Starting phenix.real_space_refine on Fri Nov 15 16:05:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jjp_36364/11_2024/8jjp_36364.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jjp_36364/11_2024/8jjp_36364.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jjp_36364/11_2024/8jjp_36364.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jjp_36364/11_2024/8jjp_36364.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jjp_36364/11_2024/8jjp_36364.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jjp_36364/11_2024/8jjp_36364.cif" } resolution = 2.9 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= 0.048 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 60 5.16 5 C 5893 2.51 5 N 1544 2.21 5 O 1668 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 9165 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2415 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 10, 'TRANS': 281} Chain: "C" Number of atoms: 1853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1853 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 2, 'TRANS': 230} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 2589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2589 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "G" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 431 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 1772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1772 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "L" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 77 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 7} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.19, per 1000 atoms: 0.68 Number of scatterers: 9165 At special positions: 0 Unit cell: (88.4, 124.95, 133.45, 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 60 16.00 O 1668 8.00 N 1544 7.00 C 5893 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 110 " - pdb=" SG CYS A 187 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " 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: 2.53 Conformation dependent library (CDL) restraints added in 1.2 seconds 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2174 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 14 sheets defined 35.6% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 35 through 65 removed outlier: 4.395A pdb=" N TRP A 39 " --> pdb=" O GLY A 35 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU A 51 " --> pdb=" O LEU A 47 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE A 53 " --> pdb=" O PHE A 49 " (cutoff:3.500A) Proline residue: A 54 - end of helix removed outlier: 3.547A pdb=" N VAL A 59 " --> pdb=" O GLY A 55 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY A 64 " --> pdb=" O ILE A 60 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE A 65 " --> pdb=" O TRP A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 89 removed outlier: 4.103A pdb=" N TRP A 75 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N PHE A 76 " --> pdb=" O THR A 72 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 99 removed outlier: 4.401A pdb=" N TYR A 93 " --> pdb=" O PHE A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 141 removed outlier: 3.738A pdb=" N LYS A 111 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N PHE A 122 " --> pdb=" O GLN A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 175 removed outlier: 3.882A pdb=" N LEU A 155 " --> pdb=" O LEU A 151 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE A 156 " --> pdb=" O LYS A 152 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL A 157 " --> pdb=" O ASN A 153 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER A 166 " --> pdb=" O TRP A 162 " (cutoff:3.500A) Proline residue: A 171 - end of helix Processing helix chain 'A' and resid 198 through 215 removed outlier: 3.560A pdb=" N ARG A 202 " --> pdb=" O LEU A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 235 removed outlier: 3.606A pdb=" N LYS A 234 " --> pdb=" O ILE A 230 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS A 235 " --> pdb=" O PHE A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 268 removed outlier: 3.654A pdb=" N TRP A 246 " --> pdb=" O SER A 242 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR A 247 " --> pdb=" O ARG A 243 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL A 251 " --> pdb=" O THR A 247 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL A 252 " --> pdb=" O ILE A 248 " (cutoff:3.500A) Proline residue: A 261 - end of helix Processing helix chain 'A' and resid 279 through 304 removed outlier: 3.723A pdb=" N GLN A 283 " --> pdb=" O HIS A 279 " (cutoff:3.500A) Proline residue: A 287 - end of helix removed outlier: 3.564A pdb=" N CYS A 298 " --> pdb=" O PHE A 294 " (cutoff:3.500A) Proline