (tp) cc_final: 0.7866 (mt) REVERT: B 451 LYS cc_start: 0.8502 (mmmt) cc_final: 0.8120 (mttp) REVERT: B 460 ARG cc_start: 0.7836 (ttt90) cc_final: 0.7633 (ttm-80) REVERT: B 467 ARG cc_start: 0.7747 (ttt90) cc_final: 0.7012 (ttp80) REVERT: C 250 THR cc_start: 0.8934 (t) cc_final: 0.8589 (p) REVERT: C 377 LEU cc_start: 0.8319 (tp) cc_final: 0.7863 (mt) REVERT: C 451 LYS cc_start: 0.8493 (mmmt) cc_final: 0.8109 (mttp) REVERT: C 460 ARG cc_start: 0.7821 (ttt90) cc_final: 0.7619 (ttm-80) REVERT: C 467 ARG cc_start: 0.7735 (ttt90) cc_final: 0.6992 (ttp80) REVERT: D 250 THR cc_start: 0.8949 (t) cc_final: 0.8609 (p) REVERT: D 377 LEU cc_start: 0.8319 (tp) cc_final: 0.7863 (mt) REVERT: D 451 LYS cc_start: 0.8502 (mmmt) cc_final: 0.8122 (mttp) REVERT: D 460 ARG cc_start: 0.7858 (ttt90) cc_final: 0.7650 (ttm-80) REVERT: D 467 ARG cc_start: 0.7762 (ttt90) cc_final: 0.6967 (ttp80) REVERT: E 12 GLU cc_start: 0.7241 (pt0) cc_final: 0.6588 (tp30) REVERT: E 72 MET cc_start: 0.7941 (tpt) cc_final: 0.7664 (tpp) REVERT: F 12 GLU cc_start: 0.7236 (pt0) cc_final: 0.6594 (tp30) REVERT: F 48 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7158 (mp0) REVERT: F 72 MET cc_start: 0.7936 (tpt) cc_final: 0.7659 (tpp) REVERT: F 123 ASP cc_start: 0.5056 (m-30) cc_final: 0.4718 (m-30) REVERT: G 12 GLU cc_start: 0.7237 (pt0) cc_final: 0.6615 (tp30) REVERT: G 48 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7222 (mp0) REVERT: G 72 MET cc_start: 0.7928 (tpt) cc_final: 0.7646 (tpp) REVERT: G 123 ASP cc_start: 0.4987 (m-30) cc_final: 0.4653 (m-30) REVERT: H 12 GLU cc_start: 0.7224 (pt0) cc_final: 0.6606 (tp30) REVERT: H 48 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7157 (mp0) REVERT: H 72 MET cc_start: 0.7937 (tpt) cc_final: 0.7662 (tpp) REVERT: H 123 ASP cc_start: 0.5021 (m-30) cc_final: 0.4681 (m-30) outliers start: 26 outliers final: 8 residues processed: 305 average time/residue: 0.1487 time to fit residues: 64.0658 Evaluate side-chains 286 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 277 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain D residue 342 THR Chi-restraints excluded: chain F residue 106 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 67 optimal weight: 2.9990 chunk 117 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 158 optimal weight: 0.3980 chunk 169 optimal weight: 0.8980 chunk 193 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 16 optimal weight: 6.9990 chunk 195 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 181 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 HIS B 483 HIS C 483 HIS D 483 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.170903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.121446 restraints weight = 16101.425| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.75 r_work: 0.3205 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2158 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= 0.118 Angle : 0.423 7.124 22144 Z= 0.226 Chirality : 0.036 0.162 2568 Planarity : 0.003 0.033 2788 Dihedral : 3.276 11.752 2212 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.65 % Allowed : 11.32 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.60 (0.19), residues: 2020 helix: 2.94 (0.13), residues: 1528 sheet: 0.93 (0.70), residues: 64 loop : 0.49 (0.33), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 87 TYR 0.006 0.001 TYR B 369 PHE 0.010 0.001 PHE D 356 TRP 0.006 0.001 TRP C 327 HIS 0.003 0.001 HIS A 448 Details of bonding type rmsd covalent geometry : bond 