Starting phenix.real_space_refine on Wed Aug 5 19:16:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c9m_45364/08_2026/9c9m_45364.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c9m_45364/08_2026/9c9m_45364.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9c9m_45364/08_2026/9c9m_45364.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c9m_45364/08_2026/9c9m_45364.map" model { file = "/net/cci-nas-00/data/ceres_data/9c9m_45364/08_2026/9c9m_45364.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c9m_45364/08_2026/9c9m_45364.cif" } resolution = 2.01 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Zn 2 6.06 5 P 72 5.49 5 Mg 4 5.21 5 S 36 5.16 5 C 7046 2.51 5 N 2040 2.21 5 O 2299 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11503 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 2049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2049 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 9, 'TRANS': 251} Chain breaks: 1 Chain: "B" Number of atoms: 1914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1914 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 7, 'TRANS': 234} Chain breaks: 3 Chain: "D" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 388 Classifications: {'peptide': 47} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 43} Chain: "E" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 384 Classifications: {'DNA': 19} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 18} Chain: "F" Number of atoms: 371 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 17, 350 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Conformer: "B" Number of residues, atoms: 17, 350 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} bond proxies already assigned to first conformer: 369 Chain: "I" Number of atoms: 2049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2049 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 9, 'TRANS': 251} Chain breaks: 1 Chain: "K" Number of atoms: 1914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1914 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 7, 'TRANS': 234} Chain breaks: 3 Chain: "M" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 388 Classifications: {'peptide': 47} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 43} Chain: "N" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 384 Classifications: {'DNA': 19} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 18} Chain: "O" Number of atoms: 371 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 17, 350 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Conformer: "B" Number of residues, atoms: 17, 350 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} bond proxies already assigned to first conformer: 369 Chain: "L" Number of atoms: 572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 572 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "C" Number of atoms: 572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 572 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'DLU': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "O" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'DLU': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "F" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "I" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "N" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "O" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "L" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 319 SG CYS A 40 42.542 92.168 31.182 1.00 17.47 S ATOM 342 SG CYS A 43 45.478 90.410 32.452 1.00 19.39 S ATOM 5425 SG CYS I 40 60.382 38.974 31.194 1.00 17.38 S ATOM 5448 SG CYS I 43 57.434 40.738 32.449 1.00 19.60 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" P A DA F 21 " occ=0.58 ... (40 atoms not shown) pdb=" C4 B DA F 21 " occ=0.42 residue: pdb=" P A DA O 21 " occ=0.56 ... (40 atoms not shown) pdb=" C4 B DA O 21 " occ=0.44 Time building chain proxies: 2.57, per 1000 atoms: 0.22 Number of scatterers: 11503 At special positions: 0 Unit cell: (103.75, 132.8, 87.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 2 29.99 S 36 16.00 P 72 15.00 Mg 4 11.99 F 4 9.00 O 2299 8.00 N 2040 7.00 C 7046 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.98 Conformation dependent library (CDL) restraints added in 401.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 303 " pdb="ZN ZN A 303 " - pdb=" ND1 HIS A 16 " pdb="ZN ZN A 303 " - pdb=" NE2 HIS A 12 " pdb="ZN ZN A 303 " - pdb=" SG CYS A 40 " pdb="ZN ZN A 303 " - pdb=" SG CYS A 43 " pdb=" ZN I 303 " pdb="ZN ZN I 303 " - pdb=" ND1 HIS I 16 " pdb="ZN ZN I 303 " - pdb=" NE2 HIS I 12 " pdb="ZN ZN I 303 " - pdb=" SG CYS I 40 " pdb="ZN ZN I 303 " - pdb=" SG CYS I 43 " Number of angles added : 4 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2292 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 12 sheets defined 47.7% alpha, 22.3% beta 32 base pairs and 60 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 2 through 16 removed outlier: 3.668A pdb=" N ASP A 6 " --> pdb=" O LEU A 2 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS A 7 " --> pdb=" O ASP A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 26 Processing helix chain 'A' and resid 29 through 39 Processing helix chain 'A' and resid 40 through 44 Processing helix chain 'A' and resid 93 through 108 Processing helix chain 'A' and resid 118 through 123 Processing helix chain 'A' and resid 123 through 133 Processing helix chain 'A' and resid 144 through 147 Processing helix chain 'A' and resid 148 through 166 Processing helix chain 'A' and resid 167 through 169 No H-bonds generated for 'chain 'A' and resid 167 through 169' Processing helix chain 'A' and resid 171 through 186 Processing helix chain 'A' and resid 190 through 194 removed outlier: 3.517A pdb=" N TYR A 194 " --> pdb=" O ILE A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 221 Processing helix chain 'B' and resid 4 through 16 Processing helix chain 'B' and resid 