Starting phenix.real_space_refine on Sat Aug 23 07:51:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ied_35380/08_2025/8ied_35380.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ied_35380/08_2025/8ied_35380.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ied_35380/08_2025/8ied_35380.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ied_35380/08_2025/8ied_35380.map" model { file = "/net/cci-nas-00/data/ceres_data/8ied_35380/08_2025/8ied_35380.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ied_35380/08_2025/8ied_35380.cif" } resolution = 3.33 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= -0.002 sd= 0.111 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 79 5.16 5 C 6888 2.51 5 N 1770 2.21 5 O 1955 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s 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: 10694 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2062 Classifications: {'peptide': 269} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 9, 'TRANS': 259} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 2250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2250 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 10, 'TRANS': 278} Chain breaks: 1 Chain: "C" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1659 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 4, 'TRANS': 210} Chain breaks: 1 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'ASP:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "D" Number of atoms: 2527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2527 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 3, 'GLN:plan1': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 53 Chain: "N" Number of atoms: 1707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1707 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 7, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "Y" Number of atoms: 385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 385 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "B" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Time building chain proxies: 2.26, per 1000 atoms: 0.21 Number of scatterers: 10694 At special positions: 0 Unit cell: (94.77, 119.88, 144.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 79 16.00 P 2 15.00 O 1955 8.00 N 1770 7.00 C 6888 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 191 " - pdb=" SG CYS A 216 " distance=2.03 Simple disulfide: pdb=" SG CYS B 191 " - pdb=" SG CYS B 216 " distance=2.03 Simple disulfide: pdb=" SG CYS N 147 " - pdb=" SG CYS N 217 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.96 Conformation dependent library (CDL) restraints added in 452.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2594 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 14 sheets defined 41.9% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 46 through 74 Processing helix chain 'A' and resid 77 through 82 Processing helix chain 'A' and resid 84 through 105 removed outlier: 3.540A pdb=" N ASN A 88 " --> pdb=" O SER A 84 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE A 89 " --> pdb=" O PRO A 85 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N VAL A 90 " --> pdb=" O ASN A 86 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR A 91 " --> pdb=" O LEU A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 151 Proline residue: A 137 - end of helix Processing helix chain 'A' and resid 161 through 187 removed outlier: 3.645A pdb=" N LEU A 165 " --> pdb=" O LYS A 161 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TRP A 183 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP A 187 " --> pdb=" O TRP A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 246 removed outlier: 3.848A pdb=" N TRP A 224 " --> pdb=" O TYR A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 280 Processing helix chain 'A' and resid 284 through 317 Proline residue: A 310 - end of helix removed outlier: 3.660A pdb=" N ALA A 317 " --> pdb=" O LYS A 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 74 Processing helix chain 'B' and resid 77 through 83 Processing helix chain 'B' and resid 84 through 105 removed outlier: 3.543A pdb=" N VAL B 90 " --> pdb=" O ASN B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 150 removed outlier: 3.870A pdb=" N MET B 126 " --> pdb=" O THR B 122 " (cutoff:3.500A) Proline residue: B 137 - end of helix Processing helix chain 'B' and resid 161 through 187 removed outlier: 3.755A pdb=" N LEU B 165 " --> pdb=" O LYS B 161 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP B 187 " --> pdb=" O TRP B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 246 removed outlier: 3.535A pdb=" N TRP B 224 " --> pdb=" O TYR B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 281 Processing helix chain 'B' and resid 284 through 315 Proline residue: B 310 - end of helix Processing helix chain 'B' and resid 316 through 319 Processing helix chain 'B' and resid 324 through 328 removed outlier: 3.552A pdb=" N ARG B 327 " --> pdb=" O THR B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 333 Processing helix chain 'C' and resid 6 through 31 Processing helix chain 'C' and resid 96 through 102 removed outlier: 3.563A pdb=" N GLU C 101 " --> pdb=" O HIS C 98 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ASP C 102 " --> pdb=" O CYS C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 129 Processing helix chain 'C' and resid 130 through 135 removed outlier: 6.292A pdb=" N PHE C 133 " --> pdb=" O ASN C 130 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE C 135 " --> pdb=" O LYS C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 153 Processing helix chain 'C' and resid 170 through 184 Processing helix chain 'C' and resid 205 through 225 Processing helix chain 'D' and resid 4 through 25 Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.581A pdb=" N SER N 31 " --> pdb=" O ALA N 28 " (cutoff:3.500A) Processing helix chain 'N' and resid 53 through 56 removed outlier: 3.722A pdb=" N GLY N 56 " --> pdb=" O SER N 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 53 through 56' Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.699A pdb=" N ASP N 90 " --> pdb=" O THR N 87 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR N 91 " --> pdb=" O SER N 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 87 through 91' Processing helix chain 'Y' and resid 9 through 24 removed outlier: 3.504A pdb=" N MET Y 21 " --> pdb=" O GLU Y 17 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU Y 22 " --> pdb=" O GLN Y 18 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA Y 23 " --> pdb=" O LEU Y 19 " (cutoff:3.500A) Processing helix chain 'Y' and resid 34 through 44 removed outlier: 3.592A pdb=" N MET Y 38 " --> pdb=" O ALA Y 34 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU Y 42 " --> pdb=" O MET Y 38 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 206 through 216 removed outlier: 4.040A pdb=" N PHE A 215 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU A 192 " --> pdb=" O PHE A 215 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU A 195 " --> pdb=" O MET B 199 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU B 195 " --> pdb=" O MET A 199 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL A 201 " --> pdb=" O GLN B 193 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN B 193 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLN B 190 " --> pdb=" O ALA B 217 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE B 215 " --> pdb=" O LEU B 192 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 54 through 55 removed outlier: 3.987A pdb=" N ALA C 105 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ILE C 139 " --> pdb=" O TYR C 194 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N HIS C 196 " --> pdb=" O ILE C 139 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU C 141 " --> pdb=" O HIS C 196 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 49 through 51 removed outlier: 3.750A pdb=" N VAL D 327 " --> pdb=" O TRP D 339 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 58 through 63 removed outlier: 3.561A pdb=" N ALA D 60 " --> pdb=" O ALA D 73 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA D 73 " --> pdb=" O ALA D 60 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LYS D 78 " --> pdb=" O SER D 74 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N LEU D 79 " --> pdb=" O ALA D 92 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ALA D 92 " --> pdb=" O LEU D 79 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ILE D 81 " --> pdb=" O VAL D 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 100 through 105 removed outlier: 6.988A pdb=" N GLY D 115 " --> pdb=" O MET D 101 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N CYS D 103 " --> pdb=" O ALA D 113 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ALA D 113 " --> pdb=" O CYS D 103 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N TYR D 105 " --> pdb=" O TYR D 111 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N TYR D 111 " --> pdb=" O TYR D 105 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLY D 116 " --> pdb=" O ILE D 120 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ILE D 120 " --> pdb=" O GLY D 116 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ARG D 137 " --> pdb=" O ILE D 123 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N ASN D 125 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL D 135 " --> pdb=" O ASN D 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 146 through 151 removed outlier: 6.648A pdb=" N SER D 160 " --> pdb=" O SER D 147 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N CYS D 149 " --> pdb=" O VAL D 158 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL D 158 " --> pdb=" O CYS D 149 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N PHE D 151 " --> pdb=" O GLN D 156 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N GLN D 156 " --> pdb=" O PHE D 151 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE D 157 " --> pdb=" O TRP D 169 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N THR D 165 " --> pdb=" O SER D 161 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N CYS D 166 " --> pdb=" O PHE D 180 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ASP D 170 " --> pdb=" O GLN D 176 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N GLN D 176 " --> pdb=" O ASP D 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 191 through 192 removed outlier: 4.021A pdb=" N SER D 207 " --> pdb=" O ALA D 203 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ALA D 208 " --> pdb=" O THR D 221 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N THR D 221 " --> pdb=" O ALA D 208 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LEU D 210 " --> pdb=" O ARG D 219 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 229 through 234 removed outlier: 3.578A pdb=" N CYS D 233 " --> pdb=" O ALA D 242 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER D 245 " --> pdb=" O THR D 249 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N THR D 249 " --> pdb=" O SER D 245 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N CYS D 250 " --> pdb=" O TYR D 264 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N MET D 262 " --> pdb=" O LEU D 252 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ASP D 254 " --> pdb=" O GLU D 260 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N GLU D 260 " --> pdb=" O ASP D 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 276 through 278 removed outlier: 3.583A pdb=" N LEU D 285 " --> pdb=" O TRP D 297 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASN D 293 " --> pdb=" O TYR D 289 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLY D 306 " --> pdb=" O VAL D 296 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'N' and resid 10 through 12 removed outlier: 5.822A pdb=" N GLY N 10 " --> pdb=" O THR N 118 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 10 through 12 removed outlier: 5.822A pdb=" N GLY N 10 " --> pdb=" O THR N 118 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N PHE N 110 " --> pdb=" O ARG N 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 142 through 147 removed outlier: 3.871A pdb=" N PHE N 200 " --> pdb=" O CYS N 147 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER N 192 " --> pdb=" O THR N 203 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 182 through 183 removed outlier: 6.529A pdb=" N TRP N 164 " --> pdb=" O LEU N 176 " (cutoff:3.500A) 590 hydrogen bonds defined for protein. 