Starting phenix.real_space_refine on Fri Jul 3 01:23:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c9m_45364/07_2026/9c9m_45364.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c9m_45364/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/9c9m_45364/07_2026/9c9m_45364.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c9m_45364/07_2026/9c9m_45364.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9c9m_45364/07_2026/9c9m_45364.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c9m_45364/07_2026/9c9m_45364.map" } 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-dev-6108/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: 2.78, per 1000 atoms: 0.24 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: 0.75 Conformation dependent library (CDL) restraints added in 263.9 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: 1.60 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: 2.41 Time building geometry restraints manager: 0.98 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: 15865 1.84 - 3.69: 324 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 14.390 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.280 ------------------------------------------------------------------------------- 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 : 0.646 12.175 16244 Z= 0.422 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 0.62823 / 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 : 0.421 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: 0.5641 time to fit residues: 136.3013 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 : 0.427 ------------------------------------------------------------------------------- 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 = 0.137379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.094205 restraints weight = 18808.829| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.90 r_work: 0.3233 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3121 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 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 = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (6 function evaluations) r_final: 0.3121 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11808 Z= 0.169 Angle : 0.646 9.725 16244 Z= 0.353 Chirality : 0.045 0.162 1780 Planarity : 0.005 0.056 1802 Dihedral : 21.301 67.290 2222 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 4.26 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: 1.28 (0.24), residues: 1208 helix: 1.74 (0.21), residues: 534 sheet: 1.34 (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 0.013 0.002 TYR K 194 PHE 0.019 0.002 PHE I 139 TRP 0.009 0.001 TRP K 19 HIS 0.008 0.001 HIS B 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.17 (11800) covalent geometry : angle 0.63891 / 0.35 (16240) hydrogen bonds : bond 0.04422 / 3.08 ( 636) hydrogen bonds : angle 4.72279 / 3.45 ( 1747) metal coordination : bond 0.00977 / 0.54 ( 8) metal coordination : angle 6.05488 / 4.49 ( 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 : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 240 LYS cc_start: 0.7884 (OUTLIER) cc_final: 0.7502 (tptp) REVERT: L 224 ARG cc_start: 0.7688 (mtt-85) cc_final: 0.7369 (mtp85) outliers start: 35 outliers final: 10 residues processed: 162 average time/residue: 0.6899 time to fit residues: 119.9657 Evaluate side-chains 132 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 121 time to evaluate : 0.397 ------------------------------------------------------------------------------- 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 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: 5.9990 chunk 54 optimal weight: 5.9990 chunk 119 optimal weight: 0.8980 chunk 95 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 68 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 87 optimal weight: 5.9990 chunk 47 optimal weight: 0.4980 chunk 13 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4057 r_free = 0.4057 target = 0.136308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.091563 restraints weight = 25203.352| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.14 r_work: 0.3179 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3033 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3033 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11808 Z= 0.140 Angle : 0.550 7.600 16244 Z= 0.306 Chirality : 0.043 0.146 1780 Planarity : 0.004 0.043 1802 Dihedral : 21.087 64.747 2220 