Starting phenix.real_space_refine on Fri Aug 22 22:04:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v6u_42999/08_2025/8v6u_42999.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v6u_42999/08_2025/8v6u_42999.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8v6u_42999/08_2025/8v6u_42999.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v6u_42999/08_2025/8v6u_42999.map" model { file = "/net/cci-nas-00/data/ceres_data/8v6u_42999/08_2025/8v6u_42999.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v6u_42999/08_2025/8v6u_42999.cif" } resolution = 3.0 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= 0.001 sd= 0.018 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 53 5.16 5 C 5264 2.51 5 N 1389 2.21 5 O 1505 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8211 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1999 Classifications: {'peptide': 260} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 9, 'TRANS': 250} Chain breaks: 2 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 3, 'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "B" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1656 Classifications: {'peptide': 211} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 4, 'TRANS': 206} Chain breaks: 4 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 4, 'PHE:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 49 Chain: "C" Number of atoms: 2466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2466 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 6, 'GLN:plan1': 5, 'ARG:plan': 7, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 107 Chain: "D" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 353 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 4, 'TRANS': 46} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "E" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1716 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain breaks: 2 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 6, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "A" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'YEQ': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.26, per 1000 atoms: 0.28 Number of scatterers: 8211 At special positions: 0 Unit cell: (90.272, 118.048, 132.804, 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 53 16.00 O 1505 8.00 N 1389 7.00 C 5264 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 148 " - pdb=" SG CYS A 227 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.05 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: 0.68 Conformation dependent library (CDL) restraints added in 470.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2042 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 13 sheets defined 38.3% alpha, 24.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 78 through 102 removed outlier: 3.710A pdb=" N ALA A 82 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 127 removed outlier: 3.682A pdb=" N LEU A 113 " --> pdb=" O THR A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 137 Processing helix chain 'A' and resid 144 through 146 No H-bonds generated for 'chain 'A' and resid 144 through 146' Processing helix chain 'A' and resid 147 through 179 removed outlier: 3.787A pdb=" N TRP A 151 " --> pdb=" O LEU A 147 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE A 152 " --> pdb=" O CYS A 148 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA A 161 " --> pdb=" O LEU A 157 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N SER A 162 " --> pdb=" O PHE A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 186 removed outlier: 3.522A pdb=" N PHE A 186 " --> pdb=" O HIS A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 207 removed outlier: 4.167A pdb=" N PHE A 193 " --> pdb=" O ARG A 189 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER A 207 " --> pdb=" O SER A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 215 removed outlier: 3.851A pdb=" N LEU A 215 " --> pdb=" O PRO A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 243 Processing helix chain 'A' and resid 243 through 262 Processing helix chain 'A' and resid 317 through 349 removed outlier: 3.501A pdb=" N MET A 335 " --> pdb=" O LEU A 331 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TRP A 336 " --> pdb=" O PHE A 332 " (cutoff:3.500A) Proline residue: A 338 - end of helix removed outlier: 3.580A pdb=" N VAL A 347 " --> pdb=" O ASN A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 372 removed outlier: 3.634A pdb=" N VAL A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N TRP A 367 " --> pdb=" O ASN A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 380 Processing helix chain 'A' and resid 384 through 393 Processing helix chain 'B' and resid 6 through 32 removed outlier: 3.611A pdb=" N ALA B 11 " --> pdb=" O ALA B 7 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER B 16 " --> pdb=" O ALA B 12 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU B 28 " --> pdb=" O ARG B 24 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LYS B 29 " --> pdb=" O GLU B 25 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA B 30 " --> pdb=" O ASP B 26 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG B 31 " --> pdb=" O GLY B 27 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 49 removed outlier: 3.989A pdb=" N ILE B 49 " --> pdb=" O LYS