Starting phenix.real_space_refine on Wed May 14 04:19:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c9m_45364/05_2025/9c9m_45364.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c9m_45364/05_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_45364/05_2025/9c9m_45364.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c9m_45364/05_2025/9c9m_45364.map" model { file = "/net/cci-nas-00/data/ceres_data/9c9m_45364/05_2025/9c9m_45364.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c9m_45364/05_2025/9c9m_45364.cif" } resolution = 2.01 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 8.07, per 1000 atoms: 0.70 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: 3.39 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 4.24 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: 3.96 Time building geometry restraints manager: 3.31 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: 2.470 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: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 34.000 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.080 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:12.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.300 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (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 TRP 0.008 0.001 TRP M 243 HIS 0.004 0.001 HIS I 51 PHE 0.011 0.001 PHE I 181 TYR 0.016 0.001 TYR I 99 ARG 0.003 0.000 ARG K 107 Details of bonding type rmsd hydrogen bonds : bond 0.11710 ( 636) hydrogen bonds : angle 5.77419 ( 1747) metal coordination : bond 0.06861 ( 8) metal coordination : angle 9.62372 ( 4) covalent geometry : bond 0.00465 (11800) covalent geometry : angle 0.57669 (16240) *********************** 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 : 1.186 Fit side-chains 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: 0.5708 (t0) outliers start: 2 outliers final: 1 residues processed: 224 average time/residue: 1.2584 time to fit residues: 304.4537 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 : 1.103 ------------------------------------------------------------------------------- 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 106 optimal weight: 0.8980 chunk 95 optimal weight: 0.8980 chunk 52 optimal weight: 0.3980 chunk 32 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 114 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4079 r_free = 0.4079 target = 0.136827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.093469 restraints weight = 20087.431| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.94 r_work: 0.3260 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3148 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3147 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11808 Z= 0.165 Angle : 0.605 9.095 16244 Z= 0.328 Chirality : 0.044 0.159 1780 Planarity : 0.004 0.045 1802 Dihedral : 21.093 61.993 2222 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 3.26 % Allowed : 15.74 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.24), residues: 1208 helix: 1.89 (0.22), residues: 534 sheet: 1.38 (0.31), residues: 286 loop : -0.70 (0.33), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP K 19 HIS 0.008 0.001 HIS B 12 PHE 0.014 0.001 PHE K 223 TYR 0.014 0.002 TYR A 83 ARG 0.008 0.001 ARG A 20 Details of bonding type rmsd hydrogen bonds : bond 0.04365 ( 636) hydrogen bonds : angle 4.59153 ( 1747) metal coordination : bond 0.01043 ( 8) metal coordination : angle 6.49584 ( 4) covalent geometry : bond 0.00365 (11800) covalent geometry : angle 0.59618 (16240) *********************** 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 188 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 154 time to evaluate : 1.104 Fit side-chains revert: symmetry clash REVERT: D 240 LYS cc_start: 0.8167 (OUTLIER) cc_final: 0.7800 (tptp) REVERT: K 22 MET cc_start: 0.5884 (OUTLIER) cc_final: 0.4948 (ptp) REVERT: L 224 ARG cc_start: 0.7802 (mtt-85) cc_final: 0.7545 (mmm-85) REVERT: C 224 ARG cc_start: 0.7881 (mtt-85) cc_final: 0.7622 (mmm-85) outliers start: 34 outliers final: 6 residues processed: 174 average time/residue: 1.5196 time to fit residues: 282.7437 Evaluate side-chains 141 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 133 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLN Chi-restraints excluded: chain A residue 32 VAL 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 C residue 220 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 112 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 10 optimal weight: 0.4980 chunk 7 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 96 optimal weight: 0.1980 chunk 117 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 ASN B 222 ASN D 254 ASN K 222 ASN L 214 GLN