Starting phenix.real_space_refine on Fri Nov 15 08:04:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8id4_35357/11_2024/8id4_35357.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8id4_35357/11_2024/8id4_35357.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8id4_35357/11_2024/8id4_35357.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8id4_35357/11_2024/8id4_35357.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8id4_35357/11_2024/8id4_35357.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8id4_35357/11_2024/8id4_35357.cif" } resolution = 3.1 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= 0.016 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: 4 Type Number sf(0) Gaussians S 58 5.16 5 C 5545 2.51 5 N 1472 2.21 5 O 1590 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 8665 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2174 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 11, 'TRANS': 273} Chain breaks: 4 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 6, 'TRP:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 63 Chain: "A" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1761 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 37 Chain: "B" Number of atoms: 2572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2572 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "Y" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 404 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "S" Number of atoms: 1733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1733 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain breaks: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "R" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 21 Unusual residues: {'EIC': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Time building chain proxies: 5.31, per 1000 atoms: 0.61 Number of scatterers: 8665 At special positions: 0 Unit cell: (106.47, 127.764, 113.568, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 58 16.00 O 1590 8.00 N 1472 7.00 C 5545 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS S 160 " - pdb=" SG CYS S 230 " distance=2.04 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 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2126 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 13 sheets defined 35.9% alpha, 23.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'R' and resid 38 through 69 removed outlier: 3.619A pdb=" N ARG R 67 " --> pdb=" O VAL R 63 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 90 removed outlier: 3.635A pdb=" N LEU R 81 " --> pdb=" O LEU R 77 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE R 82 " --> pdb=" O VAL R 78 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU R 86 " --> pdb=" O PHE R 82 " (cutoff:3.500A) Processing helix chain 'R' and resid 91 through 101 removed outlier: 4.018A pdb=" N VAL R 95 " --> pdb=" O ALA R 91 " (cutoff:3.500A) Processing helix chain 'R' and resid 109 through 112 removed outlier: 3.691A pdb=" N HIS R 112 " --> pdb=" O VAL R 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 109 through 112' Processing helix chain 'R' and resid 113 through 142 Processing helix chain 'R' and resid 152 through 171 Processing helix chain 'R' and resid 172 through 174 No H-bonds generated for 'chain 'R' and resid 172 through 174' Processing helix chain 'R' and resid 201 through 216 removed outlier: 3.662A pdb=" N SER R 206 " --> pdb=" O PRO R 202 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N TRP R 207 " --> pdb=" O GLY R 203 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR R 213 " --> pdb=" O VAL R 209 " (cutoff:3.500A) Processing helix chain 'R' and resid 216 through 244 removed outlier: 3.663A pdb=" N THR R 242 " --> pdb=" O ARG R 238 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL R 243 " --> pdb=" O LYS R 239 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N SER R 244 " --> pdb=" O ARG R 240 " (cutoff:3.500A) Processing helix chain 'R' and resid 251 through 294 removed outlier: 3.864A pdb=" N SER R 256 " --> pdb=" O GLN R 252 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ARG R 261 " --> pdb=" O GLN R 257 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N PHE R 273 " --> pdb=" O LEU R 269 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N PHE R 274 " --> pdb=" O MET R 270 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER R 278 " --> pdb=" O PHE R 274 " (cutoff:3.500A) Proline residue: R 279 - end of helix removed outlier: 3.849A pdb=" N PHE R 292 " --> pdb=" O LEU R 288 " (cutoff:3.500A) Processing helix chain 'R' and resid 301 through 321 removed outlier: 3.867A pdb=" N TRP R 305 " --> pdb=" O SER R 301 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN R 313 " --> pdb=" O PHE R 309 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N SER R 314 " --> pdb=" O THR R 310 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA R 315 " --> pdb=" O PHE R 311 " (cutoff:3.500A) Proline residue: R 318 - end of helix Processing helix chain 'A' and resid 6 through 30 Processing helix chain 'A' and resid 31 through 33 No H-bonds generated for 'chain 'A' and resid 31 through 33' Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.546A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.681A pdb=" N TRP A 211 " --> pdb=" O ARG A 208 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 removed outlier: 4.198A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.613A pdb=" N GLU A 245 " --> pdb=" O ASN A 241 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 272 No H-bonds generated for 'chain 'A' and resid 270 through 272' Processing helix chain 'A' and resid 273 through 278 removed outlier: 3.655A pdb=" N LYS A 277 " --> pdb=" O LEU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.938A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 351 removed outlier: 3.546A pdb=" N GLN A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 24 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'Y' and resid 9 through 24 removed outlier: 3.636A pdb=" N ASN Y 24 " --> pdb=" O LYS Y 20 " (cutoff:3.500A) Processing helix chain 'Y' and resid 29 through 44 Processing helix chain 'S' and resid 28 through 32 Processing sheet with id=AA1, first strand: chain 'R' and resid 177 through 181 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.093A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N CYS A 224 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 52 removed outlier: 3.638A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.850A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.754A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.516A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.937A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.534A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.557A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.692A pdb=" N THR S 118 " --> pdb=" O GLY S 10 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN S 39 " --> pdb=" O MET S 93 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 141 through 142 removed outlier: 3.522A pdb=" N ALA S 212 " --> pdb=" O SER S 209 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 147 through 149 removed outlier: 3.792A pdb=" N GLU S 247 " --> pdb=" O VAL S 148 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LEU S 179 " --> pdb=" O LEU S 188 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N LEU S 188 " --> pdb=" O LEU S 179 " (cutoff:3.500A) 419 hydrogen bonds defined for protein. 1191 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: 2.39 Time building geometry restraints manager: 2.73 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: 2378 1.33 - 1.45: 1616 1.45 - 1.57: 4759 1.57 - 1.70: 2 1.70 - 1.82: 83 Bond restraints: 8838 Sorted by residual: bond pdb=" N THR A 327 " pdb=" CA THR A 327 " ideal model delta sigma weight residual 1.457 1.529 -0.072 1.29e-02 6.01e+03 3.12e+01 bond pdb=" CA PHE R 88 " pdb=" C PHE R 88 " ideal model delta sigma weight residual 1.524 1.584 -0.061 1.27e-02 6.20e+03 2.28e+01 bond pdb=" N ALA A 326 " pdb=" CA ALA A 326 " ideal model delta sigma weight residual 1.457 1.504 -0.047 1.20e-02 6.94e+03 1.55e+01 bond pdb=" N ILE R 89 " pdb=" CA ILE R 89 " ideal model delta sigma weight residual 1.459 1.509 -0.050 1.34e-02 5.57e+03 1.42e+01 bond pdb=" CA ALA A 326 " pdb=" C ALA A 326 " ideal model delta sigma weight residual 1.524 1.560 -0.037 1.23e-02 6.61e+03 8.84e+00 ... (remaining 8833 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 11810 2.46 - 4.92: 147 4.92 - 7.38: 31 7.38 - 9.84: 2 9.84 - 12.29: 2 Bond angle restraints: 11992 Sorted by residual: angle pdb=" N ALA A 326 " pdb=" CA ALA A 326 " pdb=" C ALA A 326 " ideal model delta sigma weight residual 108.38 120.67 -12.29 1.35e+00 5.49e-01 8.29e+01 angle pdb=" N SER R 244 " pdb=" CA SER R 244 " pdb=" C SER R 244 " ideal model delta sigma weight residual 110.28 100.09 10.19 1.48e+00 4.57e-01 4.74e+01 angle pdb=" N ARG R 69 " pdb=" CA ARG R 69 " pdb=" C ARG R 69 " ideal model delta sigma weight residual 112.90 106.20 6.70 1.31e+00 5.83e-01 2.62e+01 angle pdb=" N SER R 90 " pdb=" CA SER R 90 " pdb=" C SER R 90 " ideal model delta sigma weight residual 112.34 105.71 6.63 1.30e+00 5.92e-01 2.60e+01 angle pdb=" N ILE R 89 " pdb=" CA ILE R 89 " pdb=" C ILE R 89 " ideal model delta sigma weight residual 111.44 117.93 -6.49 1.34e+00 5.57e-01 2.34e+01 ... (remaining 11987 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.82: 4753 16.82 - 33.64: 377 33.64 - 50.46: 68 50.46 - 67.29: 10 67.29 - 84.11: 9 Dihedral angle restraints: 5217 sinusoidal: 1934 harmonic: 3283 Sorted by residual: dihedral pdb=" C THR A 327 " pdb=" N THR A 327 " pdb=" CA THR A 327 " pdb=" CB THR A 327 " ideal model delta harmonic sigma weight residual -122.00 -145.78 23.78 0 2.50e+00 1.60e-01 9.05e+01 dihedral pdb=" N THR A 327 " pdb=" C THR A 327 " pdb=" CA THR A 327 " pdb=" CB THR A 327 " ideal model delta harmonic sigma weight residual 123.40 145.69 -22.29 0 2.50e+00 1.60e-01 7.95e+01 dihedral pdb=" CA ILE R 298 " pdb=" C ILE R 298 " pdb=" N TRP R 299 " pdb=" CA TRP R 299 " ideal model delta harmonic sigma weight residual 180.00 158.32 21.68 0 5.00e+00 4.00e-02 1.88e+01 ... (remaining 5214 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.171: 1391 0.171 - 0.342: 8 0.342 - 0.514: 0 0.514 - 0.685: 0 0.685 - 0.856: 1 Chirality restraints: 1400 Sorted by residual: chirality pdb=" CA THR A 327 " pdb=" N THR A 327 " pdb=" C THR A 327 " pdb=" CB THR A 327 " both_signs ideal model delta sigma weight residual False 2.53 1.67 0.86 2.00e-01 2.50e+01 1.83e+01 chirality pdb=" CB ILE R 197 " pdb=" CA ILE R 197 " pdb=" CG1 ILE R 197 " pdb=" CG2 ILE R 197 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" CA SER R 244 " pdb=" N SER R 244 " pdb=" C SER R 244 " pdb=" CB SER R 244 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 1397 not shown) Planarity restraints: 1508 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 171 " 0.052 5.00e-02 4.00e+02 7.81e-02 9.76e+00 pdb=" N PRO R 172 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO R 172 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO R 172 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 324 " 0.015 2.00e-02 2.50e+03 3.11e-02 9.70e+00 pdb=" C THR A 324 " -0.054 2.00e-02 2.50e+03 pdb=" O THR A 324 " 0.021 2.00e-02 2.50e+03 pdb=" N CYS A 325 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN S 13 " 0.050 5.00e-02 4.00e+02 7.31e-02 8.55e+00 pdb=" N PRO S 14 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO S 14 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO S 14 " 0.041 5.00e-02 4.00e+02 ... (remaining 1505 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1199 2.75 - 3.29: 8068 3.29 - 3.83: 13913 3.83 - 4.36: 16869 4.36 - 4.90: 30336 Nonbonded interactions: 70385 Sorted by model distance: nonbonded pdb=" OG1 THR B 128 " pdb=" O ASN B 132 " model vdw 2.217 3.040 nonbonded pdb=" OG SER B 108 " pdb=" OD1 ASP B 154 " model vdw 2.233 3.040 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 176 " model vdw 2.238 3.040 nonbonded pdb=" OG1 THR B 86 " pdb=" OD1 ASN B 88 " model vdw 2.242 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.252 3.040 ... (remaining 70380 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: 0.290 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: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 22.650 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 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 : 0.004 0.095 8838 Z= 0.275 Angle : 0.732 12.295 11992 Z= 0.427 Chirality : 0.053 0.856 1400 Planarity : 0.005 0.078 1508 Dihedral : 12.922 84.108 3088 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.69 % Favored : 96.13 % Rotamer: Outliers : 0.22 % Allowed : 0.88 % Favored : 98.90 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 3.12 % 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 (0.25), residues: 1112 helix: 0.33 (0.28), residues: 