Starting phenix.real_space_refine on Tue Nov 18 05:26:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c9m_45364/11_2025/9c9m_45364.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c9m_45364/11_2025/9c9m_45364.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9c9m_45364/11_2025/9c9m_45364.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c9m_45364/11_2025/9c9m_45364.map" model { file = "/net/cci-nas-00/data/ceres_data/9c9m_45364/11_2025/9c9m_45364.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c9m_45364/11_2025/9c9m_45364.cif" } resolution = 2.01 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Zn 2 6.06 5 P 72 5.49 5 Mg 4 5.21 5 S 36 5.16 5 C 7046 2.51 5 N 2040 2.21 5 O 2299 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/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: 3.13, per 1000 atoms: 0.27 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: 1.10 Conformation dependent library (CDL) restraints added in 520.4 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: 1.50 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: 2.13 Time building geometry restraints manager: 1.40 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: 15936 1.84 - 3.69: 256 3.69 - 5.53: 44 5.53 - 7.37: 2 7.37 - 9.21: 2 Bond angle restraints: 16240 Sorted by residual: angle pdb=" NBC DLU O 101 " pdb=" CBB DLU O 101 " pdb=" OAQ DLU O 101 " ideal model delta sigma weight residual 110.33 101.12 9.21 3.00e+00 1.11e-01 9.43e+00 angle pdb=" NBC DLU F 101 " pdb=" CBB DLU F 101 " pdb=" OAQ DLU F 101 " ideal model delta sigma weight residual 110.33 101.13 9.20 3.00e+00 1.11e-01 9.41e+00 angle pdb=" N LYS A 136 " pdb=" CA LYS A 136 " pdb=" C LYS A 136 " ideal model delta sigma weight residual 109.96 104.99 4.97 1.68e+00 3.54e-01 8.75e+00 angle pdb=" N ILE I 135 " pdb=" CA ILE I 135 " pdb=" C ILE I 135 " ideal model delta sigma weight residual 108.17 111.90 -3.73 1.40e+00 5.10e-01 7.10e+00 angle pdb=" C3' DT F 17 " pdb=" C2' DT F 17 " pdb=" C1' DT F 17 " ideal model delta sigma weight residual 101.60 105.23 -3.63 1.50e+00 4.44e-01 5.84e+00 ... (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 - 0.030: 1050 0.030 - 0.060: 406 0.060 - 0.089: 189 0.089 - 0.119: 119 0.119 - 0.149: 16 Chirality restraints: 1780 Sorted by residual: chirality pdb=" CA ILE I 141 " pdb=" N ILE I 141 " pdb=" C ILE I 141 " pdb=" CB ILE I 141 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.53e-01 chirality pdb=" CA ILE A 141 " pdb=" N ILE A 141 " pdb=" C ILE A 141 " pdb=" CB ILE A 141 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.28e-01 chirality pdb=" CA LYS A 136 " pdb=" N LYS A 136 " pdb=" C LYS A 136 " pdb=" CB LYS A 136 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.78e-01 ... (remaining 1777 not shown) Planarity restraints: 1802 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 155 " 0.010 2.00e-02 2.50e+03 2.02e-02 4.09e+00 pdb=" C ASN A 155 " -0.035 2.00e-02 2.50e+03 pdb=" O ASN A 155 " 0.013 2.00e-02 2.50e+03 pdb=" N LYS A 156 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 260 " -0.033 5.00e-02 4.00e+02 5.04e-02 4.07e+00 pdb=" N PRO B 261 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO B 261 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 261 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DG N 18 " -0.023 2.00e-02 2.50e+03 1.03e-02 3.19e+00 pdb=" N9 DG N 18 " 0.026 2.00e-02 2.50e+03 pdb=" C8 DG N 18 " 0.001 2.00e-02 2.50e+03 pdb=" N7 DG N 18 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DG N 18 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG N 18 " -0.003 2.00e-02 2.50e+03 pdb=" O6 DG N 18 " -0.006 2.00e-02 2.50e+03 pdb=" N1 DG N 18 " -0.000 2.00e-02 2.50e+03 pdb=" C2 DG N 18 " 0.000 2.00e-02 2.50e+03 pdb=" N2 DG N 18 " 0.000 2.00e-02 2.50e+03 pdb=" N3 DG N 18 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DG N 18 " 0.003 2.00e-02 2.50e+03 ... (remaining 1799 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 115 2.56 - 3.14: 8983 3.14 - 3.73: 18885 3.73 - 4.31: 26809 4.31 - 4.90: 41711 Nonbonded interactions: 96503 Sorted by model distance: nonbonded pdb="MG MG A 301 " pdb=" O HOH A 408 " model vdw 1.971 2.170 nonbonded pdb="MG MG I 301 " pdb=" O HOH I 407 " model vdw 1.972 2.170 nonbonded pdb="MG MG A 301 " pdb=" O HOH A 405 " model vdw 1.978 2.170 nonbonded pdb="MG MG I 301 " pdb=" O HOH I 405 " model vdw 1.978 2.170 nonbonded pdb=" OD2 ASP A 64 " pdb="MG MG A 302 " model vdw 2.025 2.170 ... (remaining 96498 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 44 or resid 57 through 140 or resid 150 through \ 268)) selection = (chain 'B' and (resid 2 through 228 or resid 236 through 268)) selection = (chain 'I' and (resid 2 through 44 or resid 57 through 140 or resid 150 through \ 268)) selection = (chain 'K' and (resid 