18 through 27 Processing helix chain 'B' and resid 29 through 40 removed outlier: 3.777A pdb=" N CYS B 40 " --> pdb=" O ILE B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 108 Processing helix chain 'B' and resid 123 through 133 Processing helix chain 'B' and resid 150 through 166 Processing helix chain 'B' and resid 167 through 169 No H-bonds generated for 'chain 'B' and resid 167 through 169' Processing helix chain 'B' and resid 171 through 187 removed outlier: 3.910A pdb=" N ARG B 187 " --> pdb=" O HIS B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 221 Processing helix chain 'I' and resid 2 through 16 Processing helix chain 'I' and resid 18 through 26 Processing helix chain 'I' and resid 29 through 39 Processing helix chain 'I' and resid 40 through 44 Processing helix chain 'I' and resid 93 through 108 Processing helix chain 'I' and resid 118 through 123 Processing helix chain 'I' and resid 123 through 133 Processing helix chain 'I' and resid 144 through 147 Processing helix chain 'I' and resid 148 through 165 Processing helix chain 'I' and resid 166 through 169 removed outlier: 3.670A pdb=" N ALA I 169 " --> pdb=" O ARG I 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 166 through 169' Processing helix chain 'I' and resid 171 through 186 Processing helix chain 'I' and resid 190 through 194 removed outlier: 3.617A pdb=" N TYR I 194 " --> pdb=" O ILE I 191 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 221 Processing helix chain 'K' and resid 4 through 16 Processing helix chain 'K' and resid 18 through 27 Processing helix chain 'K' and resid 29 through 40 removed outlier: 3.799A pdb=" N CYS K 40 " --> pdb=" O ILE K 36 " (cutoff:3.500A) Processing helix chain 'K' and resid 93 through 108 Processing helix chain 'K' and resid 118 through 123 Processing helix chain 'K' and resid 123 through 134 Processing helix chain 'K' and resid 150 through 166 Processing helix chain 'K' and resid 167 through 169 No H-bonds generated for 'chain 'K' and resid 167 through 169' Processing helix chain 'K' and resid 171 through 186 Processing helix chain 'K' and resid 195 through 222 removed outlier: 3.913A pdb=" N ASN K 222 " --> pdb=" O THR K 218 " (cutoff:3.500A) Processing helix chain 'L' and resid 213 through 223 removed outlier: 3.869A pdb=" N PHE L 223 " --> pdb=" O LYS L 219 " (cutoff:3.500A) Processing helix chain 'L' and resid 270 through 277 Processing helix chain 'C' and resid 213 through 223 removed outlier: 3.863A pdb=" N PHE C 223 " --> pdb=" O LYS C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 277 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 89 removed outlier: 3.565A pdb=" N TYR A 83 " --> pdb=" O HIS A 78 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N VAL A 72 " --> pdb=" O ILE A 89 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N TRP A 61 " --> pdb=" O HIS A 114 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N VAL A 113 " --> pdb=" O GLU A 138 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 256 through 261 removed outlier: 6.999A pdb=" N ALA A 248 " --> pdb=" O LYS A 244 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N LYS A 244 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL A 250 " --> pdb=" O LEU A 242 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 84 through 89 removed outlier: 4.273A pdb=" N VAL B 72 " --> pdb=" O ILE B 89 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 257 through 261 removed outlier: 6.260A pdb=" N GLN B 252 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N LEU B 241 " --> pdb=" O GLN B 252 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU B 241 " --> pdb=" O PHE B 223 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N PHE B 223 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 256 through 261 removed outlier: 6.818A pdb=" N GLN D 252 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N LEU D 241 " --> pdb=" O GLN D 252 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N VAL D 225 " --> pdb=" O PRO D 238 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 83 through 89 removed outlier: 3.564A pdb=" N TYR I 83 " --> pdb=" O HIS I 78 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL I 72 " --> pdb=" O ILE I 89 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N TRP I 61 " --> pdb=" O HIS I 114 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N VAL I 113 " --> pdb=" O GLU I 138 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 257 through 261 removed outlier: 7.017A pdb=" N ALA I 248 " --> pdb=" O LYS I 244 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N LYS I 244 " --> pdb=" O ALA I 248 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL I 250 " --> pdb=" O LEU I 242 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 84 through 89 removed outlier: 4.298A pdb=" N VAL K 72 " --> pdb=" O ILE K 89 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N TRP K 61 " --> pdb=" O HIS K 114 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 257 through 261 removed outlier: 6.096A pdb=" N GLN K 252 " --> pdb=" O LEU K 241 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N LEU K 241 " --> pdb=" O GLN K 252 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LEU K 241 " --> pdb=" O PHE K 223 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N PHE K 223 " --> pdb=" O LEU K 241 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'M' and resid 256 through 261 removed outlier: 6.804A pdb=" N GLN M 252 " --> pdb=" O LEU M 241 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N LEU M 241 " --> pdb=" O GLN M 252 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N VAL M 225 " --> pdb=" O PRO M 238 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 257 through 261 removed outlier: 6.989A pdb=" N ALA L 248 " --> pdb=" O LYS L 244 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N LYS L 244 " --> pdb=" O ALA L 248 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL L 250 " --> pdb=" O LEU L 242 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR L 227 " --> pdb=" O LYS L 236 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N VAL L 225 " --> pdb=" O PRO L 238 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 257 through 261 removed outlier: 6.995A pdb=" N ALA C 248 " --> pdb=" O LYS C 244 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N LYS C 244 " --> pdb=" O ALA C 248 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL C 250 " --> pdb=" O LEU C 242 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N VAL C 225 " --> pdb=" O PRO C 238 " (cutoff:3.500A) 556 hydrogen bonds defined for protein. 