Starting phenix.real_space_refine on Fri Sep 11 03:44:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7bz2_30249/09_2026/7bz2_30249.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bz2_30249/09_2026/7bz2_30249.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7bz2_30249/09_2026/7bz2_30249.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7bz2_30249/09_2026/7bz2_30249.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7bz2_30249/09_2026/7bz2_30249.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bz2_30249/09_2026/7bz2_30249.map" model { file = "/net/cci-nas-00/data/ceres_data/7bz2_30249/09_2026/7bz2_30249.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bz2_30249/09_2026/7bz2_30249.cif" } resolution = 3.82 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 44 5.16 5 C 4725 2.51 5 N 1275 2.21 5 O 1349 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7393 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1561 Classifications: {'peptide': 198} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 3, 'TRANS': 194} Chain breaks: 5 Unresolved non-hydrogen bonds: 123 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 6, 'ASN:plan1': 1, 'GLU:plan': 4, 'ASP:plan': 7, 'GLN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 81 Chain: "B" Number of atoms: 2453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2453 Classifications: {'peptide': 331} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 5, 'TRANS': 325} Chain breaks: 2 Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 6, 'GLN:plan1': 4, 'GLU:plan': 3, 'ASN:plan1': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 73 Chain: "G" Number of atoms: 246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 246 Classifications: {'peptide': 37} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 1, 'TRANS': 35} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "N" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 956 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 121} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "R" Number of atoms: 2152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2152 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 7, 'TRANS': 277} Chain breaks: 2 Unresolved non-hydrogen bonds: 152 Unresolved non-hydrogen angles: 197 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'TRP:plan': 3, 'GLU:plan': 7, 'PHE:plan': 2, 'ARG:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 2, 'ASP:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 102 Chain: "R" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'H98': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.55, per 1000 atoms: 0.21 Number of scatterers: 7393 At special positions: 0 Unit cell: (92.22, 96.46, 117.66, 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 44 16.00 O 1349 8.00 N 1275 7.00 C 4725 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS R 184 " - pdb=" SG CYS R 190 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.52 Conformation dependent library (CDL) restraints added in 471.4 milliseconds 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1842 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 12 sheets defined 33.8% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 10 through 13 Processing helix chain 'A' and resid 14 through 38 removed outlier: 3.705A pdb=" N ALA A 22 " --> pdb=" O ALA A 18 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LYS A 28 " --> pdb=" O LYS A 24 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N GLN A 31 " --> pdb=" O GLU A 27 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 279 removed outlier: 3.628A pdb=" N ALA A 269 " --> pdb=" O ARG A 265 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER A 275 " --> pdb=" O ASN A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.697A pdb=" N PHE A 315 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 312 through 316' Processing helix chain 'A' and resid 332 through 350 removed outlier: 4.822A pdb=" N ALA A 337 " --> pdb=" O ARG A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 389 removed outlier: 3.959A pdb=" N ASP A 378 " --> pdb=" O ARG A 374 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP A 381 " --> pdb=" O ASN A 377 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ILE A 382 " --> pdb=" O ASP A 378 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE A 383 " --> pdb=" O CYS A 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 25 Processing helix chain 'G' and resid 16 through 24 Processing helix chain 'G' and resid 29 through 45 removed outlier: 4.199A pdb=" N ALA G 35 " --> pdb=" O SER G 31 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N CYS G 41 " --> pdb=" O LEU G 37 " (cutoff:3.500A) Processing helix chain 'R' and resid 38 through 60 removed outlier: 3.822A pdb=" N ILE R 43 " --> pdb=" O VAL R 39 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL R 44 " --> pdb=" O MET R 40 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASN R 51 " --> pdb=" O ILE R 47 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL R 52 " --> pdb=" O VAL R 48 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU R 53 " --> pdb=" O PHE R 49 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N VAL R 54 " --> pdb=" O GLY R 50 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA R 57 " --> pdb=" O LEU R 53 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE R 58 " --> pdb=" O VAL R 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 85 removed