2 through 228 or resid 236 through 268)) } ncs_group { reference = chain 'C' selection = chain 'L' } ncs_group { reference = chain 'D' selection = chain 'M' } ncs_group { reference = chain 'E' selection = chain 'N' } ncs_group { reference = (chain 'F' and (resid 5 through 20 or resid 101)) selection = (chain 'O' and (resid 5 through 20 or resid 101)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.42 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 15.000 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 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= 0.232 Angle : 0.596 12.175 16244 Z= 0.317 Chirality : 0.044 0.149 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 covalent geometry : bond 0.00465 (11800) covalent geometry : angle 0.57669 (16240) hydrogen bonds : bond 0.11710 ( 636) hydrogen bonds : angle 5.77419 ( 1747) metal coordination : bond 0.06861 ( 8) metal coordination : angle 9.62372 ( 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 : 0.441 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: 0.6533 time to fit residues: 157.3989 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 : 0.301 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 274 GLN C 274 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.136950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.093696 restraints weight = 18974.344| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.89 r_work: 0.3257 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3154 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 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 = 0.3153 r_free = 0.3153 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3153 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11808 Z= 0.151 Angle : 0.578 9.004 16244 Z= 0.316 Chirality : 0.043 0.157 1780 Planarity : 0.004 0.045 1802 Dihedral : 20.986 64.789 2222 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.59 % Allowed : 16.03 % 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: 1.56 (0.25), residues: 1208 helix: 2.01 (0.22), residues: 534 sheet: 1.44 (0.31), residues: 286 loop : -0.70 (0.33), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 224 TYR 0.012 0.001 TYR A 83 PHE 0.011 0.001 PHE K 223 TRP 0.013 0.001 TRP K 19 HIS 0.004 0.001 HIS B 12 Details of bonding type rmsd covalent geometry : bond 0.00335 (11800) covalent geometry : angle 0.56916 (16240) hydrogen bonds : bond 0.04272 ( 636) hydrogen bonds : angle 4.61212 ( 1747) metal coordination : bond 0.00949 ( 8) metal coordination : angle 6.37190 ( 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 173 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 146 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 GLN cc_start: 0.7394 (mm-40) cc_final: 0.7126 (tp-100) REVERT: D 240 LYS cc_start: 0.8026 (OUTLIER) cc_final: 0.7684 (tptp) REVERT: L 224 ARG cc_start: 0.7819 (mtt-85) cc_final: 0.7589 (mmm-85) outliers start: 27 outliers final: 5 residues processed: 162 average time/residue: 0.7271 time to fit residues: 125.7782 Evaluate side-chains 130 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 124 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLN Chi-restraints excluded: chain D residue 240 LYS Chi-restraints excluded: chain I residue 9 GLN Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain L residue 230 SER Chi-restraints excluded: chain C residue 220 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 0.3980 chunk 54 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 47 optimal weight: 8.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 ASN B 222 ASN D 254 ASN K 222 ASN L 214 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.133978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.088056 restraints weight = 26250.491| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.21 r_work: 0.3120 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: 0.3004 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 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 = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3004 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.4033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11808 Z= 0.158 Angle : 0.546 7.343 16244 Z= 0.302 Chirality : 0.043 0.138 1780 Planarity : 0.004 0.043 1802 Dihedral : 20.986 63.006 2220 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.50 % Allowed : 16.51 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.24), residues: 1208 helix: 2.09 (0.21), residues: 534 sheet: 1.36 (0.31), residues: 286 loop : -0.70 (0.33), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 224 TYR 0.014 0.001 TYR B 83 PHE 0.028 0.002 PHE K 26 TRP 0.020 0.001 TRP B 19 HIS 0.006 0.001 HIS I 114 Details of bonding type rmsd covalent geometry : bond 0.00352 (11800) covalent geometry : angle 0.54009 (16240) hydrogen bonds : bond 0.04329 ( 636) hydrogen bonds : angle 4.57596 ( 1747) metal coordination : bond 0.01549 ( 8) metal coordination : angle 5.15316 ( 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 164 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 0.453 Fit side-chains revert: symmetry clash REVERT: A 9 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.8040 (mt0) REVERT: B 207 ASP cc_start: 0.8873 (t70) cc_final: 0.8661 (t0) REVERT: D 240 LYS cc_start: 0.8261 (mmmt) cc_final: 0.7842 (tptp) REVERT: I 9 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.7990 (mt0) REVERT: K 22 MET cc_start: 0.6110 (ptp) cc_final: 0.5381 (ptp) REVERT: L 224 ARG cc_start: 0.7860 (mtt-85) cc_final: 0.7580 (mmm-85) outliers start: 26 outliers final: 6 residues processed: 156 average time/residue: 0.7123 time to fit residues: 118.8352 Evaluate side-chains 135 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 127 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLN Chi-restraints excluded: chain B residue 137 GLN Chi-restraints excluded: chain I residue 9 GLN Chi-restraints excluded: chain L residue 230 SER Chi-restraints excluded: chain L residue 257 ILE Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 230 SER Chi-restraints excluded: chain C residue 257 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 34 optimal weight: 0.7980 chunk 95 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 70 optimal weight: 0.5980 chunk 42 optimal weight: 0.6980 chunk 4 optimal weight: 0.2980 chunk 105 optimal weight: 7.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 ASN ** B 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 214 GLN C 214 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.134297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.089926 restraints weight = 19012.944| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.89 r_work: 0.3168 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3051 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3051 r_free = 0.3051 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3051 r_free = 0.3051 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3051 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.4292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 11808 Z= 0.129 Angle : 0.509 8.432 16244 Z= 0.282 Chirality : 0.042 0.142 1780 Planarity : 0.004 0.042 1802 Dihedral : 20.962 62.272 2220 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.73 % Allowed : 16.60 % Favored : 81.67 % 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: 1.65 (0.24), residues: 1208 helix: 2.21 (0.22), residues: 534 sheet: 1.27 (0.30), residues: 286 loop : -0.65 (0.33), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 224 TYR 0.012 0.001 TYR A 83 PHE 0.025 0.002 PHE K 26 TRP 0.025 0.001 TRP B 19 HIS 0.004 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00290 (11800) covalent geometry : angle 0.50414 (16240) hydrogen bonds : bond 0.03725 ( 636) hydrogen bonds : angle 4.44892 ( 1747) metal coordination : bond 0.01057 ( 8) metal coordination : angle 4.67175 ( 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 149 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 131 time to evaluate : 0.528 Fit side-chains revert: symmetry clash REVERT: A 9 GLN cc_start: 0.8284 (OUTLIER) cc_final: 0.8045 (mt0) REVERT: D 240 LYS cc_start: 0.8254 (mmmt) cc_final: 0.7852 (tptp) REVERT: I 9 GLN cc_start: 0.8298 (OUTLIER) cc_final: 0.8036 (mt0) REVERT: K 188 LYS cc_start: 0.7144 (OUTLIER) cc_final: 0.6705 (mmtp) REVERT: L 224 ARG cc_start: 0.7821 (mtt-85) cc_final: 0.7552 (mmm-85) REVERT: C 224 ARG cc_start: 0.7857 (mtt-85) cc_final: 0.7531 (mmm-85) outliers start: 18 outliers final: 8 residues processed: 142 average time/residue: 0.7375 time to fit residues: 111.8329 Evaluate side-chains 145 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 134 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLN Chi-restraints excluded: chain B residue 137 GLN Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain I residue 9 GLN Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain K residue 188 LYS Chi-restraints excluded: chain K residue 220 ILE Chi-restraints excluded: chain 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 110 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 102 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 85 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 6 optimal weight: 0.0870 chunk 73 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 27 ASN L 214 GLN L 221 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.133689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.088789 restraints weight = 