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 2.40 % Allowed : 15.26 % Favored : 82.34 % 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: 1.60 (0.24), residues: 1208 helix: 2.13 (0.22), residues: 534 sheet: 1.44 (0.31), residues: 282 loop : -0.78 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG I 224 TYR 0.010 0.001 TYR A 83 PHE 0.014 0.002 PHE K 26 TRP 0.021 0.001 TRP B 19 HIS 0.005 0.001 HIS A 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 (11800) covalent geometry : angle 0.54388 / 0.31 (16240) hydrogen bonds : bond 0.04260 / 2.96 ( 636) hydrogen bonds : angle 4.63578 / 3.38 ( 1747) metal coordination : bond 0.01432 / 0.83 ( 8) metal coordination : angle 5.38456 / 4.27 ( 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 153 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 128 time to evaluate : 0.433 Fit side-chains revert: symmetry clash REVERT: D 231 ARG cc_start: 0.7421 (OUTLIER) cc_final: 0.7211 (mtm180) REVERT: D 240 LYS cc_start: 0.8088 (OUTLIER) cc_final: 0.7687 (tptp) REVERT: D 263 ARG cc_start: 0.9063 (OUTLIER) cc_final: 0.8723 (mtm110) REVERT: I 136 LYS cc_start: 0.8818 (tmmt) cc_final: 0.8578 (ttpp) REVERT: L 224 ARG cc_start: 0.7832 (mtt-85) cc_final: 0.7570 (mmm-85) REVERT: L 229 ASP cc_start: 0.7372 (m-30) cc_final: 0.7111 (m-30) REVERT: C 224 ARG cc_start: 0.7871 (mtt-85) cc_final: 0.7619 (mmm-85) REVERT: C 253 ASP cc_start: 0.7576 (t0) cc_final: 0.7341 (t0) outliers start: 25 outliers final: 7 residues processed: 144 average time/residue: 0.6667 time to fit residues: 103.2005 Evaluate side-chains 128 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 0.419 ------------------------------------------------------------------------------- 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: 0.6980 chunk 95 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 117 ASN B 222 ASN K 222 ASN L 214 GLN C 214 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.132723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.087876 restraints weight = 20456.531| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.96 r_work: 0.3117 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3002 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3002 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.4071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11808 Z= 0.177 Angle : 0.591 6.980 16244 Z= 0.324 Chirality : 0.045 0.186 1780 Planarity : 0.004 0.044 1802 Dihedral : 21.255 63.440 2220 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.21 % Allowed : 16.22 % 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: 1.49 (0.24), residues: 1208 helix: 2.01 (0.21), residues: 534 sheet: 1.33 (0.31), residues: 282 loop : -0.73 (0.33), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 224 TYR 0.016 0.002 TYR B 83 PHE 0.015 0.002 PHE A 100 TRP 0.022 0.002 TRP B 19 HIS 0.005 0.001 HIS I 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.18 (11800) covalent geometry : angle 0.58749 / 0.32 (16240) hydrogen bonds : bond 0.04630 / 3.16 ( 636) hydrogen bonds : angle 4.62117 / 3.37 ( 1747) metal coordination : bond 0.01751 / 1.00 ( 8) metal coordination : angle 4.20466 / 3.27 ( 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 151 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 0.410 Fit side-chains REVERT: A 9 GLN cc_start: 0.8270 (OUTLIER) cc_final: 0.8003 (mt0) REVERT: B 22 MET cc_start: 0.5825 (mtp) cc_final: 0.4631 (mtp) REVERT: D 240 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.7820 (tptp) REVERT: I 9 GLN cc_start: 0.8313 (OUTLIER) cc_final: 0.7997 (mt0) REVERT: K 188 LYS cc_start: 0.7128 (OUTLIER) cc_final: 0.6716 (mmtp) REVERT: L 224 ARG cc_start: 0.7883 (mtt-85) cc_final: 0.7592 (mmm-85) REVERT: C 224 ARG cc_start: 0.7895 (mtt-85) cc_final: 0.7627 (mmm-85) REVERT: C 236 LYS cc_start: 0.8733 (mmtp) cc_final: 0.8454 (mmtp) outliers start: 23 outliers final: 6 residues processed: 144 average time/residue: 0.6952 time to fit residues: 107.2011 Evaluate side-chains 134 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 124 time to evaluate : 0.415 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 27 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 82 optimal weight: 0.4980 chunk 85 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 73 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 137 GLN L 214 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.133514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.088600 restraints weight = 