1587 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 80 hydrogen bonds 160 hydrogen bond angles 0 basepair planarities 32 basepair parallelities 60 stacking parallelities Total time for adding SS restraints: 1.81 Time building geometry restraints manager: 1.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2889 1.33 - 1.45: 2452 1.45 - 1.57: 6265 1.57 - 1.69: 142 1.69 - 1.81: 52 Bond restraints: 11800 Sorted by residual: bond pdb=" CAN DLU F 101 " pdb=" CAV DLU F 101 " ideal model delta sigma weight residual 1.505 1.382 0.123 2.00e-02 2.50e+03 3.76e+01 bond pdb=" CAN DLU O 101 " pdb=" CAV DLU O 101 " ideal model delta sigma weight residual 1.505 1.383 0.122 2.00e-02 2.50e+03 3.74e+01 bond pdb=" CAU DLU F 101 " pdb=" FAG DLU F 101 " ideal model delta sigma weight residual 1.339 1.234 0.105 2.00e-02 2.50e+03 2.77e+01 bond pdb=" CAU DLU O 101 " pdb=" FAG DLU O 101 " ideal model delta sigma weight residual 1.339 1.235 0.104 2.00e-02 2.50e+03 2.69e+01 bond pdb=" CAR DLU F 101 " pdb=" CAX DLU F 101 " ideal model delta sigma weight residual 1.491 1.387 0.104 2.00e-02 2.50e+03 2.68e+01 ... (remaining 11795 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 15861 1.84 - 3.69: 328 3.69 - 5.53: 47 5.53 - 7.37: 2 7.37 - 9.21: 2 Bond angle restraints: 16240 Sorted by residual: angle pdb=" N3 DT N 29 " pdb=" C4 DT N 29 " pdb=" O4 DT N 29 " ideal model delta sigma weight residual 119.90 122.56 -2.66 6.00e-01 2.78e+00 1.97e+01 angle pdb=" N3 DT E 29 " pdb=" C4 DT E 29 " pdb=" O4 DT E 29 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.91e+01 angle pdb=" N3 DT N 28 " pdb=" C4 DT N 28 " pdb=" O4 DT N 28 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.76e+01 angle pdb=" N3 DT E 28 " pdb=" C4 DT E 28 " pdb=" O4 DT E 28 " ideal model delta sigma weight residual 119.90 122.42 -2.52 6.00e-01 2.78e+00 1.76e+01 angle pdb=" N3 DT O 17 " pdb=" C4 DT O 17 " pdb=" O4 DT O 17 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.73e+01 ... (remaining 16235 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.49: 6186 25.49 - 50.99: 573 50.99 - 76.48: 162 76.48 - 101.98: 19 101.98 - 127.47: 2 Dihedral angle restraints: 6942 sinusoidal: 3390 harmonic: 3552 Sorted by residual: dihedral pdb=" CA TYR A 194 " pdb=" C TYR A 194 " pdb=" N SER A 195 " pdb=" CA SER A 195 " ideal model delta harmonic sigma weight residual 180.00 154.69 25.31 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" CA TYR I 194 " pdb=" C TYR I 194 " pdb=" N SER I 195 " pdb=" CA SER I 195 " ideal model delta harmonic sigma weight residual 180.00 154.97 25.03 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CAM DLU O 101 " pdb=" CAL DLU O 101 " pdb=" OAQ DLU O 101 " pdb=" CBB DLU O 101 " ideal model delta sinusoidal sigma weight residual -69.82 57.65 -127.47 1 3.00e+01 1.11e-03 1.72e+01 ... (remaining 6939 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1128 0.034 - 0.068: 375 0.068 - 0.102: 116 0.102 - 0.135: 114 0.135 - 0.169: 47 Chirality restraints: 1780 Sorted by residual: chirality pdb=" C3' DC E 19 " pdb=" C4' DC E 19 " pdb=" O3' DC E 19 " pdb=" C2' DC E 19 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 7.15e-01 chirality pdb=" C3' DA F 12 " pdb=" C4' DA F 12 " pdb=" O3' DA F 12 " pdb=" C2' DA F 12 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 7.13e-01 chirality pdb=" C3'B DA O 21 " pdb=" C4'B DA O 21 " pdb=" O3'B DA O 21 " pdb=" C2'B DA O 21 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 7.12e-01 ... (remaining 1777 not shown) Planarity restraints: 1802 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 155 " 0.010 2.00e-02 2.50e+03 2.02e-02 4.09e+00 pdb=" C ASN A 155 " -0.035 2.00e-02 2.50e+03 pdb=" O ASN A 155 " 0.013 2.00e-02 2.50e+03 pdb=" N LYS A 156 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 260 " -0.033 5.00e-02 4.00e+02 5.04e-02 4.07e+00 pdb=" N PRO B 261 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO B 261 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 261 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DG N 18 " -0.023 2.00e-02 2.50e+03 1.03e-02 3.19e+00 pdb=" N9 DG N 18 " 0.026 2.00e-02 2.50e+03 pdb=" C8 DG N 18 " 0.001 2.00e-02 2.50e+03 pdb=" N7 DG N 18 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DG N 18 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG N 18 " -0.003 2.00e-02 2.50e+03 pdb=" O6 DG N 18 " -0.006 2.00e-02 2.50e+03 pdb=" N1 DG N 18 " -0.000 2.00e-02 2.50e+03 pdb=" C2 DG N 18 " 0.000 2.00e-02 2.50e+03 pdb=" N2 DG N 18 " 0.000 2.00e-02 2.50e+03 pdb=" N3 DG N 18 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DG N 18 " 0.003 2.00e-02 2.50e+03 ... (remaining 1799 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 115 2.56 - 3.14: 8983 3.14 - 3.73: 18885 3.73 - 4.31: 26809 4.31 - 4.90: 41711 Nonbonded interactions: 96503 Sorted by model distance: nonbonded pdb="MG MG A 301 " pdb=" O HOH A 408 " model vdw 1.971 2.170 nonbonded pdb="MG MG I 301 " pdb=" O HOH I 407 " model vdw 1.972 2.170 nonbonded pdb="MG MG A 301 " pdb=" O HOH A 405 " model vdw 1.978 2.170 nonbonded pdb="MG MG I 301 " pdb=" O HOH I 405 " model vdw 1.978 2.170 nonbonded pdb=" OD2 ASP A 64 " pdb="MG MG A 302 " model vdw 2.025 2.170 ... (remaining 96498 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 44 or resid 57 through 140 or resid 150 through \ 268)) selection = (chain 'B' and (resid 2 