Starting phenix.real_space_refine on Tue Apr 29 11:25:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vy9_43650/04_2025/8vy9_43650.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vy9_43650/04_2025/8vy9_43650.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vy9_43650/04_2025/8vy9_43650.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vy9_43650/04_2025/8vy9_43650.map" model { file = "/net/cci-nas-00/data/ceres_data/8vy9_43650/04_2025/8vy9_43650.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vy9_43650/04_2025/8vy9_43650.cif" } resolution = 2.88 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= 0.001 sd= 0.022 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: 5 Type Number sf(0) Gaussians S 60 5.16 5 C 5574 2.51 5 N 1451 2.21 5 O 1580 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 8668 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1722 Classifications: {'peptide': 224} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 22} Link IDs: {'PTRANS': 2, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 6, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "B" Number of atoms: 2458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2458 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 143 Unresolved non-hydrogen angles: 175 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 7, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 109 Chain: "C" Number of atoms: 328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 328 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 4, 'TRANS': 45} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 34 Chain: "D" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 2326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2326 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 286} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'ARG:plan': 1, 'TRP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "R" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 51 Unusual residues: {'A1AEI': 1, 'CLR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.85, per 1000 atoms: 0.67 Number of scatterers: 8668 At special positions: 0 Unit cell: (87.6, 117.384, 134.904, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 60 16.00 F 3 9.00 O 1580 8.00 N 1451 7.00 C 5574 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 217 " distance=2.03 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: 2.43 Conformation dependent library (CDL) restraints added in 1.1 seconds 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2120 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 13 sheets defined 39.1% alpha, 23.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 6 through 31 Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.687A pdb=" N GLN A 52 " --> pdb=" O THR A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.576A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TRP A 211 " --> pdb=" O ARG A 208 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.570A pdb=" N ASN A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 279 removed outlier: 4.544A pdb=" N THR A 279 " --> pdb=" O GLN A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.745A pdb=" N ILE A 285 " --> pdb=" O HIS A 282 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N CYS A 286 " --> pdb=" O LEU A 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 282 through 286' Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 4 through 26 removed outlier: 3.601A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 13 through 24 removed outlier: 3.611A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.565A pdb=" N SER D 31 " --> pdb=" O ALA D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 212 removed outlier: 3.697A pdb=" N VAL D 212 " --> pdb=" O ALA D 209 " (cutoff:3.500A) Processing helix chain 'R' and resid 2 through 37 Processing helix chain 'R' and resid 42 through 71 Processing helix chain 'R' and resid 74 through 77 Processing helix chain 'R' and resid 78 through 112 removed outlier: 4.146A pdb=" N THR R 86 " --> pdb=" O PHE R 82 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE R 95 " --> pdb=" O VAL R 91 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA R 100 " --> pdb=" O SER R 96 " (cutoff:3.500A) Processing helix chain 'R' and resid 116 through 125 removed outlier: 3.790A pdb=" N ARG R 125 " --> pdb=" O TYR R 121 " (cutoff:3.500A) Processing helix chain 'R' and resid 125 through 137 Processing helix chain 'R' and resid 137 through 160 removed outlier: 3.573A pdb=" N LEU R 141 " --> pdb=" O THR R 137 " (cutoff:3.500A) Processing helix chain 'R' and resid 175 through 213 removed outlier: 4.068A pdb=" N ILE R 179 " --> pdb=" O PHE R 175 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE R 189 " --> pdb=" O VAL R 185 " (cutoff:3.500A) Proline residue: R 190 - end of helix removed outlier: 3.760A pdb=" N LEU R 193 " --> pdb=" O ILE R 189 " (cutoff:3.500A) Processing helix chain 'R' and resid 223 through 253 removed outlier: 3.932A pdb=" N SER R 232 " --> pdb=" O ARG R 228 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N THR R 235 " --> pdb=" O LYS R 231 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR R 253 " --> pdb=" O ILE R 249 " (cutoff:3.500A) Processing helix chain 'R' and resid 261 through 282 removed outlier: 3.577A pdb=" N ALA R 271 " --> pdb=" O VAL R 267 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N