1695 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: 1.79 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1677 1.32 - 1.44: 2970 1.44 - 1.57: 6149 1.57 - 1.70: 4 1.70 - 1.83: 112 Bond restraints: 10912 Sorted by residual: bond pdb=" C39 PC1 A 601 " pdb=" C3A PC1 A 601 " ideal model delta sigma weight residual 1.524 1.318 0.206 2.00e-02 2.50e+03 1.06e+02 bond pdb=" C39 PC1 B 601 " pdb=" C3A PC1 B 601 " ideal model delta sigma weight residual 1.524 1.320 0.204 2.00e-02 2.50e+03 1.04e+02 bond pdb=" C31 PC1 B 601 " pdb=" O31 PC1 B 601 " ideal model delta sigma weight residual 1.330 1.426 -0.096 2.00e-02 2.50e+03 2.30e+01 bond pdb=" C31 PC1 A 601 " pdb=" O31 PC1 A 601 " ideal model delta sigma weight residual 1.330 1.418 -0.088 2.00e-02 2.50e+03 1.95e+01 bond pdb=" C2 PC1 B 601 " pdb=" O21 PC1 B 601 " ideal model delta sigma weight residual 1.430 1.380 0.050 2.00e-02 2.50e+03 6.19e+00 ... (remaining 10907 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.98: 14651 2.98 - 5.95: 136 5.95 - 8.93: 28 8.93 - 11.91: 1 11.91 - 14.89: 2 Bond angle restraints: 14818 Sorted by residual: angle pdb=" O12 PC1 B 601 " pdb=" P PC1 B 601 " pdb=" O14 PC1 B 601 " ideal model delta sigma weight residual 123.67 108.78 14.89 3.00e+00 1.11e-01 2.46e+01 angle pdb=" O12 PC1 A 601 " pdb=" P PC1 A 601 " pdb=" O14 PC1 A 601 " ideal model delta sigma weight residual 123.67 109.52 14.15 3.00e+00 1.11e-01 2.22e+01 angle pdb=" C PRO C 157 " pdb=" N LEU C 158 " pdb=" CA LEU C 158 " ideal model delta sigma weight residual 121.54 129.45 -7.91 1.91e+00 2.74e-01 1.71e+01 angle pdb=" C ASP C 85 " pdb=" N VAL C 86 " pdb=" CA VAL C 86 " ideal model delta sigma weight residual 121.97 129.03 -7.06 1.80e+00 3.09e-01 1.54e+01 angle pdb=" N PRO A 252 " pdb=" CA PRO A 252 " pdb=" C PRO A 252 " ideal model delta sigma weight residual 110.70 114.71 -4.01 1.22e+00 6.72e-01 1.08e+01 ... (remaining 14813 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 5821 17.72 - 35.43: 495 35.43 - 53.15: 98 53.15 - 70.86: 16 70.86 - 88.58: 12 Dihedral angle restraints: 6442 sinusoidal: 2419 harmonic: 4023 Sorted by residual: dihedral pdb=" CB CYS N 147 " pdb=" SG CYS N 147 " pdb=" SG CYS N 217 " pdb=" CB CYS N 217 " ideal model delta sinusoidal sigma weight residual 93.00 -178.42 -88.58 1 1.00e+01 1.00e-02 9.36e+01 dihedral pdb=" CA GLN N 130 " pdb=" C GLN N 130 " pdb=" N ALA N 131 " pdb=" CA ALA N 131 " ideal model delta harmonic sigma weight residual 180.00 159.33 20.67 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA ILE B 307 " pdb=" C ILE B 307 " pdb=" N PHE B 308 " pdb=" CA PHE B 308 " ideal model delta harmonic sigma weight residual -180.00 -160.91 -19.09 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 6439 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1523 0.071 - 0.141: 217 0.141 - 0.212: 6 0.212 - 0.283: 2 0.283 - 0.353: 1 Chirality restraints: 1749 Sorted by residual: chirality pdb=" CB VAL C 86 " pdb=" CA VAL C 86 " pdb=" CG1 VAL C 86 " pdb=" CG2 VAL C 86 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.12e+00 chirality pdb=" CB ILE A 189 " pdb=" CA ILE A 189 " pdb=" CG1 ILE A 189 " pdb=" CG2 ILE A 189 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CG LEU A 92 " pdb=" CB LEU A 92 " pdb=" CD1 LEU A 92 " pdb=" CD2 LEU A 92 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 1746 not shown) Planarity restraints: 1829 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 252 " -0.046 5.00e-02 4.00e+02 6.92e-02 7.66e+00 pdb=" N PRO B 253 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO B 253 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 253 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 252 " -0.044 5.00e-02 4.00e+02 6.50e-02 6.76e+00 pdb=" N PRO A 253 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 253 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 253 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE D 235 " -0.034 5.00e-02 4.00e+02 5.18e-02 4.30e+00 pdb=" N PRO D 236 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO D 236 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 236 " -0.029 5.00e-02 4.00e+02 ... (remaining 1826 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 379 2.71 - 3.26: 10148 3.26 - 3.81: 17525 3.81 - 4.35: 20751 4.35 - 4.90: 36604 Nonbonded interactions: 85407 Sorted by model distance: nonbonded pdb=" OE2 GLU D 260 " pdb=" OG1 THR D 263 " model vdw 2.166 3.040 nonbonded pdb=" O VAL A 298 " pdb=" OG1 THR A 302 " model vdw 2.198 3.040 nonbonded pdb=" OH TYR C 194 " pdb=" OD2 ASP C 215 " model vdw 2.238 3.040 nonbonded pdb=" OG SER N 149 " pdb=" O LYS N 151 " model vdw 2.247 3.040 nonbonded pdb=" O TYR B 146 " pdb=" OG1 THR B 150 " model vdw 2.254 3.040 ... (remaining 85402 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 44 through 110 or resid 115 through 601)) selection = (chain 'B' and (resid 44 through 110 or resid 115 through 150 or (resid 151 thro \ ugh 152 and (name N or name CA or name C or name O or name CB )) or resid 153 th \ rough 154 or (resid 155 and (name N or name CA or name C or name O or name CB )) \ or resid 159 through 318 or resid 601)) } 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: 4.670 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: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.970 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 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 : 0.006 0.206 10915 Z= 0.278 Angle : 0.772 14.886 14824 Z= 0.381 Chirality : 0.048 0.353 1749 Planarity : 0.005 0.069 1829 Dihedral : 14.177 85.674 3839 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % 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 aren not related in a simple way. whole: -0.47 (0.22), residues: 1374 helix: 1.10 (0.21), residues: 536 sheet: -0.52 (0.31), residues: 311 loop : -1.64 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 144 TYR 0.022 0.002 TYR N 223 PHE 0.023 0.002 PHE A 306 TRP 0.029 0.002 TRP A 229 HIS 0.006 0.001 HIS N 220 Details of bonding type rmsd covalent geometry : bond 0.00598 (10912) covalent geometry : angle 0.77142 (14818) SS BOND : bond 0.00260 ( 3) SS BOND : angle 1.51662 ( 6) hydrogen bonds : bond 0.16461 ( 588) hydrogen bonds : angle 6.71757 ( 1695) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 LYS cc_start: 0.8194 (tttp) cc_final: 0.7651 (ttpt) REVERT: B 125 SER cc_start: 0.9036 (t) cc_final: 0.8750 (p) REVERT: B 261 MET cc_start: 0.7754 (mmm) cc_final: 0.7458 (mmm) outliers start: 0 outliers final: 0 residues processed: 270 average time/residue: 0.1125 time to fit residues: 43.1141 Evaluate side-chains 175 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.2980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 GLN ** C 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 75 GLN D 225 HIS D 237 ASN N 77 ASN N 130 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.202727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.160553 restraints weight = 12521.178| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 2.83 r_work: 0.3615 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10915 Z= 0.188 Angle : 0.623 8.376 14824 Z= 0.329 Chirality : 0.044 0.188 1749 Planarity : 0.005 0.061 1829 Dihedral : 8.930 72.066 1572 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 1.84 % Allowed : 9.04 % Favored : 89.11 % 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 aren not related in a simple way. whole: 0.35 (0.24), residues: 1374 helix: 2.13 (0.22), residues: 543 sheet: -0.35 (0.31), residues: 305 loop : -1.48 (0.27), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 137 TYR 0.024 0.002 TYR N 60 PHE 0.022 0.002 PHE B 66 TRP 0.018 0.002 TRP D 211 HIS 0.004 0.001 HIS N 35 Details of bonding type rmsd covalent geometry : bond 0.00444 (10912) covalent geometry : angle 0.62323 (14818) SS BOND : bond 0.01530 ( 3) SS BOND : angle 0.90676 ( 6) hydrogen bonds : bond 0.04339 ( 588) hydrogen bonds : angle 5.05781 ( 1695) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 204 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 PHE cc_start: 0.7690 (t80) cc_final: 0.7480 (t80) REVERT: A 174 MET cc_start: 0.7740 (ptm) cc_final: 0.7228 (ppp) REVERT: B 81 LYS cc_start: 0.7790 (tttp) cc_final: 0.7139 (ttpt) REVERT: B 125 SER cc_start: 0.8973 (t) cc_final: 0.8722 (p) REVERT: B 279 ARG cc_start: 0.8521 (ttm-80) cc_final: 0.8285 (ttm170) REVERT: C 82 ARG cc_start: 0.7863 (mtp180) cc_final: 0.7644 (mtp85) REVERT: C 136 ASP cc_start: 0.8009 (t70) cc_final: 0.7729 (t0) REVERT: C 169 ASN cc_start: 0.7404 (m-40) cc_final: 0.6731 (t0) REVERT: C 202 ASP cc_start: 0.7770 (t0) cc_final: 0.7480 (t0) REVERT: D 130 GLU cc_start: 0.7540 (mt-10) cc_final: 0.7017 (mp0) REVERT: D 156 GLN cc_start: 0.7808 (mt0) cc_final: 0.7544 (mt0) REVERT: D 175 GLN cc_start: 0.6657 (mm-40) cc_final: 0.6342 (mm110) REVERT: Y 38 MET cc_start: 0.5833 (mmm) cc_final: 0.5391 (ptt) outliers start: 21 outliers final: 15 residues processed: 216 average time/residue: 0.1157 time to fit residues: 35.1459 Evaluate side-chains 188 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 173 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain N residue 126 ILE Chi-restraints excluded: chain N residue 135 VAL Chi-restraints excluded: chain N residue 192 SER Chi-restraints excluded: chain N residue 212 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 15 optimal weight: 0.2980 chunk 97 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 118 optimal weight: 0.7980 chunk 53 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 113 optimal weight: 0.7980 chunk 129 optimal weight: 1.9990 chunk 117 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.200270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.163624 restraints weight = 12879.461| |-----------------------------------------------------------------------------| r_work (start): 0.3945 rms_B_bonded: 2.62 r_work: 0.3716 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10915 Z= 0.146 Angle : 0.560 6.701 14824 Z= 0.298 Chirality : 0.043 0.197 1749 Planarity : 0.005 0.066 1829 Dihedral : 8.518 73.299 1572 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.67 % Allowed : 12.82 % Favored : 85.51 % 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 aren not related in a simple way. whole: 0.62 (0.24), residues: 1374 helix: 2.45 (0.22), residues: 545 sheet: -0.28 (0.31), residues: 306 loop : -1.42 (0.28), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 251 TYR 0.022 0.002 TYR N 223 PHE 0.013 0.001 PHE C 210 TRP 0.011 0.001 TRP D 211 HIS 0.004 0.001 HIS D 225 Details of bonding type rmsd covalent geometry : bond 0.00341 (10912) covalent geometry : angle 0.55949 (14818) SS BOND : bond 0.01599 ( 3) SS BOND : angle 1.09374 ( 6) hydrogen bonds : bond 0.03918 ( 588) hydrogen bonds : angle 4.71164 ( 1695) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 188 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 MET cc_start: 0.7331 (ptm) cc_final: 0.6966 (ppp) REVERT: B 81 LYS cc_start: 0.7955 (tttp) cc_final: 0.7381 (ttpt) REVERT: B 199 MET cc_start: 0.7326 (tmm) cc_final: 0.7105 (tpt) REVERT: C 136 ASP cc_start: 0.7962 (t70) cc_final: 0.7610 (t0) REVERT: C 169 ASN cc_start: 0.7153 (m-40) cc_final: 0.6711 (t0) REVERT: D 175 GLN cc_start: 0.6678 (mm-40) cc_final: 0.6462 (mm110) REVERT: D 339 TRP cc_start: 0.6764 (m100) cc_final: 0.6070 (m100) REVERT: N 64 VAL cc_start: 0.4130 (t) cc_final: 0.3816 (m) REVERT: Y 38 MET cc_start: 0.5624 (mmm) cc_final: 0.5409 (ptt) outliers start: 19 outliers final: 11 residues processed: 197 average time/residue: 0.1053 time to fit residues: 29.6526 Evaluate side-chains 182 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 171 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain N residue 126 ILE Chi-restraints excluded: chain N residue 190 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 116 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 