through 228 or resid 236 through 268)) selection = (chain 'I' and (resid 2 through 44 or resid 57 through 140 or resid 150 through \ 268)) selection = (chain 'K' and (resid 2 through 228 or resid 236 through 268)) } ncs_group { reference = chain 'C' selection = chain 'L' } ncs_group { reference = chain 'D' selection = chain 'M' } ncs_group { reference = chain 'E' selection = chain 'N' } ncs_group { reference = (chain 'F' and (resid 5 through 20 or resid 101)) selection = (chain 'O' and (resid 5 through 20 or resid 101)) } 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=0.42 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: 4.460 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: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 12.420 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 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 : 0.005 0.123 11808 Z= 0.340 Angle : 0.648 12.175 16244 Z= 0.425 Chirality : 0.051 0.169 1780 Planarity : 0.004 0.050 1802 Dihedral : 19.979 127.472 4650 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.19 % Allowed : 12.96 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.25), residues: 1208 helix: 1.80 (0.22), residues: 526 sheet: 1.17 (0.30), residues: 282 loop : -0.74 (0.33), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 107 TYR 0.016 0.001 TYR I 99 PHE 0.011 0.001 PHE I 181 TRP 0.008 0.001 TRP M 243 HIS 0.004 0.001 HIS I 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.34 (11800) covalent geometry : angle 0.63045 / 0.42 (16240) hydrogen bonds : bond 0.11710 / 8.19 ( 636) hydrogen bonds : angle 5.77419 / 4.19 ( 1747) metal coordination : bond 0.06861 / 3.67 ( 8) metal coordination : angle 9.62372 / 7.25 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 224 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 253 ASP cc_start: 0.6045 (t70) cc_final: 0.5461 (t0) REVERT: K 253 ASP cc_start: 0.6073 (t0) cc_final: 0.5726 (t0) outliers start: 2 outliers final: 1 residues processed: 224 average time/residue: 0.5104 time to fit residues: 123.3386 Evaluate side-chains 125 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 124 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 0.0060 chunk 113 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 123 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.3980 overall best weight: 0.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 114 HIS A 148 GLN B 27 ASN B 117 ASN B 222 ASN D 254 ASN I 114 HIS I 148 GLN K 216 GLN ** L 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 274 GLN ** C 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.137368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.094195 restraints weight = 18726.910| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 1.89 r_work: 0.3234 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3116 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (8 function evaluations) r_final: 0.3116 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 11808 Z= 0.174 Angle : 0.652 10.158 16244 Z= 0.353 Chirality : 0.045 0.154 1780 Planarity : 0.005 0.056 1802 Dihedral : 21.274 67.481 2222 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 3.36 % Allowed : 14.78 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.24), residues: 1208 helix: 1.74 (0.21), residues: 534 sheet: 1.33 (0.31), residues: 286 loop : -0.78 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 224 TYR 0.016 0.002 TYR K 227 PHE 0.018 0.002 PHE I 139 TRP 0.008 0.001 TRP M 243 HIS 0.008 0.001 HIS B 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.17 (11800) covalent geometry : angle 0.64477 / 0.35 (16240) hydrogen bonds : bond 0.04451 / 3.10 ( 636) hydrogen bonds : angle 4.72674 / 3.45 ( 1747) metal coordination : bond 0.01024 / 0.56 ( 8) metal coordination : angle 6.09506 / 4.53 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 143 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 240 LYS cc_start: 0.7885 (OUTLIER) cc_final: 0.7506 (tptp) REVERT: M 263 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.8425 (mtm110) REVERT: L 224 ARG cc_start: 0.7682 (mtt-85) cc_final: 0.7365 (mtp85) outliers start: 35 outliers final: 10 residues processed: 162 average time/residue: 0.6370 time to fit residues: 110.8625 Evaluate side-chains 133 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 121 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLN Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain D residue 240 LYS Chi-restraints excluded: chain I residue 9 GLN Chi-restraints excluded: chain K residue 22 MET Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain M residue 263 ARG Chi-restraints excluded: chain L residue 230 SER Chi-restraints excluded: chain L residue 252 GLN Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 252 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 chunk 119 optimal weight: 0.0970 chunk 95 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 7 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 47 optimal weight: 0.0970 chunk 13 optimal weight: 0.9980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 117 ASN B 137 GLN B 222 ASN L 214 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.136713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.092385 restraints weight = 25120.273| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.13 r_work: 0.3167 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3078 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3078 r_free = 0.3078 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3078 r_free = 0.3078 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3078 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11808 Z= 0.136 Angle : 0.551 7.894 16244 Z= 0.304 Chirality : 0.044 0.148 1780 Planarity : 0.004 0.048 1802 Dihedral : 21.036 66.840 2220 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 2.40 % Allowed : 16.03 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.24), residues: 