TYR R 272 " --> pdb=" O MET R 268 " (cutoff:3.500A) Proline residue: R 273 - end of helix removed outlier: 4.586A pdb=" N SER R 277 " --> pdb=" O PRO R 273 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N CYS R 278 " --> pdb=" O SER R 274 " (cutoff:3.500A) Processing helix chain 'R' and resid 284 through 302 removed outlier: 3.590A pdb=" N ARG R 299 " --> pdb=" O LEU R 295 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.833A pdb=" N CYS A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.574A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.741A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.835A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.599A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.862A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.655A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.563A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.793A pdb=" N MET D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N TYR D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 10 through 12 removed outlier: 4.312A pdb=" N PHE D 110 " --> pdb=" O ARG D 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 135 through 136 removed outlier: 3.577A pdb=" N GLU D 234 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE D 177 " --> pdb=" O TRP D 164 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU D 166 " --> pdb=" O LEU D 175 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N LEU D 175 " --> pdb=" O LEU D 166 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 143 through 147 removed outlier: 3.635A pdb=" N ALA D 199 " --> pdb=" O SER D 196 " (cutoff:3.500A) 467 hydrogen bonds defined for protein. 1326 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.54 Time building geometry restraints manager: 2.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2692 1.34 - 1.46: 1928 1.46 - 1.58: 4141 1.58 - 1.70: 2 1.70 - 1.82: 90 Bond restraints: 8853 Sorted by residual: bond pdb=" C10 A1AEI R 601 " pdb=" N11 A1AEI R 601 " ideal model delta sigma weight residual 1.364 1.457 -0.093 2.00e-02 2.50e+03 2.17e+01 bond pdb=" C13 A1AEI R 601 " pdb=" C14 A1AEI R 601 " ideal model delta sigma weight residual 1.461 1.527 -0.066 2.00e-02 2.50e+03 1.09e+01 bond pdb=" N16 A1AEI R 601 " pdb=" N17 A1AEI R 601 " ideal model delta sigma weight residual 1.275 1.335 -0.060 2.00e-02 2.50e+03 8.99e+00 bond pdb=" C16 CLR R 602 " pdb=" C17 CLR R 602 " ideal model delta sigma weight residual 1.554 1.606 -0.052 2.00e-02 2.50e+03 6.69e+00 bond pdb=" C23 CLR R 602 " pdb=" C24 CLR R 602 " ideal model delta sigma weight residual 1.525 1.571 -0.046 2.00e-02 2.50e+03 5.22e+00 ... (remaining 8848 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 11787 2.16 - 4.32: 187 4.32 - 6.49: 29 6.49 - 8.65: 9 8.65 - 10.81: 2 Bond angle restraints: 12014 Sorted by residual: angle pdb=" C ASP A 231 " pdb=" N MET A 232 " pdb=" CA MET A 232 " ideal model delta sigma weight residual 122.82 127.50 -4.68 1.42e+00 4.96e-01 1.09e+01 angle pdb=" CA TYR D 178 " pdb=" CB TYR D 178 " pdb=" CG TYR D 178 " ideal model delta sigma weight residual 113.90 119.71 -5.81 1.80e+00 3.09e-01 1.04e+01 angle pdb=" CA LEU R 261 " pdb=" CB LEU R 261 " pdb=" CG LEU R 261 " ideal model delta sigma weight residual 116.30 127.11 -10.81 3.50e+00 8.16e-02 9.54e+00 angle pdb=" N PHE R 247 " pdb=" CA PHE R 247 " pdb=" CB PHE R 247 " ideal model delta sigma weight residual 110.01 114.44 -4.43 1.45e+00 4.76e-01 9.34e+00 angle pdb=" C22 CLR R 602 " pdb=" C23 CLR R 602 " pdb=" C24 CLR R 602 " ideal model delta sigma weight residual 111.95 102.84 9.11 3.00e+00 1.11e-01 9.21e+00 ... (remaining 12009 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.63: 4922 22.63 - 45.26: 268 45.26 - 67.89: 32 67.89 - 90.52: 6 90.52 - 113.15: 3 Dihedral angle restraints: 5231 sinusoidal: 1951 harmonic: 3280 Sorted by residual: dihedral pdb=" CB CYS D 147 " pdb=" SG CYS D 147 " pdb=" SG CYS D 217 " pdb=" CB CYS D 217 " ideal model delta sinusoidal sigma weight residual 93.00 167.08 -74.08 1 1.00e+01 1.00e-02 6.97e+01 dihedral pdb=" CA ASP A 231 " pdb=" C ASP A 231 " pdb=" N MET A 232 " pdb=" CA MET A 232 " ideal model delta harmonic sigma weight residual 180.00 157.15 22.85 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" CA TYR D 178 " pdb=" C TYR D 178 " pdb=" N ARG D 179 " pdb=" CA ARG D 179 " ideal model delta harmonic sigma weight residual 180.00 157.16 22.84 0 5.00e+00 4.00e-02 2.09e+01 ... (remaining 5228 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1113 0.056 - 0.112: 233 0.112 - 0.168: 45 0.168 - 0.224: 6 0.224 - 0.280: 1 Chirality restraints: 1398 Sorted by residual: chirality pdb=" C17 CLR R 602 " pdb=" C13 CLR R 602 " pdb=" C16 CLR R 602 " pdb=" C20 CLR R 602 " both_signs ideal model delta sigma weight residual False 2.55 2.83 -0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" C13 CLR R 602 " pdb=" C12 CLR R 602 " pdb=" C14 CLR R 602 " pdb=" C17 CLR R 602 " both_signs ideal model delta sigma weight residual False -2.93 -3.13 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CB VAL R 251 " pdb=" CA VAL R 251 " pdb=" CG1 VAL R 251 " pdb=" CG2 VAL R 251 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.95e-01 ... (remaining 1395 not shown) Planarity restraints: 1490 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE R 247 " 0.028 2.00e-02 2.50e+03 2.77e-02 1.34e+01 