B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 101 removed outlier: 3.522A pdb=" N ASN B 101 " --> pdb=" O GLN B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 131 removed outlier: 3.570A pdb=" N ASN B 130 " --> pdb=" O LYS B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 156 Processing helix chain 'B' and resid 159 through 163 Processing helix chain 'B' and resid 164 through 169 Processing helix chain 'B' and resid 184 through 203 removed outlier: 4.134A pdb=" N ARG B 188 " --> pdb=" O PRO B 184 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA B 189 " --> pdb=" O ARG B 185 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N PHE B 197 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE B 200 " --> pdb=" O GLU B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 243 removed outlier: 3.555A pdb=" N PHE B 228 " --> pdb=" O ALA B 224 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP B 233 " --> pdb=" O ASN B 229 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ARG B 241 " --> pdb=" O GLN B 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 25 removed outlier: 3.972A pdb=" N GLN C 9 " --> pdb=" O ASP C 5 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG C 19 " --> pdb=" O LYS C 15 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N CYS C 25 " --> pdb=" O ALA C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'D' and resid 12 through 23 removed outlier: 4.256A pdb=" N GLU D 17 " --> pdb=" O ARG D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 44 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 4.015A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'E' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'B' and resid 69 through 76 removed outlier: 5.095A pdb=" N VAL B 86 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ARG B 35 " --> pdb=" O ALA B 105 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N ILE B 107 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU B 37 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N VAL B 109 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N LEU B 39 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 8.616A pdb=" N ASP B 111 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ILE B 106 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N PHE B 142 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N PHE B 108 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N ASN B 144 " --> pdb=" O PHE B 108 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL B 110 " --> pdb=" O ASN B 144 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 46 through 51 removed outlier: 5.285A pdb=" N THR C 47 " --> pdb=" O ASN C 340 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ASN C 340 " --> pdb=" O THR C 47 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG C 49 " --> pdb=" O ILE C 338 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N CYS C 317 " --> pdb=" O GLY C 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.585A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEU C 79 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ALA C 92 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE C 81 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.937A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG C 137 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 151 removed outlier: 3.774A pdb=" N CYS C 148 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR C 178 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.691A pdb=" N ALA C 208 " --> pdb=" O THR C 221 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N THR C 221 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU C 210 " --> pdb=" O ARG C 219 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N MET C 217 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.655A pdb=" N CYS C 250 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N THR C 263 " --> pdb=" O CYS C 250 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N LEU C 252 " --> pdb=" O LEU C 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.631A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N CYS C 294 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N VAL C 307 " --> pdb=" O CYS C 294 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL C 296 " --> pdb=" O ALA C 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.161A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 128 through 130 Processing sheet with id=AB3, first strand: chain 'E' and resid 134 through 136 removed outlier: 6.622A pdb=" N VAL E 135 " --> pdb=" O GLU E 234 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU E 162 " --> pdb=" O TYR E 178 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N TYR E 178 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 134 through 136 removed outlier: 6.622A pdb=" N VAL E 135 " --> pdb=" O GLU E 234 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N THR E 226 " --> pdb=" O GLN E 219 " (cutoff:3.500A) 405 hydrogen bonds defined for protein. 