outlier: 4.070A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR R 73 " --> pdb=" O ASN R 69 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA R 78 " --> pdb=" O SER R 74 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASP R 79 " --> pdb=" O LEU R 75 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N MET R 82 " --> pdb=" O ALA R 78 " (cutoff:3.500A) Processing helix chain 'R' and resid 86 through 97 removed outlier: 3.579A pdb=" N ALA R 92 " --> pdb=" O PRO R 88 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ILE R 94 " --> pdb=" O GLY R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 108 through 137 removed outlier: 3.671A pdb=" N VAL R 114 " --> pdb=" O THR R 110 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU R 115 " --> pdb=" O SER R 111 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR R 118 " --> pdb=" O VAL R 114 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N LEU R 124 " --> pdb=" O SER R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 142 removed outlier: 4.698A pdb=" N GLN R 142 " --> pdb=" O PRO R 138 " (cutoff:3.500A) Processing helix chain 'R' and resid 153 through 161 removed outlier: 4.246A pdb=" N ILE R 159 " --> pdb=" O LEU R 155 " (cutoff:3.500A) Processing helix chain 'R' and resid 161 through 166 Processing helix chain 'R' and resid 166 through 171 Processing helix chain 'R' and resid 198 through 203 removed outlier: 3.954A pdb=" N ALA R 202 " --> pdb=" O ALA R 198 " (cutoff:3.500A) Processing helix chain 'R' and resid 203 through 208 Processing helix chain 'R' and resid 209 through 227 removed outlier: 3.915A pdb=" N VAL R 213 " --> pdb=" O TYR R 209 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N TYR R 219 " --> pdb=" O MET R 215 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG R 221 " --> pdb=" O PHE R 217 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLU R 225 " --> pdb=" O ARG R 221 " (cutoff:3.500A) Processing helix chain 'R' and resid 232 through 236 removed outlier: 3.545A pdb=" N LYS R 235 " --> pdb=" O LYS R 232 " (cutoff:3.500A) Processing helix chain 'R' and resid 272 through 287 removed outlier: 4.915A pdb=" N THR R 281 " --> pdb=" O ILE R 277 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ALA R 285 " --> pdb=" O THR R 281 " (cutoff:3.500A) Processing helix chain 'R' and resid 288 through 299 removed outlier: 4.764A pdb=" N ILE R 294 " --> pdb=" O PHE R 290 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 309 Processing helix chain 'R' and resid 310 through 315 Processing helix chain 'R' and resid 321 through 325 Processing helix chain 'R' and resid 329 through 336 Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 42 removed outlier: 7.346A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 46 removed outlier: 3.765A pdb=" N LEU A 46 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL A 247 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE A 246 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU A 289 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N HIS A 362 " --> pdb=" O LEU A 289 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.645A pdb=" N VAL B 71 " --> pdb=" O HIS B 62 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 104 through 105 Processing sheet with id=AA5, first strand: chain 'B' and resid 158 through 159 removed outlier: 3.844A pdb=" N THR B 159 " --> pdb=" O ALA B 167 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 200 through 201 removed outlier: 3.713A pdb=" N LYS B 209 " --> pdb=" O SER B 201 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 232 removed outlier: 4.145A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 250 through 253 removed outlier: 3.715A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 276 through 277 removed outlier: 4.180A pdb=" N SER B 277 " --> pdb=" O LEU B 286 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 6 Processing sheet with id=AB2, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.194A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR N 122 " --> pdb=" O TYR N 94 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 17 through 20 removed outlier: 3.512A pdb=" N LEU N 20 " --> pdb=" O LEU N 81 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR N 78 " --> pdb=" O ASP N 73 " (cutoff:3.500A) 220 hydrogen bonds defined for protein. 624 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: 0.94 Time building geometry restraints manager: 0.75 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: 2395 1.34 - 1.46: 1787 1.46 - 1.58: 3294 1.58 - 1.70: 0 1.70 - 1.81: 62 Bond restraints: 7538 Sorted by residual: bond pdb=" C19 H98 R 401 " pdb=" N2 H98 R 401 " ideal model delta sigma weight residual 1.349 1.391 -0.042 2.00e-02 2.50e+03 4.36e+00 bond pdb=" C3 H98 R 401 " pdb=" C4 H98 R 401 " ideal model delta sigma weight residual 1.503 1.480 0.023 2.00e-02 2.50e+03 1.31e+00 bond pdb=" C13 H98 R 401 " pdb=" C14 H98 R 401 " ideal model delta sigma weight residual 1.392 1.370 0.022 2.00e-02 2.50e+03 1.23e+00 bond pdb=" CA GLY A 47 " pdb=" C GLY A 47 " ideal model delta sigma weight residual 1.514 1.499 0.015 1.41e-02 5.03e+03 1.19e+00 bond pdb=" CB TRP B 82 " pdb=" CG TRP B 82 " ideal model delta sigma weight residual 1.498 1.465 0.033 3.10e-02 1.04e+03 1.13e+00 ... (remaining 7533 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 9945 1.68 - 3.35: 251 3.35 - 5.03: 37 5.03 - 6.70: 9 6.70 - 8.38: 3 Bond angle restraints: 10245 Sorted by residual: angle pdb=" N VAL R 31 " pdb=" CA