pdb=" CG PHE R 247 " -0.065 2.00e-02 2.50e+03 pdb=" CD1 PHE R 247 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE R 247 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE R 247 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE R 247 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE R 247 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR R 240 " -0.021 2.00e-02 2.50e+03 1.31e-02 3.42e+00 pdb=" CG TYR R 240 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR R 240 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR R 240 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR R 240 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR R 240 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR R 240 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR R 240 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.030 5.00e-02 4.00e+02 4.50e-02 3.24e+00 pdb=" N PRO B 236 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.025 5.00e-02 4.00e+02 ... (remaining 1487 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1779 2.78 - 3.31: 7571 3.31 - 3.84: 14554 3.84 - 4.37: 16340 4.37 - 4.90: 29477 Nonbonded interactions: 69721 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.245 3.040 nonbonded pdb=" OD1 ASP R 221 " pdb=" OG1 THR R 224 " model vdw 2.269 3.040 nonbonded pdb=" O LEU R 133 " pdb=" OG1 THR R 137 " model vdw 2.287 3.040 nonbonded pdb=" O ILE D 126 " pdb=" OG1 THR D 226 " model vdw 2.299 3.040 nonbonded pdb=" OG SER R 254 " pdb=" OE1 GLU R 255 " model vdw 2.303 3.040 ... (remaining 69716 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: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.750 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: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.810 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 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 0.093 8854 Z= 0.226 Angle : 0.702 10.811 12016 Z= 0.358 Chirality : 0.049 0.280 1398 Planarity : 0.005 0.045 1490 Dihedral : 14.270 113.148 3108 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.24), residues: 1118 helix: 0.23 (0.23), residues: 410 sheet: 0.30 (0.31), residues: 282 loop : -1.63 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 169 HIS 0.008 0.001 HIS D 220 PHE 0.065 0.002 PHE R 247 TYR 0.030 0.002 TYR D 178 ARG 0.002 0.000 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.17015 ( 462) hydrogen bonds : angle 6.33799 ( 1326) SS BOND : bond 0.00176 ( 1) SS BOND : angle 1.09983 ( 2) covalent geometry : bond 0.00496 ( 8853) covalent geometry : angle 0.70217 (12014) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 1.000 Fit side-chains REVERT: A 186 GLU cc_start: 0.7520 (tt0) cc_final: 0.7300 (tt0) REVERT: B 70 LEU cc_start: 0.8316 (tt) cc_final: 0.8103 (tt) REVERT: B 189 SER cc_start: 0.8649 (p) cc_final: 0.8423 (t) REVERT: B 263 THR cc_start: 0.8624 (t) cc_final: 0.8280 (m) REVERT: D 21 SER cc_start: 0.8211 (m) cc_final: 0.7701 (p) REVERT: D 23 SER cc_start: 0.8253 (m) cc_final: 0.8043 (t) REVERT: D 192 SER cc_start: 0.8536 (m) cc_final: 0.8253 (t) REVERT: D 218 MET cc_start: 0.8168 (ttp) cc_final: 0.7956 (ttm) REVERT: R 152 ILE cc_start: 0.8314 (mm) cc_final: 0.7806 (tt) REVERT: R 280 LEU cc_start: 0.8725 (mt) cc_final: 0.8458 (mt) outliers start: 0 outliers final: 1 residues processed: 242 average time/residue: 0.8954 time to fit residues: 235.6367 Evaluate side-chains 207 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 206 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 19 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 57 optimal weight: 0.2980 chunk 45 optimal weight: 0.6980 chunk 87 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 101 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.134847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.117317 restraints weight = 12202.443| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 2.02 r_work: 0.3460 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8854 Z= 0.150 Angle : 0.544 6.405 12016 Z= 0.285 Chirality : 0.041 0.147 1398 Planarity : 0.004 0.036 1490 Dihedral : 5.390 48.616 1280 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.09 % Allowed : 12.47 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.25), residues: 1118 helix: 1.61 (0.25), residues: 407 sheet: 0.66 (0.30), residues: 281 loop : -1.47 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS D 220 PHE 0.033 0.002 PHE R 247 TYR 0.024 0.001 TYR D 178 ARG 0.005 0.000 ARG R 55 Details of bonding type rmsd hydrogen bonds : bond 0.04139 ( 462) hydrogen bonds : angle 4.29573 ( 1326) SS BOND : bond 0.00091 ( 1) SS BOND : angle 0.57722 ( 2) covalent geometry : bond 0.00338 ( 8853) covalent geometry : angle 0.54354 (12014) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 213 time to evaluate : 1.085 Fit side-chains REVERT: A 186 GLU cc_start: 0.7858 (tt0) cc_final: 0.7642 (tt0) REVERT: A 313 LYS cc_start: 0.8017 (OUTLIER) cc_final: 0.7809 (tttm) REVERT: D 23 SER cc_start: 0.8349 (m) cc_final: 0.8091 (p) REVERT: D 116 THR cc_start: 0.8480 (t) cc_final: 0.8274 (m) REVERT: D 192 SER cc_start: 0.8553 (m) cc_final: 0.8274 (t) REVERT: D 218 MET cc_start: 0.8221 (ttp) cc_final: 0.8021 (ttt) REVERT: R 13 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8168 (tt) REVERT: R 101 THR cc_start: 0.8819 (OUTLIER) cc_final: 0.8571 (t) REVERT: R 152 ILE cc_start: 0.8333 (mm) cc_final: 