24072.245| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.13 r_work: 0.3115 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- 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 = 0.48 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 = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2995 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.4509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11808 Z= 0.132 Angle : 0.509 7.775 16244 Z= 0.283 Chirality : 0.042 0.142 1780 Planarity : 0.004 0.042 1802 Dihedral : 20.921 62.586 2220 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.02 % Allowed : 16.60 % 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: 1.71 (0.25), residues: 1208 helix: 2.28 (0.22), residues: 534 sheet: 1.29 (0.30), residues: 282 loop : -0.63 (0.33), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 224 TYR 0.012 0.001 TYR A 83 PHE 0.010 0.001 PHE A 100 TRP 0.028 0.001 TRP B 19 HIS 0.004 0.001 HIS A 12 Details of bonding type rmsd covalent geometry : bond 0.00293 (11800) covalent geometry : angle 0.50459 (16240) hydrogen bonds : bond 0.03742 ( 636) hydrogen bonds : angle 4.43850 ( 1747) metal coordination : bond 0.00989 ( 8) metal coordination : angle 4.22418 ( 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 154 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 0.417 Fit side-chains revert: symmetry clash REVERT: A 9 GLN cc_start: 0.8283 (OUTLIER) cc_final: 0.8052 (mt0) REVERT: A 136 LYS cc_start: 0.8976 (tmmt) cc_final: 0.8772 (ttpp) REVERT: D 240 LYS cc_start: 0.8277 (OUTLIER) cc_final: 0.7860 (tptp) REVERT: I 9 GLN cc_start: 0.8268 (OUTLIER) cc_final: 0.7936 (mt0) REVERT: K 22 MET cc_start: 0.5960 (ptm) cc_final: 0.5500 (ptp) REVERT: K 188 LYS cc_start: 0.7221 (OUTLIER) cc_final: 0.6685 (mmtp) REVERT: K 253 ASP cc_start: 0.7085 (t0) cc_final: 0.6545 (t0) REVERT: L 224 ARG cc_start: 0.7831 (mtt-85) cc_final: 0.7521 (mmm-85) REVERT: C 224 ARG cc_start: 0.7858 (mtt-85) cc_final: 0.7492 (mmm-85) outliers start: 21 outliers final: 8 residues processed: 148 average time/residue: 0.7083 time to fit residues: 112.2740 Evaluate side-chains 136 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLN Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain B residue 137 GLN Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain D residue 240 LYS Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain I residue 9 GLN Chi-restraints excluded: chain K residue 188 LYS Chi-restraints excluded: chain K residue 220 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 31 optimal weight: 4.9990 chunk 119 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 49 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN B 117 ASN ** B 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 214 GLN ** K 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 214 GLN C 221 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.130146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.085523 restraints weight = 20171.611| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.94 r_work: 0.3053 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2962 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2962 r_free = 0.2962 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 = 0.2962 r_free = 0.2962 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2962 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.4810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 11808 Z= 0.237 Angle : 0.591 7.491 16244 Z= 0.325 Chirality : 0.046 0.145 1780 Planarity : 0.004 0.044 1802 Dihedral : 21.084 64.122 2220 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.30 % Allowed : 16.79 % 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: 1.44 (0.24), residues: 1208 helix: 2.01 (0.21), residues: 534 sheet: 1.15 (0.31), residues: 282 loop : -0.66 (0.33), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 263 TYR 0.016 0.002 TYR B 83 PHE 0.017 0.002 PHE A 100 TRP 0.030 0.002 TRP B 19 HIS 0.007 0.002 HIS I 16 Details of bonding type rmsd covalent geometry : bond 0.00543 (11800) covalent geometry : angle 0.58631 (16240) hydrogen bonds : bond 0.04795 ( 636) hydrogen bonds : angle 4.69381 ( 1747) metal coordination : bond 0.01835 ( 8) metal coordination : angle 4.55754 ( 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 146 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 0.426 Fit side-chains revert: symmetry clash REVERT: A 9 GLN cc_start: 0.8314 (OUTLIER) cc_final: 0.8102 (mt0) REVERT: B 27 ASN cc_start: 0.8893 (t0) cc_final: 0.8598 (t0) REVERT: B 188 LYS cc_start: 0.7405 (OUTLIER) cc_final: 0.6833 (mmtp) REVERT: D 240 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7826 (tptp) REVERT: I 9 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.8064 (mt0) REVERT: K 22 MET cc_start: 