C 221 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.134039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.090323 restraints weight = 19829.781| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.93 r_work: 0.3197 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3085 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3085 r_free = 0.3085 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3085 r_free = 0.3085 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3085 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.3901 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= 0.135 Angle : 0.525 8.929 16244 Z= 0.290 Chirality : 0.042 0.161 1780 Planarity : 0.004 0.043 1802 Dihedral : 20.955 63.130 2220 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.98 % Allowed : 16.60 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.24), residues: 1208 helix: 2.13 (0.21), residues: 534 sheet: 1.27 (0.32), residues: 266 loop : -0.46 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 19 HIS 0.005 0.001 HIS A 114 PHE 0.009 0.001 PHE I 100 TYR 0.012 0.001 TYR B 83 ARG 0.009 0.001 ARG A 20 Details of bonding type rmsd hydrogen bonds : bond 0.03945 ( 636) hydrogen bonds : angle 4.48490 ( 1747) metal coordination : bond 0.01290 ( 8) metal coordination : angle 4.91175 ( 4) covalent geometry : bond 0.00300 (11800) covalent geometry : angle 0.51926 (16240) *********************** 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 166 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 135 time to evaluate : 1.281 Fit side-chains revert: symmetry clash REVERT: A 9 GLN cc_start: 0.8233 (OUTLIER) cc_final: 0.8002 (mt0) REVERT: D 240 LYS cc_start: 0.8220 (mmmt) cc_final: 0.7837 (tptp) REVERT: I 9 GLN cc_start: 0.8259 (OUTLIER) cc_final: 0.8005 (mt0) REVERT: L 224 ARG cc_start: 0.7837 (mtt-85) cc_final: 0.7568 (mmm-85) REVERT: L 236 LYS cc_start: 0.7975 (mmtp) cc_final: 0.7775 (mttm) REVERT: C 224 ARG cc_start: 0.7919 (mtt-85) cc_final: 0.7682 (mmm-85) outliers start: 31 outliers final: 7 residues processed: 158 average time/residue: 1.3611 time to fit residues: 230.8562 Evaluate side-chains 137 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 128 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLN Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 137 GLN Chi-restraints excluded: chain I residue 9 GLN 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 39 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 104 optimal weight: 10.0000 overall best weight: 1.3788 ------------------------------------------------------------------------------- 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** ** K 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 214 GLN C 214 GLN C 221 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.131704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.086710 restraints weight = 23227.993| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.08 r_work: 0.3097 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- 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 = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2982 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.4468 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= 0.191 Angle : 0.565 9.134 16244 Z= 0.310 Chirality : 0.044 0.145 1780 Planarity : 0.004 0.043 1802 Dihedral : 21.057 63.217 2220 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.98 % Allowed : 15.74 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.24), residues: 1208 helix: 2.09 (0.21), residues: 534 sheet: 1.23 (0.31), residues: 286 loop : -0.65 (0.33), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 19 HIS 0.005 0.001 HIS I 16 PHE 0.014 0.002 PHE B 26 TYR 0.014 0.002 TYR A 83 ARG 0.006 0.001 ARG A 20 Details of bonding type rmsd hydrogen bonds : bond 0.04493 ( 636) hydrogen bonds : angle 4.60739 ( 1747) metal coordination : bond 0.01528 ( 8) metal coordination : angle 4.69835 ( 4) covalent geometry : bond 0.00434 (11800) covalent geometry : angle 0.56061 (16240) *********************** 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 154 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 123 time to evaluate : 1.104 Fit side-chains revert: symmetry clash REVERT: A 9 GLN cc_start: 0.8319 (OUTLIER) cc_final: 0.8090 (mt0) REVERT: B 188 LYS cc_start: 0.7312 (OUTLIER) cc_final: 0.6818 (mmtp) REVERT: D 240 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.7812 (tptp) REVERT: I 9 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.8051 (mt0) REVERT: K 188 LYS cc_start: 0.7305 (OUTLIER) cc_final: 0.6793 (mmtp) REVERT: L 224 ARG cc_start: 0.7897 (mtt-85) cc_final: 0.7609 (mmm-85) REVERT: C 224 ARG cc_start: 0.7909 (mtt-85) cc_final: 0.7633 (mmm-85) outliers start: 31 