0.00269 (16368) covalent geometry : angle 0.42306 (22136) SS BOND : bond 0.00106 ( 4) SS BOND : angle 0.12726 ( 8) hydrogen bonds : bond 0.03613 ( 1233) hydrogen bonds : angle 3.14075 ( 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 320 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 292 time to evaluate : 0.523 Fit side-chains revert: symmetry clash REVERT: A 250 THR cc_start: 0.8962 (t) cc_final: 0.8621 (p) REVERT: A 377 LEU cc_start: 0.8325 (tp) cc_final: 0.7869 (mt) REVERT: A 451 LYS cc_start: 0.8501 (mmmt) cc_final: 0.8119 (mttp) REVERT: A 460 ARG cc_start: 0.7853 (ttt90) cc_final: 0.7650 (ttm-80) REVERT: A 467 ARG cc_start: 0.7745 (ttt90) cc_final: 0.6935 (ttp80) REVERT: B 250 THR cc_start: 0.8957 (t) cc_final: 0.8618 (p) REVERT: B 377 LEU cc_start: 0.8322 (tp) cc_final: 0.7864 (mt) REVERT: B 451 LYS cc_start: 0.8499 (mmmt) cc_final: 0.8117 (mttp) REVERT: B 460 ARG cc_start: 0.7830 (ttt90) cc_final: 0.7625 (ttm-80) REVERT: B 467 ARG cc_start: 0.7736 (ttt90) cc_final: 0.6934 (ttp80) REVERT: C 250 THR cc_start: 0.8938 (t) cc_final: 0.8596 (p) REVERT: C 377 LEU cc_start: 0.8324 (tp) cc_final: 0.7867 (mt) REVERT: C 451 LYS cc_start: 0.8500 (mmmt) cc_final: 0.8120 (mttp) REVERT: C 460 ARG cc_start: 0.7831 (ttt90) cc_final: 0.7625 (ttm-80) REVERT: C 467 ARG cc_start: 0.7715 (ttt90) cc_final: 0.6904 (ttp80) REVERT: D 250 THR cc_start: 0.8956 (t) cc_final: 0.8620 (p) REVERT: D 377 LEU cc_start: 0.8323 (tp) cc_final: 0.7864 (mt) REVERT: D 451 LYS cc_start: 0.8505 (mmmt) cc_final: 0.8126 (mttp) REVERT: D 460 ARG cc_start: 0.7854 (ttt90) cc_final: 0.7652 (ttm-80) REVERT: D 467 ARG cc_start: 0.7752 (ttt90) cc_final: 0.6938 (ttp80) REVERT: E 12 GLU cc_start: 0.7232 (pt0) cc_final: 0.6602 (tp30) REVERT: E 72 MET cc_start: 0.7928 (tpt) cc_final: 0.7654 (tpp) REVERT: F 12 GLU cc_start: 0.7216 (pt0) cc_final: 0.6600 (tp30) REVERT: F 48 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7205 (mp0) REVERT: F 72 MET cc_start: 0.7923 (tpt) cc_final: 0.7648 (tpp) REVERT: F 123 ASP cc_start: 0.5149 (m-30) cc_final: 0.4809 (m-30) REVERT: G 12 GLU cc_start: 0.7231 (pt0) cc_final: 0.6603 (tp30) REVERT: G 48 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7215 (mp0) REVERT: G 72 MET cc_start: 0.7946 (tpt) cc_final: 0.7669 (tpp) REVERT: G 123 ASP cc_start: 0.5067 (m-30) cc_final: 0.4720 (m-30) REVERT: G 141 GLU cc_start: 0.7894 (mp0) cc_final: 0.7645 (mp0) REVERT: H 12 GLU cc_start: 0.7214 (pt0) cc_final: 0.6588 (tp30) REVERT: H 48 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7190 (mp0) REVERT: H 72 MET cc_start: 0.7945 (tpt) cc_final: 0.7676 (tpp) REVERT: H 123 ASP cc_start: 0.5037 (m-30) cc_final: 0.4693 (m-30) outliers start: 28 outliers final: 13 residues processed: 306 average time/residue: 0.1210 time to fit residues: 53.6003 Evaluate side-chains 294 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 281 time to evaluate : 0.434 ------------------------------------------------------------------------------- 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 342 THR Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 342 THR 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 Chi-restraints excluded: chain F residue 106 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 184 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 151 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 119 optimal weight: 0.6980 chunk 76 optimal weight: 0.8980 chunk 66 optimal weight: 0.5980 chunk 164 