Starting phenix.real_space_refine on Fri May 9 18:06:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b3a_44133/05_2025/9b3a_44133_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b3a_44133/05_2025/9b3a_44133.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b3a_44133/05_2025/9b3a_44133.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b3a_44133/05_2025/9b3a_44133.map" model { file = "/net/cci-nas-00/data/ceres_data/9b3a_44133/05_2025/9b3a_44133_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b3a_44133/05_2025/9b3a_44133_neut.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 2190 2.51 5 N 555 2.21 5 O 570 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 3345 Number of models: 1 Model: "" Number of chains: 45 Chain: "A" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 156 Unusual residues: {'ACE': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 2, 'TRANS': 18} Chain: "B" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 58 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Chain: "C" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 156 Unusual residues: {'ACE': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 2, 'TRANS': 18} Chain: "D" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 58 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Chain: "E" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 156 Unusual residues: {'ACE': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 2, 'TRANS': 18} Chain: "F" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 58 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Chain: "G" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 156 Unusual residues: {'ACE': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 2, 'TRANS': 18} Chain: "H" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 58 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Chain: "I" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 156 Unusual residues: {'ACE': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 2, 'TRANS': 18} Chain: "J" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 58 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Chain: "K" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 156 Unusual residues: {'ACE': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 2, 'TRANS': 18} Chain: "L" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 58 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Chain: "M" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 156 Unusual residues: {'ACE': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 2, 'TRANS': 18} Chain: "N" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 58 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Chain: "O" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 156 Unusual residues: {'ACE': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 2, 'TRANS': 18} Chain: "P" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 58 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Chain: "Q" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 156 Unusual residues: {'ACE': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 2, 'TRANS': 18} Chain: "R" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 58 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Chain: "S" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 156 Unusual residues: {'ACE': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 2, 'TRANS': 18} Chain: "T" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 58 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Chain: "U" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 156 Unusual residues: {'ACE': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 2, 'TRANS': 18} Chain: "V" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 58 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Chain: "W" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 156 Unusual residues: {'ACE': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 2, 'TRANS': 18} Chain: "X" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 58 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Chain: "Y" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 156 Unusual residues: {'ACE': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 2, 'TRANS': 18} Chain: "Z" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 58 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Chain: "a" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 156 Unusual residues: {'ACE': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 2, 'TRANS': 18} Chain: "b" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 58 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Chain: "c" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 156 Unusual residues: {'ACE': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 2, 'TRANS': 18} Chain: "d" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 58 