outliers final: 12 residues processed: 148 average time/residue: 1.4678 time to fit residues: 231.9902 Evaluate side-chains 138 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 1.258 ------------------------------------------------------------------------------- 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 32 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain B residue 40 CYS 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 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 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 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 113 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 94 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 115 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 67 optimal weight: 0.4980 chunk 39 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN B 222 ASN K 222 ASN C 216 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 = 0.4011 r_free = 0.4011 target = 0.132712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.088918 restraints weight = 17159.046| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.82 r_work: 0.3147 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3030 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3030 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.4637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11808 Z= 0.139 Angle : 0.521 7.948 16244 Z= 0.288 Chirality : 0.042 0.143 1780 Planarity : 0.004 0.042 1802 Dihedral : 20.952 63.636 2220 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.69 % Allowed : 16.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.24), residues: 1208 helix: 2.20 (0.22), residues: 534 sheet: 1.19 (0.30), residues: 282 loop : -0.64 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 19 HIS 0.004 0.001 HIS A 12 PHE 0.017 0.001 PHE B 26 TYR 0.012 0.001 TYR A 83 ARG 0.004 0.000 ARG A 20 Details of bonding type rmsd hydrogen bonds : bond 0.03869 ( 636) hydrogen bonds : angle 4.49311 ( 1747) metal coordination : bond 0.01224 ( 8) metal coordination : angle 4.53811 ( 4) covalent geometry : bond 0.00311 (11800) covalent geometry : angle 0.51638 (16240) *********************** 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 151 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 123 time to evaluate : 1.200 Fit side-chains REVERT: A 9 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.8050 (mt0) REVERT: B 27 ASN cc_start: 0.8916 (t0) cc_final: 0.8605 (t0) REVERT: D 240 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7948 (tptm) REVERT: D 258 LYS cc_start: 0.8675 (mttt) cc_final: 0.8469 (mttm) REVERT: I 9 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.8024 (mt0) REVERT: K 188 LYS cc_start: 0.7328 (OUTLIER) cc_final: 0.6800 (mmtp) REVERT: M 258 LYS cc_start: 0.8683 (mttt) cc_final: 0.8476 (mttm) REVERT: L 224 ARG cc_start: 0.7853 (mtt-85) cc_final: 0.7561 (mmm-85) REVERT: C 224 ARG cc_start: 0.7866 (mtt-85) cc_final: 0.7598 (mmm-85) outliers start: 28 outliers final: 13 residues processed: 142 average time/residue: 1.5181 time to fit residues: 231.8990 Evaluate side-chains 139 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 1.226 ------------------------------------------------------------------------------- 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 32 VAL Chi-restraints excluded: chain B residue 40 CYS 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 I residue 31 VAL Chi-restraints excluded: chain K residue 188 LYS Chi-restraints excluded: chain K residue 220 ILE Chi-restraints excluded: chain M residue 231 ARG Chi-restraints excluded: chain L residue 220 ILE Chi-restraints excluded: chain L residue 230 SER Chi-restraints excluded: chain C residue 220 ILE Chi-restraints excluded: chain C residue 230 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 67 optimal weight: 0.2980 chunk 53 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 3 optimal weight: 0.2980 chunk 1 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 48 optimal weight: 9.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 221 GLN C 221 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.133581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.089372 restraints weight = 23590.015| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.09 r_work: 0.3153 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3007 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3007 r_free = 0.3007 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 = 0.3007 r_free = 0.3007 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3007 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.4758 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= 0.119 Angle : 0.503 7.780 16244 Z= 0.278 Chirality : 0.042 0.141 1780 Planarity : 0.003 0.041 1802 Dihedral : 20.882 65.646 2220 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.78 % Allowed : 17.27 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.25), residues: 1208 helix: 2.30 (0.22), residues: 534 sheet: 1.22 (0.30), residues: 282 loop : -0.63 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 19 HIS 0.004 0.001 HIS A 12 PHE 0.019 0.001 PHE B 26 TYR 0.012 0.001 TYR A 83 ARG 0.003 0.000 ARG L 224 Details of bonding type rmsd hydrogen bonds : bond 0.03541 ( 636) hydrogen bonds : angle 4.39952 ( 1747) metal coordination : bond 0.00928 ( 8) metal coordination : angle 4.36105 ( 4) covalent geometry : bond 0.00261 (11800) covalent geometry : angle 0.49807 (16240) *********************** 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 152 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 123 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.8101 (mt0) REVERT: B 27 ASN cc_start: 0.8874 (t0) cc_final: 0.8560 (t0) REVERT: D 240 LYS cc_start: 0.8303 (OUTLIER) cc_final: 0.8041 (tptp) REVERT: I 9 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.8100 (mt0) REVERT: K 27 ASN cc_start: 0.8874 (t0) cc_final: 0.8606 (t0) REVERT: L 224 ARG cc_start: 0.7881 (mtt-85) cc_final: 0.7582 (mmm-85) REVERT: C 224 ARG cc_start: 0.7920 (mtt-85) cc_final: 0.7649 (mmm-85) outliers start: 29 outliers final: 14 residues processed: 142 average time/residue: 1.4682 time to fit residues: 223.3429 Evaluate side-chains 141 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 1.187 ------------------------------------------------------------------------------- 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 32 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 42 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 44 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 103 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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 = 0.3976 r_free = 0.3976 target = 0.130225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.085793 restraints weight = 20545.742| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.96 r_work: 0.3057 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2968 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2968 r_free = 0.2968 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 = 0.2968 r_free = 0.2968 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2968 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.4900 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= 0.217 Angle : 0.576 7.722 16244 Z= 0.316 Chirality : 0.045 0.144 1780 Planarity : 0.004 0.044 1802 Dihedral : 21.064 64.342 2220 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.21 % Allowed : 17.56 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.24), residues: 1208 helix: 2.07 (0.21), residues: 534 sheet: 1.14 (0.31), residues: 282 loop : -0.65 (0.33), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 19 HIS 0.006 0.001 HIS A 16 PHE 0.018 0.002 PHE B 26 TYR 0.015 0.002 TYR A 83 ARG 0.005 0.000 ARG M 263 Details of bonding type rmsd hydrogen bonds : bond 0.04593 ( 636) hydrogen bonds : angle 4.62772 ( 1747) metal coordination : bond 0.01891 ( 8) metal coordination : angle 4.28618 ( 4) covalent geometry : bond 0.00496 (11800) covalent geometry : angle 0.57210 (16240) *********************** 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 : 1.102 Fit side-chains revert: symmetry clash REVERT: A 9 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.8110 (mt0) REVERT: A 156 LYS cc_start: 0.9050 (OUTLIER) cc_final: 0.8725 (tmmm) REVERT: B 27 ASN cc_start: 0.8815 (t0) cc_final: 0.8506 (t0) REVERT: D 240 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.8013 (tptm) REVERT: I 9 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.8080 (mt0) REVERT: K 27 ASN cc_start: 0.8795 (t0) cc_final: 0.8523 (t0) REVERT: L 224 ARG cc_start: 0.7907 (mtt-85) cc_final: 0.7604 (mmm-85) REVERT: C 224 ARG cc_start: 0.7911 (mtt-85) cc_final: 0.7632 (mmm-85) outliers start: 23 outliers final: 14 residues processed: 137 average time/residue: 1.4941 time to fit residues: 218.5319 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 : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLN Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 42 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 172 LEU Chi-restraints excluded: chain K residue 220 ILE Chi-restraints excluded: chain M residue 231 ARG Chi-restraints excluded: chain L residue 220 ILE Chi-restraints excluded: chain 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 26 optimal weight: 0.3980 chunk 77 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 24 optimal weight: 8.9990 chunk 115 