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.171249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.121692 restraints weight = 16054.324| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.75 r_work: 0.3215 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16372 Z= 0.122 Angle : 0.422 7.050 22144 Z= 0.228 Chirality : 0.036 0.134 2568 Planarity : 0.003 0.033 2788 Dihedral : 3.277 11.992 2212 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.36 % Allowed : 11.26 % 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 aren not related in a simple way. whole: 3.61 (0.19), residues: 2020 helix: 2.88 (0.13), residues: 1552 sheet: 0.91 (0.70), residues: 64 loop : 0.67 (0.34), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 87 TYR 0.006 0.001 TYR B 369 PHE 0.010 0.001 PHE D 356 TRP 0.006 0.001 TRP C 327 HIS 0.003 0.001 HIS B 448 Details of bonding type rmsd covalent geometry : bond 0.00281 (16368) covalent geometry : angle 0.42194 (22136) SS BOND : bond 0.00009 ( 4) SS BOND : angle 0.23287 ( 8) hydrogen bonds : bond 0.03615 ( 1233) hydrogen bonds : angle 3.15602 ( 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 305 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 282 time to evaluate : 0.562 Fit side-chains revert: symmetry clash REVERT: A 250 THR cc_start: 0.8958 (t) cc_final: 0.8600 (p) REVERT: A 377 LEU cc_start: 0.8306 (tp) cc_final: 0.7873 (mt) REVERT: A 451 LYS cc_start: 0.8521 (mmmt) cc_final: 0.8135 (mttp) REVERT: A 467 ARG cc_start: 0.7750 (ttt90) cc_final: 0.6890 (ttp80) REVERT: B 250 THR cc_start: 0.8962 (t) cc_final: 0.8601 (p) REVERT: B 377 LEU cc_start: 0.8336 (tp) cc_final: 0.7879 (mt) REVERT: B 451 LYS cc_start: 0.8514 (mmmt) cc_final: 0.8123 (mttp) REVERT: B 467 ARG cc_start: 0.7754 (ttt90) cc_final: 0.6898 (ttp80) REVERT: C 250 THR cc_start: 0.8955 (t) cc_final: 0.8590 (p) REVERT: C 377 LEU cc_start: 0.8332 (tp) cc_final: 0.7872 (mt) REVERT: C 451 LYS cc_start: 0.8510 (mmmt) cc_final: 0.8121 (mttp) REVERT: C 467 ARG cc_start: 0.7755 (ttt90) cc_final: 0.6887 (ttp80) REVERT: D 250 THR cc_start: 0.8958 (t) cc_final: 0.8599 (p) REVERT: D 377 LEU cc_start: 0.8333 (tp) cc_final: 0.7872 (mt) REVERT: D 451 LYS cc_start: 0.8518 (mmmt) cc_final: 0.8135 (mttp) REVERT: D 467 ARG cc_start: 0.7753 (ttt90) cc_final: 0.6892 (ttp80) REVERT: E 12 GLU cc_start: 0.7211 (pt0) cc_final: 0.6555 (tp30) REVERT: E 72 MET cc_start: 0.7905 (tpt) cc_final: 0.7622 (tpp) REVERT: E 106 LEU cc_start: 0.7157 (OUTLIER) cc_final: 0.6878 (mm) REVERT: F 12 GLU cc_start: 0.7208 (pt0) cc_final: 0.6562 (tp30) REVERT: F 48 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7197 (mp0) REVERT: F 72 MET cc_start: 0.7921 (tpt) cc_final: 0.7640 (tpp) REVERT: F 123 ASP cc_start: 0.5189 (m-30) cc_final: 0.4861 (m-30) REVERT: G 12 GLU cc_start: 0.7204 (pt0) cc_final: 0.6580 (tp30) REVERT: G 48 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7222 (mp0) REVERT: G 72 MET cc_start: 0.7956 (tpt) cc_final: 0.7680 (tpp) REVERT: G 123 ASP cc_start: 0.5247 (m-30) cc_final: 0.4898 (m-30) REVERT: G 141 GLU cc_start: 0.7796 (mp0) cc_final: 0.7558 (mp0) REVERT: H 12 GLU cc_start: 0.7202 (pt0) cc_final: 0.6571 (tp30) REVERT: H 48 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7183 (mp0) REVERT: H 72 MET cc_start: 0.7923 (tpt) cc_final: 0.7645 (tpp) REVERT: H 123 ASP cc_start: 0.5146 (m-30) cc_final: 0.4784 (m-30) outliers start: 23 outliers final: 17 residues processed: 300 average time/residue: 0.1289 time to fit residues: 56.1479 Evaluate side-chains 294 