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 9 Unusual residues: {'8VH': 1, 'NH2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 9 Unusual residues: {'8VH': 1, 'NH2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 9 Unusual residues: {'8VH': 1, 'NH2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 9 Unusual residues: {'8VH': 1, 'NH2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 9 Unusual residues: {'8VH': 1, 'NH2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 9 Unusual residues: {'8VH': 1, 'NH2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 9 Unusual residues: {'8VH': 1, 'NH2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 9 Unusual residues: {'8VH': 1, 'NH2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 9 Unusual residues: {'8VH': 1, 'NH2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 9 Unusual residues: {'8VH': 1, 'NH2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 9 Unusual residues: {'8VH': 1, 'NH2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 9 Unusual residues: {'8VH': 1, 'NH2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 9 Unusual residues: {'8VH': 1, 'NH2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "a" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 9 Unusual residues: {'8VH': 1, 'NH2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "c" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 9 Unusual residues: {'8VH': 1, 'NH2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.89, per 1000 atoms: 0.86 Number of scatterers: 3345 At special positions: 0 Unit cell: (76.446, 78.09, 41.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 30 16.00 O 570 8.00 N 555 7.00 C 2190 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=45, symmetry=0 Number of additional bonds: simple=45, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.93 Conformation dependent library (CDL) restraints added in 379.8 milliseconds 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 750 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 9 sheets defined 0.0% alpha, 32.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'M' and resid 295 through 297 removed outlier: 6.797A pdb=" N ILE M 297 " --> pdb=" O ASN E 296 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ILE E 297 " --> pdb=" O ASN A 296 " (cutoff:3.500A) removed outlier: 8.689A pdb=" N ASP A 295 " --> pdb=" O ASN W 296 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ILE W 297 " --> pdb=" O ASN S 296 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'M' and resid 306 through 310 removed outlier: 6.720A pdb=" N GLN A 307 " --> pdb=" O ILE E 308 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N TYR E 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL A 309 " --> pdb=" O TYR E 310 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N VAL A 306 " --> pdb=" O GLN W 307 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N VAL W 309 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ILE A 308 " --> pdb=" O VAL W 309 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N GLN S 307 " --> pdb=" O ILE W 308 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N TYR W 310 " --> pdb=" O GLN S 307 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL S 309 " --> pdb=" O TYR W 310 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'N' and resid 307 through 310 removed outlier: 6.432A pdb=" N GLN F 307 " --> pdb=" O ILE N 308 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N TYR N 310 " --> pdb=" O GLN F 307 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL F 309 " --> pdb=" O TYR N 310 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLN B 307 " --> pdb=" O ILE F 308 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N TYR F 310 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N VAL B 309 " --> pdb=" O TYR F 310 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLN T 307 " --> pdb=" O ILE X 308 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N TYR X 310 " --> pdb=" O GLN T 307 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N VAL T 309 " --> pdb=" O TYR X 310 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'O' and resid 295 through 297 removed outlier: 6.775A pdb=" N ILE O 297 " --> pdb=" O ASN K 296 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ILE K 297 " --> pdb=" O ASN C 296 " (cutoff:3.500A) removed outlier: 8.574A pdb=" N ASP C 295 " --> pdb=" O ASN c 296 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ILE c 297 " --> pdb=" O ASN U 296 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'O' and resid 306 through 310 removed outlier: 6.625A pdb=" N GLN K 307 " --> pdb=" O ILE O 308 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N TYR O 310 " --> pdb=" O GLN K 307 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL K 309 " --> pdb=" O TYR O 310 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLN C 307 " --> pdb=" O ILE K 308 