VAL R 31 " pdb=" C VAL R 31 " ideal model delta sigma weight residual 113.53 109.98 3.55 9.80e-01 1.04e+00 1.31e+01 angle pdb=" C GLU B 172 " pdb=" N THR B 173 " pdb=" CA THR B 173 " ideal model delta sigma weight residual 121.54 128.13 -6.59 1.91e+00 2.74e-01 1.19e+01 angle pdb=" C15 H98 R 401 " pdb=" N2 H98 R 401 " pdb=" C19 H98 R 401 " ideal model delta sigma weight residual 129.13 120.75 8.38 3.00e+00 1.11e-01 7.80e+00 angle pdb=" N GLY B 162 " pdb=" CA GLY B 162 " pdb=" C GLY B 162 " ideal model delta sigma weight residual 113.18 107.08 6.10 2.37e+00 1.78e-01 6.62e+00 angle pdb=" CA LEU A 393 " pdb=" CB LEU A 393 " pdb=" CG LEU A 393 " ideal model delta sigma weight residual 116.30 124.44 -8.14 3.50e+00 8.16e-02 5.40e+00 ... (remaining 10240 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 3938 17.95 - 35.90: 383 35.90 - 53.85: 61 53.85 - 71.81: 13 71.81 - 89.76: 5 Dihedral angle restraints: 4400 sinusoidal: 1561 harmonic: 2839 Sorted by residual: dihedral pdb=" CA PHE R 290 " pdb=" C PHE R 290 " pdb=" N ILE R 291 " pdb=" CA ILE R 291 " ideal model delta harmonic sigma weight residual 180.00 154.15 25.85 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CB CYS R 184 " pdb=" SG CYS R 184 " pdb=" SG CYS R 190 " pdb=" CB CYS R 190 " ideal model delta sinusoidal sigma weight residual -86.00 -47.65 -38.35 1 1.00e+01 1.00e-02 2.07e+01 dihedral pdb=" CA ASN R 69 " pdb=" C ASN R 69 " pdb=" N TYR R 70 " pdb=" CA TYR R 70 " ideal model delta harmonic sigma weight residual 180.00 157.62 22.38 0 5.00e+00 4.00e-02 2.00e+01 ... (remaining 4397 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 627 0.030 - 0.060: 364 0.060 - 0.091: 128 0.091 - 0.121: 64 0.121 - 0.151: 11 Chirality restraints: 1194 Sorted by residual: chirality pdb=" CG LEU A 291 " pdb=" CB LEU A 291 " pdb=" CD1 LEU A 291 " pdb=" CD2 LEU A 291 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.70e-01 chirality pdb=" CA ILE B 58 " pdb=" N ILE B 58 " pdb=" C ILE B 58 " pdb=" CB ILE B 58 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.02e-01 chirality pdb=" CA TYR R 219 " pdb=" N TYR R 219 " pdb=" C TYR R 219 " pdb=" CB TYR R 219 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.81e-01 ... (remaining 1191 not shown) Planarity restraints: 1295 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 167 " -0.033 5.00e-02 4.00e+02 5.02e-02 4.03e+00 pdb=" N PRO R 168 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO R 168 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO R 168 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.032 5.00e-02 4.00e+02 4.86e-02 3.79e+00 pdb=" N PRO B 236 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS N 87 " 0.024 5.00e-02 4.00e+02 3.64e-02 2.12e+00 pdb=" N PRO N 88 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO N 88 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO N 88 " 0.020 5.00e-02 4.00e+02 ... (remaining 1292 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 146 2.66 - 3.22: 7103 3.22 - 3.78: 10470 3.78 - 4.34: 14131 4.34 - 4.90: 23768 Nonbonded interactions: 55618 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.101 3.040 nonbonded pdb=" OD2 ASP B 247 " pdb=" OG1 THR B 249 " model vdw 2.134 3.040 nonbonded pdb=" OG1 THR N 104 " pdb=" OD1 ASP N 106 " model vdw 2.193 3.040 nonbonded pdb=" OD1 ASP B 291 " pdb=" ND2 ASN B 293 " model vdw 2.204 3.120 nonbonded pdb=" OG SER R 203 " pdb=" O2 H98 R 401 " model vdw 2.221 3.040 ... (remaining 55613 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 group one per residue 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: 0.360 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.030 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 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 0.042 7540 Z= 0.185 Angle : 0.680 8.376 10249 Z= 0.376 Chirality : 0.046 0.151 1194 Planarity : 0.004 0.050 1295 Dihedral : 14.754 89.757 2552 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.21 % Favored : 89.79 % Rotamer: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.04 (0.20), residues: 950 helix: -3.35 (0.21), residues: 342 sheet: -4.69 (0.26), residues: 190 loop : -4.15 (0.21), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 118 TYR 0.013 0.001 TYR B 59 PHE 0.014 0.002 PHE N 108 TRP 0.018 0.002 TRP R 109 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 ( 7538) covalent geometry : angle 0.67970 / 0.38 (10245) SS BOND : bond 0.00143 / 0.07 ( 2) SS BOND : angle 0.35880 / 0.21 ( 4) hydrogen bonds : bond 0.15042 / 9.74 ( 220) hydrogen bonds : angle 6.82933 / 4.87 ( 624) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.261 Fit side-chains revert: symmetry clash REVERT: B 111 TYR cc_start: 0.7918 (m-80) cc_final: 0.7697 (m-80) REVERT: R 227 LYS cc_start: 0.8479 (ttpt) cc_final: 0.7850 (tttt) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.0845 time to fit residues: 20.8935 Evaluate side-chains 144 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 0.0970 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 74 optimal weight: 7.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 GLN A 220 HIS A 371 ASN B 176 GLN B 230 ASN N 39 GLN R 142 GLN R 148 ASN R 312 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.179930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.153805 restraints weight = 8243.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.150175 restraints weight = 14152.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.151324 restraints weight = 13276.