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 276 time to evaluate : 0.586 ------------------------------------------------------------------------------- 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 A residue 342 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 B residue 342 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 Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain F residue 106 LEU 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: 5.9990 chunk 28 optimal weight: 4.9990 chunk 195 optimal weight: 0.9980 chunk 87 optimal weight: 0.8980 chunk 178 optimal weight: 0.0000 chunk 37 optimal weight: 5.9990 chunk 142 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 187 optimal weight: 0.9990 chunk 117 optimal weight: 0.6980 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.171487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.121937 restraints weight = 16187.806| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.76 r_work: 0.3278 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16372 Z= 0.118 Angle : 0.430 6.984 22144 Z= 0.229 Chirality : 0.036 0.133 2568 Planarity : 0.003 0.033 2788 Dihedral : 3.263 13.232 2212 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.53 % Allowed : 11.14 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.66 (0.19), residues: 2020 helix: 2.88 (0.13), residues: 1556 sheet: 0.87 (0.70), residues: 64 loop : 0.81 (0.34), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 87 TYR 0.006 0.001 TYR B 369 PHE 0.010 0.001 PHE D 356 TRP 0.006 0.001 TRP C 327 HIS 0.002 0.001 HIS B 448 Details of bonding type rmsd covalent geometry : bond 0.00269 (16368) covalent geometry : angle 0.43020 (22136) SS BOND : bond 0.00070 ( 4) SS BOND : angle 0.09869 ( 8) hydrogen bonds : bond 0.03550 ( 1233) hydrogen bonds : angle 3.12477 ( 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 308 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 282 time to evaluate : 0.534 Fit side-chains revert: symmetry clash REVERT: A 250 THR cc_start: 0.8933 (t) cc_final: 0.8576 (p) REVERT: A 377 LEU cc_start: 0.8291 (tp) cc_final: 0.7823 (mt) REVERT: A 451 LYS cc_start: 0.8465 (mmmt) cc_final: 0.8059 (mttp) REVERT: A 467 ARG cc_start: 0.7644 (ttt90) cc_final: 0.6803 (ttp80) REVERT: B 250 THR cc_start: 0.8932 (t) cc_final: 0.8571 (p) REVERT: B 377 LEU cc_start: 0.8296 (tp) cc_final: 0.7829 (mt) REVERT: B 451 LYS cc_start: 0.8457 (mmmt) cc_final: 0.8052 (mttp) REVERT: B 467 ARG cc_start: 0.7643 (ttt90) cc_final: 0.6804 (ttp80) REVERT: C 250 THR cc_start: 0.8934 (t) cc_final: 0.8565 (p) REVERT: C 377 LEU cc_start: 0.8296 (tp) cc_final: 0.7828 (mt) REVERT: C 451 LYS cc_start: 0.8450 (mmmt) cc_final: 0.8042 (mttp) REVERT: C 467 ARG cc_start: 0.7645 (ttt90) cc_final: 0.6796 (ttp80) REVERT: D 250 THR cc_start: 0.8934 (t) cc_final: 0.8578 (p) REVERT: D 377 LEU cc_start: 0.8291 (tp) cc_final: 0.7820 (mt) REVERT: D 451 LYS cc_start: 0.8454 (mmmt) cc_final: 0.8051 (mttp) REVERT: D 467 ARG cc_start: 0.7645 (ttt90) cc_final: 0.6793 (ttp80) REVERT: E 12 GLU cc_start: 0.7161 (pt0) cc_final: 0.6519 (tp30) REVERT: E 72 MET cc_start: 0.7900 (tpt) cc_final: 0.7618 (tpp) REVERT: F 12 GLU cc_start: 0.7148 (pt0) cc_final: 0.6512 (tp30) REVERT: F 48 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7207 (mp0) REVERT: F 72 MET cc_start: 0.7878 (tpt) cc_final: 0.7577 (tpp) REVERT: F 123 ASP cc_start: 0.5190 (m-30) cc_final: 0.4789 (m-30) REVERT: G 12 GLU cc_start: 0.7133 (pt0) cc_final: 0.6519 (tp30) REVERT: G 48 