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N TYR K 310 " --> pdb=" O GLN C 307 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL C 309 " --> pdb=" O TYR K 310 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N GLN U 307 " --> pdb=" O ILE c 308 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N TYR c 310 " --> pdb=" O GLN U 307 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL U 309 " --> pdb=" O TYR c 310 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'P' and resid 307 through 310 removed outlier: 6.563A pdb=" N GLN L 307 " --> pdb=" O ILE P 308 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N TYR P 310 " --> pdb=" O GLN L 307 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N VAL L 309 " --> pdb=" O TYR P 310 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLN D 307 " --> pdb=" O ILE L 308 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N TYR L 310 " --> pdb=" O GLN D 307 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N VAL D 309 " --> pdb=" O TYR L 310 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N GLN V 307 " --> pdb=" O ILE d 308 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N TYR d 310 " --> pdb=" O GLN V 307 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N VAL V 309 " --> pdb=" O TYR d 310 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'Q' and resid 295 through 297 removed outlier: 6.808A pdb=" N ILE Q 297 " --> pdb=" O ASN I 296 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ILE I 297 " --> pdb=" O ASN G 296 " (cutoff:3.500A) removed outlier: 8.648A pdb=" N ASP G 295 " --> pdb=" O ASN a 296 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ILE a 297 " --> pdb=" O ASN Y 296 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'Q' and resid 306 through 310 removed outlier: 6.694A pdb=" N GLN G 307 " --> pdb=" O ILE I 308 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N TYR I 310 " --> pdb=" O GLN G 307 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N VAL G 309 " --> pdb=" O TYR I 310 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL G 306 " --> pdb=" O GLN a 307 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N VAL a 309 " --> pdb=" O VAL G 306 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ILE G 308 " --> pdb=" O VAL a 309 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N GLN Y 307 " --> pdb=" O ILE a 308 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N TYR a 310 " --> pdb=" O GLN Y 307 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL Y 309 " --> pdb=" O TYR a 310 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 307 through 310 removed outlier: 6.567A pdb=" N GLN J 307 " --> pdb=" O ILE R 308 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N TYR R 310 " --> pdb=" O GLN J 307 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL J 309 " --> pdb=" O TYR R 310 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLN H 307 " --> pdb=" O ILE J 308 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N TYR J 310 " --> pdb=" O GLN H 307 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N VAL H 309 " --> pdb=" O TYR J 310 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N GLN Z 307 " --> pdb=" O ILE b 308 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N TYR b 310 " --> pdb=" O GLN Z 307 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N VAL Z 309 " --> pdb=" O TYR b 310 " (cutoff:3.500A) 30 hydrogen bonds defined for protein. 90 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: 0.93 Time building geometry restraints manager: 1.08 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: 990 1.34 - 1.46: 647 1.46 - 1.58: 1708 1.58 - 1.69: 0 1.69 - 1.81: 30 Bond restraints: 3375 Sorted by residual: bond pdb=" C ACE G 293 " pdb=" O ACE G 293 " ideal model delta sigma weight residual 1.199 1.230 -0.031 2.00e-02 2.50e+03 2.41e+00 bond pdb=" C ACE A 293 " pdb=" O ACE A 293 " ideal model delta sigma weight residual 1.199 1.229 -0.030 2.00e-02 2.50e+03 2.27e+00 bond pdb=" C ACE O 293 " pdb=" O ACE O 293 " ideal model delta sigma weight residual 1.199 1.229 -0.030 2.00e-02 2.50e+03 2.26e+00 bond pdb=" C ACE Y 293 " pdb=" O ACE Y 293 " ideal model delta sigma weight residual 1.199 1.229 -0.030 2.00e-02 2.50e+03 2.24e+00 bond pdb=" C ACE I 293 " pdb=" O ACE I 293 " ideal model delta sigma weight residual 1.199 1.229 -0.030 2.00e-02 2.50e+03 2.24e+00 ... (remaining 3370 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.74: 4281 0.74 - 1.49: 174 1.49 - 2.23: 30 2.23 - 2.98: 30 2.98 - 3.72: 15 Bond angle restraints: 4530 Sorted by residual: angle pdb=" C TYR Y 310 " pdb=" N LYS Y 311 " pdb=" CA LYS Y 311 " ideal model delta sigma weight residual 122.83 125.29 -2.46 1.08e+00 8.57e-01 5.20e+00 angle pdb=" C TYR I 310 " pdb=" N LYS I 311 " pdb=" CA LYS I 311 " ideal model delta sigma weight residual 122.83 125.27 -2.44 1.08e+00 8.57e-01 5.11e+00 angle pdb=" C TYR c 310 " pdb=" N LYS c 311 " pdb=" CA LYS c 311 " ideal model delta sigma weight residual 122.83 125.23 -2.40 1.08e+00 8.57e-01 4.96e+00 angle pdb=" C TYR O 310 " pdb=" N LYS O 311 " pdb=" CA LYS O 311 " ideal model delta sigma weight residual 122.83 125.22 -2.39 1.08e+00 8.57e-01 4.90e+00 angle pdb=" C TYR A 310 " pdb=" N LYS A 311 " pdb=" CA LYS A 311 " ideal model delta sigma weight residual 122.83 125.21 -2.38 1.08e+00 8.57e-01 4.88e+00 ... (remaining 4525 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.30: 1713 8.30 - 16.59: 162 16.59 - 24.89: 15 24.89 - 33.18: 45 33.18 - 41.48: 15 Dihedral angle restraints: 1950 sinusoidal: 780 harmonic: 1170 Sorted by residual: dihedral pdb=" CA LYS G 298 " pdb=" CB LYS G 298 " pdb=" CG LYS G 298 " pdb=" CD LYS G 298 " ideal model delta sinusoidal sigma weight residual 180.00 149.09 30.91 3 1.50e+01 4.44e-03 4.97e+00 dihedral pdb=" CA LYS Y 298 " pdb=" CB LYS Y 298 " pdb=" CG LYS Y 298 " pdb=" CD LYS Y 298 " ideal model delta sinusoidal sigma weight residual 180.00 149.09 30.91 3 1.50e+01 4.44e-03 4.97e+00 dihedral pdb=" CA LYS Q 298 " pdb=" CB LYS Q 298 " pdb=" CG LYS Q 298 " pdb=" CD LYS Q 298 " ideal model delta sinusoidal sigma weight residual 180.00 149.11 30.89 3 1.50e+01 4.44e-03 4.96e+00 ... (remaining 1947 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 242 0.023 - 0.046: 117 0.046 - 0.069: 16 0.069 - 0.092: 1 0.092 - 0.114: 134 Chirality restraints: 510 Sorted by residual: chirality pdb=" CA ILE E 297 " pdb=" N ILE E 297 " pdb=" C ILE E 297 " pdb=" CB ILE E 297 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.28e-01 chirality pdb=" CA ILE c 297 " pdb=" N ILE c 297 " pdb=" C ILE c 297 " pdb=" CB ILE c 297 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.26e-01 chirality pdb=" CA ILE M 297 " pdb=" N ILE M 297 " pdb=" C ILE M 297 " pdb=" CB ILE M 297 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.22e-01 ... (remaining 507 not shown) Planarity restraints: 555 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL U 300 " -0.012 5.00e-02 4.00e+02 1.76e-02 4.95e-01 pdb=" N PRO U 301 " 0.030 5.00e-02 4.00e+02 pdb=" CA PRO U 301 " -0.009 5.00e-02 4.00e+02 pdb=" CD PRO U 301 " -0.010 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E 300 " -0.012 5.00e-02 4.00e+02 1.76e-02 4.95e-01 pdb=" N PRO E 301 " 0.030 5.00e-02 4.00e+02 pdb=" CA PRO E 301 " -0.009 5.00e-02 4.00e+02 pdb=" CD PRO E 301 " -0.010 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL K 300 " -0.012 5.00e-02 4.00e+02 1.75e-02 4.89e-01 pdb=" N PRO K 301 " 0.030 5.00e-02 4.00e+02 pdb=" CA PRO K 301 " -0.009 5.00e-02 4.00e+02 pdb=" CD PRO K 301 " -0.010 5.00e-02 4.00e+02 ... (remaining 552 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.92: 1300 2.92 - 3.42: 2790 3.42 - 3.91: 5746 3.91 - 4.41: 6085 4.41 - 4.90: 10820 Nonbonded interactions: 26741 Sorted by model distance: nonbonded pdb=" NZ LYS U 311 " pdb=" OD1 ASP a 295 " model vdw 2.430 3.120 nonbonded pdb=" NZ LYS C 311 " pdb=" OD1 ASP I 295 " model vdw 2.431 3.120 nonbonded pdb=" OD1 ASP E 295 " pdb=" NZ LYS G 311 " model vdw 2.457 3.120 nonbonded pdb=" OD1 ASP W 295 " pdb=" NZ LYS Y 311 " model vdw 2.458 3.120 nonbonded pdb=" NZ LYS K 311 " pdb=" OD1 ASP Q 295 " model vdw 2.461 3.120 ... (remaining 26736 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' selection = chain 'Y' selection = chain 'a' selection = chain 'c' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'X' selection = chain 'Z' selection = chain 'b' selection = chain 'd' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.370 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.200 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.117 3420 Z= 0.779 Angle : 0.431 3.721 4530 Z= 0.240 Chirality : 0.058 0.114 510 Planarity : 0.003 0.018 555 Dihedral : 9.127 41.475 1200 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.39), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.75 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS O 299 TYR 0.003 0.001 TYR Z 310 Details of bonding type rmsd hydrogen bonds : bond 0.18376 ( 30) hydrogen bonds : angle 7.46618 ( 90) covalent geometry : bond 0.00306 ( 3375) covalent geometry : angle 0.43136 ( 4530) Misc. bond : bond 0.06660 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.408 Fit side-chains REVERT: S 298 LYS cc_start: 0.7832 (mttt) cc_final: 0.7575 (pttm) REVERT: Y 295 ASP cc_start: 0.8101 (m-30) cc_final: 0.7806 (m-30) REVERT: a 295 ASP cc_start: 0.8059 (m-30) cc_final: 0.7580 (m-30) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.1742 time to fit residues: 23.8687 Evaluate side-chains 73 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 7 optimal weight: 0.3980 chunk 15 optimal weight: 0.0270 chunk 23 optimal weight: 9.9990 chunk 9 optimal weight: 0.0870 chunk 14 optimal weight: 0.1980 chunk 17 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 overall best weight: 0.2816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 307 GLN R 