1208 helix: 2.19 (0.22), residues: 534 sheet: 1.43 (0.31), residues: 282 loop : -0.78 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 224 TYR 0.010 0.001 TYR A 83 PHE 0.022 0.002 PHE K 26 TRP 0.023 0.001 TRP B 19 HIS 0.004 0.001 HIS A 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.14 (11800) covalent geometry : angle 0.54390 / 0.30 (16240) hydrogen bonds : bond 0.04173 / 2.90 ( 636) hydrogen bonds : angle 4.61290 / 3.36 ( 1747) metal coordination : bond 0.01375 / 0.80 ( 8) metal coordination : angle 5.51964 / 4.38 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 231 ARG cc_start: 0.7371 (OUTLIER) cc_final: 0.7046 (mtm180) REVERT: D 240 LYS cc_start: 0.8052 (OUTLIER) cc_final: 0.7638 (tptp) REVERT: D 263 ARG cc_start: 0.9031 (OUTLIER) cc_final: 0.8647 (mtm110) REVERT: I 136 LYS cc_start: 0.8797 (tmmt) cc_final: 0.8567 (ttpp) REVERT: L 224 ARG cc_start: 0.7762 (mtt-85) cc_final: 0.7488 (mmm-85) REVERT: L 229 ASP cc_start: 0.7309 (m-30) cc_final: 0.7057 (m-30) outliers start: 25 outliers final: 7 residues processed: 141 average time/residue: 0.6900 time to fit residues: 104.2345 Evaluate side-chains 131 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 121 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLN Chi-restraints excluded: chain D residue 231 ARG Chi-restraints excluded: chain D residue 240 LYS Chi-restraints excluded: chain D residue 263 ARG Chi-restraints excluded: chain I residue 9 GLN Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain M residue 231 ARG Chi-restraints excluded: chain L residue 220 ILE Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 230 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 34 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 2 optimal weight: 0.0970 chunk 0 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 105 optimal weight: 7.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 117 ASN B 222 ASN I 148 GLN K 222 ASN L 214 GLN C 214 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.132211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.086700 restraints weight = 21128.542| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.00 r_work: 0.3102 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2985 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2985 r_free = 0.2985 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2985 r_free = 0.2985 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2985 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.4216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11808 Z= 0.195 Angle : 0.626 7.869 16244 Z= 0.340 Chirality : 0.047 0.161 1780 Planarity : 0.005 0.046 1802 Dihedral : 21.298 64.296 2220 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.30 % Allowed : 16.31 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.24), residues: 1208 helix: 1.97 (0.21), residues: 534 sheet: 1.20 (0.30), residues: 286 loop : -0.76 (0.33), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 224 TYR 0.017 0.002 TYR B 83 PHE 0.017 0.002 PHE I 100 TRP 0.024 0.002 TRP B 19 HIS 0.007 0.002 HIS I 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.19 (11800) covalent geometry : angle 0.62232 / 0.34 (16240) hydrogen bonds : bond 0.05003 / 3.39 ( 636) hydrogen bonds : angle 4.68250 / 3.41 ( 1747) metal coordination : bond 0.01908 / 1.10 ( 8) metal coordination : angle 4.14875 / 3.21 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 129 time to evaluate : 0.296 Fit side-chains REVERT: A 9 GLN cc_start: 0.8288 (OUTLIER) cc_final: 0.8022 (mt0) REVERT: B 22 MET cc_start: 0.5814 (mtp) cc_final: 0.4609 (mtp) REVERT: D 240 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7825 (tptp) REVERT: I 9 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.7999 (mt0) REVERT: K 188 LYS cc_start: 0.7138 (OUTLIER) cc_final: 0.6713 (mmtp) REVERT: L 224 ARG cc_start: 0.7879 (mtt-85) cc_final: 0.7584 (mmm-85) REVERT: C 224 ARG cc_start: 0.7897 (mtt-85) cc_final: 0.7591 (mmm-85) REVERT: C 236 LYS cc_start: 0.8729 (mmtp) cc_final: 0.8451 (mmtp) outliers start: 24 outliers final: 7 residues processed: 146 average time/residue: 0.6384 time to fit residues: 99.6563 Evaluate side-chains 131 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLN Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain D residue 240 LYS Chi-restraints excluded: chain I residue 9 GLN Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 172 LEU Chi-restraints excluded: chain K residue 188 LYS Chi-restraints excluded: chain L residue 220 ILE Chi-restraints excluded: chain L residue 230 SER Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 230 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 110 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 85 optimal weight: 0.0980 chunk 92 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 73 optimal weight: 0.5980 chunk 7 optimal weight: 4.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 117 ASN B 137 GLN K 155 ASN L 214 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.132471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.087473 restraints weight = 23661.500| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.10 r_work: 0.3113 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2999 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2999 r_free = 0.2999 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2999 r_free = 0.2999 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.2999 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.4405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11808 Z= 0.148 Angle : 0.552 9.339 16244 Z= 0.303 Chirality : 0.044 0.144 1780 Planarity : 0.004 0.042 1802 Dihedral : 21.162 63.053 2220 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.11 % Allowed : 16.70 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.24), residues: 1208 helix: 2.12 (0.21), residues: 534 sheet: 1.16 (0.30), residues: 282 loop : -0.71 (0.33), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 