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.151365 restraints weight = 9767.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.151651 restraints weight = 8058.301| |-----------------------------------------------------------------------------| r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7540 Z= 0.130 Angle : 0.604 8.965 10249 Z= 0.319 Chirality : 0.044 0.140 1194 Planarity : 0.004 0.048 1295 Dihedral : 6.104 71.741 1046 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 2.45 % Allowed : 18.12 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.98 (0.23), residues: 950 helix: -2.34 (0.26), residues: 339 sheet: -4.37 (0.28), residues: 186 loop : -3.53 (0.23), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 72 TYR 0.013 0.001 TYR G 40 PHE 0.030 0.002 PHE R 208 TRP 0.015 0.002 TRP R 313 HIS 0.006 0.001 HIS B 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 ( 7538) covalent geometry : angle 0.60436 / 0.32 (10245) SS BOND : bond 0.00321 / 0.16 ( 2) SS BOND : angle 0.63978 / 0.36 ( 4) hydrogen bonds : bond 0.03916 / 2.56 ( 220) hydrogen bonds : angle 5.33790 / 3.78 ( 624) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 161 time to evaluate : 0.253 Fit side-chains REVERT: B 111 TYR cc_start: 0.7872 (m-80) cc_final: 0.7273 (m-80) REVERT: B 154 ASP cc_start: 0.7948 (m-30) cc_final: 0.7396 (t0) outliers start: 18 outliers final: 11 residues processed: 171 average time/residue: 0.0761 time to fit residues: 17.8632 Evaluate side-chains 158 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 147 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 40 MET Chi-restraints excluded: chain R residue 205 ILE Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 312 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 82 optimal weight: 0.0570 chunk 52 optimal weight: 5.9990 chunk 69 optimal weight: 0.6980 chunk 4 optimal weight: 10.0000 chunk 50 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 81 optimal weight: 0.0770 chunk 0 optimal weight: 20.0000 chunk 45 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 75 optimal weight: 0.0770 overall best weight: 0.3214 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 371 ASN B 176 GLN B 183 HIS B 220 GLN R 142 GLN R 148 ASN R 170 GLN R 293 ASN R 312 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.183284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.159309 restraints weight = 8032.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.156739 restraints weight = 13321.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.156651 restraints weight = 11820.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.155230 restraints weight = 10673.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.156331 restraints weight = 8924.357| |-----------------------------------------------------------------------------| r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7540 Z= 0.097 Angle : 0.554 8.427 10249 Z= 0.288 Chirality : 0.042 0.138 1194 Planarity : 0.003 0.047 1295 Dihedral : 5.610 68.553 1046 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 4.09 % Allowed : 19.48 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.23 (0.24), residues: 950 helix: -1.88 (0.26), residues: 345 sheet: -3.71 (0.30), residues: 196 loop : -3.05 (0.26), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 72 TYR 0.009 0.001 TYR G 40 PHE 0.017 0.001 PHE A 222 TRP 0.024 0.001 TRP R 109 HIS 0.004 0.001 HIS R 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.10 ( 7538) covalent geometry : angle 0.55370 / 0.29 (10245) SS BOND : bond 0.00235 / 0.11 ( 2) SS BOND : angle 0.46661 / 0.25 ( 4) hydrogen bonds : bond 0.03268 / 2.11 ( 220) hydrogen bonds : angle 4.89454 / 3.44 ( 624) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 154 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 111 TYR cc_start: 0.7749 (m-80) cc_final: 0.7294 (m-80) REVERT: B 154 ASP cc_start: 0.7848 (m-30) cc_final: 0.7357 (t0) REVERT: R 300 ASP cc_start: 0.7606 (OUTLIER) cc_final: 0.7051 (m-30) REVERT: R 312 ASN cc_start: 0.6282 (OUTLIER) cc_final: 0.5638 (t0) outliers start: 30 outliers final: 12 residues processed: 171 average time/residue: 0.0600 time to fit residues: 14.5662 Evaluate side-chains 150 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 136 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 40 MET Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 125 VAL Chi-restraints excluded: chain R residue 205 ILE Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 300 ASP Chi-restraints excluded: chain R residue 312 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 45 optimal weight: 2.9990 chunk 84 optimal weight: 0.5980 chunk 21 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 15 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 70 optimal weight: 0.4980 chunk 16 optimal weight: 3.9990 chunk 81 optimal weight: 0.0370 chunk 67 optimal weight: 20.0000 overall best weight: 0.6260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 371 ASN B 176 GLN B 183 HIS N 39 GLN R 312 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.183875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.152003 restraints weight = 8113.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.150774 restraints weight = 8345.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.152295 restraints weight = 8221.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.153150 restraints weight = 6880.