Starting phenix.real_space_refine on Fri Feb 14 21:42:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ied_35380/02_2025/8ied_35380.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ied_35380/02_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_35380/02_2025/8ied_35380.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ied_35380/02_2025/8ied_35380.map" model { file = "/net/cci-nas-00/data/ceres_data/8ied_35380/02_2025/8ied_35380.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ied_35380/02_2025/8ied_35380.cif" } resolution = 3.33 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 2, 'ASP: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: {'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 4, 'ASP:plan': 3} 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: {'GLN:plan1': 1, 'GLU:plan': 7, '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: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP: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: 7.23, per 1000 atoms: 0.68 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: 2.59 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.05 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: 3.40 Time building geometry restraints manager: 3.01 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 318 or resid 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: 3.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 26.950 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.730 ------------------------------------------------------------------------------- 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 10912 Z= 0.416 Angle : 0.771 14.886 14818 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (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 TRP 0.029 0.002 TRP A 229 HIS 0.006 0.001 HIS N 220 PHE 0.023 0.002 PHE A 306 TYR 0.022 0.002 TYR N 223 ARG 0.004 0.000 ARG B 144 *********************** 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 : 1.188 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: 0.2313 time to fit residues: 87.8913 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 : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 0.0870 chunk 103 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 64 optimal weight: 0.0970 chunk 79 optimal weight: 3.9990 chunk 123 optimal weight: 0.9980 overall best weight: 0.8360 ------------------------------------------------------------------------------- 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 = 0.4356 r_free = 0.4356 target = 0.205780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.164335 restraints weight = 12380.212| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 2.80 r_work: 0.3635 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10912 Z= 0.269 Angle : 0.607 8.743 14818 Z= 0.320 Chirality : 0.044 0.189 1749 Planarity : 0.005 0.060 1829 Dihedral : 8.905 72.395 1572 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.76 % Allowed : 9.04 % Favored : 89.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.24), residues: 1374 helix: 2.15 (0.22), residues: 542 sheet: -0.28 (0.31), residues: 303 loop : -1.46 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 211 HIS 0.004 0.001 HIS N 35 PHE 0.022 0.002 PHE B 66 TYR 0.029 0.002 TYR N 60 ARG 0.007 0.001 ARG D 137 *********************** 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 220 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 200 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 MET cc_start: 0.7744 (ptm) cc_final: 0.7223 (ppp) REVERT: B 81 LYS cc_start: 0.7773 (tttp) cc_final: 0.7134 (ttpt) REVERT: B 125 SER cc_start: 0.8954 (t) cc_final: 0.8712 (p) REVERT: C 136 ASP cc_start: 0.7976 (t70) cc_final: 0.7706 (t0) REVERT: C 169 ASN cc_start: 0.7330 (m-40) cc_final: 0.6723 (t0) REVERT: C 202 ASP cc_start: 0.7649 (t0) cc_final: 0.7384 (t0) REVERT: D 65 THR cc_start: 0.7245 (p) cc_final: 0.6812 (t) REVERT: D 130 GLU cc_start: 0.7483 (mt-10) cc_final: 0.7013 (mp0) REVERT: D 156 GLN cc_start: 0.7770 (mt0) cc_final: 0.7505 (mt0) REVERT: N 72 ARG cc_start: 0.5768 (ptm160) cc_final: 0.4976 (ptm160) REVERT: Y 38 MET cc_start: 0.6005 (mmm) cc_final: 0.5393 (ptt) outliers start: 20 outliers final: 14 residues processed: 211 average time/residue: 0.2327 time to fit residues: 69.2211 Evaluate side-chains 191 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 177 time to evaluate : 1.078 ------------------------------------------------------------------------------- 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 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 26 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 104 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 129 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 85 optimal weight: 0.0570 chunk 40 optimal weight: 0.9980 overall best weight: 0.6498 ------------------------------------------------------------------------------- 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 = 0.4236 r_free = 0.4236 target = 0.195816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.152933 restraints weight = 12947.955| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 2.82 r_work: 0.3698 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10912 Z= 0.216 Angle : 0.553 6.497 14818 Z= 0.295 Chirality : 0.043 0.202 1749 Planarity : 0.004 0.065 1829 Dihedral : 8.506 73.449 1572 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 1.93 % Allowed : 11.59 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.24), residues: 1374 helix: 2.48 (0.22), residues: 545 sheet: -0.13 (0.31), residues: 295 loop : -1.40 (0.28), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 169 HIS 0.004 0.001 HIS D 225 PHE 0.017 0.001 PHE A 70 TYR 0.021 0.002 