0.6031 (ptm) cc_final: 0.5653 (ptp) REVERT: K 188 LYS cc_start: 0.7429 (OUTLIER) cc_final: 0.6803 (mmtp) REVERT: K 258 LYS cc_start: 0.6744 (OUTLIER) cc_final: 0.6387 (ptpp) REVERT: L 224 ARG cc_start: 0.7903 (mtt-85) cc_final: 0.7601 (mmm-85) REVERT: C 224 ARG cc_start: 0.7920 (mtt-85) cc_final: 0.7596 (mmm-85) outliers start: 24 outliers final: 12 residues processed: 137 average time/residue: 0.7601 time to fit residues: 111.1338 Evaluate side-chains 138 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLN Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain B residue 137 GLN Chi-restraints excluded: chain B residue 188 LYS Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain D residue 231 ARG Chi-restraints excluded: chain D residue 240 LYS Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain I residue 9 GLN Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 172 LEU Chi-restraints excluded: chain K residue 188 LYS Chi-restraints excluded: chain K residue 220 ILE Chi-restraints excluded: chain K residue 258 LYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 43 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 91 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 10 optimal weight: 0.0670 chunk 64 optimal weight: 0.9990 chunk 81 optimal weight: 0.4980 chunk 72 optimal weight: 1.9990 overall best weight: 0.6522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 222 ASN K 222 ASN C 221 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.132566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.088080 restraints weight = 24848.606| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.14 r_work: 0.3127 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2982 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2982 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.4889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11808 Z= 0.130 Angle : 0.510 7.645 16244 Z= 0.285 Chirality : 0.042 0.152 1780 Planarity : 0.003 0.041 1802 Dihedral : 20.942 64.707 2220 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.21 % Allowed : 17.27 % 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: 1.61 (0.25), residues: 1208 helix: 2.23 (0.22), residues: 534 sheet: 1.15 (0.30), residues: 282 loop : -0.64 (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 0.018 0.001 PHE B 26 TRP 0.034 0.001 TRP B 19 HIS 0.005 0.001 HIS K 183 Details of bonding type rmsd covalent geometry : bond 0.00288 (11800) covalent geometry : angle 0.50489 (16240) hydrogen bonds : bond 0.03719 ( 636) hydrogen bonds : angle 4.50187 ( 1747) metal coordination : bond 0.01178 ( 8) metal coordination : angle 4.42245 ( 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 146 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.449 Fit side-chains revert: symmetry clash REVERT: A 9 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.8085 (mt0) REVERT: A 156 LYS cc_start: 0.9066 (OUTLIER) cc_final: 0.8859 (tmmm) REVERT: B 27 ASN cc_start: 0.8839 (t0) cc_final: 0.8545 (t0) REVERT: D 240 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.7878 (tptp) REVERT: I 9 GLN cc_start: 0.8339 (OUTLIER) cc_final: 0.8087 (mt0) REVERT: K 22 MET cc_start: 0.5933 (ptm) cc_final: 0.5598 (ptp) REVERT: L 215 LYS cc_start: 0.8473 (ttmm) cc_final: 0.8135 (ttpp) REVERT: L 224 ARG cc_start: 0.7891 (mtt-85) cc_final: 0.7595 (mmm-85) REVERT: C 224 ARG cc_start: 0.7941 (mtt-85) cc_final: 0.7601 (mmm-85) outliers start: 23 outliers final: 11 residues processed: 137 average time/residue: 0.7827 time to fit residues: 114.2597 Evaluate side-chains 138 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 0.407 ------------------------------------------------------------------------------- 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 156 LYS 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 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 Chi-restraints excluded: chain C residue 230 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 125 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 23 optimal weight: 0.0470 chunk 98 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 51 optimal weight: 0.0670 chunk 57 optimal weight: 2.9990 overall best weight: 1.0220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 216 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.131517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.086082 restraints weight = 30477.806| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.35 r_work: 0.3058 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2942 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2942 r_free = 0.2942 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 = 0.2942 r_free = 0.2942 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2942 