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.153304 restraints weight = 6217.725| |-----------------------------------------------------------------------------| r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7540 Z= 0.101 Angle : 0.545 7.917 10249 Z= 0.283 Chirality : 0.042 0.130 1194 Planarity : 0.003 0.045 1295 Dihedral : 5.503 68.966 1046 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 4.09 % Allowed : 21.25 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.82 (0.25), residues: 950 helix: -1.56 (0.27), residues: 348 sheet: -3.47 (0.32), residues: 197 loop : -2.79 (0.27), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 256 TYR 0.009 0.001 TYR G 40 PHE 0.014 0.001 PHE R 193 TRP 0.024 0.001 TRP R 109 HIS 0.003 0.001 HIS R 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 ( 7538) covalent geometry : angle 0.54473 / 0.28 (10245) SS BOND : bond 0.00229 / 0.11 ( 2) SS BOND : angle 0.48643 / 0.26 ( 4) hydrogen bonds : bond 0.03000 / 1.96 ( 220) hydrogen bonds : angle 4.75485 / 3.33 ( 624) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 141 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7787 (mp0) REVERT: B 111 TYR cc_start: 0.7742 (m-80) cc_final: 0.7348 (m-80) REVERT: B 154 ASP cc_start: 0.7791 (m-30) cc_final: 0.7275 (t0) REVERT: B 188 MET cc_start: 0.7836 (mmm) cc_final: 0.7332 (mmm) REVERT: R 36 MET cc_start: 0.6915 (mmt) cc_final: 0.6480 (mmm) REVERT: R 64 LEU cc_start: 0.7163 (OUTLIER) cc_final: 0.6830 (mt) REVERT: R 300 ASP cc_start: 0.7573 (OUTLIER) cc_final: 0.6871 (m-30) REVERT: R 312 ASN cc_start: 0.6224 (OUTLIER) cc_final: 0.5757 (t0) outliers start: 30 outliers final: 15 residues processed: 158 average time/residue: 0.0773 time to fit residues: 17.2640 Evaluate side-chains 148 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 44 HIS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 40 MET Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 125 VAL Chi-restraints excluded: chain R residue 205 ILE Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 300 ASP Chi-restraints excluded: chain R residue 312 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 31 optimal weight: 10.0000 chunk 88 optimal weight: 0.5980 chunk 82 optimal weight: 10.0000 chunk 85 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 92 optimal weight: 0.3980 chunk 70 optimal weight: 4.9990 chunk 76 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 371 ASN B 183 HIS R 142 GLN R 312 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.185082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.157512 restraints weight = 8180.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.154935 restraints weight = 12383.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.156285 restraints weight = 10136.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.155934 restraints weight = 8204.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.156210 restraints weight = 6993.179| |-----------------------------------------------------------------------------| r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7540 Z= 0.111 Angle : 0.546 8.465 10249 Z= 0.283 Chirality : 0.042 0.187 1194 Planarity : 0.003 0.045 1295 Dihedral : 5.435 67.570 1046 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 4.36 % Allowed : 22.89 % Favored : 72.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.53 (0.25), residues: 950 helix: -1.31 (0.27), residues: 348 sheet: -3.36 (0.32), residues: 197 loop : -2.59 (0.28), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 256 TYR 0.011 0.001 TYR A 339 PHE 0.012 0.001 PHE A 222 TRP 0.024 0.002 TRP R 313 HIS 0.003 0.001 HIS R 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 ( 7538) covalent geometry : angle 0.54617 / 0.28 (10245) SS BOND : bond 0.00227 / 0.11 ( 2) SS BOND : angle 0.51525 / 0.28 ( 4) hydrogen bonds : bond 0.03056 / 2.00 ( 220) hydrogen bonds : angle 4.74879 / 3.31 ( 624) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 135 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7757 (mp0) REVERT: B 101 MET cc_start: 0.8886 (mmm) cc_final: 0.8618 (mtt) REVERT: B 111 TYR cc_start: 0.7784 (m-80) cc_final: 0.7306 (m-80) REVERT: B 154 ASP cc_start: 0.7857 (m-30) cc_final: 0.7389 (t0) REVERT: B 256 ARG cc_start: 0.7203 (mmm160) cc_final: 0.6712 (mtm180) REVERT: N 60 TYR cc_start: 0.8770 (m-80) cc_final: 0.8419 (m-80) REVERT: R 64 LEU cc_start: 0.7180 (OUTLIER) cc_final: 0.6847 (mt) REVERT: R 300 ASP cc_start: 0.7464 (OUTLIER) cc_final: 0.6802 (m-30) REVERT: R 312 ASN cc_start: 0.6566 (OUTLIER) cc_final: 0.5969 (t0) outliers start: 32 outliers final: 22 residues processed: 155 average time/residue: 0.0738 time to fit residues: 16.2816 Evaluate side-chains 155 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 338 LYS Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 44 HIS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 125 VAL Chi-restraints excluded: chain R residue 159 ILE Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 300 ASP Chi-restraints excluded: chain R residue 312 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 59 optimal weight: 0.4980 chunk 50 optimal weight: 5.9990 chunk 83 optimal weight: 9.9990 chunk 90 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 49 optimal weight: 5.9990 chunk 40 optimal weight: 8.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 371 ASN R 312 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.184215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.157677 restraints weight = 8206.