23507.247| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.08 r_work: 0.3112 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2995 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2995 r_free = 0.2995 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2995 r_free = 0.2995 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (11 function evaluations) r_final: 0.2995 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.4304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11808 Z= 0.129 Angle : 0.532 9.843 16244 Z= 0.295 Chirality : 0.043 0.142 1780 Planarity : 0.004 0.040 1802 Dihedral : 21.149 62.960 2220 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.54 % Allowed : 17.08 % 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: 1.61 (0.24), residues: 1208 helix: 2.19 (0.22), residues: 534 sheet: 1.25 (0.30), residues: 282 loop : -0.68 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 224 TYR 0.013 0.001 TYR A 83 PHE 0.022 0.001 PHE B 26 TRP 0.026 0.001 TRP B 19 HIS 0.005 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 (11800) covalent geometry : angle 0.52670 / 0.29 (16240) hydrogen bonds : bond 0.03914 / 2.72 ( 636) hydrogen bonds : angle 4.54288 / 3.33 ( 1747) metal coordination : bond 0.01282 / 0.76 ( 8) metal coordination : angle 4.81908 / 3.83 ( 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 142 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 0.431 Fit side-chains REVERT: A 9 GLN cc_start: 0.8238 (OUTLIER) cc_final: 0.7994 (mt0) REVERT: B 188 LYS cc_start: 0.7289 (OUTLIER) cc_final: 0.6790 (mmtp) REVERT: D 240 LYS cc_start: 0.8222 (mmmt) cc_final: 0.7796 (tptp) REVERT: I 9 GLN cc_start: 0.8261 (OUTLIER) cc_final: 0.7989 (mt0) REVERT: L 224 ARG cc_start: 0.7813 (mtt-85) cc_final: 0.7504 (mmm-85) REVERT: C 224 ARG cc_start: 0.7840 (mtt-85) cc_final: 0.7560 (mmm-85) outliers start: 16 outliers final: 8 residues processed: 136 average time/residue: 0.7273 time to fit residues: 105.5712 Evaluate side-chains 134 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 123 time to evaluate : 0.462 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 85 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 chunk 49 optimal weight: 9.9990 chunk 22 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 84 optimal weight: 0.3980 chunk 74 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 222 ASN L 214 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.132025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.087273 restraints weight = 20010.731| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.94 r_work: 0.3087 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3003 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.3003 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.4467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11808 Z= 0.158 Angle : 0.555 9.477 16244 Z= 0.306 Chirality : 0.044 0.142 1780 Planarity : 0.004 0.043 1802 Dihedral : 21.148 63.496 2220 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.54 % Allowed : 17.18 % Favored : 81.29 % 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: 1.57 (0.24), residues: 1208 helix: 2.15 (0.21), residues: 534 sheet: 1.23 (0.31), residues: 282 loop : -0.66 (0.33), 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 0.002 PHE B 26 TRP 0.024 0.001 TRP K 19 HIS 0.006 0.001 HIS I 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.16 (11800) covalent geometry : angle 0.55172 / 0.31 (16240) hydrogen bonds : bond 0.04335 / 2.96 ( 636) hydrogen bonds : angle 4.54319 / 3.33 ( 1747) metal coordination : bond 0.01495 / 0.89 ( 8) metal coordination : angle 4.10458 / 3.20 ( 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 138 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 0.307 Fit side-chains REVERT: A 9 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.7965 (mt0) REVERT: D 240 LYS cc_start: 0.8259 (mmmt) cc_final: 0.7826 (tptp) REVERT: I 9 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7982 (mt0) REVERT: K 188 LYS cc_start: 0.7221 (OUTLIER) cc_final: 0.6692 (mmtp) REVERT: L 224 ARG cc_start: 0.7834 (mtt-85) cc_final: 0.7539 (mmm-85) REVERT: C 224 ARG cc_start: 0.7817 (mtt-85) cc_final: 0.7524 (mmm-85) outliers start: 16 outliers final: 9 residues processed: 130 average time/residue: 0.6470 time to fit residues: 89.9455 Evaluate side-chains 132 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 120 time to evaluate : 0.275 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 43 