0.7833 (tt) REVERT: R 267 VAL cc_start: 0.7877 (t) cc_final: 0.7670 (p) REVERT: R 280 LEU cc_start: 0.8694 (mt) cc_final: 0.8456 (mt) REVERT: R 286 LYS cc_start: 0.8179 (ttmm) cc_final: 0.7873 (ttpt) outliers start: 28 outliers final: 11 residues processed: 222 average time/residue: 0.9351 time to fit residues: 224.4150 Evaluate side-chains 211 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 197 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 313 LYS Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain R residue 12 VAL Chi-restraints excluded: chain R residue 13 LEU Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain R residue 145 ILE Chi-restraints excluded: chain R residue 184 THR Chi-restraints excluded: chain R residue 292 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 11 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.134148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.116108 restraints weight = 12135.141| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.03 r_work: 0.3419 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 8854 Z= 0.240 Angle : 0.588 10.254 12016 Z= 0.306 Chirality : 0.044 0.166 1398 Planarity : 0.004 0.037 1490 Dihedral : 5.392 52.736 1278 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.42 % Allowed : 16.45 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.25), residues: 1118 helix: 1.77 (0.25), residues: 410 sheet: 0.61 (0.31), residues: 275 loop : -1.39 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.005 0.001 HIS D 35 PHE 0.030 0.002 PHE R 247 TYR 0.034 0.002 TYR D 178 ARG 0.006 0.000 ARG R 55 Details of bonding type rmsd hydrogen bonds : bond 0.04329 ( 462) hydrogen bonds : angle 4.20698 ( 1326) SS BOND : bond 0.00163 ( 1) SS BOND : angle 0.89526 ( 2) covalent geometry : bond 0.00554 ( 8853) covalent geometry : angle 0.58810 (12014) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 207 time to evaluate : 0.963 Fit side-chains REVERT: A 234 LEU cc_start: 0.7547 (mm) cc_final: 0.7333 (mm) REVERT: A 341 ASP cc_start: 0.8306 (t70) cc_final: 0.8058 (t70) REVERT: A 345 LYS cc_start: 0.8404 (mtmt) cc_final: 0.8193 (mtmm) REVERT: B 49 ARG cc_start: 0.8555 (mmt-90) cc_final: 0.8176 (mpt180) REVERT: B 155 ASN cc_start: 0.8508 (t0) cc_final: 0.8232 (t0) REVERT: D 21 SER cc_start: 0.8409 (m) cc_final: 0.8003 (p) REVERT: D 23 SER cc_start: 0.8366 (m) cc_final: 0.8158 (p) REVERT: D 116 THR cc_start: 0.8530 (OUTLIER) cc_final: 0.8302 (m) REVERT: D 192 SER cc_start: 0.8616 (m) cc_final: 0.8349 (t) REVERT: R 13 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8263 (tt) REVERT: R 101 THR cc_start: 0.8860 (OUTLIER) cc_final: 0.8659 (t) REVERT: R 152 ILE cc_start: 0.8322 (mm) cc_final: 0.7856 (tt) REVERT: R 211 LYS cc_start: 0.7180 (OUTLIER) cc_final: 0.6917 (ttpp) REVERT: R 280 LEU cc_start: 0.8769 (mt) cc_final: 0.8450 (mt) REVERT: R 286 LYS cc_start: 0.8125 (ttmm) cc_final: 0.7875 (ttmt) outliers start: 31 outliers final: 13 residues processed: 217 average time/residue: 0.8886 time to fit residues: 209.5754 Evaluate side-chains 216 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 199 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain R residue 12 VAL Chi-restraints excluded: chain R residue 13 LEU Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain R residue 211 LYS Chi-restraints excluded: chain R residue 292 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 41 optimal weight: 0.0270 chunk 71 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 59 optimal weight: 0.0870 chunk 13 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 104 optimal weight: 0.8980 chunk 31 optimal weight: 0.0980 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.134562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.116605 restraints weight = 12271.047| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.05 r_work: 0.3427 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8854 Z= 0.117 Angle : 0.511 7.935 12016 Z= 0.265 Chirality : 0.040 0.139 1398 Planarity : 0.003 0.034 1490 Dihedral : 5.016 49.191 1278 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.98 % Allowed : 18.87 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.26), residues: 1118 helix: 2.22 (0.25), residues: 410 sheet: 0.77 (0.31), residues: 280 loop : -1.32 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.002 0.001 HIS R 94 PHE 0.031 0.002 PHE R 17 TYR 0.020 0.001 TYR D 178 ARG 0.005 0.000 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.03492 ( 462) hydrogen bonds : angle 3.97765 ( 1326) SS BOND : bond 0.00085 ( 1) SS BOND : angle 0.35256 ( 2) covalent geometry : bond 0.00256 ( 8853) covalent geometry : angle 0.51138 (12014) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 206 time to evaluate : 1.042 Fit side-chains REVERT: A 274 PHE cc_start: 0.8477 (t80) cc_final: 0.8240 (t80) REVERT: A 318 GLU cc_start: 0.7557 (mm-30) cc_final: 0.7353 (mm-30) REVERT: A 323 MET cc_start: 0.8427 (mtt) cc_final: 0.8106 (mtt) REVERT: A 350 ASP cc_start: 0.7651 (p0) cc_final: 0.7261 (p0) REVERT: B 14 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8153 (mm) REVERT: B 49 ARG cc_start: 0.8529 (mmt-90) cc_final: 0.8203 (mpt180) REVERT: B 50 THR cc_start: 0.8559 (t) cc_final: 0.8349 (m) REVERT: B 70 LEU cc_start: 0.8213 (tt) cc_final: 0.7979 (tp) REVERT: B 136 SER cc_start: 0.8580 (t) cc_final: 0.8368 (p) REVERT: B 155 ASN cc_start: 