1125 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: 1.36 Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2136 1.33 - 1.46: 1841 1.46 - 1.59: 4326 1.59 - 1.71: 1 1.71 - 1.84: 78 Bond restraints: 8382 Sorted by residual: bond pdb=" C02 YEQ A 501 " pdb=" N03 YEQ A 501 " ideal model delta sigma weight residual 1.454 1.209 0.245 2.00e-02 2.50e+03 1.50e+02 bond pdb=" C06 YEQ A 501 " pdb=" C07 YEQ A 501 " ideal model delta sigma weight residual 1.528 1.422 0.106 2.00e-02 2.50e+03 2.81e+01 bond pdb=" C05 YEQ A 501 " pdb=" C06 YEQ A 501 " ideal model delta sigma weight residual 1.534 1.455 0.079 2.00e-02 2.50e+03 1.58e+01 bond pdb=" C07 YEQ A 501 " pdb=" C09 YEQ A 501 " ideal model delta sigma weight residual 1.507 1.581 -0.074 2.00e-02 2.50e+03 1.38e+01 bond pdb=" C12 YEQ A 501 " pdb=" O13 YEQ A 501 " ideal model delta sigma weight residual 1.350 1.423 -0.073 2.00e-02 2.50e+03 1.33e+01 ... (remaining 8377 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.09: 10511 3.09 - 6.18: 864 6.18 - 9.26: 22 9.26 - 12.35: 2 12.35 - 15.44: 1 Bond angle restraints: 11400 Sorted by residual: angle pdb=" CA ASP C 186 " pdb=" CB ASP C 186 " pdb=" CG ASP C 186 " ideal model delta sigma weight residual 112.60 121.20 -8.60 1.00e+00 1.00e+00 7.39e+01 angle pdb=" C PHE E 108 " pdb=" N ASP E 109 " pdb=" CA ASP E 109 " ideal model delta sigma weight residual 120.29 130.02 -9.73 1.42e+00 4.96e-01 4.70e+01 angle pdb=" CA ASP C 228 " pdb=" CB ASP C 228 " pdb=" CG ASP C 228 " ideal model delta sigma weight residual 112.60 119.28 -6.68 1.00e+00 1.00e+00 4.46e+01 angle pdb=" CA PHE E 68 " pdb=" CB PHE E 68 " pdb=" CG PHE E 68 " ideal model delta sigma weight residual 113.80 119.57 -5.77 1.00e+00 1.00e+00 3.33e+01 angle pdb=" CA ASP C 163 " pdb=" CB ASP C 163 " pdb=" CG ASP C 163 " ideal model delta sigma weight residual 112.60 117.89 -5.29 1.00e+00 1.00e+00 2.80e+01 ... (remaining 11395 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 4503 18.00 - 35.99: 328 35.99 - 53.98: 77 53.98 - 71.98: 9 71.98 - 89.97: 6 Dihedral angle restraints: 4923 sinusoidal: 1766 harmonic: 3157 Sorted by residual: dihedral pdb=" CA LYS C 78 " pdb=" C LYS C 78 " pdb=" N LEU C 79 " pdb=" CA LEU C 79 " ideal model delta harmonic sigma weight residual 180.00 150.62 29.38 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA SER E 52 " pdb=" C SER E 52 " pdb=" N SER E 53 " pdb=" CA SER E 53 " ideal model delta harmonic sigma weight residual 180.00 152.73 27.27 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA THR C 165 " pdb=" C THR C 165 " pdb=" N CYS C 166 " pdb=" CA CYS C 166 " ideal model delta harmonic sigma weight residual 180.00 154.15 25.85 0 5.00e+00 4.00e-02 2.67e+01 ... (remaining 4920 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 986 0.088 - 0.176: 289 0.176 - 0.263: 47 0.263 - 0.351: 7 0.351 - 0.439: 6 Chirality restraints: 1335 Sorted by residual: chirality pdb=" CA PHE C 292 " pdb=" N PHE C 292 " pdb=" C PHE C 292 " pdb=" CB PHE C 292 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.82e+00 chirality pdb=" CA THR C 164 " pdb=" N THR C 164 " pdb=" C THR C 164 " pdb=" CB THR C 164 " both_signs ideal model delta sigma weight residual False 2.53 2.12 0.41 2.00e-01 2.50e+01 4.20e+00 chirality pdb=" CA SER C 334 " pdb=" N SER C 334 " pdb=" C SER C 334 " pdb=" CB SER C 334 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.93e+00 ... (remaining 1332 not shown) Planarity restraints: 1432 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 332 " 0.138 2.00e-02 2.50e+03 7.53e-02 1.42e+02 pdb=" CG TRP C 332 " -0.006 2.00e-02 2.50e+03 pdb=" CD1 TRP C 332 " -0.046 2.00e-02 2.50e+03 pdb=" CD2 TRP C 332 " -0.060 2.00e-02 2.50e+03 pdb=" NE1 TRP C 332 " -0.060 2.00e-02 2.50e+03 pdb=" CE2 TRP C 332 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 332 " -0.098 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 332 " 0.102 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 332 " -0.046 2.00e-02 2.50e+03 pdb=" CH2 TRP C 332 " 0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 94 " -0.121 2.00e-02 2.50e+03 6.85e-02 9.39e+01 pdb=" CG TYR E 94 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR E 94 " 0.068 2.00e-02 2.50e+03 pdb=" CD2 TYR E 94 " 0.050 2.00e-02 2.50e+03 pdb=" CE1 TYR E 94 " 0.036 2.00e-02 2.50e+03 pdb=" CE2 TYR E 94 " 0.050 2.00e-02 2.50e+03 pdb=" CZ TYR E 94 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR E 94 " -0.107 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 82 " -0.120 2.00e-02 2.50e+03 5.71e-02 8.15e+01 pdb=" CG TRP C 82 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP C 82 " 0.041 2.00e-02 2.50e+03 pdb=" CD2 TRP C 82 " 0.066 2.00e-02 2.50e+03 pdb=" NE1 TRP C 82 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP C 82 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP C 82 " 0.071 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 82 " -0.058 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 82 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP C 82 " -0.051 2.00e-02 2.50e+03 ... (remaining 1429 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 13 2.58 - 3.16: 6055 3.16 - 3.74: 11828 3.74 - 4.32: 16339 4.32 - 4.90: 28229 Nonbonded interactions: 62464 Sorted by model distance: nonbonded pdb=" OD1 ASP A 172 " pdb=" OH TYR B 243 " model vdw 1.999 3.040 nonbonded pdb=" OD1 ASN A 110 " pdb=" OH TYR A 387 " model vdw 2.212 3.040 nonbonded pdb=" O ILE A 197 " pdb=" OG1 THR A 201 " model vdw 2.337 3.040 nonbonded pdb=" O SER A 219 " pdb=" OG SER A 219 " model vdw 2.464 3.040 nonbonded pdb=" C06 YEQ A 501 " pdb=" C15 YEQ A 501 " model vdw 2.499 2.992 ... (remaining 62459 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.540 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.520 Find NCS groups from input model: 0.050 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:6.