224 TYR 0.014 0.001 TYR A 83 PHE 0.022 0.002 PHE B 26 TRP 0.027 0.002 TRP K 19 HIS 0.005 0.001 HIS A 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 (11800) covalent geometry : angle 0.54737 / 0.30 (16240) hydrogen bonds : bond 0.04178 / 2.89 ( 636) hydrogen bonds : angle 4.61085 / 3.37 ( 1747) metal coordination : bond 0.01617 / 0.97 ( 8) metal coordination : angle 4.71466 / 3.73 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 0.356 Fit side-chains REVERT: A 9 GLN cc_start: 0.8289 (OUTLIER) cc_final: 0.8055 (mt0) REVERT: B 188 LYS cc_start: 0.7368 (OUTLIER) cc_final: 0.6864 (mmtp) REVERT: D 240 LYS cc_start: 0.8308 (mmmt) cc_final: 0.7894 (tptp) REVERT: I 9 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.7978 (mt0) REVERT: K 188 LYS cc_start: 0.7198 (OUTLIER) cc_final: 0.6710 (mmtp) REVERT: L 224 ARG cc_start: 0.7880 (mtt-85) cc_final: 0.7581 (mmm-85) REVERT: C 224 ARG cc_start: 0.7900 (mtt-85) cc_final: 0.7620 (mmm-85) outliers start: 22 outliers final: 9 residues processed: 139 average time/residue: 0.7092 time to fit residues: 105.3014 Evaluate side-chains 134 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLN Chi-restraints excluded: chain B residue 188 LYS Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain I residue 9 GLN Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain K residue 188 LYS Chi-restraints excluded: chain K residue 220 ILE Chi-restraints excluded: chain M residue 231 ARG Chi-restraints excluded: chain L residue 220 ILE Chi-restraints excluded: chain L residue 230 SER Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 230 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 31 optimal weight: 4.9990 chunk 119 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 74 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 137 GLN I 148 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.132584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.088394 restraints weight = 20134.530| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.92 r_work: 0.3107 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2990 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.4514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11808 Z= 0.135 Angle : 0.542 9.266 16244 Z= 0.298 Chirality : 0.043 0.141 1780 Planarity : 0.004 0.042 1802 Dihedral : 21.105 63.586 2220 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.73 % Allowed : 17.08 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.24), residues: 1208 helix: 2.18 (0.22), residues: 534 sheet: 1.16 (0.30), residues: 282 loop : -0.69 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 224 TYR 0.014 0.001 TYR A 83 PHE 0.010 0.001 PHE A 100 TRP 0.023 0.001 TRP K 19 HIS 0.004 0.001 HIS A 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (11800) covalent geometry : angle 0.53751 / 0.30 (16240) hydrogen bonds : bond 0.04063 / 2.80 ( 636) hydrogen bonds : angle 4.54218 / 3.33 ( 1747) metal coordination : bond 0.01275 / 0.76 ( 8) metal coordination : angle 4.45909 / 3.52 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 0.339 Fit side-chains REVERT: A 9 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.7906 (mt0) REVERT: D 240 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.7850 (tptp) REVERT: I 9 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7982 (mt0) REVERT: K 22 MET cc_start: 0.6085 (ptm) cc_final: 0.5725 (ptp) REVERT: L 224 ARG cc_start: 0.7807 (mtt-85) cc_final: 0.7520 (mmm-85) REVERT: C 224 ARG cc_start: 0.7810 (mtt-85) cc_final: 0.7513 (mmm-85) outliers start: 18 outliers final: 11 residues processed: 133 average time/residue: 0.6472 time to fit residues: 92.1372 Evaluate side-chains 136 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLN Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain D residue 231 ARG Chi-restraints excluded: chain D residue 240 LYS Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain I residue 9 GLN Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 172 LEU Chi-restraints excluded: chain K residue 220 ILE Chi-restraints excluded: chain M residue 231 ARG Chi-restraints excluded: chain L residue 220 ILE Chi-restraints excluded: chain L residue 230 SER Chi-restraints excluded: chain C residue 220 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 43 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 120 optimal weight: 2.9990 chunk 111 optimal weight: 20.0000 chunk 91 optimal weight: 0.6980 chunk 101 optimal weight: 5.9990 chunk 115 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 64 optimal weight: 0.4980 chunk 81 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.131500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.086271 restraints weight = 27284.796| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.23 r_work: 0.3086 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2971 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2971 r_free = 0.2971 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2971 r_free = 0.2971 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2971 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.4660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11808 Z= 0.162 Angle : 0.567 8.963 16244 Z= 0.310 Chirality : 0.044 0.142 1780 Planarity : 0.004 0.044 1802 Dihedral : 21.136 64.124 2220 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.30 % Allowed : 16.60 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.24), residues: 1208 helix: 2.16 (0.21), residues: 534 sheet: 1.16 (0.30), residues: 282 loop : -0.69 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 224 TYR 0.014 0.002 TYR A 83 PHE 0.013 0.001 PHE A 100 TRP 0.032 0.002 TRP B 19 HIS 0.006 0.001 HIS I 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 (11800) covalent geometry : angle 0.56295 / 0.31 (16240) hydrogen bonds : bond 0.04313 / 2.94 ( 636) hydrogen bonds : angle 4.58474 / 3.35 ( 1747) metal coordination : bond 0.01690 / 1.02 ( 8) metal