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.151726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.121628 restraints weight = 4105.124| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 2.68 r_work: 0.3603 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3420 Z= 0.083 Angle : 0.473 5.229 4530 Z= 0.240 Chirality : 0.059 0.140 510 Planarity : 0.003 0.023 555 Dihedral : 7.758 42.338 450 Min Nonbonded Distance : 2.666 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 5.87 % Allowed : 9.07 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.40), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.81 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS M 299 TYR 0.010 0.001 TYR M 310 Details of bonding type rmsd hydrogen bonds : bond 0.02563 ( 30) hydrogen bonds : angle 5.92709 ( 90) covalent geometry : bond 0.00195 ( 3375) covalent geometry : angle 0.47308 ( 4530) Misc. bond : bond 0.00021 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 72 time to evaluate : 0.417 Fit side-chains revert: symmetry clash REVERT: M 298 LYS cc_start: 0.7307 (tppt) cc_final: 0.6648 (ttmt) REVERT: Y 295 ASP cc_start: 0.8142 (m-30) cc_final: 0.7869 (m-30) REVERT: Y 310 TYR cc_start: 0.8574 (t80) cc_final: 0.8233 (t80) outliers start: 22 outliers final: 10 residues processed: 84 average time/residue: 0.1644 time to fit residues: 16.6479 Evaluate side-chains 75 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain H residue 308 ILE Chi-restraints excluded: chain J residue 308 ILE Chi-restraints excluded: chain R residue 308 ILE Chi-restraints excluded: chain V residue 308 ILE Chi-restraints excluded: chain V residue 309 VAL Chi-restraints excluded: chain Y residue 306 VAL Chi-restraints excluded: chain Z residue 308 ILE Chi-restraints excluded: chain a residue 306 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 27 optimal weight: 6.9990 chunk 29 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 5 optimal weight: 7.9990 chunk 23 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.150008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.120080 restraints weight = 4104.051| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 2.62 r_work: 0.3589 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 3420 Z= 0.101 Angle : 0.466 3.717 4530 Z= 0.238 Chirality : 0.059 0.179 510 Planarity : 0.003 0.024 555 Dihedral : 7.883 44.376 450 Min Nonbonded Distance : 2.662 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 6.13 % Allowed : 9.87 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.40), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.75 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS I 299 TYR 0.012 0.001 TYR M 310 Details of bonding type rmsd hydrogen bonds : bond 0.02315 ( 30) hydrogen bonds : angle 5.47039 ( 90) covalent geometry : bond 0.00251 ( 3375) covalent geometry : angle 0.46611 ( 4530) Misc. bond : bond 0.00042 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 63 time to evaluate : 0.392 Fit side-chains REVERT: M 298 LYS cc_start: 0.7370 (tppt) cc_final: 0.6754 (ttmt) REVERT: Y 295 ASP cc_start: 0.8087 (m-30) cc_final: 0.7797 (m-30) outliers start: 23 outliers final: 10 residues processed: 77 average time/residue: 0.1598 time to fit residues: 14.9227 Evaluate side-chains 71 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain G residue 295 ASP Chi-restraints excluded: chain J residue 308 ILE Chi-restraints excluded: chain L residue 309 VAL Chi-restraints excluded: chain R residue 308 ILE Chi-restraints excluded: chain V residue 309 VAL Chi-restraints excluded: chain Y residue 306 VAL Chi-restraints excluded: chain Z residue 308 ILE Chi-restraints excluded: chain b residue 308 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 9 optimal weight: 0.9980 chunk 19 optimal weight: 0.0040 chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 0.0870 chunk 18 optimal weight: 10.0000 chunk 1 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 chunk 7 optimal weight: 0.0970 chunk 26 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 overall best weight: 0.3968 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.151095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.121238 restraints weight = 4186.115| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 2.64 r_work: 0.3613 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3420 Z= 0.077 Angle : 0.452 3.621 4530 Z= 0.230 Chirality : 0.059 0.167 510 Planarity : 0.003 0.023 555 Dihedral : 7.802 44.736 450 Min Nonbonded Distance : 2.670 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.53 % Allowed : 11.73 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.41), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.77 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS O 299 TYR 0.010 0.001 TYR M 310 Details of bonding type rmsd hydrogen bonds : bond 0.02340 ( 30) hydrogen bonds : angle 4.98398 ( 90) covalent geometry : bond 0.00181 ( 3375) covalent