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 111 optimal weight: 20.0000 chunk 91 optimal weight: 0.2980 chunk 101 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 64 optimal weight: 0.5980 chunk 81 optimal weight: 7.9990 chunk 72 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 27 ASN B 137 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.132921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.088004 restraints weight = 27774.519| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.25 r_work: 0.3121 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2976 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 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 = 0.2976 r_free = 0.2976 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: 0.2976 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.4580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11808 Z= 0.125 Angle : 0.530 9.166 16244 Z= 0.294 Chirality : 0.043 0.143 1780 Planarity : 0.004 0.041 1802 Dihedral : 21.114 63.745 2220 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.82 % Allowed : 17.27 % Favored : 80.90 % 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: 1.67 (0.25), residues: 1208 helix: 2.25 (0.22), residues: 534 sheet: 1.26 (0.31), residues: 282 loop : -0.65 (0.33), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 224 TYR 0.013 0.001 TYR A 83 PHE 0.009 0.001 PHE A 100 TRP 0.030 0.001 TRP B 19 HIS 0.004 0.001 HIS A 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.13 (11800) covalent geometry : angle 0.52531 / 0.29 (16240) hydrogen bonds : bond 0.03855 / 2.66 ( 636) hydrogen bonds : angle 4.49826 / 3.30 ( 1747) metal coordination : bond 0.01173 / 0.70 ( 8) metal coordination : angle 4.49367 / 3.55 ( 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 142 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 0.438 Fit side-chains REVERT: A 9 GLN cc_start: 0.8339 (OUTLIER) cc_final: 0.8104 (mt0) REVERT: D 240 LYS cc_start: 0.8330 (mmmt) cc_final: 0.7939 (tptp) REVERT: I 9 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.8086 (mt0) REVERT: K 22 MET cc_start: 0.6152 (ptm) cc_final: 0.5761 (ptp) REVERT: K 188 LYS cc_start: 0.7283 (OUTLIER) cc_final: 0.6763 (mmtp) REVERT: K 212 GLU cc_start: 0.8568 (mm-30) cc_final: 0.8358 (mm-30) REVERT: L 224 ARG cc_start: 0.7895 (mtt-85) cc_final: 0.7623 (mmm-85) REVERT: C 224 ARG cc_start: 0.7907 (mtt-85) cc_final: 0.7640 (mmm-85) outliers start: 19 outliers final: 9 residues processed: 134 average time/residue: 0.7676 time to fit residues: 109.6243 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 : 0.439 ------------------------------------------------------------------------------- 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 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 C residue 220 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 125 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 99 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 78 optimal weight: 10.0000 chunk 23 optimal weight: 0.9980 chunk 98 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 27 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.132408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.086897 restraints weight = 34220.974| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.46 r_work: 0.3093 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2948 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2948 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.4669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11808 Z= 0.137 Angle : 0.535 8.826 16244 Z= 0.297 Chirality : 0.043 0.153 1780 Planarity : 0.004 0.041 1802 Dihedral : 21.081 64.058 2220 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.82 % Allowed : 17.66 % Favored : 80.52 % 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: 1.67 (0.25), residues: 1208 helix: 2.26 (0.22), residues: 534 sheet: 1.24 (0.31), residues: 282 loop : -0.64 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 224 TYR 0.014 0.001 TYR A 83 PHE 0.014 0.001 PHE B 26 TRP 0.042 0.002 TRP K 19 HIS 0.004 0.001 HIS I 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.14 (11800) covalent geometry : angle 0.53106 / 0.30 (16240) hydrogen bonds : bond 0.04012 / 2.75 ( 636) hydrogen bonds : angle 4.50073 / 3.30 ( 1747) metal coordination : bond 0.01273 / 0.75 ( 8) metal coordination : angle 4.04674 / 3.19 ( 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 141 