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7204 (mp0) REVERT: G 72 MET cc_start: 0.7912 (tpt) cc_final: 0.7616 (tpp) REVERT: G 123 ASP cc_start: 0.5181 (m-30) cc_final: 0.4788 (m-30) REVERT: G 141 GLU cc_start: 0.7739 (mp0) cc_final: 0.7506 (mp0) REVERT: H 12 GLU cc_start: 0.7158 (pt0) cc_final: 0.6541 (tp30) REVERT: H 48 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7191 (mp0) REVERT: H 72 MET cc_start: 0.7893 (tpt) cc_final: 0.7594 (tpp) REVERT: H 123 ASP cc_start: 0.5213 (m-30) cc_final: 0.4816 (m-30) outliers start: 26 outliers final: 15 residues processed: 299 average time/residue: 0.1267 time to fit residues: 54.9507 Evaluate side-chains 293 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 278 time to evaluate : 0.560 ------------------------------------------------------------------------------- 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 342 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 B residue 342 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: 0.7980 chunk 174 optimal weight: 2.9990 chunk 176 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 163 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 179 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 118 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.173157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.124260 restraints weight = 16039.352| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.71 r_work: 0.3233 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16372 Z= 0.130 Angle : 0.447 7.048 22144 Z= 0.236 Chirality : 0.037 0.134 2568 Planarity : 0.003 0.033 2788 Dihedral : 3.309 13.707 2212 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.36 % Allowed : 11.26 % 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 aren not related in a simple way. whole: 3.61 (0.19), residues: 2020 helix: 2.83 (0.13), residues: 1556 sheet: 0.90 (0.70), residues: 64 loop : 0.87 (0.34), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 87 TYR 0.007 0.001 TYR B 369 PHE 0.011 0.001 PHE D 356 TRP 0.005 0.001 TRP B 327 HIS 0.003 0.001 HIS D 189 Details of bonding type rmsd covalent geometry : bond 0.00306 (16368) covalent geometry : angle 0.44727 (22136) SS BOND : bond 0.00110 ( 4) SS BOND : angle 0.07444 ( 8) hydrogen bonds : bond 0.03655 ( 1233) hydrogen bonds : angle 3.15115 ( 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 298 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 275 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 377 LEU cc_start: 0.8330 (tp) cc_final: 0.7903 (mt) REVERT: A 451 LYS cc_start: 0.8553 (mmmt) cc_final: 0.8177 (mttp) REVERT: A 467 ARG cc_start: 0.7721 (ttt90) cc_final: 0.6917 (ttp80) REVERT: B 377 LEU cc_start: 0.8328 (tp) cc_final: 0.7904 (mt) REVERT: B 451 LYS cc_start: 0.8549 (mmmt) cc_final: 0.8174 (mttp) REVERT: B 467 ARG cc_start: 0.7722 (ttt90) cc_final: 0.6922 (ttp80) REVERT: C 250 THR cc_start: 0.8996 (t) cc_final: 0.8620 (p) REVERT: C 377 LEU cc_start: 0.8330 (tp) cc_final: 0.7905 (mt) REVERT: C 451 LYS cc_start: 0.8539 (mmmt) cc_final: 0.8157 (mttp) REVERT: C 467 ARG cc_start: 0.7712 (ttt90) cc_final: 0.6907 (ttp80) REVERT: D 377 LEU cc_start: 0.8324 (tp) cc_final: 0.7898 (mt) REVERT: D 451 LYS cc_start: 0.8547 (mmmt) cc_final: 0.8168 (mttp) REVERT: D 467 ARG cc_start: 0.7729 (ttt90) cc_final: 0.6921 (ttp80) REVERT: E 12 GLU cc_start: 0.7253 (pt0) cc_final: 0.6622 (tp30) REVERT: E 35 THR cc_start: 0.8315 (t) cc_final: 0.8066 (p) REVERT: E 72 MET cc_start: 0.7966 (tpt) cc_final: 