residue: A 301 - end of helix Processing helix chain 'A' and resid 308 through 325 removed outlier: 3.821A pdb=" N SER A 318 " --> pdb=" O ARG A 314 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLU A 321 " --> pdb=" O SER A 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 30 removed outlier: 3.841A pdb=" N ALA C 11 " --> pdb=" O ALA C 7 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA C 12 " --> pdb=" O GLU C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 53 removed outlier: 4.343A pdb=" N MET C 53 " --> pdb=" O ILE C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 212 removed outlier: 4.129A pdb=" N TRP C 211 " --> pdb=" O GLU C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 216 Processing helix chain 'C' and resid 241 through 255 Processing helix chain 'C' and resid 270 through 279 removed outlier: 3.974A pdb=" N LYS C 279 " --> pdb=" O GLU C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 286 removed outlier: 3.589A pdb=" N ILE C 285 " --> pdb=" O PRO C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 309 Processing helix chain 'C' and resid 329 through 351 removed outlier: 3.716A pdb=" N GLN C 333 " --> pdb=" O THR C 329 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N CYS C 351 " --> pdb=" O ASN C 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 9 through 22 Processing helix chain 'G' and resid 23 through 25 No H-bonds generated for 'chain 'G' and resid 23 through 25' Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 removed outlier: 4.008A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'S' and resid 28 through 32 Processing sheet with id=AA1, first strand: chain 'A' and resid 176 through 181 Processing sheet with id=AA2, first strand: chain 'C' and resid 185 through 190 removed outlier: 3.632A pdb=" N ALA C 220 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ILE C 221 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N PHE C 267 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N PHE C 223 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N ASN C 269 " --> pdb=" O PHE C 223 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N VAL C 225 " --> pdb=" O ASN C 269 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N ILE C 264 " --> pdb=" O TYR C 320 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N HIS C 322 " --> pdb=" O ILE C 264 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU C 266 " --> pdb=" O HIS C 322 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.498A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.618A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.570A 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: 7.099A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.894A 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 151 removed outlier: 3.518A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.693A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N MET B 217 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.575A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.802A 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: 3.678A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (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 11 through 12 removed outlier: 6.015A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 11 through 12 removed outlier: 4.317A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 140 through 141 Processing sheet with id=AB5, first strand: chain 'S' and resid 146 through 148 removed outlier: 3.757A pdb=" N GLU S 246 " --> pdb=" O VAL S 147 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LEU S 174 " --> pdb=" O TYR S 190 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N TYR S 190 " --> pdb=" O LEU S 174 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) 420 hydrogen bonds defined for protein. 1188 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: 2.83 Time building geometry restraints manager: 2.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2904 1.34 - 1.46: 2366 1.46 - 1.58: 4029 1.58 - 1.70: 1 1.70 - 1.82: 86 Bond restraints: 9386 Sorted by residual: bond pdb=" CG PRO A 301 " pdb=" CD PRO A 301 " ideal model delta sigma weight residual 1.503 1.368 0.135 3.40e-02 8.65e+02 1.58e+01 bond pdb=" CB PRO A 301 " pdb=" CG PRO A 301 " ideal model delta sigma weight residual 1.492 1.664 -0.172 5.00e-02 4.00e+02 1.19e+01 bond pdb=" N PRO A 301 " pdb=" CD PRO A 301 " ideal model delta sigma weight residual 1.473 1.518 -0.045 1.40e-02 5.10e+03 1.05e+01 bond pdb=" N PRO A 301 " pdb=" CA PRO A 301 " ideal model delta sigma weight residual 1.469 1.443 0.025 1.28e-02 6.10e+03 3.97e+00 bond pdb=" C LEU A 90 " pdb=" N PRO A 91 " ideal model delta sigma weight residual 1.334 1.368 -0.034 2.34e-02 1.83e+03 