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 122 time to evaluate : 0.398 Fit side-chains REVERT: A 9 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.8146 (mt0) REVERT: D 240 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.7912 (tptp) REVERT: I 9 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.8053 (mt0) REVERT: K 188 LYS cc_start: 0.7319 (OUTLIER) cc_final: 0.6735 (mmtp) REVERT: L 224 ARG cc_start: 0.7944 (mtt-85) cc_final: 0.7658 (mmm-85) REVERT: L 262 ARG cc_start: 0.8976 (OUTLIER) cc_final: 0.8044 (tpm170) REVERT: C 224 ARG cc_start: 0.7931 (mtt-85) cc_final: 0.7654 (mmm-85) outliers start: 19 outliers final: 11 residues processed: 132 average time/residue: 0.7113 time to fit residues: 100.2971 Evaluate side-chains 138 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 0.613 ------------------------------------------------------------------------------- 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 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 L residue 262 ARG Chi-restraints excluded: chain C residue 220 ILE 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: 3.9990 chunk 123 optimal weight: 0.7980 chunk 76 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 59 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.3997 r_free = 0.3997 target = 0.131783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.086650 restraints weight = 28409.240| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.26 r_work: 0.3094 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2975 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2975 r_free = 0.2975 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 = 0.2975 r_free = 0.2975 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: 0.2975 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.4763 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= 0.152 Angle : 0.550 8.782 16244 Z= 0.305 Chirality : 0.044 0.142 1780 Planarity : 0.004 0.042 1802 Dihedral : 21.135 64.413 2220 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.82 % Allowed : 17.47 % Favored : 80.71 % 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: 1.62 (0.25), residues: 1208 helix: 2.21 (0.22), residues: 534 sheet: 1.22 (0.31), residues: 282 loop : -0.65 (0.33), 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 0.020 0.002 PHE K 26 TRP 0.037 0.002 TRP K 19 HIS 0.005 0.001 HIS I 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (11800) covalent geometry : angle 0.54670 / 0.30 (16240) hydrogen bonds : bond 0.04110 / 2.82 ( 636) hydrogen bonds : angle 4.55224 / 3.33 ( 1747) metal coordination : bond 0.01489 / 0.90 ( 8) metal coordination : angle 4.05803 / 3.18 ( 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 141 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 122 time to evaluate : 0.424 Fit side-chains REVERT: A 9 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.8142 (mt0) REVERT: B 27 ASN cc_start: 0.8792 (t0) cc_final: 0.8576 (t0) REVERT: D 240 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.8046 (tptm) REVERT: I 9 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.8068 (mt0) REVERT: K 188 LYS cc_start: 0.7345 (OUTLIER) cc_final: 0.6744 (mmtp) REVERT: L 224 ARG cc_start: 0.7925 (mtt-85) cc_final: 0.7628 (mmm-85) REVERT: L 262 ARG cc_start: 0.8978 (OUTLIER) cc_final: 0.8246 (tpm170) REVERT: C 224 ARG cc_start: 0.7923 (mtt-85) cc_final: 0.7641 (mmm-85) outliers start: 19 outliers final: 11 residues processed: 132 average time/residue: 0.7247 time to fit residues: 102.3987 Evaluate side-chains 138 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 0.411 ------------------------------------------------------------------------------- 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 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 L residue 262 ARG Chi-restraints excluded: chain C residue 220 ILE 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: 0.0970 chunk 17 optimal weight: 0.3980 chunk 20 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 116 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 50 optimal weight: 0.1980 overall best weight: 0.4178 ------------------------------------------------------------------------------- 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 = 0.4025 r_free = 0.4025 target = 0.133654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.089197 restraints weight = 27671.163| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.24 r_work: 0.3118 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3032 