370 sheet: -0.43 (0.31), residues: 276 loop : -1.68 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.004 0.001 HIS B 91 PHE 0.022 0.002 PHE R 25 TYR 0.024 0.001 TYR S 176 ARG 0.012 0.001 ARG S 161 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 131 time to evaluate : 1.065 Fit side-chains REVERT: A 28 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7674 (mt-10) REVERT: B 134 ARG cc_start: 0.8079 (ptt90) cc_final: 0.7575 (ptt-90) REVERT: B 221 THR cc_start: 0.8845 (t) cc_final: 0.8308 (m) outliers start: 2 outliers final: 0 residues processed: 133 average time/residue: 0.2588 time to fit residues: 45.6440 Evaluate side-chains 118 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.4980 chunk 84 optimal weight: 0.9980 chunk 46 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 44 optimal weight: 0.0170 chunk 87 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 52 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 chunk 100 optimal weight: 7.9990 overall best weight: 0.9022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 215 ASN A 306 GLN B 17 GLN B 91 HIS S 82 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.0949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8838 Z= 0.181 Angle : 0.552 7.948 11992 Z= 0.296 Chirality : 0.042 0.233 1400 Planarity : 0.004 0.063 1508 Dihedral : 5.476 70.342 1227 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.24 % Favored : 96.58 % Rotamer: Outliers : 1.10 % Allowed : 6.91 % Favored : 92.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.62 (0.25), residues: 1112 helix: 0.83 (0.28), residues: 376 sheet: -0.18 (0.29), residues: 278 loop : -1.60 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 207 HIS 0.003 0.001 HIS B 225 PHE 0.019 0.001 PHE R 25 TYR 0.016 0.001 TYR S 176 ARG 0.005 0.000 ARG R 240 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 131 time to evaluate : 0.962 Fit side-chains REVERT: A 28 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7591 (mt-10) REVERT: A 29 LYS cc_start: 0.7869 (ttmt) cc_final: 0.7405 (tttp) REVERT: A 197 LYS cc_start: 0.8071 (mmtt) cc_final: 0.7607 (mmtt) REVERT: B 17 GLN cc_start: 0.8070 (OUTLIER) cc_final: 0.7756 (pp30) REVERT: S 82 GLN cc_start: 0.7610 (tp40) cc_final: 0.6454 (mp10) outliers start: 10 outliers final: 7 residues processed: 134 average time/residue: 0.2517 time to fit residues: 44.7939 Evaluate side-chains 127 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 119 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 157 VAL Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 271 VAL Chi-restraints excluded: chain R residue 323 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain S residue 6 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 83 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 chunk 109 optimal weight: 0.8980 chunk 89 optimal weight: 6.9990 chunk 34 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8838 Z= 0.235 Angle : 0.557 7.799 11992 Z= 0.297 Chirality : 0.043 0.231 1400 Planarity : 0.004 0.058 1508 Dihedral : 5.357 70.459 1227 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.51 % Favored : 96.31 % Rotamer: Outliers : 1.32 % Allowed : 9.65 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.52 (0.25), residues: 1112 helix: 1.04 (0.28), residues: 372 sheet: -0.15 (0.29), residues: 279 loop : -1.63 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS B 225 PHE 0.012 0.001 PHE B 151 TYR 0.013 0.001 TYR S 191 ARG 0.004 0.000 ARG R 68 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 121 time to evaluate : 1.045 Fit side-chains REVERT: A 28 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7719 (mt-10) REVERT: A 197 LYS cc_start: 0.8208 (mmtt) cc_final: 0.7984 (mttm) REVERT: B 17 GLN cc_start: 0.8308 (pp30) cc_final: 0.8094 (pp30) REVERT: B 325 MET cc_start: 0.8060 (mtt) cc_final: 0.7647 (mtm) REVERT: S 46 GLU cc_start: 0.7888 (tt0) cc_final: 0.7658 (tt0) REVERT: S 82 GLN cc_start: 0.7665 (tp40) cc_final: 0.6469 (mp10) outliers start: 12 outliers final: 8 residues processed: 128 average time/residue: 0.2626 time to fit residues: 44.4782 Evaluate side-chains 124 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 116 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 157 VAL Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 271 