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.153871 restraints weight = 13376.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.155735 restraints weight = 12498.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.155861 restraints weight = 8438.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.155928 restraints weight = 7389.784| |-----------------------------------------------------------------------------| r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7540 Z= 0.118 Angle : 0.542 8.290 10249 Z= 0.283 Chirality : 0.042 0.141 1194 Planarity : 0.003 0.045 1295 Dihedral : 5.415 67.752 1046 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 3.95 % Allowed : 24.52 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.31 (0.26), residues: 950 helix: -1.09 (0.28), residues: 345 sheet: -3.20 (0.32), residues: 199 loop : -2.52 (0.28), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 256 TYR 0.016 0.001 TYR R 308 PHE 0.013 0.001 PHE A 222 TRP 0.025 0.001 TRP R 109 HIS 0.003 0.001 HIS R 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 ( 7538) covalent geometry : angle 0.54167 / 0.28 (10245) SS BOND : bond 0.00237 / 0.11 ( 2) SS BOND : angle 0.51055 / 0.27 ( 4) hydrogen bonds : bond 0.03085 / 2.02 ( 220) hydrogen bonds : angle 4.68296 / 3.29 ( 624) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 129 time to evaluate : 0.272 Fit side-chains REVERT: A 27 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7780 (mp0) REVERT: A 212 PHE cc_start: 0.7198 (p90) cc_final: 0.6934 (p90) REVERT: B 88 ASN cc_start: 0.8653 (m-40) cc_final: 0.8149 (m110) REVERT: B 101 MET cc_start: 0.8891 (mmm) cc_final: 0.8677 (mtt) REVERT: B 154 ASP cc_start: 0.7915 (m-30) cc_final: 0.7707 (m-30) REVERT: N 60 TYR cc_start: 0.8752 (m-80) cc_final: 0.8397 (m-80) REVERT: R 64 LEU cc_start: 0.7174 (OUTLIER) cc_final: 0.6829 (mt) REVERT: R 300 ASP cc_start: 0.7424 (OUTLIER) cc_final: 0.6739 (m-30) REVERT: R 312 ASN cc_start: 0.6463 (OUTLIER) cc_final: 0.5916 (t0) outliers start: 29 outliers final: 20 residues processed: 149 average time/residue: 0.0751 time to fit residues: 15.9303 Evaluate side-chains 151 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 44 HIS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 125 VAL Chi-restraints excluded: chain R residue 159 ILE Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 300 ASP Chi-restraints excluded: chain R residue 312 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 89 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 67 optimal weight: 8.9990 chunk 62 optimal weight: 7.9990 chunk 15 optimal weight: 4.9990 chunk 87 optimal weight: 0.4980 chunk 64 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 82 optimal weight: 0.3980 chunk 4 optimal weight: 20.0000 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 371 ASN R 142 GLN R 312 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.183833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.159453 restraints weight = 8055.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.155903 restraints weight = 11051.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.157545 restraints weight = 11577.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.157613 restraints weight = 7846.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.157823 restraints weight = 6667.083| |-----------------------------------------------------------------------------| r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7540 Z= 0.101 Angle : 0.542 8.013 10249 Z= 0.278 Chirality : 0.042 0.181 1194 Planarity : 0.003 0.045 1295 Dihedral : 5.312 66.341 1046 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 3.68 % Allowed : 25.75 % Favored : 70.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.03 (0.26), residues: 950 helix: -0.92 (0.28), residues: 349 sheet: -2.98 (0.33), residues: 199 loop : -2.35 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 256 TYR 0.017 0.001 TYR B 111 PHE 0.011 0.001 PHE A 222 TRP 0.032 0.002 TRP R 313 HIS 0.003 0.001 HIS R 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 ( 7538) covalent geometry : angle 0.54174 / 0.28 (10245) SS BOND : bond 0.00205 / 0.10 ( 2) SS BOND : angle 0.44976 / 0.24 ( 4) hydrogen bonds : bond 0.02958 / 1.94 ( 220) hydrogen bonds : angle 4.60337 / 3.24 ( 624) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 0.290 Fit side-chains REVERT: A 27 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7773 (mp0) REVERT: A 212 PHE cc_start: 0.7164 (p90) cc_final: 0.6908 (p90) REVERT: B 88 ASN cc_start: 0.8647 (m-40) cc_final: 0.8150 (m110) REVERT: B 111 TYR cc_start: 0.7593 (m-80) cc_final: 0.7000 (m-80) REVERT: B 154 ASP cc_start: 0.7932 (m-30) cc_final: 0.7488 (t0) REVERT: N 35 ASN cc_start: 0.8383 (p0) cc_final: 0.7907 (p0) REVERT: N 60 TYR cc_start: 0.8775 (m-80) cc_final: 0.8457 (m-80) REVERT: R 64 LEU cc_start: 0.7120 (OUTLIER) cc_final: 0.6780 (mt) REVERT: R 300 ASP cc_start: 0.7335 (OUTLIER) cc_final: 0.6695 (m-30) REVERT: R 312 ASN cc_start: 0.6329 (OUTLIER) cc_final: 0.5770 (t0) outliers start: 27 outliers final: 17 residues processed: 148 average time/residue: 0.0718 time to fit residues: 15.1826 Evaluate side-chains 145 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 44 HIS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 159 ILE Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 281 THR Chi-restraints excluded: chain R residue 300 ASP Chi-restraints excluded: chain R residue 312 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 28 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 42 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 371 ASN B 183 HIS R 312 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.183451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.158351 restraints weight = 8225.