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 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 = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3032 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.4828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11808 Z= 0.112 Angle : 0.514 8.586 16244 Z= 0.288 Chirality : 0.042 0.153 1780 Planarity : 0.003 0.040 1802 Dihedral : 21.071 64.480 2220 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.63 % Allowed : 17.66 % Favored : 80.71 % 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: 1.72 (0.25), residues: 1208 helix: 2.31 (0.22), residues: 534 sheet: 1.27 (0.31), residues: 282 loop : -0.62 (0.33), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 224 TYR 0.012 0.001 TYR A 83 PHE 0.024 0.001 PHE B 223 TRP 0.047 0.002 TRP B 19 HIS 0.004 0.001 HIS K 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.11 (11800) covalent geometry : angle 0.50942 / 0.29 (16240) hydrogen bonds : bond 0.03580 / 2.48 ( 636) hydrogen bonds : angle 4.46217 / 3.27 ( 1747) metal coordination : bond 0.00863 / 0.51 ( 8) metal coordination : angle 4.55440 / 3.61 ( 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 144 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 127 time to evaluate : 0.457 Fit side-chains REVERT: A 9 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.8049 (mt0) REVERT: B 27 ASN cc_start: 0.8775 (t0) cc_final: 0.8547 (t0) REVERT: D 240 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.8036 (tptp) REVERT: I 9 GLN cc_start: 0.8319 (OUTLIER) cc_final: 0.7993 (mt0) REVERT: I 136 LYS cc_start: 0.8909 (ttpt) cc_final: 0.8688 (tmmt) REVERT: K 188 LYS cc_start: 0.7312 (OUTLIER) cc_final: 0.6735 (mmtp) REVERT: L 224 ARG cc_start: 0.7867 (mtt-85) cc_final: 0.7550 (mmm-85) REVERT: L 262 ARG cc_start: 0.8938 (OUTLIER) cc_final: 0.8241 (tpm170) REVERT: C 224 ARG cc_start: 0.7868 (mtt-85) cc_final: 0.7573 (mmm-85) outliers start: 17 outliers final: 12 residues processed: 135 average time/residue: 0.7571 time to fit residues: 109.1952 Evaluate side-chains 140 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 0.418 ------------------------------------------------------------------------------- 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 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 L residue 262 ARG Chi-restraints excluded: chain C residue 220 ILE 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: 0.7980 chunk 107 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 48 optimal weight: 30.0000 chunk 51 optimal weight: 0.0470 chunk 4 optimal weight: 0.5980 chunk 58 optimal weight: 4.9990 chunk 65 optimal weight: 0.0870 chunk 64 optimal weight: 0.7980 chunk 101 optimal weight: 0.8980 overall best weight: 0.4656 ------------------------------------------------------------------------------- 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 = 0.4025 r_free = 0.4025 target = 0.133587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.089696 restraints weight = 20802.807| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.95 r_work: 0.3142 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3025 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3025 r_free = 0.3025 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 = 0.3025 r_free = 0.3025 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: 0.3025 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.4881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11808 Z= 0.116 Angle : 0.517 8.568 16244 Z= 0.289 Chirality : 0.042 0.167 1780 Planarity : 0.004 0.041 1802 Dihedral : 21.024 64.293 2220 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.63 % Allowed : 17.95 % Favored : 80.42 % 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: 1.76 (0.25), residues: 1208 helix: 2.31 (0.22), residues: 534 sheet: 1.31 (0.31), residues: 282 loop : -0.59 (0.33), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 224 TYR 0.013 0.001 TYR A 83 PHE 0.030 0.001 PHE B 26 TRP 0.045 0.001 TRP K 19 HIS 0.004 0.001 HIS K 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.12 (11800) covalent geometry : angle 0.51300 / 0.29 (16240) hydrogen bonds : bond 0.03628 / 2.50 ( 636) hydrogen bonds : angle 4.44191 / 3.25 ( 1747) metal coordination : bond 0.00881 / 0.50 ( 8) metal coordination : angle 3.97615 / 3.14 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10248.12 seconds wall clock time: 174 minutes 19.92 seconds (10459.92 seconds total)