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 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 : 0.011 0.245 8384 Z= 0.699 Angle : 1.670 15.442 11404 Z= 1.100 Chirality : 0.086 0.439 1335 Planarity : 0.012 0.115 1432 Dihedral : 14.064 89.972 2875 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 1.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.14 % Favored : 95.77 % Rotamer: Outliers : 1.31 % Allowed : 11.53 % Favored : 87.16 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 3.23 % 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 aren not related in a simple way. whole: 0.40 (0.25), residues: 1064 helix: 0.58 (0.27), residues: 349 sheet: 1.45 (0.34), residues: 222 loop : -0.48 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 117 TYR 0.121 0.016 TYR E 94 PHE 0.068 0.008 PHE C 151 TRP 0.138 0.018 TRP C 332 HIS 0.015 0.004 HIS C 62 Details of bonding type rmsd covalent geometry : bond 0.01148 ( 8382) covalent geometry : angle 1.66956 (11400) SS BOND : bond 0.01633 ( 2) SS BOND : angle 2.17539 ( 4) hydrogen bonds : bond 0.19589 ( 403) hydrogen bonds : angle 6.59245 ( 1125) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 152 time to evaluate : 0.282 Fit side-chains REVERT: A 208 MET cc_start: 0.7086 (mmm) cc_final: 0.6841 (mmm) REVERT: A 242 SER cc_start: 0.8572 (p) cc_final: 0.8240 (p) REVERT: B 22 ASN cc_start: 0.7935 (t0) cc_final: 0.7673 (m110) REVERT: B 200 ILE cc_start: 0.7590 (OUTLIER) cc_final: 0.7390 (tt) REVERT: C 35 ASN cc_start: 0.7678 (t0) cc_final: 0.7068 (m-40) REVERT: C 156 GLN cc_start: 0.8643 (mt0) cc_final: 0.8419 (mt0) REVERT: C 333 ASP cc_start: 0.7362 (p0) cc_final: 0.7067 (p0) REVERT: E 215 TYR cc_start: 0.7622 (m-80) cc_final: 0.7350 (m-80) outliers start: 11 outliers final: 9 residues processed: 161 average time/residue: 0.5933 time to fit residues: 101.4372 Evaluate side-chains 115 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 105 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 237 GLN Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 228 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 0.5980 chunk 106 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 183 HIS B 146 GLN C 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.114706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.100913 restraints weight = 15727.966| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.80 r_work: 0.3360 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8384 Z= 0.191 Angle : 0.673 9.788 11404 Z= 0.358 Chirality : 0.046 0.147 1335 Planarity : 0.004 0.040 1432 Dihedral : 6.866 58.087 1202 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.40 % Allowed : 17.00 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 aren not related in a simple way. whole: 0.85 (0.26), residues: 1064 helix: 1.27 (0.28), residues: 358 sheet: 1.22 (0.31), residues: 268 loop : -0.39 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 31 TYR 0.018 0.002 TYR E 178 PHE 0.020 0.002 PHE C 235 TRP 0.019 0.002 TRP C 82 HIS 0.010 0.002 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00442 ( 8382) covalent geometry : angle 0.67178 (11400) SS BOND : bond 0.00708 ( 2) SS BOND : angle 2.10503 ( 4) hydrogen bonds : bond 0.05909 ( 403) hydrogen bonds : angle 4.81487 ( 1125) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 117 time to evaluate : 0.388 Fit side-chains REVERT: A 242 SER cc_start: 0.8561 (p) cc_final: 0.8255 (p) REVERT: A 330 PHE cc_start: 0.7017 (OUTLIER) cc_final: 0.6694 (t80) REVERT: B 10 LYS cc_start: 0.7308 (tttm) cc_final: 0.7008 (mtmt) REVERT: B 80 ASN cc_start: 0.7118 (p0) cc_final: 0.6856 (p0) REVERT: C 35 ASN cc_start: 0.7936 (t0) cc_final: 0.7450 (m-40) REVERT: C 156 GLN cc_start: 0.8926 (mt0) cc_final: 0.8657 (mt0) REVERT: C 333 ASP cc_start: 0.7482 (p0) cc_final: 0.7190 (p0) REVERT: D 51 LEU cc_start: 0.6976 (OUTLIER) cc_final: 0.6570 (tm) REVERT: E 202 LEU cc_start: 0.7741 (OUTLIER) cc_final: 0.7404 (tp) REVERT: E 215 TYR cc_start: 0.7801 (m-80) cc_final: 0.7573 (m-80) outliers start: 37 outliers final: 12 residues processed: 142 average time/residue: 0.5196 time to fit residues: 79.1486 Evaluate side-chains 120 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 PHE Chi-restraints excluded: chain A residue 336 TRP Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 237 GLN Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain E residue 202 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 0.0040 chunk 91 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 102 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 106 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.114126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.100419 restraints weight = 15638.143| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.80 r_work: 0.3372 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8384 Z= 0.160 Angle : 0.603 8.830 11404 Z= 0.320 Chirality : 0.044 0.142 1335 Planarity : 0.004 0.048 1432 Dihedral : 5.738 58.255 1189 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.88 % Allowed : 18.79 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 aren not related in a simple way. whole: 0.93 (0.26), residues: 1064 helix: 1.62 (0.28), residues: 352 sheet: 0.97 (0.31), residues: 278 loop : -0.42 