geometry : angle 0.45207 ( 4530) Misc. bond : bond 0.00014 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 60 time to evaluate : 0.396 Fit side-chains REVERT: C 300 VAL cc_start: 0.8067 (t) cc_final: 0.7815 (m) REVERT: M 298 LYS cc_start: 0.7419 (tppt) cc_final: 0.6835 (ttmt) REVERT: X 309 VAL cc_start: 0.7424 (t) cc_final: 0.7127 (m) REVERT: Y 295 ASP cc_start: 0.8066 (m-30) cc_final: 0.7800 (m-30) REVERT: b 307 GLN cc_start: 0.7153 (mt0) cc_final: 0.6496 (tp-100) outliers start: 17 outliers final: 10 residues processed: 73 average time/residue: 0.1659 time to fit residues: 14.6461 Evaluate side-chains 68 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain H residue 308 ILE Chi-restraints excluded: chain J residue 308 ILE Chi-restraints excluded: chain M residue 306 VAL Chi-restraints excluded: chain R residue 308 ILE Chi-restraints excluded: chain V residue 309 VAL Chi-restraints excluded: chain Y residue 306 VAL Chi-restraints excluded: chain Z residue 308 ILE Chi-restraints excluded: chain b residue 308 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 0 optimal weight: 10.0000 chunk 15 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 24 optimal weight: 8.9990 chunk 25 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.143855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.114479 restraints weight = 4184.961| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.67 r_work: 0.3496 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 3420 Z= 0.276 Angle : 0.607 5.502 4530 Z= 0.315 Chirality : 0.061 0.156 510 Planarity : 0.004 0.026 555 Dihedral : 8.980 52.437 450 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 4.80 % Allowed : 11.73 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.41), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.71 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS Y 299 TYR 0.014 0.002 TYR M 310 Details of bonding type rmsd hydrogen bonds : bond 0.03463 ( 30) hydrogen bonds : angle 5.55439 ( 90) covalent geometry : bond 0.00712 ( 3375) covalent geometry : angle 0.60744 ( 4530) Misc. bond : bond 0.00084 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 59 time to evaluate : 0.398 Fit side-chains REVERT: M 298 LYS cc_start: 0.7410 (tppt) cc_final: 0.6804 (ttmt) REVERT: Y 295 ASP cc_start: 0.8137 (m-30) cc_final: 0.7849 (m-30) outliers start: 18 outliers final: 9 residues processed: 70 average time/residue: 0.1682 time to fit residues: 14.2777 Evaluate side-chains 65 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain J residue 308 ILE Chi-restraints excluded: chain L residue 309 VAL Chi-restraints excluded: chain M residue 306 VAL Chi-restraints excluded: chain R residue 308 ILE Chi-restraints excluded: chain S residue 306 VAL Chi-restraints excluded: chain Z residue 308 ILE Chi-restraints excluded: chain a residue 305 SER Chi-restraints excluded: chain a residue 306 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 7.9990 chunk 24 optimal weight: 7.9990 chunk 7 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 chunk 3 optimal weight: 0.7980 chunk 12 optimal weight: 0.0370 chunk 10 optimal weight: 4.9990 chunk 19 optimal weight: 0.0570 chunk 29 optimal weight: 0.8980 chunk 20 optimal weight: 0.1980 overall best weight: 0.3976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.150978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.121134 restraints weight = 4050.749| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 2.61 r_work: 0.3573 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 3420 Z= 0.081 Angle : 0.477 3.813 4530 Z= 0.245 Chirality : 0.060 0.192 510 Planarity : 0.003 0.023 555 Dihedral : 8.385 53.147 450 Min Nonbonded Distance : 2.677 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Rotamer: Outliers : 3.73 % Allowed : 15.20 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.41), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.83 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS c 299 TYR 0.017 0.001 TYR X 310 Details of bonding type rmsd hydrogen bonds : bond 0.02209 ( 30) hydrogen bonds : angle 4.95544 ( 90) covalent geometry : bond 0.00184 ( 3375) covalent geometry : angle 0.47697 ( 4530) Misc. bond : bond 0.00014 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 0.364 Fit side-chains REVERT: M 298 LYS cc_start: 0.7572 (tppt) cc_final: 0.6977 (ttmt) REVERT: Y 295 ASP cc_start: 0.7985 (m-30) cc_final: 0.7766 (m-30) outliers start: 14 outliers final: 10 residues processed: 68 average time/residue: 0.1679 time to fit residues: 13.8024 Evaluate side-chains 67 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain H residue 308 ILE Chi-restraints excluded: chain J residue 308 ILE Chi-restraints excluded: chain L residue 309 VAL Chi-restraints excluded: chain M residue 306 VAL Chi-restraints excluded: chain R residue 308 ILE Chi-restraints excluded: chain S residue 306 VAL Chi-restraints excluded: chain Z residue 308 ILE Chi-restraints excluded: chain a residue 306 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 0.0170 chunk 11 optimal weight: 7.9990 chunk 13 optimal weight: 8.9990 chunk 6 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 22 optimal weight: 8.9990 chunk 3 optimal weight: 0.9990 overall best weight: 2.