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain S residue 6 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 1.9990 chunk 52 optimal weight: 0.0970 chunk 11 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 67 optimal weight: 0.3980 chunk 101 optimal weight: 4.9990 chunk 107 optimal weight: 0.5980 chunk 96 optimal weight: 0.1980 chunk 28 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 156 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 8838 Z= 0.129 Angle : 0.485 6.963 11992 Z= 0.260 Chirality : 0.041 0.221 1400 Planarity : 0.004 0.054 1508 Dihedral : 5.026 70.702 1227 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.70 % Favored : 97.12 % Rotamer: Outliers : 1.75 % Allowed : 10.86 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.14 (0.25), residues: 1112 helix: 1.43 (0.28), residues: 373 sheet: 0.02 (0.29), residues: 284 loop : -1.47 (0.27), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 207 HIS 0.002 0.000 HIS A 188 PHE 0.021 0.001 PHE R 25 TYR 0.013 0.001 TYR S 191 ARG 0.004 0.000 ARG S 87 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 1.036 Fit side-chains REVERT: A 28 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7552 (mt-10) REVERT: A 197 LYS cc_start: 0.8217 (mmtt) cc_final: 0.7983 (mttm) REVERT: B 17 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.7899 (pp30) REVERT: B 221 THR cc_start: 0.8886 (t) cc_final: 0.8324 (m) REVERT: Y 21 MET cc_start: 0.5727 (ttm) cc_final: 0.5479 (ttp) REVERT: S 46 GLU cc_start: 0.7881 (tt0) cc_final: 0.7641 (tt0) REVERT: S 82 GLN cc_start: 0.7724 (tp40) cc_final: 0.6666 (mp10) outliers start: 16 outliers final: 11 residues processed: 137 average time/residue: 0.2582 time to fit residues: 46.6070 Evaluate side-chains 132 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 120 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 271 VAL Chi-restraints excluded: chain R residue 323 MET Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 97 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 40.0000 chunk 79 optimal weight: 4.9990 chunk 44 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 chunk 74 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 54 optimal weight: 4.9990 chunk 96 optimal weight: 6.9990 chunk 27 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 156 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 8838 Z= 0.343 Angle : 0.590 7.325 11992 Z= 0.315 Chirality : 0.045 0.223 1400 Planarity : 0.004 0.062 1508 Dihedral : 5.385 70.995 1227 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.87 % Favored : 96.04 % Rotamer: Outliers : 2.08 % Allowed : 12.39 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.27 (0.25), residues: 1112 helix: 1.15 (0.27), residues: 376 sheet: 0.00 (0.29), residues: 286 loop : -1.44 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.005 0.001 HIS S 35 PHE 0.017 0.002 PHE R 51 TYR 0.010 0.002 TYR B 85 ARG 0.006 0.001 ARG R 68 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.996 Fit side-chains REVERT: A 28 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7758 (mt-10) REVERT: A 197 LYS cc_start: 0.8319 (mmtt) cc_final: 0.8072 (mttm) REVERT: S 46 GLU cc_start: 0.7915 (tt0) cc_final: 0.7682 (tt0) REVERT: S 82 GLN cc_start: 0.7660 (tp40) cc_final: 0.6492 (mp10) outliers start: 19 outliers final: 14 residues processed: 129 average time/residue: 0.2389 time to fit residues: 41.9322 Evaluate side-chains 131 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 157 VAL Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 271 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 113 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 8 optimal weight: 0.0670 chunk 35 optimal weight: 0.0040 chunk 56 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 12 optimal weight: 9.9990 chunk 61 optimal weight: 0.8980 overall best weight: 0.5530 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 156 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8838 Z= 0.137 Angle : 0.487 5.925 11992 Z= 0.261 Chirality : 0.041 0.254 1400 Planarity : 0.004 0.054 1508 Dihedral : 5.052 71.123 1227 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.08 % Allowed : 13.05 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.04 (0.25), residues: 1112 helix: 1.48 (0.28), residues: 378 sheet: 0.15 (0.30), residues: 281 loop : -1.30 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 207 HIS 0.003 0.001 HIS A 188 PHE 0.022 0.001 PHE R 25 TYR 0.012 0.001 TYR S 191 ARG 0.007 0.000 ARG R 68 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.938 Fit side-chains REVERT: A 28 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7588 (mt-10) REVERT: A 197 LYS cc_start: 0.8202 (mmtt) cc_final: 0.7779 (mttp) REVERT: S 46 GLU cc_start: 0.7896 (tt0) cc_final: 0.7651 (tt0) REVERT: S 82 GLN cc_start: 0.7581 (tp40) cc_final: 0.6483 (mp10) outliers start: 19 outliers final: 12 residues processed: 129 average time/residue: 0.2400 time to fit residues: 41.5582 Evaluate side-chains 128 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 271 VAL Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 97 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 106 optimal weight: 8.9990 chunk 66 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 42 optimal weight: 9.9990 chunk 63 optimal weight: 0.9990 chunk 32 optimal weight: 10.0000 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 156 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8838 Z= 0.239 Angle : 0.536 5.956 11992 Z= 0.286 Chirality : 0.043 0.265 1400 Planarity : 0.004 0.057 1508 Dihedral : 5.161 71.518 1227 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.08 % Allowed : 13.38 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.05 (0.25), residues: 1112 helix: 1.44 (0.27), residues: 378 sheet: 0.13 (0.29), residues: 293 loop : -1.26 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS B 225 PHE 0.012 0.001 PHE B 151 TYR 0.010 0.001 TYR S 191 ARG 0.007 0.000 ARG R 68 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 1.050 Fit side-chains REVERT: A 28 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7689 (mt-10) REVERT: A 197 LYS cc_start: 0.8259 (mmtt) cc_final: 0.7825 (mttp) REVERT: B 234 PHE cc_start: 0.9019 (OUTLIER) cc_final: 0.8658 (m-80) REVERT: Y 21 MET cc_start: 0.5848 (ttm) cc_final: 0.5612 (ttp) REVERT: S 46 GLU cc_start: 0.7910 (tt0) cc_final: 0.7675 (tt0) REVERT: S 82 GLN cc_start: 0.7723 (tp40) cc_final: 0.6509 (mp10) outliers start: 19 outliers final: 13 residues processed: 128 average time/residue: 0.2492 time to fit residues: 42.5684 Evaluate side-chains 133 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 157 VAL Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 271 VAL Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 97 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 72 optimal weight: 0.3980 chunk 52 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 156 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8838 Z= 0.201 Angle : 0.519 6.407 11992 Z= 0.278 Chirality : 0.042 0.277 1400 Planarity : 0.004 0.055 1508 Dihedral : 5.116 71.725 1227 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.08 % Allowed : 13.93 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.12 (0.25), residues: 1112 helix: 1.52 (0.27), residues: 377 sheet: 0.16 (0.29), residues: 292 loop : -1.24 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS B 225 PHE 0.012 0.001 PHE B 151 TYR 0.011 0.001 TYR S 191 ARG 0.008 0.000 ARG R 68 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.991 Fit side-chains REVERT: A 28 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7700 (mt-10) REVERT: A 197 LYS cc_start: 0.8229 (mmtt) cc_final: 0.7815 (mttp) REVERT: B 17 GLN cc_start: 0.8289 (OUTLIER) cc_final: 0.7946 (pp30) REVERT: B 234 PHE cc_start: 0.9010 (OUTLIER) cc_final: 0.8664 (m-80) REVERT: Y 21 MET cc_start: 0.5720 (ttm) cc_final: 0.5466 (ttp) REVERT: S 46 GLU cc_start: 0.7910 (tt0) cc_final: 0.7666 (tt0) REVERT: S 82 GLN cc_start: 0.7709 (tp40) cc_final: 0.6504 (mp10) outliers start: 19 outliers final: 15 residues processed: 130 average time/residue: 0.2328 time to fit residues: 40.7228 Evaluate side-chains 135 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 137 MET Chi-restraints excluded: chain R residue 157 VAL Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 271 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 113 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 105 optimal weight: 0.5980 chunk 64 optimal weight: 3.