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 148 TYR 0.017 0.002 TYR E 178 PHE 0.016 0.002 PHE C 235 TRP 0.020 0.002 TRP C 82 HIS 0.007 0.002 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 8382) covalent geometry : angle 0.60209 (11400) SS BOND : bond 0.00575 ( 2) SS BOND : angle 2.04500 ( 4) hydrogen bonds : bond 0.05289 ( 403) hydrogen bonds : angle 4.50706 ( 1125) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 110 time to evaluate : 0.236 Fit side-chains REVERT: C 23 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7640 (tmmm) REVERT: C 35 ASN cc_start: 0.7977 (t0) cc_final: 0.7671 (t0) REVERT: C 156 GLN cc_start: 0.8946 (mt0) cc_final: 0.8656 (mt0) REVERT: C 217 MET cc_start: 0.8555 (OUTLIER) cc_final: 0.7563 (ppp) REVERT: C 258 ASP cc_start: 0.8321 (t0) cc_final: 0.8042 (t0) REVERT: C 315 VAL cc_start: 0.8544 (OUTLIER) cc_final: 0.8312 (m) REVERT: D 51 LEU cc_start: 0.7192 (OUTLIER) cc_final: 0.6738 (tm) outliers start: 41 outliers final: 16 residues processed: 137 average time/residue: 0.4970 time to fit residues: 72.9416 Evaluate side-chains 123 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 103 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain B residue 73 LYS Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 237 GLN Chi-restraints excluded: chain C residue 23 LYS Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain E residue 211 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 80 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 66 optimal weight: 0.5980 chunk 96 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 65 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 86 optimal weight: 0.0030 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 268 ASN E 159 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.114626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.100644 restraints weight = 16008.252| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 1.87 r_work: 0.3375 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8384 Z= 0.139 Angle : 0.559 8.241 11404 Z= 0.295 Chirality : 0.043 0.137 1335 Planarity : 0.004 0.048 1432 Dihedral : 5.444 58.332 1189 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 4.28 % Allowed : 20.57 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 aren not related in a simple way. whole: 1.07 (0.26), residues: 1064 helix: 2.01 (0.28), residues: 346 sheet: 1.01 (0.31), residues: 264 loop : -0.47 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 31 TYR 0.016 0.001 TYR E 178 PHE 0.014 0.002 PHE C 199 TRP 0.017 0.002 TRP C 82 HIS 0.006 0.001 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 8382) covalent geometry : angle 0.55742 (11400) SS BOND : bond 0.00543 ( 2) SS BOND : angle 1.96782 ( 4) hydrogen bonds : bond 0.04702 ( 403) hydrogen bonds : angle 4.31723 ( 1125) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 110 time to evaluate : 0.342 Fit side-chains REVERT: B 126 LYS cc_start: 0.8334 (tppt) cc_final: 0.7467 (ptpt) REVERT: C 23 LYS cc_start: 0.8157 (OUTLIER) cc_final: 0.7611 (tmmm) REVERT: C 35 ASN cc_start: 0.7995 (t0) cc_final: 0.7688 (t0) REVERT: C 156 GLN cc_start: 0.8964 (mt0) cc_final: 0.8678 (mt0) REVERT: C 217 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.7582 (ppp) REVERT: C 258 ASP cc_start: 0.8253 (t0) cc_final: 0.8001 (t0) REVERT: D 51 LEU cc_start: 0.7229 (OUTLIER) cc_final: 0.6816 (tm) outliers start: 36 outliers final: 15 residues processed: 136 average time/residue: 0.5116 time to fit residues: 74.6328 Evaluate side-chains 123 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 336 TRP Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain B residue 73 LYS Chi-restraints excluded: chain B residue 115 TYR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 237 GLN Chi-restraints excluded: chain C residue 23 LYS Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain E residue 202 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 48 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 62 optimal weight: 0.3980 chunk 64 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 0 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 268 ASN E 159 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.113293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.099476 restraints weight = 15900.599| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 1.82 r_work: 0.3356 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8384 Z= 0.166 Angle : 0.588 8.520 11404 Z= 0.308 Chirality : 0.044 0.144 1335 Planarity : 0.004 0.048 1432 Dihedral : 5.530 58.093 1189 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 4.88 % Allowed : 21.40 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 aren not related in a simple way. whole: 0.89 (0.26), residues: 1064 helix: 1.95 (0.28), residues: 347 sheet: 0.85 (0.31), residues: 264 loop : -0.64 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 148 TYR 0.018 0.002 TYR E 178 PHE 0.024 0.002 PHE A 255 TRP 0.019 0.002 TRP C 82 HIS 0.007 0.002 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 8382) covalent geometry : angle 0.58648 (11400) SS BOND : bond 0.00575 ( 2) SS BOND : angle 2.04335 ( 4) hydrogen bonds : bond 0.05075 ( 403) hydrogen bonds : angle 4.38059 ( 1125) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 107 time to evaluate : 0.378 Fit side-chains REVERT: A 255 PHE cc_start: 0.7783 (t80) cc_final: 