53 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 112 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 chunk 12 optimal weight: 4.9990 chunk 45 optimal weight: 0.5980 chunk 70 optimal weight: 0.8980 chunk 10 optimal weight: 0.0000 chunk 8 optimal weight: 0.5980 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.201663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.160330 restraints weight = 12670.451| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 2.85 r_work: 0.3587 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10915 Z= 0.128 Angle : 0.540 8.399 14824 Z= 0.287 Chirality : 0.042 0.212 1749 Planarity : 0.004 0.064 1829 Dihedral : 8.019 71.622 1572 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.28 % Allowed : 12.91 % Favored : 84.81 % 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 aren not related in a simple way. whole: 0.61 (0.24), residues: 1374 helix: 2.44 (0.22), residues: 552 sheet: -0.34 (0.32), residues: 292 loop : -1.40 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 129 TYR 0.021 0.001 TYR N 223 PHE 0.012 0.001 PHE C 74 TRP 0.010 0.001 TRP D 169 HIS 0.005 0.001 HIS D 225 Details of bonding type rmsd covalent geometry : bond 0.00297 (10912) covalent geometry : angle 0.53934 (14818) SS BOND : bond 0.00491 ( 3) SS BOND : angle 0.92986 ( 6) hydrogen bonds : bond 0.03670 ( 588) hydrogen bonds : angle 4.51325 ( 1695) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 178 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 174 MET cc_start: 0.7727 (ptm) cc_final: 0.7193 (ppp) REVERT: B 81 LYS cc_start: 0.7615 (tttp) cc_final: 0.6924 (ttpt) REVERT: C 136 ASP cc_start: 0.8181 (t70) cc_final: 0.7873 (t0) REVERT: C 169 ASN cc_start: 0.7414 (m-40) cc_final: 0.6781 (t0) REVERT: D 130 GLU cc_start: 0.7670 (mp0) cc_final: 0.7265 (mp0) REVERT: D 175 GLN cc_start: 0.6672 (mm-40) cc_final: 0.6333 (mm110) REVERT: D 260 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7317 (tt0) REVERT: D 283 ARG cc_start: 0.5665 (mmm160) cc_final: 0.5099 (mmm160) REVERT: D 339 TRP cc_start: 0.6828 (m100) cc_final: 0.5684 (m100) REVERT: N 64 VAL cc_start: 0.4240 (t) cc_final: 0.4026 (p) REVERT: Y 21 MET cc_start: 0.6553 (tpp) cc_final: 0.6052 (tmm) REVERT: Y 38 MET cc_start: 0.5914 (mmm) cc_final: 0.5582 (ptt) outliers start: 26 outliers final: 17 residues processed: 195 average time/residue: 0.1126 time to fit residues: 31.2451 Evaluate side-chains 185 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 167 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 181 MET Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain N residue 126 ILE Chi-restraints excluded: chain N residue 190 ARG Chi-restraints excluded: chain N residue 192 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 102 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 87 optimal weight: 0.2980 chunk 9 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 HIS C 196 HIS D 75 GLN N 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.200164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.158749 restraints weight = 12687.810| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 2.79 r_work: 0.3590 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10915 Z= 0.144 Angle : 0.566 7.840 14824 Z= 0.297 Chirality : 0.043 0.231 1749 Planarity : 0.004 0.064 1829 Dihedral : 7.750 70.876 1572 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.11 % Allowed : 13.96 % Favored : 83.93 % 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 aren not related in a simple way. whole: 0.55 (0.24), residues: 1374 helix: 2.43 (0.22), residues: 551 sheet: -0.38 (0.31), residues: 308 loop : -1.49 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 219 TYR 0.021 0.002 TYR N 223 PHE 0.013 0.001 PHE C 74 TRP 0.011 0.001 TRP D 211 HIS 0.005 0.001 HIS D 225 Details of bonding type rmsd covalent geometry : bond 0.00341 (10912) covalent geometry : angle 0.56624 (14818) SS BOND : bond 0.00181 ( 3) SS BOND : angle 0.91133 ( 6) hydrogen bonds : bond 0.03662 ( 588) hydrogen bonds : angle 4.44663 ( 1695) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 182 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 174 MET cc_start: 0.7737 (ptm) cc_final: 0.7185 (ppp) REVERT: A 197 VAL cc_start: 0.8789 (OUTLIER) cc_final: 0.8516 (p) REVERT: A 279 ARG cc_start: 0.8221 (ttm-80) cc_final: 0.7949 (ttt90) REVERT: B 81 LYS cc_start: 0.7638 (tttp) cc_final: 0.6963 (ttpt) REVERT: C 136 ASP cc_start: 0.8251 (t70) cc_final: 0.7903 (t0) REVERT: C 169 ASN cc_start: 0.7380 (m-40) cc_final: 0.6703 (t0) REVERT: C 202 ASP cc_start: 0.7629 (t0) cc_final: 0.7396 (t0) REVERT: D 32 GLN cc_start: 0.4864 (OUTLIER) cc_final: 0.4407 (tp40) REVERT: D 130 GLU cc_start: 0.7709 (mp0) cc_final: 0.7134 (mp0) REVERT: D 155 ASN cc_start: 0.7957 (t0) cc_final: 0.7721 (t0) REVERT: D 175 GLN cc_start: 0.6658 (mm-40) cc_final: 0.6333 (mm110) REVERT: D 339 TRP cc_start: 0.6844 (m100) cc_final: 0.5632 (m100) REVERT: N 82 GLN cc_start: 0.6148 (tp40) cc_final: 0.5738 (tp40) REVERT: N 218 MET cc_start: 0.7778 (ttp) cc_final: 0.7572 (ttp) REVERT: Y 21 MET cc_start: 0.6528 (tpp) cc_final: 0.6041 (tmm) REVERT: Y 38 MET cc_start: 0.6007 (mmm) cc_final: 0.5617 (ptt) outliers start: 24 outliers final: 16 residues processed: 199 average time/residue: 0.1017 time to fit residues: 29.1410 Evaluate side-chains 185 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 167 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 73 HIS Chi-restraints excluded: chain C residue 126 ASP Chi-restraints excluded: chain D residue 32 GLN Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain N residue 126 ILE Chi-restraints excluded: chain N residue 190 ARG Chi-restraints excluded: chain N residue 192 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 47 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 107 optimal weight: 9.9990 chunk 96 optimal weight: 0.0870 chunk 41 optimal weight: 9.9990 chunk 63 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 GLN ** C 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.199514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.157995 