2.08e+00 ... (remaining 9381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.57: 12688 3.57 - 7.13: 40 7.13 - 10.70: 4 10.70 - 14.27: 1 14.27 - 17.83: 1 Bond angle restraints: 12734 Sorted by residual: angle pdb=" CA PRO A 301 " pdb=" N PRO A 301 " pdb=" CD PRO A 301 " ideal model delta sigma weight residual 112.00 94.17 17.83 1.40e+00 5.10e-01 1.62e+02 angle pdb=" N PRO A 301 " pdb=" CD PRO A 301 " pdb=" CG PRO A 301 " ideal model delta sigma weight residual 103.20 92.27 10.93 1.50e+00 4.44e-01 5.31e+01 angle pdb=" CA PRO A 301 " pdb=" CB PRO A 301 " pdb=" CG PRO A 301 " ideal model delta sigma weight residual 104.50 96.53 7.97 1.90e+00 2.77e-01 1.76e+01 angle pdb=" CA GLU S 222 " pdb=" CB GLU S 222 " pdb=" CG GLU S 222 " ideal model delta sigma weight residual 114.10 120.03 -5.93 2.00e+00 2.50e-01 8.79e+00 angle pdb=" CA TYR A 96 " pdb=" CB TYR A 96 " pdb=" CG TYR A 96 " ideal model delta sigma weight residual 113.90 119.13 -5.23 1.80e+00 3.09e-01 8.43e+00 ... (remaining 12729 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.45: 5017 22.45 - 44.90: 435 44.90 - 67.35: 80 67.35 - 89.80: 12 89.80 - 112.25: 3 Dihedral angle restraints: 5547 sinusoidal: 2178 harmonic: 3369 Sorted by residual: dihedral pdb=" CB CYS A 110 " pdb=" SG CYS A 110 " pdb=" SG CYS A 187 " pdb=" CB CYS A 187 " ideal model delta sinusoidal sigma weight residual 93.00 -178.92 -88.08 1 1.00e+01 1.00e-02 9.28e+01 dihedral pdb=" CA TRP B 332 " pdb=" C TRP B 332 " pdb=" N ASP B 333 " pdb=" CA ASP B 333 " ideal model delta harmonic sigma weight residual 180.00 157.69 22.31 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 160.53 19.47 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 5544 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 839 0.029 - 0.057: 386 0.057 - 0.086: 118 0.086 - 0.115: 72 0.115 - 0.144: 23 Chirality restraints: 1438 Sorted by residual: chirality pdb=" CA THR A 260 " pdb=" N THR A 260 " pdb=" C THR A 260 " pdb=" CB THR A 260 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.14 2.00e-01 2.50e+01 5.16e-01 chirality pdb=" CA HIS A 279 " pdb=" N HIS A 279 " pdb=" C HIS A 279 " pdb=" CB HIS A 279 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.14e-01 chirality pdb=" CB ILE A 240 " pdb=" CA ILE A 240 " pdb=" CG1 ILE A 240 " pdb=" CG2 ILE A 240 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 4.98e-01 ... (remaining 1435 not shown) Planarity restraints: 1591 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 300 " 0.119 5.00e-02 4.00e+02 1.62e-01 4.20e+01 pdb=" N PRO A 301 " -0.279 5.00e-02 4.00e+02 pdb=" CA PRO A 301 " 0.080 5.00e-02 4.00e+02 pdb=" CD PRO A 301 " 0.080 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 286 " 0.068 5.00e-02 4.00e+02 1.02e-01 1.66e+01 pdb=" N PRO A 287 " -0.176 5.00e-02 4.00e+02 pdb=" CA PRO A 287 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO A 287 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 170 " 0.033 5.00e-02 4.00e+02 5.01e-02 4.01e+00 pdb=" N PRO A 171 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 171 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 171 " 0.028 5.00e-02 4.00e+02 ... (remaining 1588 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 738 2.74 - 3.28: 8612 3.28 - 3.82: 14619 3.82 - 4.36: 17758 4.36 - 4.90: 31588 Nonbonded interactions: 73315 Sorted by model distance: nonbonded pdb=" O ILE A 286 " pdb=" OG1 THR A 290 " model vdw 2.202 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.241 3.040 nonbonded pdb=" NH1 ARG A 176 " pdb=" OG SER L 137 " model vdw 2.248 3.120 nonbonded pdb=" OE2 GLU C 8 " pdb=" OH TYR S 175 " model vdw 2.250 3.040 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.254 3.040 ... (remaining 73310 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: 1.790 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: 0.410 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 24.310 Find NCS groups from input model: 0.100 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: 0.010 Load rotamer database and sin/cos tables:11.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 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 : 0.003 0.172 9386 Z= 0.208 Angle : 0.598 17.832 12734 Z= 0.326 Chirality : 0.042 0.144 1438 Planarity : 0.006 0.162 1591 Dihedral : 16.865 112.246 3364 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.84 % Allowed : 24.47 % Favored : 71.69 % 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: 0.22 (0.25), residues: 1144 helix: 1.35 (0.29), residues: 366 sheet: 0.64 (0.30), residues: 278 loop : -1.05 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 268 HIS 0.008 0.001 HIS A 244 PHE 0.018 0.001 PHE A 62 TYR 0.030 0.002 TYR A 45 ARG 0.010 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 101 