0.6987 (m-80) REVERT: C 23 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7672 (tmmm) REVERT: C 35 ASN cc_start: 0.8030 (t0) cc_final: 0.7746 (t0) REVERT: C 156 GLN cc_start: 0.8907 (mt0) cc_final: 0.8636 (mt0) REVERT: C 217 MET cc_start: 0.8470 (OUTLIER) cc_final: 0.7566 (ppp) REVERT: C 258 ASP cc_start: 0.8254 (t0) cc_final: 0.8012 (t0) REVERT: E 11 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7782 (tt) outliers start: 41 outliers final: 21 residues processed: 138 average time/residue: 0.4964 time to fit residues: 73.5859 Evaluate side-chains 125 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 336 TRP Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain B residue 115 TYR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 237 GLN Chi-restraints excluded: chain C residue 23 LYS Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 194 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 15 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 60 optimal weight: 0.0570 chunk 30 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 6 optimal weight: 0.3980 chunk 38 optimal weight: 0.7980 chunk 59 optimal weight: 0.4980 chunk 26 optimal weight: 0.8980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 ASN C 268 ASN E 159 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.113911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.100029 restraints weight = 15663.052| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.82 r_work: 0.3377 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8384 Z= 0.136 Angle : 0.545 8.134 11404 Z= 0.288 Chirality : 0.043 0.135 1335 Planarity : 0.004 0.048 1432 Dihedral : 5.335 58.015 1189 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.99 % Allowed : 22.35 % Favored : 72.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 aren not related in a simple way. whole: 0.89 (0.26), residues: 1064 helix: 1.99 (0.28), residues: 349 sheet: 0.96 (0.31), residues: 260 loop : -0.75 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 31 TYR 0.016 0.001 TYR E 178 PHE 0.018 0.002 PHE A 255 TRP 0.016 0.002 TRP C 82 HIS 0.006 0.001 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 8382) covalent geometry : angle 0.54395 (11400) SS BOND : bond 0.00524 ( 2) SS BOND : angle 1.96545 ( 4) hydrogen bonds : bond 0.04604 ( 403) hydrogen bonds : angle 4.26774 ( 1125) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 110 time to evaluate : 0.323 Fit side-chains REVERT: A 255 PHE cc_start: 0.7775 (t80) cc_final: 0.6963 (m-80) REVERT: B 24 ARG cc_start: 0.8267 (ttm110) cc_final: 0.7677 (ttp-110) REVERT: B 126 LYS cc_start: 0.8288 (tppt) cc_final: 0.7426 (ptpt) REVERT: C 18 ILE cc_start: 0.6432 (OUTLIER) cc_final: 0.6092 (tp) REVERT: C 23 LYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7601 (tmmm) REVERT: C 35 ASN cc_start: 0.8057 (t0) cc_final: 0.7810 (t0) REVERT: C 156 GLN cc_start: 0.8900 (mt0) cc_final: 0.8623 (mt0) REVERT: C 217 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.7594 (ppp) REVERT: E 11 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7788 (tt) outliers start: 42 outliers final: 24 residues processed: 139 average time/residue: 0.5311 time to fit residues: 79.0516 Evaluate side-chains 130 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 102 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 336 TRP Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain B residue 73 LYS Chi-restraints excluded: chain B residue 115 TYR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 237 GLN Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 23 LYS Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 159 ASN Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain E residue 202 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 71 optimal weight: 0.3980 chunk 105 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 132 ASN E 159 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.113424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.099422 restraints weight = 15874.668| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.86 r_work: 0.3360 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 8384 Z= 0.155 Angle : 0.580 8.189 11404 Z= 0.304 Chirality : 0.043 0.139 1335 Planarity : 0.004 0.047 1432 Dihedral : 5.357 57.923 1189 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.52 % Allowed : 23.07 % Favored : 72.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 aren not related in a simple way. whole: 0.90 (0.26), residues: 1064 helix: 2.05 (0.28), residues: 347 sheet: 0.86 (0.31), residues: 262 loop : -0.70 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 134 TYR 0.017 0.001 TYR E 178 PHE 0.017 0.002 PHE A 255 TRP 0.017 0.002 TRP C 82 HIS 0.006 0.002 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 8382) covalent geometry : angle 0.57891 (11400) SS BOND : bond 0.00546 ( 2) SS BOND : angle 2.01819 ( 4) hydrogen bonds : bond 0.04790 ( 403) hydrogen bonds : angle 4.32319 ( 1125) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 100 time to evaluate : 0.241 Fit side-chains REVERT: A 255 PHE cc_start: 0.7789 (t80) cc_final: 0.6972 (m-80) REVERT: A 341 ILE cc_start: 0.7357 (mm) cc_final: 0.6839 (tp) REVERT: B 24 ARG cc_start: 0.8285 (ttm110) cc_final: 0.7685 (ttp-110) REVERT: C 23 LYS cc_start: 0.8162 (OUTLIER) cc_final: 0.7649 (tmmm) REVERT: C 35 ASN cc_start: 0.8082 (t0) cc_final: 