0.8542 (t0) cc_final: 0.8320 (t0) REVERT: D 116 THR cc_start: 0.8481 (OUTLIER) cc_final: 0.8270 (m) REVERT: D 192 SER cc_start: 0.8586 (m) cc_final: 0.8279 (t) REVERT: R 13 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8178 (tt) REVERT: R 17 PHE cc_start: 0.7394 (t80) cc_final: 0.7050 (t80) REVERT: R 101 THR cc_start: 0.8820 (OUTLIER) cc_final: 0.8616 (t) REVERT: R 110 LYS cc_start: 0.8430 (mttm) cc_final: 0.7855 (mttm) REVERT: R 152 ILE cc_start: 0.8300 (mm) cc_final: 0.7846 (tt) REVERT: R 280 LEU cc_start: 0.8741 (mt) cc_final: 0.8413 (mt) REVERT: R 286 LYS cc_start: 0.8100 (ttmm) cc_final: 0.7884 (ttmt) outliers start: 27 outliers final: 10 residues processed: 216 average time/residue: 0.9102 time to fit residues: 213.3643 Evaluate side-chains 210 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 196 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain R residue 12 VAL Chi-restraints excluded: chain R residue 13 LEU Chi-restraints excluded: chain R residue 19 ILE Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain R residue 292 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 78 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 chunk 77 optimal weight: 0.7980 chunk 31 optimal weight: 0.0070 chunk 69 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.133905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.115976 restraints weight = 12358.778| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.04 r_work: 0.3427 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8854 Z= 0.138 Angle : 0.515 7.760 12016 Z= 0.267 Chirality : 0.041 0.141 1398 Planarity : 0.003 0.032 1490 Dihedral : 5.005 50.180 1278 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.87 % Allowed : 20.20 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.26), residues: 1118 helix: 2.40 (0.25), residues: 410 sheet: 0.82 (0.32), residues: 271 loop : -1.29 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS D 35 PHE 0.018 0.001 PHE R 63 TYR 0.023 0.001 TYR D 178 ARG 0.007 0.000 ARG R 55 Details of bonding type rmsd hydrogen bonds : bond 0.03494 ( 462) hydrogen bonds : angle 3.94359 ( 1326) SS BOND : bond 0.00037 ( 1) SS BOND : angle 0.40690 ( 2) covalent geometry : bond 0.00314 ( 8853) covalent geometry : angle 0.51511 (12014) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 206 time to evaluate : 0.967 Fit side-chains REVERT: A 323 MET cc_start: 0.8409 (mtt) cc_final: 0.8116 (mtt) REVERT: B 14 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8190 (mm) REVERT: B 49 ARG cc_start: 0.8553 (mmt-90) cc_final: 0.8218 (mpt180) REVERT: B 70 LEU cc_start: 0.8230 (tt) cc_final: 0.7996 (tp) REVERT: B 136 SER cc_start: 0.8568 (t) cc_final: 0.8365 (p) REVERT: B 155 ASN cc_start: 0.8556 (t0) cc_final: 0.8269 (t0) REVERT: D 21 SER cc_start: 0.8368 (m) cc_final: 0.7974 (p) REVERT: D 116 THR cc_start: 0.8477 (OUTLIER) cc_final: 0.8274 (m) REVERT: D 183 LEU cc_start: 0.8750 (mt) cc_final: 0.8539 (mm) REVERT: D 192 SER cc_start: 0.8609 (m) cc_final: 0.8310 (t) REVERT: R 13 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8158 (tt) REVERT: R 17 PHE cc_start: 0.7496 (t80) cc_final: 0.7107 (t80) REVERT: R 101 THR cc_start: 0.8825 (OUTLIER) cc_final: 0.8618 (t) REVERT: R 110 LYS cc_start: 0.8421 (mttm) cc_final: 0.8194 (mttm) REVERT: R 127 LYS cc_start: 0.7479 (mmtm) cc_final: 0.7195 (mmtt) REVERT: R 152 ILE cc_start: 0.8321 (mm) cc_final: 0.7878 (tt) REVERT: R 280 LEU cc_start: 0.8741 (mt) cc_final: 0.8433 (mt) REVERT: R 286 LYS cc_start: 0.8123 (ttmm) cc_final: 0.7883 (ttpt) outliers start: 26 outliers final: 15 residues processed: 216 average time/residue: 0.8865 time to fit residues: 208.1676 Evaluate side-chains 218 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 199 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 313 LYS Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain R residue 12 VAL Chi-restraints excluded: chain R residue 13 LEU Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain R residue 292 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 36 optimal weight: 0.0570 chunk 99 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 83 optimal weight: 0.8980 chunk 94 optimal weight: 0.9980 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.133512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.115562 restraints weight = 12142.373| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.01 r_work: 0.3426 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8854 Z= 0.163 Angle : 0.528 7.643 12016 Z= 0.275 Chirality : 0.041 0.151 1398 Planarity : 0.003 0.032 1490 Dihedral : 5.063 51.432 1278 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 3.09 % Allowed : 20.75 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.26), residues: 1118 helix: 2.37 (0.25), residues: 411 sheet: 0.87 (0.31), residues: 281 loop : -1.30 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS D 35 PHE 0.023 0.002 PHE R 119 TYR 0.024 0.001 TYR D 178 ARG 0.010 0.000 ARG R 55 Details of bonding type rmsd hydrogen bonds : bond 0.03623 ( 462) hydrogen bonds : angle 3.96241 ( 1326) SS BOND : bond 0.00073 ( 1) SS BOND : angle 0.44428 ( 2) covalent geometry : bond 0.00372 ( 8853) covalent geometry : angle 0.52851 (12014) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 209 time to evaluate : 0.926 Fit side-chains REVERT: B 14 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8252 (mm) REVERT: B 49 ARG cc_start: 0.8573 (mmt-90) cc_final: 0.8189 (mpt180) REVERT: B 70 LEU cc_start: 0.8218 (tt) cc_final: 0.7990 (tp) REVERT: B 136 SER cc_start: 0.8584 (t) cc_final: 0.8382 (p) REVERT: B 155 ASN cc_start: 0.8539 (t0) cc_final: 0.8321 (t0) REVERT: B 188 MET cc_start: 0.8450 (mmm) cc_final: 0.8223 (mmm) REVERT: B 256 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.7705 (mtt180) REVERT: D 21 SER cc_start: 0.8383 (m) cc_final: 0.7972 (p) REVERT: D 34 MET cc_start: 0.8595 (mmp) cc_final: 0.8313 (mmm) REVERT: D 128 MET cc_start: 0.8748 (mmm) cc_final: 0.7696 (mmm) REVERT: D 183 LEU cc_start: 0.8777 (mt) cc_final: 0.8571 (mm) REVERT: D 192 SER cc_start: 0.8603 (m) cc_final: 0.8328 (t) REVERT: D 201 THR cc_start: 0.8437 (m) cc_final: 0.8156 (p) REVERT: R 13 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8190 (tt) REVERT: R 17 PHE cc_start: 0.7401 (t80) cc_final: 0.7118 (t80) REVERT: R 127 LYS cc_start: 0.7492 (mmtm) cc_final: 0.7180 (mmtt) REVERT: R 152 ILE cc_start: 0.8331 (mm) cc_final: 0.7922 (tt) REVERT: R 286 LYS cc_start: 0.8149 (ttmm) cc_final: 0.7901 (ttpt) REVERT: R 301 MET cc_start: 0.6423 (tpt) cc_final: 0.6078 (tpt) outliers start: 28 outliers final: 13 residues processed: 219 average time/residue: 0.9554 time to fit residues: 227.0628 Evaluate side-chains 219 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 203 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 313 LYS Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 345 LYS Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain R residue 12 VAL Chi-restraints excluded: chain R residue 13 LEU Chi-restraints excluded: chain R residue 131 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 73 optimal weight: 0.1980 chunk 39 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 86 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 65 optimal weight: 0.4980 chunk 32 optimal weight: 0.7980 chunk 89 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.133445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.115498 restraints weight = 12465.250| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.05 r_work: 0.3407 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8854 Z= 0.145 Angle : 0.526 7.530 12016 Z= 0.273 Chirality : 0.041 0.143 1398 Planarity : 0.003 0.032 1490 Dihedral : 5.030 51.196 1278 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.09 % Allowed : 22.08 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.26), residues: 1118 helix: 2.39 (0.25), residues: 411 sheet: 0.87 (0.31), residues: 281 loop : -1.29 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS D 35 PHE 0.015 0.001 PHE R 247 TYR 0.024 0.001 TYR D 178 ARG 0.006 0.000 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.03487 ( 462) hydrogen bonds : angle 3.96914 ( 1326) SS BOND : bond 0.00051 ( 1) SS BOND : angle 0.43159 ( 2) covalent geometry : bond 0.00332 ( 8853) covalent geometry : angle 0.52567 (12014) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 205 time to evaluate : 1.123 Fit side-chains REVERT: B 14 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8196 (mm) REVERT: B 49 ARG cc_start: 0.8531 (mmt-90) cc_final: 0.8147 (mpt180) REVERT: B 70 LEU cc_start: 0.8210 (tt) cc_final: 0.7985 (tp) REVERT: B 155 ASN cc_start: 0.8576 (t0) cc_final: 0.8291 (t0) REVERT: B 188 MET cc_start: 0.8472 (mmm) cc_final: 0.8245 (mmm) REVERT: B 256 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.7689 (mtt180) REVERT: B 333 ASP cc_start: 0.7996 (p0) cc_final: 0.7706 (p0) REVERT: D 21 SER cc_start: 0.8359 (m) cc_final: 0.7972 (p) REVERT: D 34 MET cc_start: 0.8599 (mmp) cc_final: 0.8328 (mmm) REVERT: D 128 MET cc_start: 0.8752 (mmm) cc_final: 0.7706 (mmm) REVERT: D 183 LEU cc_start: 0.8782 (mt) cc_final: 0.8579 (mm) REVERT: D 192 SER cc_start: 0.8643 (m) cc_final: 0.8341 (t) REVERT: D 201 THR cc_start: 0.8447 (m) cc_final: 0.8168 (p) REVERT: R 13 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8182 (tt) REVERT: R 75 LEU cc_start: 0.6857 (tp) cc_final: 0.6410 (tm) REVERT: R 81 MET cc_start: 0.7578 (OUTLIER) cc_final: 0.7053 (ttm) REVERT: R 127 LYS cc_start: 0.7490 (OUTLIER) cc_final: 0.7180 (mmtt) REVERT: R 152 ILE cc_start: 0.8317 (mm) cc_final: 0.7907 (tt) REVERT: R 286 LYS cc_start: 0.8090 (ttmm) cc_final: 0.7851 (ttpt) REVERT: R 301 MET cc_start: 0.6444 (tpt) cc_final: 0.6083 (tpt) outliers start: 28 outliers final: 15 residues processed: 214 average time/residue: 1.0465 time to fit residues: 244.0792 Evaluate side-chains 219 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 199 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 313 LYS Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 345 LYS Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain R residue 12 VAL Chi-restraints excluded: chain R residue 13 LEU Chi-restraints excluded: chain R residue 81 MET Chi-restraints excluded: chain R residue 127 LYS Chi-restraints excluded: chain R residue 179 ILE Chi-restraints excluded: chain R residue 292 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 102 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 32 optimal weight: 0.4980 chunk 14 optimal weight: 0.0770 chunk 107 optimal weight: 0.0970 chunk 29 optimal weight: 0.5980 chunk 91 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 overall best weight: 0.3736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.135369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.117060 