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: S 158 SER cc_start: 0.8703 (m) cc_final: 0.8327 (p) REVERT: S 192 MET cc_start: 0.8591 (ttt) cc_final: 0.8284 (tmm) outliers start: 38 outliers final: 34 residues processed: 133 average time/residue: 1.0809 time to fit residues: 156.9733 Evaluate side-chains 135 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 101 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 309 LYS Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 241 ASN Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain S residue 23 SER Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 106 SER Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 150 THR Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 214 LEU Chi-restraints excluded: chain S residue 226 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 2.9990 chunk 85 optimal weight: 8.9990 chunk 47 optimal weight: 0.8980 chunk 29 optimal weight: 0.3980 chunk 57 optimal weight: 0.1980 chunk 45 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 34 optimal weight: 0.2980 chunk 53 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 chunk 102 optimal weight: 1.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 HIS A 296 ASN B 340 ASN G 59 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.0738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9386 Z= 0.157 Angle : 0.537 7.617 12734 Z= 0.282 Chirality : 0.042 0.137 1438 Planarity : 0.004 0.071 1591 Dihedral : 6.751 72.590 1366 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 4.25 % Allowed : 21.84 % Favored : 73.91 % 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: 0.43 (0.25), residues: 1144 helix: 1.54 (0.28), residues: 373 sheet: 0.73 (0.31), residues: 285 loop : -0.99 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 268 HIS 0.007 0.001 HIS A 244 PHE 0.013 0.001 PHE A 62 TYR 0.028 0.001 TYR A 45 ARG 0.007 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 109 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 303 LEU cc_start: 0.7882 (mp) cc_final: 0.7634 (mt) REVERT: B 198 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8105 (pt) REVERT: B 256 ARG cc_start: 0.7522 (OUTLIER) cc_final: 0.6310 (mtp85) outliers start: 42 outliers final: 17 residues processed: 136 average time/residue: 1.0215 time to fit residues: 150.8464 Evaluate side-chains 120 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 PHE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 309 LYS Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 155 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 85 optimal weight: 20.0000 chunk 69 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 102 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 HIS A 296 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9386 Z= 0.329 Angle : 0.616 8.898 12734 Z= 0.321 Chirality : 0.045 0.147 1438 Planarity : 0.004 0.052 1591 Dihedral : 5.701 58.805 1328 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 4.75 % Allowed : 22.14 % Favored : 73.10 % 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: 0.32 (0.25), residues: 1144 helix: 1.42 (0.28), residues: 374 sheet: 0.66 (0.30), residues: 293 loop : -1.06 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 268 HIS 0.005 0.001 HIS A 244 PHE 0.015 0.002 PHE C 189 TYR 0.017 0.002 TYR A 96 ARG 0.008 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 100 time to evaluate : 1.095 Fit side-chains revert: symmetry clash REVERT: A 139 LEU cc_start: 0.7415 (OUTLIER) cc_final: 0.6802 (mp) REVERT: A 279 HIS cc_start: 0.7032 (m90) cc_final: 0.6805 (m90) REVERT: B 198 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8049 (pt) REVERT: B 256 ARG cc_start: 0.7690 (OUTLIER) cc_final: 0.6465 (mtp85) outliers start: 47 outliers final: 22 residues processed: 132 average time/residue: 0.9967 time to fit residues: 143.2678 Evaluate side-chains 123 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 98 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 PHE Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 309 LYS Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 214 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 49 optimal weight: 0.0030 chunk 69 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 97 optimal weight: 0.4980 chunk 29 optimal weight: 0.0170 chunk 90 optimal weight: 0.7980 overall best weight: 0.3828 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 HIS ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 273 HIS A 296 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9386 Z= 0.139 Angle : 0.513 6.790 12734 Z= 0.272 Chirality : 0.041 0.198 1438 Planarity : 0.004 0.050 1591 Dihedral : 5.163 57.842 1325 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.84 % Allowed : 22.85 % Favored : 73.31 % 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: 0.46 (0.25), residues: 1144 helix: 1.62 (0.28), residues: 375 sheet: 0.63 (0.30), residues: 290 loop : -0.96 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.007 0.001 HIS A 244 PHE 0.023 0.001 PHE A 84 TYR 0.015 0.001 TYR A 96 ARG 0.008 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 105 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 139 LEU cc_start: 0.7254 (OUTLIER) cc_final: 0.6575 (mp) REVERT: A 303 LEU cc_start: 0.7921 (mp) cc_final: 0.7695 (mt) REVERT: B 198 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8045 (pt) REVERT: B 256 ARG cc_start: 0.7549 (OUTLIER) cc_final: 0.6325 (mtp85) outliers start: 38 outliers final: 22 residues processed: 130 average time/residue: 1.0409 time to fit residues: 146.9521 Evaluate side-chains 121 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 96 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 62 PHE Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 309 LYS Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 241 ASN Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 155 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 0.7980 chunk 1 optimal weight: 0.2980 chunk 81 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 75 optimal weight: 0.0000 chunk 0 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 184 HIS ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9386 Z= 0.155 Angle : 0.507 6.632 12734 Z= 0.268 Chirality : 0.041 0.157 1438 Planarity : 0.004 0.050 1591 Dihedral : 5.013 52.961 1325 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 4.75 % Allowed : 21.94 % Favored : 73.31 % 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: 0.57 (0.25), residues: 1144 helix: 1.75 (0.28), residues: 375 sheet: 0.68 (0.30), residues: 289 loop : -0.91 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.006 0.001 HIS A 244 PHE 0.028 0.001 PHE A 84 TYR 0.012 0.001 TYR S 190 ARG 0.009 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 104 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 SER cc_start: 0.8792 (m) cc_final: 0.8588 (p) REVERT: A 139 LEU cc_start: 0.7155 (OUTLIER) cc_final: 0.6495 (mp) REVERT: A 303 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7711 (mt) REVERT: C 324 THR cc_start: 0.7746 (OUTLIER) cc_final: 0.7398 (m) REVERT: B 198 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8026 (pt) REVERT: B 256 ARG cc_start: 0.7527 (OUTLIER) cc_final: 0.6307 (mtp85) REVERT: S 192 MET cc_start: 0.8734 (ttt) cc_final: 0.8474 (tmm) outliers start: 47 outliers final: 27 residues processed: 135 average time/residue: 1.0401 time to fit residues: 152.8481 Evaluate side-chains 133 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 101 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 62 PHE Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 309 LYS Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 241 ASN Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 150 THR Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 184 SER Chi-restraints excluded: chain S residue 214 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9386 Z= 0.335 Angle : 0.611 8.477 12734 Z= 0.320 Chirality : 0.045 0.149 1438 Planarity : 0.004 0.050 1591 Dihedral : 5.314 47.613 1324 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 5.16 % Allowed : 22.14 % Favored : 72.70 % 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: 0.46 (0.25), residues: 1144 helix: 1.64 (0.28), residues: 372 sheet: 0.67 (0.30), residues: 292 loop : -1.01 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.005 0.001 HIS S 35 PHE 0.030 0.002 PHE A 84 TYR 0.012 0.002 TYR B 59 ARG 0.008 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 99 time to evaluate : 1.069 Fit side-chains revert: symmetry clash REVERT: A 67 TRP cc_start: 0.8182 (OUTLIER) cc_final: 0.7459 (t-100) REVERT: A 139 LEU cc_start: 0.7422 (OUTLIER) cc_final: 0.6651 (mp) REVERT: C 298 GLU cc_start: 0.7838 (tp30) cc_final: 0.6837 (tp30) REVERT: B 46 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7827 (mtt-85) REVERT: B 198 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8042 (pt) REVERT: B 256 ARG cc_start: 0.7616 (OUTLIER) cc_final: 0.6427 (mtp85) outliers start: 51 outliers final: 28 residues processed: 136 average time/residue: 0.9838 time to fit residues: 145.4815 Evaluate side-chains 127 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 94 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 62 PHE Chi-restraints excluded: chain A residue 67 TRP Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 309 LYS Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 241 ASN Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 150 THR Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 