0.7845 (t0) REVERT: C 156 GLN cc_start: 0.8893 (mt0) cc_final: 0.8614 (mt0) REVERT: C 217 MET cc_start: 0.8472 (OUTLIER) cc_final: 0.7577 (ppp) REVERT: E 11 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7757 (tt) outliers start: 38 outliers final: 29 residues processed: 133 average time/residue: 0.5145 time to fit residues: 73.2777 Evaluate side-chains 130 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 98 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 336 TRP Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain B residue 73 LYS Chi-restraints excluded: chain B residue 115 TYR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 237 GLN Chi-restraints excluded: chain C residue 23 LYS Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 159 ASN Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain E residue 202 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 82 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 chunk 23 optimal weight: 0.0470 chunk 79 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 88 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 268 ASN E 159 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.113864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.100076 restraints weight = 15699.069| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 1.81 r_work: 0.3375 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 8384 Z= 0.141 Angle : 0.556 8.026 11404 Z= 0.293 Chirality : 0.043 0.136 1335 Planarity : 0.004 0.046 1432 Dihedral : 5.291 57.890 1189 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.99 % Allowed : 22.59 % Favored : 72.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 aren not related in a simple way. whole: 0.91 (0.26), residues: 1064 helix: 2.07 (0.28), residues: 349 sheet: 0.84 (0.31), residues: 262 loop : -0.73 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 31 TYR 0.016 0.001 TYR E 178 PHE 0.016 0.002 PHE A 255 TRP 0.016 0.002 TRP C 82 HIS 0.006 0.001 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 8382) covalent geometry : angle 0.55474 (11400) SS BOND : bond 0.00528 ( 2) SS BOND : angle 2.02107 ( 4) hydrogen bonds : bond 0.04605 ( 403) hydrogen bonds : angle 4.28647 ( 1125) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 100 time to evaluate : 0.314 Fit side-chains REVERT: A 255 PHE cc_start: 0.7789 (t80) cc_final: 0.6980 (m-80) REVERT: A 341 ILE cc_start: 0.7359 (mm) cc_final: 0.6855 (tp) REVERT: B 24 ARG cc_start: 0.8269 (ttm110) cc_final: 0.7681 (ttp-110) REVERT: C 18 ILE cc_start: 0.6446 (OUTLIER) cc_final: 0.6129 (tp) REVERT: C 23 LYS cc_start: 0.8163 (OUTLIER) cc_final: 0.7636 (tmmm) REVERT: C 35 ASN cc_start: 0.8031 (t0) cc_final: 0.7820 (t0) REVERT: C 156 GLN cc_start: 0.8869 (mt0) cc_final: 0.8655 (mt0) REVERT: C 217 MET cc_start: 0.8452 (OUTLIER) cc_final: 0.7605 (ppp) REVERT: E 11 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7745 (tt) outliers start: 42 outliers final: 29 residues processed: 136 average time/residue: 0.5109 time to fit residues: 74.6409 Evaluate side-chains 130 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 97 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 336 TRP Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain B residue 73 LYS Chi-restraints excluded: chain B residue 115 TYR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 237 GLN Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 23 LYS Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 159 ASN Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain E residue 202 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 94 optimal weight: 0.0770 chunk 41 optimal weight: 0.8980 chunk 105 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 83 optimal weight: 0.0270 chunk 82 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 159 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.114288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.100347 restraints weight = 15730.222| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 1.84 r_work: 0.3376 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 8384 Z= 0.128 Angle : 0.546 9.167 11404 Z= 0.288 Chirality : 0.042 0.134 1335 Planarity : 0.004 0.046 1432 Dihedral : 5.196 57.806 1189 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 4.28 % Allowed : 23.54 % Favored : 72.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 aren not related in a simple way. whole: 0.96 (0.26), residues: 1064 helix: 2.14 (0.29), residues: 349 sheet: 0.91 (0.31), residues: 260 loop : -0.74 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 134 TYR 0.015 0.001 TYR E 178 PHE 0.015 0.001 PHE A 255 TRP 0.015 0.002 TRP C 82 HIS 0.005 0.001 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 8382) covalent geometry : angle 0.54475 (11400) SS BOND : bond 0.00488 ( 2) SS BOND : angle 1.95904 ( 4) hydrogen bonds : bond 0.04382 ( 403) hydrogen bonds : angle 4.24484 ( 1125) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 99 time to evaluate : 0.349 Fit side-chains REVERT: A 255 PHE cc_start: 0.7799 (t80) cc_final: 0.6967 (m-80) REVERT: A 341 ILE cc_start: 0.7295 (mm) cc_final: 0.6814 (tp) REVERT: B 24 ARG cc_start: 0.8253 (ttm110) cc_final: 0.7656 (ttp-110) REVERT: B 166 GLU cc_start: 0.6308 (mm-30) cc_final: 0.5810 (pt0) REVERT: C 18 ILE cc_start: 0.6408 (OUTLIER) cc_final: 0.6093 (tp) REVERT: C 23 LYS cc_start: 0.8135 (OUTLIER) cc_final: 0.7614 (tmmm) REVERT: C 35 ASN cc_start: 0.8070 (t0) cc_final: 0.7858 (t0) REVERT: C 132 ASN cc_start: 0.8235 (m-40) cc_final: 0.7664 (p0) REVERT: C 156 GLN cc_start: 0.8866 (mt0) cc_final: 0.8614 (mt0) REVERT: C 217 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.7610 (ppp) REVERT: E 11 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7716 (tt) outliers start: 36 outliers final: 26 residues processed: 129 average time/residue: 0.5366 time to fit residues: 74.1406 Evaluate side-chains 128 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 98 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain B residue 73 LYS Chi-restraints excluded: chain B residue 115 TYR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 237 GLN Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 23 LYS Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 159 ASN Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain E residue 202 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 21 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 0 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 33 optimal weight: 0.0980 chunk 5 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 103 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 340 ASN E 159 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.113467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.099646 restraints weight = 15676.213| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 1.80 r_work: 0.3363 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 8384 Z= 0.161 Angle : 0.578 8.072 11404 Z= 0.304 Chirality : 0.044 0.163 1335 Planarity : 0.004 0.046 1432 Dihedral : 5.245 57.753 1188 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.92 % Allowed : 24.14 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 aren not related in a simple way. whole: 0.86 (0.26), residues: 1064 helix: 2.05 (0.28), residues: 349 sheet: 0.75 (0.30), residues: 267 loop : -0.73 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 31 TYR 0.018 0.002 TYR E 178 PHE 0.016 0.002 PHE A 255 TRP 0.017 0.002 TRP C 82 HIS 0.006 0.002 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 8382) covalent geometry : angle 0.57713 (11400) SS BOND : bond 0.00559 ( 2) SS BOND : angle 2.07532 ( 4) hydrogen bonds : bond 0.04776 ( 403) hydrogen bonds : angle 4.34146 ( 1125) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 95 time to evaluate : 0.217 Fit side-chains REVERT: A 255 PHE cc_start: 0.7800 (t80) cc_final: 0.6983 (m-80) REVERT: A 341 ILE cc_start: 0.7413 (mm) cc_final: 0.6909 (tp) REVERT: B 24 ARG cc_start: 0.8272 (ttm110) cc_final: 0.7684 (ttp-110) REVERT: B 166 GLU cc_start: 0.6288 (mm-30) cc_final: 0.5797 (pt0) REVERT: C 18 ILE cc_start: 0.6435 (OUTLIER) cc_final: 0.6112 (tp) REVERT: C 23 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7687 (tmmm) REVERT: C 35 ASN cc_start: 0.8066 (t0) cc_final: 0.7861 (t0) REVERT: C 134 ARG cc_start: 0.7418 (ptt-90) cc_final: 0.7173 (ptt-90) REVERT: C 156 GLN cc_start: 0.8873 (mt0) cc_final: 0.8573 (mt0) REVERT: C 217 MET cc_start: 0.8455 (OUTLIER) cc_final: 0.7616 (ppp) REVERT: E 11 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7706 (tt) outliers start: 33 outliers final: 27 residues processed: 121 average time/residue: 0.5449 time to fit residues: 70.4538 Evaluate side-chains 126 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 95 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain B residue 73 LYS Chi-restraints excluded: chain B residue 115 TYR Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 237 GLN Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 23 LYS Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 87 ARG Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 150 SER Chi-restraints excluded: chain E residue 159 ASN Chi-restraints excluded: chain E residue 172 SER Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain E residue 202 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 22 optimal weight: 0.2980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 103 optimal weight: 0.0970 chunk 46 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 268 ASN E 159 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.114235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.100364 restraints weight = 15824.633| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 1.82 r_work: 0.3378 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 8384 Z= 0.131 Angle : 0.548 8.607 11404 Z= 0.289 Chirality : 0.042 0.161 1335 Planarity : 0.004 0.046 1432 Dihedral : 5.152 57.743 1188 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.92 % Allowed : 24.14 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 aren not related in a simple way. whole: 0.94 (0.26), residues: 1064 helix: 2.15 (0.28), residues: 349 sheet: 0.80 (0.31), residues: 265 loop : -0.71 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 31 TYR 0.015 0.001 TYR E 178 PHE 0.015 0.001 PHE A 255 TRP 0.015 0.002 TRP C 82 HIS 0.005 0.001 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 8382) covalent geometry : angle 0.54696 (11400) SS BOND : bond 0.00517 ( 2) SS BOND : angle 1.96638 ( 4) hydrogen bonds : bond 0.04410 ( 403) hydrogen bonds : angle 4.25789 ( 1125) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3225.95 seconds wall clock time: 55 minutes 46.27 seconds (3346.27 seconds total)