0.7675 (tpp) REVERT: F 12 GLU cc_start: 0.7262 (pt0) cc_final: 0.6636 (tp30) REVERT: F 35 THR cc_start: 0.8338 (t) cc_final: 0.8106 (p) REVERT: F 48 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7222 (mp0) REVERT: F 72 MET cc_start: 0.7959 (tpt) cc_final: 0.7665 (tpp) REVERT: G 12 GLU cc_start: 0.7247 (pt0) cc_final: 0.6642 (tp30) REVERT: G 35 THR cc_start: 0.8353 (t) cc_final: 0.8124 (p) REVERT: G 48 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7199 (mp0) REVERT: G 72 MET cc_start: 0.7982 (tpt) cc_final: 0.7705 (tpp) REVERT: G 123 ASP cc_start: 0.5209 (m-30) cc_final: 0.4839 (m-30) REVERT: H 12 GLU cc_start: 0.7239 (pt0) cc_final: 0.6639 (tp30) REVERT: H 35 THR cc_start: 0.8366 (t) cc_final: 0.8137 (p) REVERT: H 48 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7191 (mp0) REVERT: H 72 MET cc_start: 0.7968 (tpt) cc_final: 0.7673 (tpp) REVERT: H 123 ASP cc_start: 0.5201 (m-30) cc_final: 0.4846 (m-30) outliers start: 23 outliers final: 20 residues processed: 294 average time/residue: 0.1282 time to fit residues: 54.9376 Evaluate side-chains 294 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 274 time to evaluate : 0.563 ------------------------------------------------------------------------------- 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 A residue 342 THR Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 342 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 189 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 100 optimal weight: 0.0970 chunk 158 optimal weight: 7.9990 chunk 163 optimal weight: 0.3980 chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 147 optimal weight: 8.9990 chunk 98 optimal weight: 1.9990 chunk 166 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.174231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.125444 restraints weight = 16007.966| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.71 r_work: 0.3246 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 16372 Z= 0.109 Angle : 0.431 6.929 22144 Z= 0.227 Chirality : 0.036 0.134 2568 Planarity : 0.003 0.033 2788 Dihedral : 3.278 12.980 2212 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.24 % Allowed : 11.50 % 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 aren not related in a simple way. whole: 3.76 (0.19), residues: 2020 helix: 2.94 (0.13), residues: 1556 sheet: 0.92 (0.69), residues: 64 loop : 0.90 (0.34), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 87 TYR 0.005 0.001 TYR A 369 PHE 0.010 0.001 PHE D 356 TRP 0.007 0.001 TRP D 327 HIS 0.002 0.001 HIS B 448 Details of bonding type rmsd covalent geometry : bond 0.00246 (16368) covalent geometry : angle 0.43124 (22136) SS BOND : bond 0.00021 ( 4) SS BOND : angle 0.13917 ( 8) hydrogen bonds : bond 0.03441 ( 1233) hydrogen bonds : angle 3.10710 ( 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 306 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 285 time to evaluate : 0.617 Fit side-chains revert: symmetry clash REVERT: A 250 THR cc_start: 0.8972 (t) cc_final: 0.8624 (p) REVERT: A 377 LEU cc_start: 0.8350 (tp) cc_final: 0.7904 (mt) REVERT: A 451 LYS cc_start: 0.8530 (mmmt) cc_final: 0.8158 (mttp) REVERT: A 467 ARG cc_start: 0.7721 (ttt90) cc_final: 0.6920 (ttp80) REVERT: B 250 THR cc_start: 0.8969 (t) cc_final: 0.8621 (p) REVERT: B 377 LEU cc_start: 0.8342 (tp) cc_final: 0.7852 (mt) REVERT: B 451 LYS cc_start: 0.8524 (mmmt) cc_final: 0.8149 (mttp) REVERT: B 467 ARG cc_start: 0.7727 (ttt90) cc_final: 0.6926 (ttp80) REVERT: C 250 THR cc_start: 0.8966 (t) cc_final: 0.8615 (p) REVERT: C 377 LEU cc_start: 0.8345 (tp) cc_final: 0.7856 (mt) REVERT: C 451 LYS cc_start: 0.8522 (mmmt) cc_final: 0.8147 (mttp) REVERT: C 467 ARG cc_start: 0.7719 (ttt90) cc_final: 0.6915 (ttp80) REVERT: D 250 THR cc_start: 0.8972 (t) cc_final: 0.8625 (p) REVERT: D 377 LEU cc_start: 0.8338 (tp) cc_final: 0.7849 (mt) REVERT: D 451 LYS cc_start: 0.8526 (mmmt) cc_final: 0.8155 (mttp) REVERT: D 467 ARG cc_start: 0.7726 (ttt90) cc_final: 0.6917 (ttp80) REVERT: E 12 GLU cc_start: 0.7235 (pt0) cc_final: 0.6627 (tp30) REVERT: E 35 THR cc_start: 0.8381 (t) cc_final: 0.8155 (p) REVERT: E 72 MET cc_start: 0.7985 (tpt) cc_final: 0.7707 (tpp) REVERT: E 141 GLU cc_start: 0.7933 (mp0) cc_final: 0.7718 (mp0) REVERT: F 12 GLU cc_start: 0.7206 (pt0) cc_final: 0.6598 (tp30) REVERT: F 35 THR cc_start: 0.8343 (t) cc_final: 0.8059 (p) REVERT: F 48 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7238 (mp0) REVERT: F 72 MET cc_start: 0.7974 (tpt) cc_final: 0.7690 (tpp) REVERT: G 12 GLU cc_start: 0.7217 (pt0) cc_final: 0.6639 (tp30) REVERT: G 48 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7215 (mp0) REVERT: G 72 MET cc_start: 0.8007 (tpt) cc_final: 0.7719 (tpp) REVERT: H 12 GLU cc_start: 0.7220 (pt0) cc_final: 0.6636 (tp30) REVERT: H 48 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7209 (mp0) REVERT: H 72 MET cc_start: 0.7973 (tpt) cc_final: 0.7694 (tpp) REVERT: H 123 ASP cc_start: 0.5164 (m-30) cc_final: 0.4788 (m-30) outliers start: 21 outliers final: 16 residues processed: 301 average time/residue: 0.1336 time to fit residues: 57.5350 Evaluate side-chains 296 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 280 time to evaluate : 0.601 ------------------------------------------------------------------------------- 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 A residue 342 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 B residue 342 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 33 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 140 optimal weight: 0.5980 chunk 95 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 158 optimal weight: 7.9990 chunk 90 optimal weight: 0.0470 chunk 67 optimal weight: 1.9990 chunk 189 optimal weight: 0.9990 chunk 163 optimal weight: 1.9990 overall best weight: 0.9282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.170848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.121208 restraints weight = 16046.303| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.75 r_work: 0.3298 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16372 Z= 0.138 Angle : 0.454 7.029 22144 Z= 0.239 Chirality : 0.037 0.134 2568 Planarity : 0.003 0.034 2788 Dihedral : 3.374 15.470 2212 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 0.94 % Allowed : 12.21 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.65 (0.19), residues: 2020 helix: 2.85 (0.13), residues: 1556 sheet: 0.83 (0.69), residues: 64 loop : 0.93 (0.34), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 87 TYR 0.007 0.001 TYR C 369 PHE 0.011 0.001 PHE C 356 TRP 0.005 0.001 TRP C 327 HIS 0.003 0.001 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00328 (16368) covalent geometry : angle 0.45384 (22136) SS BOND : bond 0.00136 ( 4) SS BOND : angle 0.08453 ( 8) hydrogen bonds : bond 0.03696 ( 1233) hydrogen bonds : angle 3.16158 ( 3639) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4300.39 seconds wall clock time: 74 minutes 3.79 seconds (4443.79 seconds total)