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 156 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8838 Z= 0.303 Angle : 0.573 6.749 11992 Z= 0.306 Chirality : 0.044 0.275 1400 Planarity : 0.004 0.060 1508 Dihedral : 5.301 72.051 1227 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.08 % Allowed : 14.25 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.03 (0.25), residues: 1112 helix: 1.42 (0.27), residues: 372 sheet: 0.16 (0.29), residues: 290 loop : -1.38 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.004 0.001 HIS S 35 PHE 0.014 0.002 PHE B 151 TYR 0.010 0.002 TYR S 191 ARG 0.008 0.001 ARG R 68 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 0.996 Fit side-chains REVERT: A 28 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7739 (mt-10) REVERT: A 197 LYS cc_start: 0.8259 (mmtt) cc_final: 0.7849 (mttp) REVERT: B 17 GLN cc_start: 0.8210 (OUTLIER) cc_final: 0.7813 (pp30) REVERT: B 234 PHE cc_start: 0.9062 (OUTLIER) cc_final: 0.8672 (m-80) REVERT: Y 21 MET cc_start: 0.5730 (ttm) cc_final: 0.5494 (ttp) REVERT: S 46 GLU cc_start: 0.7918 (tt0) cc_final: 0.7682 (tt0) REVERT: S 82 GLN cc_start: 0.7741 (tp40) cc_final: 0.6520 (mp10) outliers start: 19 outliers final: 14 residues processed: 129 average time/residue: 0.2344 time to fit residues: 41.2389 Evaluate side-chains 133 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 157 VAL Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 271 VAL Chi-restraints excluded: chain R residue 323 MET Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 113 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 9.9990 chunk 73 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 88 optimal weight: 7.9990 chunk 9 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 53 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 156 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8838 Z= 0.210 Angle : 0.535 7.528 11992 Z= 0.285 Chirality : 0.043 0.278 1400 Planarity : 0.004 0.058 1508 Dihedral : 5.206 72.275 1227 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.54 % Allowed : 14.58 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.08 (0.25), residues: 1112 helix: 1.58 (0.27), residues: 373 sheet: 0.12 (0.29), residues: 292 loop : -1.31 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS B 225 PHE 0.012 0.001 PHE B 151 TYR 0.011 0.001 TYR S 191 ARG 0.009 0.000 ARG R 68 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2224 Ramachandran restraints generated. 1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.985 Fit side-chains REVERT: A 28 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7711 (mt-10) REVERT: A 197 LYS cc_start: 0.8247 (mmtt) cc_final: 0.7833 (mttp) REVERT: B 234 PHE cc_start: 0.9009 (OUTLIER) cc_final: 0.8612 (m-80) REVERT: Y 21 MET cc_start: 0.5656 (ttm) cc_final: 0.5399 (ttp) REVERT: S 46 GLU cc_start: 0.7915 (tt0) cc_final: 0.7670 (tt0) REVERT: S 82 GLN cc_start: 0.7721 (tp40) cc_final: 0.6506 (mp10) outliers start: 14 outliers final: 13 residues processed: 124 average time/residue: 0.2426 time to fit residues: 40.2003 Evaluate side-chains 128 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 157 VAL Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 271 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 97 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 88 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.0170 chunk 77 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 overall best weight: 0.7222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 156 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.172139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.131734 restraints weight = 9207.524| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.96 r_work: 0.3071 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8838 Z= 0.155 Angle : 0.506 7.398 11992 Z= 0.270 Chirality : 0.041 0.257 1400 Planarity : 0.004 0.053 1508 Dihedral : 5.059 72.699 1227 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.86 % Allowed : 14.69 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.23 (0.25), residues: 1112 helix: 1.78 (0.28), residues: 372 sheet: 0.19 (0.29), residues: 292 loop : -1.27 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.002 0.001 HIS B 225 PHE 0.011 0.001 PHE B 199 TYR 0.011 0.001 TYR S 191 ARG 0.009 0.000 ARG R 68 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2042.44 seconds wall clock time: 38 minutes 5.95 seconds (2285.95 seconds total)