184 SER Chi-restraints excluded: chain S residue 214 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 61 optimal weight: 0.5980 chunk 92 optimal weight: 0.6980 chunk 108 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9386 Z= 0.182 Angle : 0.529 6.983 12734 Z= 0.279 Chirality : 0.042 0.143 1438 Planarity : 0.004 0.049 1591 Dihedral : 5.076 48.970 1324 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 4.35 % Allowed : 23.66 % Favored : 71.99 % 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: 0.55 (0.25), residues: 1144 helix: 1.77 (0.28), residues: 374 sheet: 0.63 (0.30), residues: 291 loop : -0.94 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.006 0.001 HIS A 244 PHE 0.032 0.001 PHE A 84 TYR 0.013 0.001 TYR S 190 ARG 0.009 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 102 time to evaluate : 1.080 Fit side-chains revert: symmetry clash REVERT: A 67 TRP cc_start: 0.8113 (OUTLIER) cc_final: 0.7490 (t-100) REVERT: A 139 LEU cc_start: 0.7328 (OUTLIER) cc_final: 0.6618 (mp) REVERT: C 298 GLU cc_start: 0.7759 (tp30) cc_final: 0.6776 (tp30) REVERT: C 306 GLN cc_start: 0.7843 (mm110) cc_final: 0.7045 (mp10) REVERT: B 46 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7844 (mtt-85) REVERT: B 198 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8049 (pt) REVERT: B 256 ARG cc_start: 0.7560 (OUTLIER) cc_final: 0.6333 (mtp85) outliers start: 43 outliers final: 29 residues processed: 133 average time/residue: 1.0577 time to fit residues: 152.5120 Evaluate side-chains 131 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 97 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 62 PHE Chi-restraints excluded: chain A residue 67 TRP Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 309 LYS Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 241 ASN Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 150 THR Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 184 SER Chi-restraints excluded: chain S residue 214 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 85 optimal weight: 10.0000 chunk 99 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN G 59 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 9386 Z= 0.368 Angle : 0.627 8.742 12734 Z= 0.328 Chirality : 0.046 0.153 1438 Planarity : 0.004 0.050 1591 Dihedral : 5.376 47.832 1324 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 4.75 % Allowed : 24.06 % Favored : 71.18 % 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: 0.41 (0.25), residues: 1144 helix: 1.63 (0.28), residues: 372 sheet: 0.65 (0.30), residues: 292 loop : -1.06 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.005 0.001 HIS S 35 PHE 0.032 0.002 PHE A 84 TYR 0.012 0.002 TYR B 59 ARG 0.008 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 100 time to evaluate : 1.013 Fit side-chains revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8005 (ptmm) cc_final: 0.7572 (pttp) REVERT: A 67 TRP cc_start: 0.8140 (OUTLIER) cc_final: 0.7390 (t-100) REVERT: A 139 LEU cc_start: 0.7460 (OUTLIER) cc_final: 0.6681 (mp) REVERT: C 298 GLU cc_start: 0.7767 (tp30) cc_final: 0.6788 (tp30) REVERT: B 46 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7828 (mtt-85) REVERT: B 198 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8055 (pt) REVERT: B 256 ARG cc_start: 0.7625 (OUTLIER) cc_final: 0.6411 (mtp85) outliers start: 47 outliers final: 30 residues processed: 136 average time/residue: 1.0568 time to fit residues: 155.8761 Evaluate side-chains 128 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 93 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 62 PHE Chi-restraints excluded: chain A residue 67 TRP Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 309 LYS Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 241 ASN Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 150 THR Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 184 SER Chi-restraints excluded: chain S residue 214 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 91 optimal weight: 0.4980 chunk 95 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 107 optimal weight: 0.5980 chunk 65 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 340 ASN G 59 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9386 Z= 0.177 Angle : 0.539 7.490 12734 Z= 0.282 Chirality : 0.042 0.166 1438 Planarity : 0.004 0.050 1591 Dihedral : 5.107 48.634 1324 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.74 % Allowed : 24.77 % Favored : 71.49 % 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: 0.50 (0.25), residues: 1144 helix: 1.73 (0.28), residues: 374 sheet: 0.62 (0.30), residues: 291 loop : -0.98 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 63 HIS 0.006 0.001 HIS A 244 PHE 0.036 0.001 PHE A 84 TYR 0.013 0.001 TYR S 190 