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.152439 restraints weight = 15135.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.149575 restraints weight = 10565.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.149831 restraints weight = 10129.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.150876 restraints weight = 7785.311| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7540 Z= 0.137 Angle : 0.572 8.537 10249 Z= 0.295 Chirality : 0.043 0.164 1194 Planarity : 0.003 0.044 1295 Dihedral : 5.433 66.778 1046 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 4.22 % Allowed : 24.66 % Favored : 71.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.02 (0.26), residues: 950 helix: -0.96 (0.28), residues: 352 sheet: -2.88 (0.35), residues: 199 loop : -2.36 (0.29), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 256 TYR 0.015 0.001 TYR R 308 PHE 0.013 0.001 PHE A 222 TRP 0.035 0.002 TRP R 313 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 7538) covalent geometry : angle 0.57209 / 0.30 (10245) SS BOND : bond 0.00221 / 0.11 ( 2) SS BOND : angle 0.51315 / 0.28 ( 4) hydrogen bonds : bond 0.03117 / 2.03 ( 220) hydrogen bonds : angle 4.70007 / 3.31 ( 624) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 129 time to evaluate : 0.287 Fit side-chains REVERT: A 27 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7827 (mp0) REVERT: A 45 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8421 (tt) REVERT: A 212 PHE cc_start: 0.7277 (p90) cc_final: 0.7013 (p90) REVERT: A 390 GLN cc_start: 0.8463 (tp-100) cc_final: 0.8252 (tp-100) REVERT: B 88 ASN cc_start: 0.8557 (m-40) cc_final: 0.8164 (m110) REVERT: B 111 TYR cc_start: 0.7665 (m-80) cc_final: 0.7218 (m-80) REVERT: B 154 ASP cc_start: 0.8095 (m-30) cc_final: 0.7578 (t0) REVERT: N 35 ASN cc_start: 0.8436 (p0) cc_final: 0.7965 (p0) REVERT: R 64 LEU cc_start: 0.7285 (OUTLIER) cc_final: 0.6940 (mt) REVERT: R 300 ASP cc_start: 0.7441 (OUTLIER) cc_final: 0.6756 (m-30) REVERT: R 312 ASN cc_start: 0.6618 (OUTLIER) cc_final: 0.6090 (t0) outliers start: 31 outliers final: 20 residues processed: 150 average time/residue: 0.0734 time to fit residues: 15.8041 Evaluate side-chains 152 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 44 HIS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 159 ILE Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 281 THR Chi-restraints excluded: chain R residue 300 ASP Chi-restraints excluded: chain R residue 312 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 76 optimal weight: 0.6980 chunk 83 optimal weight: 7.9990 chunk 44 optimal weight: 4.9990 chunk 4 optimal weight: 20.0000 chunk 73 optimal weight: 10.0000 chunk 34 optimal weight: 0.0570 chunk 79 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 overall best weight: 1.7102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 371 ASN R 142 GLN R 312 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.180587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.146828 restraints weight = 8159.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.145783 restraints weight = 8805.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.145711 restraints weight = 8414.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.145713 restraints weight = 7746.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.145713 restraints weight = 7739.649| |-----------------------------------------------------------------------------| r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7540 Z= 0.164 Angle : 0.621 10.188 10249 Z= 0.317 Chirality : 0.045 0.149 1194 Planarity : 0.004 0.044 1295 Dihedral : 5.577 67.187 1046 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 4.09 % Allowed : 26.02 % Favored : 69.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.10 (0.26), residues: 950 helix: -1.02 (0.28), residues: 352 sheet: -2.89 (0.34), residues: 206 loop : -2.41 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 304 TYR 0.016 0.001 TYR R 308 PHE 0.015 0.002 PHE A 222 TRP 0.039 0.002 TRP R 313 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.16 ( 7538) covalent geometry : angle 0.62059 / 0.32 (10245) SS BOND : bond 0.00250 / 0.12 ( 2) SS BOND : angle 0.55289 / 0.30 ( 4) hydrogen bonds : bond 0.03311 / 2.16 ( 220) hydrogen bonds : angle 4.81530 / 3.39 ( 624) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 139 time to evaluate : 0.168 Fit side-chains REVERT: A 27 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7889 (mp0) REVERT: A 239 ASN cc_start: 0.8650 (p0) cc_final: 0.8352 (p0) REVERT: B 88 ASN cc_start: 0.8516 (m-40) cc_final: 0.8061 (m110) REVERT: B 111 TYR cc_start: 0.7708 (m-80) cc_final: 0.7326 (m-80) REVERT: B 154 ASP cc_start: 0.8111 (m-30) cc_final: 0.7586 (t0) REVERT: B 188 MET cc_start: 0.7931 (mmp) cc_final: 0.7649 (mmm) REVERT: N 35 ASN cc_start: 0.8489 (p0) cc_final: 0.8006 (p0) REVERT: R 36 MET cc_start: 0.7351 (tpp) cc_final: 0.7050 (tpp) REVERT: R 64 LEU cc_start: 0.7333 (OUTLIER) cc_final: 0.7010 (mt) REVERT: R 196 ASN cc_start: 0.7763 (p0) cc_final: 0.7557 (p0) REVERT: R 300 ASP cc_start: 0.7603 (OUTLIER) cc_final: 0.6930 (m-30) REVERT: R 312 ASN cc_start: 0.6885 (OUTLIER) cc_final: 0.6577 (t0) outliers