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 94 optimal weight: 0.2980 chunk 57 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 214 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 = 0.4011 r_free = 0.4011 target = 0.132641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.088070 restraints weight = 26985.802| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.22 r_work: 0.3128 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2984 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2984 r_free = 0.2984 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 = 0.2984 r_free = 0.2984 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2984 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.4970 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= 0.125 Angle : 0.510 7.784 16244 Z= 0.283 Chirality : 0.042 0.140 1780 Planarity : 0.003 0.042 1802 Dihedral : 20.942 65.999 2220 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.50 % Allowed : 17.37 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.25), residues: 1208 helix: 2.23 (0.22), residues: 534 sheet: 1.19 (0.31), residues: 282 loop : -0.64 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP K 19 HIS 0.005 0.001 HIS K 183 PHE 0.023 0.001 PHE B 26 TYR 0.012 0.001 TYR A 83 ARG 0.003 0.000 ARG C 224 Details of bonding type rmsd hydrogen bonds : bond 0.03601 ( 636) hydrogen bonds : angle 4.46529 ( 1747) metal coordination : bond 0.01113 ( 8) metal coordination : angle 4.39185 ( 4) covalent geometry : bond 0.00276 (11800) covalent geometry : angle 0.50535 (16240) *********************** 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 149 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 123 time to evaluate : 1.111 Fit side-chains revert: symmetry clash REVERT: A 9 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.8098 (mt0) REVERT: B 27 ASN cc_start: 0.8800 (t0) cc_final: 0.8505 (t0) REVERT: D 240 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.8102 (tptp) REVERT: I 9 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.8093 (mt0) REVERT: K 26 PHE cc_start: 0.7836 (m-80) cc_final: 0.7624 (m-80) REVERT: K 27 ASN cc_start: 0.8770 (t0) cc_final: 0.8504 (t0) REVERT: L 224 ARG cc_start: 0.7916 (mtt-85) cc_final: 0.7624 (mmm-85) REVERT: C 224 ARG cc_start: 0.7941 (mtt-85) cc_final: 0.7682 (mmm-85) outliers start: 26 outliers final: 15 residues processed: 141 average time/residue: 1.4388 time to fit residues: 217.3596 Evaluate side-chains 139 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 9 GLN Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 42 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 11 optimal weight: 0.7980 chunk 83 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 36 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 115 optimal weight: 0.9980 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 = 0.3976 r_free = 0.3976 target = 0.130225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.084712 restraints weight = 32680.812| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.42 r_work: 0.3057 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2937 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2937 r_free = 0.2937 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2937 r_free = 0.2937 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2937 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.5042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 11808 Z= 0.201 Angle : 0.568 7.782 16244 Z= 0.313 Chirality : 0.045 0.145 1780 Planarity : 0.004 0.044 1802 Dihedral : 21.063 64.857 2220 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.92 % Allowed : 17.95 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.24), residues: 1208 helix: 2.07 (0.22), residues: 534 sheet: 1.13 (0.31), residues: 282 loop : -0.62 (0.33), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 19 HIS 0.006 0.001 HIS A 16 PHE 0.028 0.002 PHE B 26 TYR 0.014 0.002 TYR A 83 ARG 0.002 0.000 ARG M 263 Details of bonding type rmsd hydrogen bonds : bond 0.04444 ( 636) hydrogen bonds : angle 4.61260 ( 1747) metal coordination : bond 0.01858 ( 8) metal coordination : angle 4.19800 ( 4) covalent geometry : bond 0.00459 (11800) covalent geometry : angle 0.56435 (16240) *********************** 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 145 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 1.214 Fit side-chains revert: symmetry clash REVERT: A 9 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.8179 (mt0) REVERT: B 27 ASN cc_start: 0.8650 (t0) cc_final: 0.8376 (t0) REVERT: D 240 LYS cc_start: 0.8387 (OUTLIER) cc_final: 0.8128 (tptm) REVERT: I 9 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.8142 (mt0) REVERT: K 27 ASN cc_start: 0.8731 (t0) cc_final: 0.8453 (t0) REVERT: L 224 ARG cc_start: 0.7980 (mtt-85) cc_final: 0.7685 (mmm-85) REVERT: C 224 ARG cc_start: 0.7978 (mtt-85) cc_final: 0.7698 (mmm-85) outliers start: 20 outliers final: 16 residues processed: 136 average time/residue: 1.4520 time to fit residues: 211.6895 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 : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 9 GLN Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 42 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 78 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 36 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.3982 r_free = 0.3982 target = 0.130582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.085586 restraints weight = 28626.749| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.28 r_work: 0.3077 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2961 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2961 r_free = 0.2961 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2961 r_free = 0.2961 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2961 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.5090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11808 Z= 0.178 Angle : 0.555 7.814 16244 Z= 0.307 Chirality : 0.044 0.191 1780 Planarity : 0.004 0.043 1802 Dihedral : 21.061 65.466 2220 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.92 % Allowed : 18.14 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.24), residues: 1208 helix: 2.08 (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 TRP 0.043 0.002 TRP K 19 HIS 0.005 0.001 HIS I 16 PHE 0.029 0.002 PHE B 26 TYR 0.014 0.002 TYR A 83 ARG 0.003 0.000 ARG M 263 Details of bonding type rmsd hydrogen bonds : bond 0.04172 ( 636) hydrogen bonds : angle 4.57867 ( 1747) metal coordination : bond 0.01596 ( 8) metal coordination : angle 4.19571 ( 4) covalent geometry : bond 0.00405 (11800) covalent geometry : angle 0.55162 (16240) ********************** 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 143 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 1.261 Fit side-chains revert: symmetry clash REVERT: A 9 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.8141 (mt0) REVERT: B 27 ASN cc_start: 0.8630 (t0) cc_final: 0.8372 (t0) REVERT: D 240 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.8125 (tptm) REVERT: I 9 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.8098 (mt0) REVERT: K 27 ASN cc_start: 0.8730 (t0) cc_final: 0.8457 (t0) REVERT: L 224 ARG cc_start: 0.7954 (mtt-85) cc_final: 0.7658 (mmm-85) REVERT: C 224 ARG cc_start: 0.7948 (mtt-85) cc_final: 0.7672 (mmm-85) outliers start: 20 outliers final: 15 residues processed: 134 average time/residue: 1.4618 time to fit residues: 210.0967 Evaluate side-chains 139 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 1.144 ------------------------------------------------------------------------------- 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 32 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 42 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 35 optimal weight: 0.3980 chunk 120 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 119 optimal weight: 0.4980 chunk 8 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 125 optimal weight: 0.3980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.4012 r_free = 0.4012 target = 0.132581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.087957 restraints weight = 26168.980| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.20 r_work: 0.3132 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3016 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3016 r_free = 0.3016 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 = 0.3016 r_free = 0.3016 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3016 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.5151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11808 Z= 0.123 Angle : 0.514 7.684 16244 Z= 0.286 Chirality : 0.042 0.161 1780 Planarity : 0.003 0.042 1802 Dihedral : 20.962 66.227 2220 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.73 % Allowed : 18.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.25), residues: 1208 helix: 2.21 (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 TRP 0.045 0.001 TRP K 19 HIS 0.004 0.001 HIS K 183 PHE 0.031 0.002 PHE B 26 TYR 0.012 0.001 TYR A 83 ARG 0.002 0.000 ARG C 224 Details of bonding type rmsd hydrogen bonds : bond 0.03554 ( 636) hydrogen bonds : angle 4.44559 ( 1747) metal coordination : bond 0.00998 ( 8) metal coordination : angle 4.46552 ( 4) covalent geometry : bond 0.00270 (11800) covalent geometry : angle 0.50915 (16240) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20092.28 seconds wall clock time: 343 minutes 34.43 seconds (20614.43 seconds total)