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.4960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11808 Z= 0.158 Angle : 0.532 7.676 16244 Z= 0.296 Chirality : 0.043 0.142 1780 Planarity : 0.004 0.042 1802 Dihedral : 20.981 64.225 2220 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.73 % Allowed : 18.04 % Favored : 80.23 % 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: 1.58 (0.24), residues: 1208 helix: 2.19 (0.22), residues: 534 sheet: 1.12 (0.30), residues: 282 loop : -0.63 (0.33), 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 0.019 0.002 PHE B 26 TRP 0.036 0.002 TRP B 19 HIS 0.005 0.001 HIS I 16 Details of bonding type rmsd covalent geometry : bond 0.00357 (11800) covalent geometry : angle 0.52842 (16240) hydrogen bonds : bond 0.04004 ( 636) hydrogen bonds : angle 4.53935 ( 1747) metal coordination : bond 0.01329 ( 8) metal coordination : angle 4.15657 ( 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 138 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 0.449 Fit side-chains revert: symmetry clash REVERT: A 9 GLN cc_start: 0.8318 (OUTLIER) cc_final: 0.8088 (mt0) REVERT: B 27 ASN cc_start: 0.8791 (t0) cc_final: 0.8487 (t0) REVERT: D 240 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.7867 (tptp) REVERT: I 9 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.8051 (mt0) REVERT: K 22 MET cc_start: 0.5762 (ptm) cc_final: 0.5429 (ptp) REVERT: L 224 ARG cc_start: 0.7893 (mtt-85) cc_final: 0.7571 (mmm-85) REVERT: C 224 ARG cc_start: 0.7939 (mtt-85) cc_final: 0.7569 (mmm-85) outliers start: 18 outliers final: 11 residues processed: 130 average time/residue: 0.7557 time to fit residues: 104.8352 Evaluate side-chains 133 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLN Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain B residue 137 GLN Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain D residue 231 ARG Chi-restraints excluded: chain D residue 240 LYS Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain I residue 9 GLN Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain 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 Chi-restraints excluded: chain C residue 230 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 12 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 50 optimal weight: 0.4980 chunk 59 optimal weight: 0.3980 chunk 52 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 216 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.132425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.087342 restraints weight = 29498.728| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.31 r_work: 0.3087 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2969 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2969 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.5027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11808 Z= 0.133 Angle : 0.512 7.587 16244 Z= 0.286 Chirality : 0.042 0.141 1780 Planarity : 0.004 0.042 1802 Dihedral : 20.943 64.158 2220 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.44 % Allowed : 18.43 % Favored : 80.13 % 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: 1.64 (0.25), residues: 1208 helix: 2.24 (0.22), residues: 534 sheet: 1.16 (0.30), residues: 282 loop : -0.60 (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 0.026 0.001 PHE B 26 TRP 0.042 0.001 TRP K 19 HIS 0.004 0.001 HIS K 183 Details of bonding type rmsd covalent geometry : bond 0.00296 (11800) covalent geometry : angle 0.50799 (16240) hydrogen bonds : bond 0.03673 ( 636) hydrogen bonds : angle 4.47843 ( 1747) metal coordination : bond 0.01046 ( 8) metal coordination : angle 4.25245 ( 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 136 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 0.423 Fit side-chains revert: symmetry clash REVERT: A 9 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.8092 (mt0) REVERT: B 27 ASN cc_start: 0.8672 (t0) cc_final: 0.8390 (t0) REVERT: D 240 LYS cc_start: 0.8314 (OUTLIER) cc_final: 0.7914 (tptp) REVERT: I 9 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.8024 (mt0) REVERT: L 224 ARG cc_start: 0.7880 (mtt-85) cc_final: 0.7563 (mmm-85) REVERT: C 224 ARG cc_start: 0.7943 (mtt-85) cc_final: 0.7575 (mmm-85) outliers start: 15 outliers final: 11 residues processed: 128 average time/residue: 0.7515 time to fit residues: 102.6679 Evaluate side-chains 133 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLN Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain B residue 137 GLN Chi-restraints excluded: chain B residue 220 ILE Chi-restraints excluded: chain D residue 231 ARG Chi-restraints excluded: chain D residue 240 LYS Chi-restraints excluded: chain I residue 5 ILE Chi-restraints excluded: chain I residue 9 GLN Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain 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 Chi-restraints excluded: chain C residue 230 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 122 optimal weight: 0.9990 chunk 124 optimal weight: 0.2980 chunk 30 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 chunk 116 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 chunk 50 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 216 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.132994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.087770 restraints weight = 32668.937| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.40 r_work: 0.3092 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3005 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3005 r_free = 0.3005 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3005 r_free = 0.3005 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3005 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.5084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11808 Z= 0.128 Angle : 0.514 7.677 16244 Z= 0.287 Chirality : 0.042 0.188 1780 Planarity : 0.003 0.042 1802 Dihedral : 20.898 63.742 2220 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.44 % Allowed : 18.71 % Favored : 79.85 % 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: 1.71 (0.25), residues: 1208 helix: 2.29 (0.22), residues: 534 sheet: 1.22 (0.31), residues: 282 loop : -0.58 (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 0.028 0.001 PHE B 26 TRP 0.045 0.001 TRP K 19 HIS 0.004 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00282 (11800) covalent geometry : angle 0.51054 (16240) hydrogen bonds : bond 0.03564 ( 636) hydrogen bonds : angle 4.45084 ( 1747) metal coordination : bond 0.00999 ( 8) metal coordination : angle 4.06034 ( 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 136 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 0.452 Fit side-chains revert: symmetry clash REVERT: A 9 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.8117 (mt0) REVERT: B 27 ASN cc_start: 0.8616 (t0) cc_final: 0.8364 (t0) REVERT: D 240 LYS cc_start: 0.8329 (OUTLIER) cc_final: 0.8059 (tptm) REVERT: I 9 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.8063 (mt0) REVERT: L 215 LYS cc_start: 0.8411 (ttmm) cc_final: 0.8119 (ttpp) REVERT: L 224 ARG cc_start: 0.7891 (mtt-85) cc_final: 0.7577 (mmm-85) REVERT: C 215 LYS cc_start: 0.8468 (ttmm) cc_final: 0.8192 (ttpt) REVERT: C 224 ARG cc_start: 0.7944 (mtt-85) cc_final: 0.7568 (mmm-85) outliers start: 15 outliers final: 11 residues processed: 128 average time/residue: 0.7220 time to fit residues: 99.0224 Evaluate side-chains 131 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 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 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 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 Chi-restraints excluded: chain C residue 230 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 56 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 48 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 58 optimal weight: 0.6980 chunk 65 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 chunk 101 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 221 GLN C 216 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.132317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.087228 restraints weight = 28509.177| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.28 r_work: 0.3086 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2967 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2967 r_free = 0.2967 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 = 0.2967 r_free = 0.2967 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2967 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.5131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11808 Z= 0.140 Angle : 0.524 7.663 16244 Z= 0.292 Chirality : 0.043 0.166 1780 Planarity : 0.004 0.042 1802 Dihedral : 20.949 63.840 2220 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.54 % Allowed : 18.52 % Favored : 79.94 % 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: 1.68 (0.25), residues: 1208 helix: 2.25 (0.22), residues: 534 sheet: 1.20 (0.30), residues: 282 loop : -0.55 (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 0.022 0.001 PHE K 26 TRP 0.044 0.002 TRP K 19 HIS 0.004 0.001 HIS A 12 Details of bonding type rmsd covalent geometry : bond 0.00314 (11800) covalent geometry : angle 0.52008 (16240) hydrogen bonds : bond 0.03731 ( 636) hydrogen bonds : angle 4.48034 ( 1747) metal coordination : bond 0.01079 ( 8) metal coordination : angle 3.93137 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10727.69 seconds wall clock time: 182 minutes 1.46 seconds (10921.46 seconds total)