coordination : angle 4.11169 / 3.22 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 0.418 Fit side-chains REVERT: A 9 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.8113 (mt0) REVERT: D 240 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.7979 (tptm) REVERT: I 9 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.8029 (mt0) REVERT: K 22 MET cc_start: 0.6042 (ptm) cc_final: 0.5665 (ptp) REVERT: K 188 LYS cc_start: 0.7348 (OUTLIER) cc_final: 0.6776 (mmtp) REVERT: L 224 ARG cc_start: 0.7915 (mtt-85) cc_final: 0.7631 (mmm-85) REVERT: C 224 ARG cc_start: 0.7920 (mtt-85) cc_final: 0.7630 (mmm-85) outliers start: 24 outliers final: 13 residues processed: 142 average time/residue: 0.6409 time to fit residues: 97.5267 Evaluate side-chains 141 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLN Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain D residue 231 ARG Chi-restraints excluded: chain D residue 240 LYS Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain I residue 9 GLN Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 172 LEU Chi-restraints excluded: chain K residue 188 LYS Chi-restraints excluded: chain K residue 220 ILE Chi-restraints excluded: chain M residue 231 ARG Chi-restraints excluded: chain L residue 220 ILE Chi-restraints excluded: chain L residue 230 SER Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 230 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 125 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 99 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.130893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.086401 restraints weight = 33018.277| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.41 r_work: 0.3112 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2997 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2997 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8875 moved from start: 0.4736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11808 Z= 0.135 Angle : 0.541 8.691 16244 Z= 0.298 Chirality : 0.043 0.142 1780 Planarity : 0.004 0.041 1802 Dihedral : 21.099 64.520 2220 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.92 % Allowed : 16.99 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.24), residues: 1208 helix: 2.23 (0.22), residues: 534 sheet: 1.15 (0.30), residues: 282 loop : -0.66 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 224 TYR 0.014 0.001 TYR A 83 PHE 0.020 0.002 PHE B 223 TRP 0.028 0.001 TRP K 19 HIS 0.004 0.001 HIS A 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (11800) covalent geometry : angle 0.53659 / 0.30 (16240) hydrogen bonds : bond 0.03934 / 2.71 ( 636) hydrogen bonds : angle 4.52986 / 3.32 ( 1747) metal coordination : bond 0.01293 / 0.78 ( 8) metal coordination : angle 4.44481 / 3.52 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 0.248 Fit side-chains REVERT: A 9 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.8127 (mt0) REVERT: D 240 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.8035 (tptm) REVERT: I 9 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.8071 (mt0) REVERT: K 22 MET cc_start: 0.5935 (ptm) cc_final: 0.5522 (ptp) REVERT: L 224 ARG cc_start: 0.7954 (mtt-85) cc_final: 0.7683 (mmm-85) REVERT: C 224 ARG cc_start: 0.7935 (mtt-85) cc_final: 0.7668 (mmm-85) outliers start: 20 outliers final: 13 residues processed: 137 average time/residue: 0.6176 time to fit residues: 90.4771 Evaluate side-chains 141 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLN Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain B residue 137 GLN Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain D residue 231 ARG Chi-restraints excluded: chain D residue 240 LYS Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain I residue 9 GLN Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 172 LEU Chi-restraints excluded: chain K residue 220 ILE Chi-restraints excluded: chain M residue 231 ARG Chi-restraints excluded: chain L residue 220 ILE Chi-restraints excluded: chain L residue 230 SER Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 230 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 12 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 123 optimal weight: 0.7980 chunk 76 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 109 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 59 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.130803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.086255 restraints weight = 29000.064| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.28 r_work: 0.3113 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3007 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3007 r_free = 0.3007 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3007 r_free = 0.3007 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3007 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.4818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11808 Z= 0.155 Angle : 0.561 8.543 16244 Z= 0.309 Chirality : 0.044 0.143 1780 Planarity : 0.004 0.043 1802 Dihedral : 21.112 64.703 2220 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.82 % Allowed : 17.18 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.24), residues: 1208 helix: 2.16 (0.21), residues: 534 sheet: 1.11 (0.30), residues: 282 loop : -0.65 (0.33), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 224 TYR 0.014 0.002 TYR A 83 PHE 0.021 0.002 PHE B 26 TRP 0.043 0.002 TRP B 19 HIS 0.005 0.001 HIS I 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (11800) covalent geometry : angle 0.55774 / 0.31 (16240) hydrogen bonds : bond 0.04197 / 2.87 ( 636) hydrogen bonds : angle 4.56876 / 3.34 ( 1747) metal coordination : bond 0.01489 / 0.90 ( 8) metal coordination : angle 4.07598 / 3.20 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 0.266 Fit side-chains REVERT: A 9 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.8157 (mt0) REVERT: B 27 ASN cc_start: 0.8817 (t0) cc_final: 0.8615 (t0) REVERT: D 240 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.8057 (tptm) REVERT: I 9 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.8109 (mt0) REVERT: L 224 ARG cc_start: 0.7958 (mtt-85) cc_final: 0.7681 (mmm-85) REVERT: C 224 ARG cc_start: 0.7951 (mtt-85) cc_final: 0.7674 (mmm-85) outliers start: 19 outliers final: 14 residues processed: 137 average time/residue: 0.6703 time to fit residues: 98.0638 Evaluate side-chains 142 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLN Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain B residue 137 GLN Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain D residue 231 ARG Chi-restraints excluded: chain D residue 240 LYS Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain I residue 9 GLN Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 172 LEU Chi-restraints excluded: chain K residue 220 ILE Chi-restraints excluded: chain M residue 231 ARG Chi-restraints excluded: chain L residue 220 ILE Chi-restraints excluded: chain L residue 230 SER Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 230 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 122 optimal weight: 1.9990 chunk 124 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 221 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.130988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.086746 restraints weight = 27592.066| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.21 r_work: 0.3125 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3015 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3015 r_free = 0.3015 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3015 r_free = 0.3015 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3015 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.4887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11808 Z= 0.147 Angle : 0.555 8.551 16244 Z= 0.306 Chirality : 0.044 0.146 1780 Planarity : 0.004 0.042 1802 Dihedral : 21.119 64.931 2220 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.92 % Allowed : 17.08 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.24), residues: 1208 helix: 2.17 (0.22), residues: 534 sheet: 1.13 (0.30), residues: 282 loop : -0.66 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 224 TYR 0.014 0.001 TYR A 83 PHE 0.024 0.002 PHE B 26 TRP 0.043 0.002 TRP K 19 HIS 0.004 0.001 HIS A 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.15 (11800) covalent geometry : angle 0.55118 / 0.31 (16240) hydrogen bonds : bond 0.04043 / 2.78 ( 636) hydrogen bonds : angle 4.56859 / 3.34 ( 1747) metal coordination : bond 0.01394 / 0.83 ( 8) metal coordination : angle 4.27870 / 3.37 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 0.415 Fit side-chains REVERT: A 9 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.8114 (mt0) REVERT: B 27 ASN cc_start: 0.8757 (t0) cc_final: 0.8523 (t0) REVERT: D 240 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.8060 (tptm) REVERT: I 9 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.8064 (mt0) REVERT: L 224 ARG cc_start: 0.7936 (mtt-85) cc_final: 0.7659 (mmm-85) REVERT: L 262 ARG cc_start: 0.8975 (OUTLIER) cc_final: 0.8058 (tpm170) REVERT: C 224 ARG cc_start: 0.7928 (mtt-85) cc_final: 0.7652 (mmm-85) outliers start: 20 outliers final: 14 residues processed: 137 average time/residue: 0.6052 time to fit residues: 88.7171 Evaluate side-chains 139 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLN Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain B residue 137 GLN Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain D residue 231 ARG Chi-restraints excluded: chain D residue 240 LYS Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain I residue 9 GLN Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 172 LEU Chi-restraints excluded: chain K residue 220 ILE Chi-restraints excluded: chain M residue 231 ARG Chi-restraints excluded: chain L residue 220 ILE Chi-restraints excluded: chain L residue 230 SER Chi-restraints excluded: chain L residue 262 ARG Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 230 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 56 optimal weight: 5.9990 chunk 34 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 48 optimal weight: 10.0000 chunk 51 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 65 optimal weight: 0.4980 chunk 64 optimal weight: 0.4980 chunk 101 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 221 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.132231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.088940 restraints weight = 20102.789| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.94 r_work: 0.3177 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3064 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3064 r_free = 0.3064 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3064 r_free = 0.3064 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3064 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8838 moved from start: 0.4939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 11808 Z= 0.121 Angle : 0.533 8.352 16244 Z= 0.296 Chirality : 0.043 0.161 1780 Planarity : 0.004 0.041 1802 Dihedral : 21.054 64.817 2220 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.92 % Allowed : 17.75 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.24), residues: 1208 helix: 2.25 (0.22), residues: 534 sheet: 1.16 (0.30), residues: 282 loop : -0.63 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 224 TYR 0.014 0.001 TYR A 83 PHE 0.032 0.001 PHE B 26 TRP 0.047 0.002 TRP K 19 HIS 0.004 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 (11800) covalent geometry : angle 0.52877 / 0.30 (16240) hydrogen bonds : bond 0.03695 / 2.55 ( 636) hydrogen bonds : angle 4.51461 / 3.30 ( 1747) metal coordination : bond 0.01062 / 0.63 ( 8) metal coordination : angle 4.47223 / 3.54 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9077.80 seconds wall clock time: 153 minutes 58.50 seconds (9238.50 seconds total)