ARG 0.009 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 99 time to evaluate : 1.111 Fit side-chains revert: symmetry clash REVERT: A 67 TRP cc_start: 0.8109 (OUTLIER) cc_final: 0.7687 (t-100) REVERT: A 139 LEU cc_start: 0.7306 (OUTLIER) cc_final: 0.6630 (mp) REVERT: C 298 GLU cc_start: 0.7744 (tp30) cc_final: 0.6769 (tp30) REVERT: C 306 GLN cc_start: 0.7884 (mm110) cc_final: 0.7096 (mp10) REVERT: B 46 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.7831 (mtt-85) REVERT: B 198 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8059 (pt) REVERT: B 256 ARG cc_start: 0.7535 (OUTLIER) cc_final: 0.6346 (mtp85) outliers start: 37 outliers final: 27 residues processed: 125 average time/residue: 1.1428 time to fit residues: 154.1741 Evaluate side-chains 127 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 95 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 62 PHE Chi-restraints excluded: chain A residue 67 TRP Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 309 LYS Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 241 ASN Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 150 THR Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 184 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 2.9990 chunk 74 optimal weight: 0.4980 chunk 112 optimal weight: 0.0570 chunk 103 optimal weight: 0.9980 chunk 89 optimal weight: 0.0030 chunk 9 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 71 optimal weight: 0.7980 chunk 95 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.4108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9386 Z= 0.145 Angle : 0.517 10.527 12734 Z= 0.269 Chirality : 0.041 0.148 1438 Planarity : 0.004 0.050 1591 Dihedral : 4.905 49.074 1324 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.13 % Allowed : 25.48 % Favored : 71.39 % 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: 0.64 (0.25), residues: 1144 helix: 1.83 (0.28), residues: 374 sheet: 0.62 (0.30), residues: 296 loop : -0.85 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.007 0.001 HIS A 244 PHE 0.038 0.001 PHE A 84 TYR 0.014 0.001 TYR S 190 ARG 0.010 0.000 ARG B 197 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2288 Ramachandran restraints generated. 1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 103 time to evaluate : 1.232 Fit side-chains revert: symmetry clash REVERT: A 67 TRP cc_start: 0.8039 (OUTLIER) cc_final: 0.7607 (t-100) REVERT: C 306 GLN cc_start: 0.7879 (mm110) cc_final: 0.7042 (mp10) REVERT: C 324 THR cc_start: 0.7781 (OUTLIER) cc_final: 0.7485 (m) REVERT: B 46 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.7815 (mtt-85) REVERT: B 198 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8056 (pt) REVERT: B 256 ARG cc_start: 0.7402 (OUTLIER) cc_final: 0.6220 (mtp85) REVERT: S 192 MET cc_start: 0.8762 (ttp) cc_final: 0.8545 (tmm) outliers start: 31 outliers final: 25 residues processed: 125 average time/residue: 1.1234 time to fit residues: 151.9584 Evaluate side-chains 128 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 98 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 62 PHE Chi-restraints excluded: chain A residue 67 TRP Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 309 LYS Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain C residue 241 ASN Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 118 THR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 144 THR Chi-restraints excluded: chain S residue 150 THR Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 184 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 92 optimal weight: 0.0570 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 0.4980 chunk 78 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 overall best weight: 0.6100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 HIS B 75 GLN B 175 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.178528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.107937 restraints weight = 9923.127| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.19 r_work: 0.3086 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9386 Z= 0.173 Angle : 0.531 9.374 12734 Z= 0.276 Chirality : 0.042 0.142 1438 Planarity : 0.004 0.050 1591 Dihedral : 4.915 49.337 1324 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.84 % Allowed : 24.87 % Favored : 71.28 % 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: 0.67 (0.25), residues: 1144 helix: 1.85 (0.28), residues: 374 sheet: 0.66 (0.30), residues: 294 loop : -0.84 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.006 0.001 HIS A 244 PHE 0.038 0.001 PHE A 84 TYR 0.013 0.001 TYR S 190 ARG 0.009 0.000 ARG B 197 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3558.48 seconds wall clock time: 64 minutes 33.10 seconds (3873.10 seconds total)