restraints weight = 12447.354| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.06 r_work: 0.3436 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8854 Z= 0.115 Angle : 0.522 9.822 12016 Z= 0.265 Chirality : 0.040 0.138 1398 Planarity : 0.003 0.030 1490 Dihedral : 4.933 50.198 1278 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.54 % Allowed : 22.96 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 1.06 (0.26), residues: 1118 helix: 2.49 (0.25), residues: 412 sheet: 0.84 (0.31), residues: 277 loop : -1.23 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS R 94 PHE 0.021 0.001 PHE R 63 TYR 0.019 0.001 TYR D 178 ARG 0.006 0.000 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.03242 ( 462) hydrogen bonds : angle 3.91913 ( 1326) SS BOND : bond 0.00030 ( 1) SS BOND : angle 0.50227 ( 2) covalent geometry : bond 0.00255 ( 8853) covalent geometry : angle 0.52230 (12014) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 202 time to evaluate : 0.954 Fit side-chains REVERT: A 277 LYS cc_start: 0.8531 (ttpp) cc_final: 0.8233 (ttmt) REVERT: A 323 MET cc_start: 0.8365 (mtt) cc_final: 0.8069 (mtt) REVERT: B 14 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8153 (mm) REVERT: B 49 ARG cc_start: 0.8472 (mmt-90) cc_final: 0.8135 (mpt180) REVERT: B 70 LEU cc_start: 0.8192 (tt) cc_final: 0.7978 (tp) REVERT: B 155 ASN cc_start: 0.8546 (t0) cc_final: 0.8331 (t0) REVERT: B 188 MET cc_start: 0.8429 (mmm) cc_final: 0.8185 (mmm) REVERT: B 256 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.7695 (mtt180) REVERT: B 333 ASP cc_start: 0.7995 (p0) cc_final: 0.7703 (p0) REVERT: D 21 SER cc_start: 0.8374 (m) cc_final: 0.7982 (p) REVERT: D 34 MET cc_start: 0.8555 (mmp) cc_final: 0.8340 (mmm) REVERT: D 128 MET cc_start: 0.8729 (mmm) cc_final: 0.7690 (mmm) REVERT: D 183 LEU cc_start: 0.8736 (mt) cc_final: 0.8528 (mm) REVERT: D 192 SER cc_start: 0.8596 (m) cc_final: 0.8271 (t) REVERT: D 201 THR cc_start: 0.8411 (m) cc_final: 0.8141 (p) REVERT: R 13 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8183 (tt) REVERT: R 17 PHE cc_start: 0.7463 (t80) cc_final: 0.7220 (t80) REVERT: R 75 LEU cc_start: 0.6843 (tp) cc_final: 0.6349 (tm) REVERT: R 81 MET cc_start: 0.7537 (OUTLIER) cc_final: 0.6997 (ttm) REVERT: R 110 LYS cc_start: 0.8457 (mttm) cc_final: 0.8245 (mttm) REVERT: R 127 LYS cc_start: 0.7486 (OUTLIER) cc_final: 0.7197 (mmtt) REVERT: R 152 ILE cc_start: 0.8284 (mm) cc_final: 0.7873 (tt) REVERT: R 286 LYS cc_start: 0.8086 (ttmm) cc_final: 0.7846 (ttpt) REVERT: R 301 MET cc_start: 0.6461 (tpt) cc_final: 0.6088 (tpt) outliers start: 23 outliers final: 14 residues processed: 209 average time/residue: 0.9415 time to fit residues: 213.0952 Evaluate side-chains 216 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 197 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 313 LYS Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 345 LYS Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain R residue 12 VAL Chi-restraints excluded: chain R residue 13 LEU Chi-restraints excluded: chain R residue 81 MET Chi-restraints excluded: chain R residue 127 LYS Chi-restraints excluded: chain R residue 179 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 28 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 57 optimal weight: 0.5980 chunk 44 optimal weight: 0.8980 chunk 105 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.134267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.115971 restraints weight = 12295.376| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.05 r_work: 0.3414 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8854 Z= 0.158 Angle : 0.544 8.457 12016 Z= 0.278 Chirality : 0.042 0.144 1398 Planarity : 0.003 0.032 1490 Dihedral : 5.037 52.259 1278 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.43 % Allowed : 23.73 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 1.04 (0.26), residues: 1118 helix: 2.39 (0.25), residues: 414 sheet: 0.90 (0.31), residues: 279 loop : -1.23 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS D 35 PHE 0.019 0.002 PHE R 63 TYR 0.023 0.001 TYR D 178 ARG 0.004 0.000 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.03522 ( 462) hydrogen bonds : angle 3.96621 ( 1326) SS BOND : bond 0.00048 ( 1) SS BOND : angle 0.39730 ( 2) covalent geometry : bond 0.00362 ( 8853) covalent geometry : angle 0.54388 (12014) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 199 time to evaluate : 0.966 Fit side-chains REVERT: A 248 LYS cc_start: 0.8034 (tttp) cc_final: 0.7691 (mtpp) REVERT: A 277 LYS cc_start: 0.8537 (ttpp) cc_final: 0.8303 (ttmt) REVERT: B 14 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8218 (mm) REVERT: B 49 ARG cc_start: 0.8493 (mmt-90) cc_final: 0.8081 (mpt180) REVERT: B 70 LEU cc_start: 0.8203 (tt) cc_final: 0.7993 (tp) REVERT: B 155 ASN cc_start: 0.8553 (t0) cc_final: 0.8276 (t0) REVERT: B 188 MET cc_start: 0.8457 (mmm) cc_final: 0.8218 (mmm) REVERT: B 256 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.7678 (mtt180) REVERT: B 333 ASP cc_start: 0.7993 (p0) cc_final: 0.7691 (p0) REVERT: D 21 SER cc_start: 0.8409 (m) cc_final: 0.8009 (p) REVERT: D 34 MET cc_start: 0.8604 (mmp) cc_final: 0.8355 (mmm) REVERT: D 128 MET cc_start: 0.8738 (mmm) cc_final: 0.7696 (mmm) REVERT: D 183 LEU cc_start: 0.8751 (mt) cc_final: 0.8545 (mm) REVERT: D 192 SER cc_start: 0.8603 (m) cc_final: 0.8291 (t) REVERT: R 13 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8206 (tt) REVERT: R 123 LYS cc_start: 0.8308 (tttp) cc_final: 0.8091 (ttpt) REVERT: R 127 LYS cc_start: 0.7517 (OUTLIER) cc_final: 0.7203 (mmtt) REVERT: R 152 ILE cc_start: 0.8310 (mm) cc_final: 0.7896 (tt) REVERT: R 286 LYS cc_start: 0.8108 (ttmm) cc_final: 0.7867 (ttpt) REVERT: R 301 MET cc_start: 0.6474 (tpt) cc_final: 0.6096 (tpt) outliers start: 22 outliers final: 15 residues processed: 206 average time/residue: 0.9323 time to fit residues: 207.9143 Evaluate side-chains 216 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 197 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 313 LYS Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 345 LYS Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain R residue 12 VAL Chi-restraints excluded: chain R residue 13 LEU Chi-restraints excluded: chain R residue 127 LYS Chi-restraints excluded: chain R residue 179 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 41 optimal weight: 0.0470 chunk 23 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 87 optimal weight: 0.7980 chunk 86 optimal weight: 0.6980 chunk 46 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.134560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.116204 restraints weight = 12387.467| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.06 r_work: 0.3426 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8854 Z= 0.142 Angle : 0.547 8.258 12016 Z= 0.278 Chirality : 0.041 0.140 1398 Planarity : 0.003 0.031 1490 Dihedral : 5.020 51.810 1278 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.32 % Allowed : 23.62 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 1.08 (0.26), residues: 1118 helix: 2.43 (0.25), residues: 414 sheet: 0.90 (0.31), residues: 279 loop : -1.21 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.003 0.001 HIS R 94 PHE 0.033 0.001 PHE R 63 TYR 0.023 0.001 TYR D 178 ARG 0.004 0.000 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.03448 ( 462) hydrogen bonds : angle 3.95490 ( 1326) SS BOND : bond 0.00041 ( 1) SS BOND : angle 0.44133 ( 2) covalent geometry : bond 0.00324 ( 8853) covalent geometry : angle 0.54730 (12014) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 199 time to evaluate : 0.921 Fit side-chains REVERT: A 248 LYS cc_start: 0.8023 (tttp) cc_final: 0.7680 (mtpp) REVERT: A 277 LYS cc_start: 0.8536 (ttpp) cc_final: 0.8304 (ttmt) REVERT: B 14 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8197 (mm) REVERT: B 49 ARG cc_start: 0.8499 (mmt-90) cc_final: 0.8096 (mpt180) REVERT: B 70 LEU cc_start: 0.8208 (tt) cc_final: 0.7989 (tp) REVERT: B 155 ASN cc_start: 0.8531 (t0) cc_final: 0.8290 (t0) REVERT: B 188 MET cc_start: 0.8445 (mmm) cc_final: 0.8208 (mmm) REVERT: B 256 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.7694 (mtt180) REVERT: B 333 ASP cc_start: 0.7975 (p0) cc_final: 0.7686 (p0) REVERT: D 21 SER cc_start: 0.8396 (m) cc_final: 0.7996 (p) REVERT: D 34 MET cc_start: 0.8597 (mmp) cc_final: 0.8334 (mmm) REVERT: D 128 MET cc_start: 0.8740 (mmm) cc_final: 0.7602 (mmm) REVERT: D 183 LEU cc_start: 0.8755 (mt) cc_final: 0.8548 (mm) REVERT: D 192 SER cc_start: 0.8601 (m) cc_final: 0.8277 (t) REVERT: D 201 THR cc_start: 0.8425 (m) cc_final: 0.8143 (p) REVERT: R 13 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8244 (tt) REVERT: R 127 LYS cc_start: 0.7497 (OUTLIER) cc_final: 0.7181 (mmtt) REVERT: R 152 ILE cc_start: 0.8288 (mm) cc_final: 0.7877 (tt) REVERT: R 286 LYS cc_start: 0.8105 (ttmm) cc_final: 0.7863 (ttpt) REVERT: R 301 MET cc_start: 0.6506 (tpt) cc_final: 0.6130 (tpt) outliers start: 21 outliers final: 15 residues processed: 206 average time/residue: 0.9281 time to fit residues: 207.1502 Evaluate side-chains 216 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 197 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 313 LYS Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 345 LYS Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain R residue 12 VAL Chi-restraints excluded: chain R residue 13 LEU Chi-restraints excluded: chain R residue 127 LYS Chi-restraints excluded: chain R residue 179 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 22 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.132284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.114164 restraints weight = 12494.054| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.05 r_work: 0.3389 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8854 Z= 0.225 Angle : 0.607 10.269 12016 Z= 0.308 Chirality : 0.044 0.155 1398 Planarity : 0.003 0.037 1490 Dihedral : 5.255 54.357 1278 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.32 % Allowed : 23.84 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.25), residues: 1118 helix: 2.22 (0.25), residues: 413 sheet: 0.81 (0.31), residues: 271 loop : -1.25 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 82 HIS 0.004 0.001 HIS D 35 PHE 0.044 0.002 PHE R 63 TYR 0.029 0.002 TYR D 178 ARG 0.005 0.000 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.03980 ( 462) hydrogen bonds : angle 4.10581 ( 1326) SS BOND : bond 0.00155 ( 1) SS BOND : angle 0.59987 ( 2) covalent geometry : bond 0.00522 ( 8853) covalent geometry : angle 0.60706 (12014) Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 7239.96 seconds wall clock time: 124 minutes 29.58 seconds (7469.58 seconds total)