start: 30 outliers final: 21 residues processed: 159 average time/residue: 0.0692 time to fit residues: 15.8008 Evaluate side-chains 163 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 44 HIS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 159 ILE Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 281 THR Chi-restraints excluded: chain R residue 300 ASP Chi-restraints excluded: chain R residue 312 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 23 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 chunk 13 optimal weight: 0.5980 chunk 62 optimal weight: 6.9990 chunk 80 optimal weight: 6.9990 chunk 17 optimal weight: 0.0870 chunk 59 optimal weight: 8.9990 chunk 14 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 overall best weight: 0.9360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 220 HIS A 371 ASN B 220 GLN R 142 GLN R 312 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.184048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.155710 restraints weight = 8089.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.151761 restraints weight = 13713.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.152834 restraints weight = 12696.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.153067 restraints weight = 9154.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.153631 restraints weight = 7485.497| |-----------------------------------------------------------------------------| r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7540 Z= 0.117 Angle : 0.601 9.510 10249 Z= 0.303 Chirality : 0.043 0.146 1194 Planarity : 0.003 0.044 1295 Dihedral : 5.440 65.924 1046 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 3.95 % Allowed : 26.70 % Favored : 69.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.93 (0.27), residues: 950 helix: -0.85 (0.28), residues: 352 sheet: -2.88 (0.35), residues: 195 loop : -2.35 (0.29), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 256 TYR 0.012 0.001 TYR R 308 PHE 0.013 0.001 PHE A 222 TRP 0.030 0.002 TRP R 109 HIS 0.003 0.001 HIS R 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 7538) covalent geometry : angle 0.60135 / 0.30 (10245) SS BOND : bond 0.00222 / 0.11 ( 2) SS BOND : angle 0.49925 / 0.27 ( 4) hydrogen bonds : bond 0.03134 / 2.04 ( 220) hydrogen bonds : angle 4.68639 / 3.30 ( 624) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 135 time to evaluate : 0.267 Fit side-chains REVERT: A 27 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7879 (mp0) REVERT: A 212 PHE cc_start: 0.7260 (p90) cc_final: 0.7023 (p90) REVERT: A 239 ASN cc_start: 0.8627 (p0) cc_final: 0.8320 (p0) REVERT: B 88 ASN cc_start: 0.8559 (m-40) cc_final: 0.8117 (m110) REVERT: B 111 TYR cc_start: 0.7646 (m-80) cc_final: 0.7269 (m-80) REVERT: B 154 ASP cc_start: 0.8049 (m-30) cc_final: 0.7596 (t0) REVERT: N 35 ASN cc_start: 0.8382 (p0) cc_final: 0.7823 (p0) REVERT: R 64 LEU cc_start: 0.7245 (OUTLIER) cc_final: 0.6950 (mt) REVERT: R 300 ASP cc_start: 0.7418 (OUTLIER) cc_final: 0.6744 (m-30) REVERT: R 312 ASN cc_start: 0.6625 (OUTLIER) cc_final: 0.6331 (t0) outliers start: 29 outliers final: 22 residues processed: 155 average time/residue: 0.0711 time to fit residues: 15.8435 Evaluate side-chains 157 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 44 HIS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 159 ILE Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 281 THR Chi-restraints excluded: chain R residue 300 ASP Chi-restraints excluded: chain R residue 312 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 14 optimal weight: 0.7980 chunk 27 optimal weight: 0.0050 chunk 8 optimal weight: 0.9990 chunk 17 optimal weight: 0.0030 chunk 24 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 77 optimal weight: 0.3980 chunk 40 optimal weight: 6.9990 chunk 90 optimal weight: 0.6980 chunk 81 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 overall best weight: 0.3804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 220 HIS A 371 ASN R 312 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.175601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.146805 restraints weight = 8234.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.143359 restraints weight = 12668.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.145613 restraints weight = 11872.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.145576 restraints weight = 8432.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.145715 restraints weight = 7445.915| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7540 Z= 0.101 Angle : 0.588 9.561 10249 Z= 0.296 Chirality : 0.042 0.140 1194 Planarity : 0.003 0.044 1295 Dihedral : 5.303 63.667 1046 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 3.68 % Allowed : 26.70 % Favored : 69.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.74 (0.27), residues: 950 helix: -0.68 (0.29), residues: 355 sheet: -2.77 (0.35), residues: 195 loop : -2.25 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 304 TYR 0.010 0.001 TYR G 40 PHE 0.027 0.001 PHE R 289 TRP 0.037 0.002 TRP R 313 HIS 0.007 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 ( 7538) covalent geometry : angle 0.58826 / 0.30 (10245) SS BOND : bond 0.00178 / 0.09 ( 2) SS BOND : angle 0.42728 / 0.23 ( 4) hydrogen bonds : bond 0.02936 / 1.92 ( 220) hydrogen bonds : angle 4.56817 / 3.21 ( 624) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1266.60 seconds wall clock time: 22 minutes 36.97 seconds (1356.97 seconds total)