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.144113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.115322 restraints weight = 4137.487| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 2.58 r_work: 0.3511 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 3420 Z= 0.218 Angle : 0.563 4.365 4530 Z= 0.293 Chirality : 0.061 0.216 510 Planarity : 0.004 0.025 555 Dihedral : 9.129 56.451 450 Min Nonbonded Distance : 2.653 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 4.53 % Allowed : 14.67 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.41), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.77 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS Y 299 TYR 0.011 0.002 TYR M 310 Details of bonding type rmsd hydrogen bonds : bond 0.03198 ( 30) hydrogen bonds : angle 5.28100 ( 90) covalent geometry : bond 0.00551 ( 3375) covalent geometry : angle 0.56269 ( 4530) Misc. bond : bond 0.00112 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 59 time to evaluate : 0.398 Fit side-chains REVERT: M 298 LYS cc_start: 0.7561 (tppt) cc_final: 0.6946 (ttmt) REVERT: Y 295 ASP cc_start: 0.8065 (m-30) cc_final: 0.7817 (m-30) REVERT: Y 310 TYR cc_start: 0.8605 (t80) cc_final: 0.8393 (t80) outliers start: 17 outliers final: 11 residues processed: 69 average time/residue: 0.1686 time to fit residues: 14.0941 Evaluate side-chains 68 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain H residue 308 ILE Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain J residue 308 ILE Chi-restraints excluded: chain L residue 309 VAL Chi-restraints excluded: chain M residue 306 VAL Chi-restraints excluded: chain R residue 308 ILE Chi-restraints excluded: chain S residue 306 VAL Chi-restraints excluded: chain a residue 305 SER Chi-restraints excluded: chain a residue 306 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 8 optimal weight: 0.2980 chunk 4 optimal weight: 8.9990 chunk 14 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.145592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.117223 restraints weight = 4100.086| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 2.48 r_work: 0.3555 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3420 Z= 0.120 Angle : 0.487 3.914 4530 Z= 0.250 Chirality : 0.059 0.193 510 Planarity : 0.003 0.026 555 Dihedral : 8.826 57.645 450 Min Nonbonded Distance : 2.673 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Rotamer: Outliers : 4.53 % Allowed : 15.47 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.41), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.77 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS Q 299 TYR 0.010 0.001 TYR X 310 Details of bonding type rmsd hydrogen bonds : bond 0.02587 ( 30) hydrogen bonds : angle 4.99678 ( 90) covalent geometry : bond 0.00292 ( 3375) covalent geometry : angle 0.48675 ( 4530) Misc. bond : bond 0.00048 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 0.435 Fit side-chains REVERT: F 310 TYR cc_start: 0.6126 (t80) cc_final: 0.5861 (t80) REVERT: M 298 LYS cc_start: 0.7571 (tppt) cc_final: 0.6966 (ttmt) REVERT: Y 295 ASP cc_start: 0.8024 (m-30) cc_final: 0.7789 (m-30) REVERT: Y 310 TYR cc_start: 0.8583 (t80) cc_final: 0.8195 (t80) outliers start: 17 outliers final: 13 residues processed: 75 average time/residue: 0.1685 time to fit residues: 15.2644 Evaluate side-chains 73 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain H residue 308 ILE Chi-restraints excluded: chain I residue 298 LYS Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain J residue 308 ILE Chi-restraints excluded: chain L residue 309 VAL Chi-restraints excluded: chain M residue 306 VAL Chi-restraints excluded: chain R residue 308 ILE Chi-restraints excluded: chain S residue 306 VAL Chi-restraints excluded: chain Y residue 305 SER Chi-restraints excluded: chain Y residue 306 VAL Chi-restraints excluded: chain a residue 306 VAL Chi-restraints excluded: chain b residue 308 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 18 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 0.5980 chunk 25 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.145483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.116873 restraints weight = 4198.054| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 2.54 r_work: 0.3533 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3420 Z= 0.146 Angle : 0.501 4.099 4530 Z= 0.260 Chirality : 0.059 0.181 510 Planarity : 0.003 0.026 555 Dihedral : 9.042 59.780 450 Min Nonbonded Distance : 2.658 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Rotamer: Outliers : 4.00 % Allowed : 15.73 