restraints weight = 12783.764| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 2.83 r_work: 0.3602 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10915 Z= 0.141 Angle : 0.552 7.867 14824 Z= 0.291 Chirality : 0.042 0.224 1749 Planarity : 0.004 0.063 1829 Dihedral : 7.651 70.756 1572 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.07 % Allowed : 13.87 % Favored : 83.06 % 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 aren not related in a simple way. whole: 0.57 (0.24), residues: 1374 helix: 2.50 (0.22), residues: 548 sheet: -0.40 (0.31), residues: 306 loop : -1.51 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 137 TYR 0.022 0.001 TYR N 223 PHE 0.013 0.001 PHE C 74 TRP 0.010 0.001 TRP D 63 HIS 0.012 0.001 HIS C 73 Details of bonding type rmsd covalent geometry : bond 0.00333 (10912) covalent geometry : angle 0.55161 (14818) SS BOND : bond 0.00204 ( 3) SS BOND : angle 0.97869 ( 6) hydrogen bonds : bond 0.03611 ( 588) hydrogen bonds : angle 4.39573 ( 1695) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 180 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 174 MET cc_start: 0.7720 (ptm) cc_final: 0.7176 (ppp) REVERT: A 197 VAL cc_start: 0.8768 (OUTLIER) cc_final: 0.8492 (p) REVERT: B 81 LYS cc_start: 0.7664 (tttp) cc_final: 0.6986 (ttpt) REVERT: C 35 LYS cc_start: 0.7864 (mtmm) cc_final: 0.7660 (mttp) REVERT: C 124 LEU cc_start: 0.7742 (tp) cc_final: 0.7539 (tp) REVERT: C 136 ASP cc_start: 0.8318 (t70) cc_final: 0.7952 (t0) REVERT: C 169 ASN cc_start: 0.7393 (m-40) cc_final: 0.6710 (t0) REVERT: C 202 ASP cc_start: 0.7726 (t0) cc_final: 0.7515 (t0) REVERT: D 32 GLN cc_start: 0.4680 (OUTLIER) cc_final: 0.4301 (tp40) REVERT: D 130 GLU cc_start: 0.7740 (mp0) cc_final: 0.7176 (mp0) REVERT: D 155 ASN cc_start: 0.7839 (t0) cc_final: 0.7560 (t0) REVERT: D 175 GLN cc_start: 0.6744 (mm-40) cc_final: 0.6403 (mm110) REVERT: D 243 THR cc_start: 0.6880 (OUTLIER) cc_final: 0.6630 (m) REVERT: D 339 TRP cc_start: 0.6903 (m100) cc_final: 0.5615 (m100) REVERT: N 130 GLN cc_start: 0.7309 (OUTLIER) cc_final: 0.6194 (pt0) REVERT: Y 21 MET cc_start: 0.6474 (tpp) cc_final: 0.6046 (tmm) REVERT: Y 38 MET cc_start: 0.6027 (mmm) cc_final: 0.5677 (ptt) outliers start: 35 outliers final: 21 residues processed: 205 average time/residue: 0.0969 time to fit residues: 28.5399 Evaluate side-chains 198 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 173 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 126 ASP Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain D residue 32 GLN Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 264 TYR Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain N residue 126 ILE Chi-restraints excluded: chain N residue 130 GLN Chi-restraints excluded: chain N residue 190 ARG Chi-restraints excluded: chain N residue 192 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 120 optimal weight: 6.9990 chunk 85 optimal weight: 0.8980 chunk 116 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 135 optimal weight: 0.0050 chunk 17 optimal weight: 0.4980 chunk 1 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 HIS C 196 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.199480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.157479 restraints weight = 12696.633| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 2.87 r_work: 0.3581 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10915 Z= 0.131 Angle : 0.543 8.165 14824 Z= 0.286 Chirality : 0.042 0.267 1749 Planarity : 0.004 0.062 1829 Dihedral : 7.502 72.176 1572 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.99 % Allowed : 14.66 % Favored : 82.35 % 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 aren not related in a simple way. whole: 0.62 (0.24), residues: 1374 helix: 2.48 (0.22), residues: 552 sheet: -0.25 (0.32), residues: 298 loop : -1.51 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 137 TYR 0.022 0.001 TYR N 223 PHE 0.016 0.001 PHE A 275 TRP 0.012 0.001 TRP D 63 HIS 0.003 0.001 HIS C 73 Details of bonding type rmsd covalent geometry : bond 0.00310 (10912) covalent geometry : angle 0.54309 (14818) SS BOND : bond 0.00319 ( 3) SS BOND : angle 1.00250 ( 6) hydrogen bonds : bond 0.03522 ( 588) hydrogen bonds : angle 4.33954 ( 1695) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 176 time to evaluate : 0.358 Fit side-chains revert: symmetry clash REVERT: A 174 MET cc_start: 0.7770 (ptm) cc_final: 0.7192 (ppp) REVERT: A 197 VAL cc_start: 0.8759 (OUTLIER) cc_final: 0.8478 (p) REVERT: B 62 LEU cc_start: 0.7238 (mt) cc_final: 0.6631 (tt) REVERT: C 136 ASP cc_start: 0.8363 (t70) cc_final: 0.8002 (t0) REVERT: C 169 ASN cc_start: 0.7407 (m-40) cc_final: 0.6616 (t0) REVERT: C 202 ASP cc_start: 0.7833 (t0) cc_final: 0.7603 (t0) REVERT: D 17 GLN cc_start: 0.8547 (tm-30) cc_final: 0.7867 (pt0) REVERT: D 32 GLN cc_start: 0.4659 (OUTLIER) cc_final: 0.4215 (tp-100) REVERT: D 130 GLU cc_start: 0.7743 (mp0) cc_final: 0.7154 (mp0) REVERT: D 155 ASN cc_start: 0.7819 (t0) cc_final: 0.7576 (t0) REVERT: D 175 GLN cc_start: 0.6795 (mm-40) cc_final: 0.6424 (mm110) REVERT: D 243 THR cc_start: 0.6811 (OUTLIER) cc_final: 0.6511 (m) REVERT: D 339 TRP cc_start: 0.6952 (m100) cc_final: 0.5585 (m100) REVERT: N 69 THR cc_start: 0.5608 (p) cc_final: 0.5374 (t) REVERT: N 130 GLN cc_start: 0.7238 (OUTLIER) cc_final: 0.6118 (pt0) REVERT: N 219 GLN cc_start: 0.7501 (pp30) cc_final: 0.6960 (pp30) REVERT: Y 21 MET cc_start: 0.6443 (tpp) cc_final: 0.6049 (tmm) REVERT: Y 38 MET cc_start: 0.6045 (mmm) cc_final: 0.5678 (ptt) outliers start: 34 outliers final: 24 residues processed: 198 average time/residue: 0.0973 time to fit residues: 28.0065 Evaluate side-chains 197 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 169 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 126 ASP Chi-restraints excluded: chain C residue 165 TYR Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain D residue 32 GLN Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 264 TYR Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain N residue 126 ILE Chi-restraints excluded: chain N residue 130 GLN Chi-restraints excluded: chain N residue 146 SER Chi-restraints excluded: chain N residue 166 LEU Chi-restraints excluded: chain N residue 190 ARG Chi-restraints excluded: chain N residue 192 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 111 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 129 optimal weight: 0.5980 chunk 47 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 121 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 48 optimal weight: 0.8980 chunk 128 optimal weight: 4.9990 chunk 93 optimal weight: 0.5980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.196849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.153645 restraints weight = 12766.598| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 2.93 r_work: 0.3574 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10915 Z= 0.167 Angle : 0.579 8.079 14824 Z= 0.304 Chirality : 0.043 0.232 1749 Planarity : 0.005 0.061 1829 Dihedral : 7.586 72.378 1572 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.99 % Allowed : 15.28 % Favored : 81.74 % 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 aren not related in a simple way. whole: 0.52 (0.24), residues: 1374 helix: 2.40 (0.22), residues: 549 sheet: -0.41 (0.31), residues: 310 loop : -1.48 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 304 TYR 0.024 0.002 TYR N 223 PHE 0.028 0.002 PHE N 200 TRP 0.013 0.001 TRP D 211 HIS 0.003 0.001 HIS C 73 Details of bonding type rmsd covalent geometry : bond 0.00403 (10912) covalent geometry : angle 0.57845 (14818) SS BOND : bond 0.00218 ( 3) SS BOND : angle 0.97668 ( 6) hydrogen bonds : bond 0.03713 ( 588) hydrogen bonds : angle 4.40020 ( 1695) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 174 time to evaluate : 0.330 Fit side-chains REVERT: A 174 MET cc_start: 0.7759 (ptm) cc_final: 0.7187 (ppp) REVERT: A 197 VAL cc_start: 0.8764 (OUTLIER) cc_final: 0.8483 (p) REVERT: B 62 LEU cc_start: 0.7265 (mt) cc_final: 0.6689 (tt) REVERT: C 136 ASP cc_start: 0.8475 (t70) cc_final: 0.8118 (t0) REVERT: C 169 ASN cc_start: 0.7435 (m-40) cc_final: 0.6613 (t0) REVERT: C 202 ASP cc_start: 0.7851 (t0) cc_final: 0.7644 (t0) REVERT: D 130 GLU cc_start: 0.7824 (mp0) cc_final: 0.7199 (mp0) REVERT: D 155 ASN cc_start: 0.7787 (t0) cc_final: 0.7550 (t0) REVERT: D 175 GLN cc_start: 0.6849 (mm-40) cc_final: 0.6485 (mm110) REVERT: D 243 THR cc_start: 0.6915 (OUTLIER) cc_final: 0.6691 (m) REVERT: D 339 TRP cc_start: 0.6948 (m100) cc_final: 0.5600 (m100) REVERT: N 69 THR cc_start: 0.5621 (p) cc_final: 0.5377 (t) REVERT: N 130 GLN cc_start: 0.7421 (OUTLIER) cc_final: 0.6349 (pt0) REVERT: N 219 GLN cc_start: 0.7504 (pp30) cc_final: 0.6887 (pp30) REVERT: Y 21 MET cc_start: 0.6552 (tpp) cc_final: 0.6116 (tmm) REVERT: Y 38 MET cc_start: 0.5984 (mmm) cc_final: 0.5654 (ptt) outliers start: 34 outliers final: 27 residues processed: 197 average time/residue: 0.0849 time to fit residues: 24.5437 Evaluate side-chains 196 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 166 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 165 TYR Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 228 TYR Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 264 TYR Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain N residue 126 ILE Chi-restraints excluded: chain N residue 130 GLN Chi-restraints excluded: chain N residue 146 SER Chi-restraints excluded: chain N residue 166 LEU Chi-restraints excluded: chain N residue 190 ARG Chi-restraints excluded: chain N residue 192 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 87 optimal weight: 0.5980 chunk 86 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 29 optimal weight: 0.4980 chunk 54 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 42 optimal weight: 10.0000 chunk 118 optimal weight: 0.3980 chunk 77 optimal weight: 8.9990 chunk 62 optimal weight: 0.5980 chunk 104 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.193216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.151198 restraints weight = 12825.876| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 3.16 r_work: 0.3650 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.4114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10915 Z= 0.133 Angle : 0.567 8.231 14824 Z= 0.297 Chirality : 0.043 0.252 1749 Planarity : 0.004 0.060 1829 Dihedral : 7.413 72.887 1572 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.81 % Allowed : 16.86 % Favored : 80.33 % 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 aren not related in a simple way. whole: 0.60 (0.24), residues: 1374 helix: 2.47 (0.22), residues: 549 sheet: -0.28 (0.31), residues: 303 loop : -1.50 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 219 TYR 0.022 0.001 TYR N 223 PHE 0.022 0.001 PHE C 74 TRP 0.014 0.001 TRP D 63 HIS 0.004 0.001 HIS C 73 Details of bonding type rmsd covalent geometry : bond 0.00315 (10912) covalent geometry : angle 0.56707 (14818) SS BOND : bond 0.00209 ( 3) SS BOND : angle 1.04078 ( 6) hydrogen bonds : bond 0.03529 ( 588) hydrogen bonds : angle 4.30837 ( 1695) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 179 time to evaluate : 0.336 Fit side-chains REVERT: A 174 MET cc_start: 0.7768 (ptm) cc_final: 0.7184 (ppp) REVERT: A 197 VAL cc_start: 0.8757 (OUTLIER) cc_final: 0.8479 (p) REVERT: A 219 ARG cc_start: 0.8506 (mtp85) cc_final: 0.8250 (ttt90) REVERT: A 275 PHE cc_start: 0.6028 (m-80) cc_final: 0.5045 (t80) REVERT: B 62 LEU cc_start: 0.7184 (mt) cc_final: 0.6641 (tt) REVERT: C 136 ASP cc_start: 0.8431 (t70) cc_final: 0.8084 (t0) REVERT: C 169 ASN cc_start: 0.7415 (m-40) cc_final: 0.6598 (t0) REVERT: D 17 GLN cc_start: 0.8536 (tm-30) cc_final: 0.7860 (pt0) REVERT: D 130 GLU cc_start: 0.7775 (mp0) cc_final: 0.7211 (mp0) REVERT: D 183 HIS cc_start: 0.4627 (OUTLIER) cc_final: 0.4305 (m-70) REVERT: D 243 THR cc_start: 0.6850 (OUTLIER) cc_final: 0.6543 (m) REVERT: D 339 TRP cc_start: 0.6950 (m100) cc_final: 0.5535 (m100) REVERT: N 69 THR cc_start: 0.5524 (p) cc_final: 0.5288 (t) REVERT: N 130 GLN cc_start: 0.7191 (OUTLIER) cc_final: 0.6060 (pt0) REVERT: N 219 GLN cc_start: 0.7517 (pp30) cc_final: 0.6994 (pp30) REVERT: Y 21 MET cc_start: 0.6536 (tpp) cc_final: 0.6040 (tmm) REVERT: Y 38 MET cc_start: 0.6092 (mmm) cc_final: 0.5693 (ptt) outliers start: 32 outliers final: 25 residues processed: 199 average time/residue: 0.0854 time to fit residues: 24.7982 Evaluate side-chains 200 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 171 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 165 TYR Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 183 HIS Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 264 TYR Chi-restraints excluded: chain N residue 126 ILE Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 130 GLN Chi-restraints excluded: chain N residue 146 SER Chi-restraints excluded: chain N residue 166 LEU Chi-restraints excluded: chain N residue 190 ARG Chi-restraints excluded: chain N residue 192 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 63 optimal weight: 0.5980 chunk 64 optimal weight: 0.0270 chunk 6 optimal weight: 4.9990 chunk 119 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 90 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 76 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 107 optimal weight: 8.9990 overall best weight: 0.6640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 155 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.193580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.151854 restraints weight = 12792.497| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 2.86 r_work: 0.3597 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.4232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10915 Z= 0.138 Angle : 0.575 8.092 14824 Z= 0.299 Chirality : 0.043 0.251 1749 Planarity : 0.004 0.060 1829 Dihedral : 7.354 73.235 1572 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.72 % Allowed : 17.30 % Favored : 79.98 % 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 aren not related in a simple way. whole: 0.64 (0.24), residues: 1374 helix: 2.53 (0.22), residues: 543 sheet: -0.26 (0.31), residues: 303 loop : -1.48 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 137 TYR 0.020 0.001 TYR N 223 PHE 0.021 0.001 PHE C 74 TRP 0.013 0.001 TRP D 63 HIS 0.004 0.001 HIS C 73 Details of bonding type rmsd covalent geometry : bond 0.00330 (10912) covalent geometry : angle 0.57486 (14818) SS BOND : bond 0.00182 ( 3) SS BOND : angle 1.04623 ( 6) hydrogen bonds : bond 0.03550 ( 588) hydrogen bonds : angle 4.29560 ( 1695) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2748 Ramachandran restraints generated. 1374 Oldfield, 0 Emsley, 1374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 170 time to evaluate : 0.434 Fit side-chains revert: symmetry clash REVERT: A 174 MET cc_start: 0.7722 (ptm) cc_final: 0.7159 (ppp) REVERT: A 197 VAL cc_start: 0.8730 (OUTLIER) cc_final: 0.8451 (p) REVERT: A 219 ARG cc_start: 0.8514 (mtp85) cc_final: 0.8277 (ttt90) REVERT: B 62 LEU cc_start: 0.7211 (mt) cc_final: 0.6685 (tt) REVERT: C 136 ASP cc_start: 0.8481 (t70) cc_final: 0.8127 (t0) REVERT: C 169 ASN cc_start: 0.7346 (m-40) cc_final: 0.6562 (t0) REVERT: C 202 ASP cc_start: 0.7927 (t0) cc_final: 0.7685 (t0) REVERT: D 17 GLN cc_start: 0.8544 (tm-30) cc_final: 0.7864 (pt0) REVERT: D 130 GLU cc_start: 0.7820 (mp0) cc_final: 0.7265 (mp0) REVERT: D 183 HIS cc_start: 0.4731 (OUTLIER) cc_final: 0.4500 (m-70) REVERT: D 243 THR cc_start: 0.6901 (OUTLIER) cc_final: 0.6622 (m) REVERT: D 339 TRP cc_start: 0.6958 (m100) cc_final: 0.5556 (m-10) REVERT: N 130 GLN cc_start: 0.7211 (OUTLIER) cc_final: 0.6106 (pt0) REVERT: N 219 GLN cc_start: 0.7542 (pp30) cc_final: 0.7018 (pp30) REVERT: Y 38 MET cc_start: 0.6174 (mmm) cc_final: 0.5727 (ptt) outliers start: 31 outliers final: 27 residues processed: 189 average time/residue: 0.1031 time to fit residues: 27.7686 Evaluate side-chains 194 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 163 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 165 TYR Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 183 HIS Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 264 TYR Chi-restraints excluded: chain D residue 292 PHE Chi-restraints excluded: chain N residue 126 ILE Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 130 GLN Chi-restraints excluded: chain N residue 146 SER Chi-restraints excluded: chain N residue 166 LEU Chi-restraints excluded: chain N residue 190 ARG Chi-restraints excluded: chain N residue 192 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 81 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 77 optimal weight: 0.0470 chunk 83 optimal weight: 0.5980 chunk 45 optimal weight: 0.5980 chunk 85 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 13 optimal weight: 0.3980 chunk 103 optimal weight: 0.6980 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 ASN A 248 HIS ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.199740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.157486 restraints weight = 12646.126| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 2.89 r_work: 0.3618 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.4322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10915 Z= 0.122 Angle : 0.558 9.157 14824 Z= 0.291 Chirality : 0.042 0.254 1749 Planarity : 0.004 0.060 1829 Dihedral : 7.191 73.408 1572 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.55 % Allowed : 17.56 % Favored : 79.89 % 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 aren not related in a simple way. whole: 0.73 (0.24), residues: 1374 helix: 2.59 (0.22), residues: 543 sheet: -0.19 (0.31), residues: 303 loop : -1.42 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 137 TYR 0.023 0.001 TYR N 223 PHE 0.019 0.001 PHE N 200 TRP 0.015 0.001 TRP D 63 HIS 0.012 0.001 HIS A 248 Details of bonding type rmsd covalent geometry : bond 0.00286 (10912) covalent geometry : angle 0.55806 (14818) SS BOND : bond 0.00153 ( 3) SS BOND : angle 1.10754 ( 6) hydrogen bonds : bond 0.03437 ( 588) hydrogen bonds : angle 4.21978 ( 1695) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2667.01 seconds wall clock time: 46 minutes 37.18 seconds (2797.18 seconds total)