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.42), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.77 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS Q 299 TYR 0.019 0.001 TYR a 310 Details of bonding type rmsd hydrogen bonds : bond 0.02830 ( 30) hydrogen bonds : angle 4.97339 ( 90) covalent geometry : bond 0.00369 ( 3375) covalent geometry : angle 0.50109 ( 4530) Misc. bond : bond 0.00048 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 0.417 Fit side-chains REVERT: F 310 TYR cc_start: 0.6346 (t80) cc_final: 0.6128 (t80) REVERT: Y 295 ASP cc_start: 0.8034 (m-30) cc_final: 0.7800 (m-30) outliers start: 15 outliers final: 12 residues processed: 70 average time/residue: 0.1846 time to fit residues: 15.4363 Evaluate side-chains 70 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain H residue 308 ILE Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain J residue 308 ILE Chi-restraints excluded: chain L residue 309 VAL Chi-restraints excluded: chain M residue 306 VAL Chi-restraints excluded: chain R residue 308 ILE Chi-restraints excluded: chain S residue 306 VAL Chi-restraints excluded: chain Y residue 305 SER Chi-restraints excluded: chain Y residue 306 VAL Chi-restraints excluded: chain a residue 306 VAL Chi-restraints excluded: chain b residue 308 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 0 optimal weight: 10.0000 chunk 21 optimal weight: 0.0980 chunk 14 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 7 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.149482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.120271 restraints weight = 4021.766| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 2.43 r_work: 0.3559 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3394 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3420 Z= 0.112 Angle : 0.506 8.801 4530 Z= 0.257 Chirality : 0.059 0.196 510 Planarity : 0.003 0.025 555 Dihedral : 8.872 59.307 450 Min Nonbonded Distance : 2.672 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Rotamer: Outliers : 3.73 % Allowed : 15.73 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.42), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.77 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS Q 299 TYR 0.017 0.001 TYR a 310 Details of bonding type rmsd hydrogen bonds : bond 0.02635 ( 30) hydrogen bonds : angle 4.83559 ( 90) covalent geometry : bond 0.00284 ( 3375) covalent geometry : angle 0.50646 ( 4530) Misc. bond : bond 0.00033 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.371 Fit side-chains REVERT: B 310 TYR cc_start: 0.6045 (t80) cc_final: 0.5746 (t80) REVERT: M 298 LYS cc_start: 0.7610 (tppt) cc_final: 0.6904 (tttt) REVERT: N 310 TYR cc_start: 0.5947 (t80) cc_final: 0.5686 (t80) REVERT: Y 295 ASP cc_start: 0.8151 (m-30) cc_final: 0.7944 (m-30) outliers start: 14 outliers final: 13 residues processed: 70 average time/residue: 0.1600 time to fit residues: 13.5565 Evaluate side-chains 70 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain H residue 308 ILE Chi-restraints excluded: chain I residue 305 SER Chi-restraints excluded: chain J residue 308 ILE Chi-restraints excluded: chain L residue 309 VAL Chi-restraints excluded: chain M residue 306 VAL Chi-restraints excluded: chain R residue 308 ILE Chi-restraints excluded: chain S residue 306 VAL Chi-restraints excluded: chain Y residue 305 SER Chi-restraints excluded: chain Y residue 306 VAL Chi-restraints excluded: chain a residue 306 VAL Chi-restraints excluded: chain b residue 308 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 23 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 chunk 15 optimal weight: 0.1980 chunk 3 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 13 optimal weight: 0.0980 chunk 27 optimal weight: 0.8980 chunk 5 optimal weight: 0.4980 chunk 20 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.152375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.122964 restraints weight = 4123.708| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 2.47 r_work: 0.3592 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.3286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 3420 Z= 0.086 Angle : 0.489 8.022 4530 Z= 0.249 Chirality : 0.059 0.177 510 Planarity : 0.003 0.025 555 Dihedral : 8.638 57.874 450 Min Nonbonded Distance : 2.674 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Rotamer: Outliers : 3.73 % Allowed : 16.00 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.42), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.82 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS K 299 TYR 0.011 0.001 TYR a 310 Details of bonding type rmsd hydrogen bonds : bond 0.02433 ( 30) hydrogen bonds : angle 4.57061 ( 90) covalent geometry : bond 0.00213 ( 3375) covalent geometry : angle 0.48868 ( 4530) Misc. bond : bond 0.00021 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1950.70 seconds wall clock time: 34 minutes 38.28 seconds (2078.28 seconds total)