TYR N 223 ARG 0.006 0.000 ARG D 96 *********************** 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 217 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 195 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 174 MET cc_start: 0.7746 (ptm) cc_final: 0.7239 (ppp) REVERT: A 199 MET cc_start: 0.6940 (ttm) cc_final: 0.6719 (mmm) REVERT: B 75 ARG cc_start: 0.6847 (ptp-170) cc_final: 0.6525 (mtp180) REVERT: B 81 LYS cc_start: 0.7729 (tttp) cc_final: 0.7058 (ttpt) REVERT: B 125 SER cc_start: 0.8963 (t) cc_final: 0.8750 (p) REVERT: B 199 MET cc_start: 0.7737 (tmm) cc_final: 0.7320 (tpt) REVERT: C 136 ASP cc_start: 0.8111 (t70) cc_final: 0.7835 (t0) REVERT: C 169 ASN cc_start: 0.7374 (m-40) cc_final: 0.6775 (t0) REVERT: C 202 ASP cc_start: 0.7812 (t0) cc_final: 0.7542 (t0) REVERT: D 130 GLU cc_start: 0.7505 (mt-10) cc_final: 0.7122 (mp0) REVERT: D 175 GLN cc_start: 0.6701 (mm-40) cc_final: 0.6371 (mm110) REVERT: D 262 MET cc_start: 0.4777 (tpp) cc_final: 0.4551 (tpp) REVERT: D 283 ARG cc_start: 0.5823 (mmm160) cc_final: 0.5252 (mmm160) REVERT: D 289 TYR cc_start: 0.6596 (m-80) cc_final: 0.6337 (m-80) REVERT: N 64 VAL cc_start: 0.4468 (t) cc_final: 0.4123 (m) REVERT: Y 38 MET cc_start: 0.5954 (mmm) cc_final: 0.5534 (ptt) outliers start: 22 outliers final: 16 residues processed: 205 average time/residue: 0.2344 time to fit residues: 67.4108 Evaluate side-chains 188 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 172 time to evaluate : 1.091 ------------------------------------------------------------------------------- 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 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 212 ASP Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain N residue 126 ILE Chi-restraints excluded: chain N residue 135 VAL Chi-restraints excluded: chain N residue 190 ARG Chi-restraints excluded: chain N residue 212 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 86 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 40 optimal weight: 0.4980 chunk 12 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 110 optimal weight: 0.0050 chunk 5 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 107 optimal weight: 8.9990 chunk 112 optimal weight: 1.9990 overall best weight: 1.1000 ------------------------------------------------------------------------------- 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 181 GLN ** C 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4283 r_free = 0.4283 target = 0.197735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.155942 restraints weight = 12688.301| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 2.78 r_work: 0.3564 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 10912 Z= 0.302 Angle : 0.605 7.266 14818 Z= 0.320 Chirality : 0.045 0.217 1749 Planarity : 0.005 0.065 1829 Dihedral : 8.227 69.169 1572 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 3.07 % Allowed : 12.82 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.24), residues: 1374 helix: 2.39 (0.22), residues: 541 sheet: -0.41 (0.32), residues: 291 loop : -1.50 (0.27), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 211 HIS 0.007 0.001 HIS D 225 PHE 0.017 0.002 PHE A 70 TYR 0.022 0.002 TYR N 223 ARG 0.005 0.001 ARG D 251 *********************** 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 229 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 194 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 MET cc_start: 0.7698 (ptm) cc_final: 0.7166 (ppp) REVERT: A 199 MET cc_start: 0.6996 (ttm) cc_final: 0.6681 (mmm) REVERT: B 62 LEU cc_start: 0.7197 (mt) cc_final: 0.6615 (tt) REVERT: B 75 ARG cc_start: 0.7128 (ptp-170) cc_final: 0.6906 (mtp180) REVERT: B 125 SER cc_start: 0.8922 (t) cc_final: 0.8716 (p) REVERT: B 200 THR cc_start: 0.6147 (OUTLIER) cc_final: 0.5890 (p) REVERT: C 124 LEU cc_start: 0.7895 (tp) cc_final: 0.7687 (tp) REVERT: C 136 ASP cc_start: 0.8302 (t70) cc_final: 0.7949 (t0) REVERT: C 169 ASN cc_start: 0.7494 (m-40) cc_final: 0.6775 (t0) REVERT: C 202 ASP cc_start: 0.7936 (t0) cc_final: 0.7719 (t0) REVERT: D 127 LYS cc_start: 0.8162 (OUTLIER) cc_final: 0.7866 (mmtt) REVERT: D 130 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7172 (mp0) REVERT: D 155 ASN cc_start: 0.7921 (t0) cc_final: 0.7695 (t0) REVERT: D 175 GLN cc_start: 0.6724 (mm-40) cc_final: 0.6384 (mm110) REVERT: D 289 TYR cc_start: 0.6810 (m-80) cc_final: 0.6447 (m-80) REVERT: D 339 TRP cc_start: 0.6874 (m100) cc_final: 0.5779 (m100) REVERT: N 64 VAL cc_start: 0.4546 (t) cc_final: 0.4074 (m) REVERT: Y 21 MET cc_start: 0.6536 (tpp) cc_final: 0.6055 (tmm) REVERT: Y 38 MET cc_start: 0.5978 (mmm) cc_final: 0.5632 (ptt) outliers start: 35 outliers final: 20 residues processed: 213 average time/residue: 0.2325 time to fit residues: 69.6514 Evaluate side-chains 198 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 176 time to evaluate : 1.103 ------------------------------------------------------------------------------- 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 259 THR Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 104 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 C residue 34 VAL Chi-restraints excluded: chain C residue 228 TYR Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 126 ILE Chi-restraints excluded: chain N residue 135 VAL Chi-restraints excluded: chain N residue 190 ARG Chi-restraints excluded: chain N residue 192 SER Chi-restraints excluded: chain N residue 212 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 104 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 chunk 7 optimal weight: 0.5980 chunk 127 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 114 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4281 r_free = 0.4281 target = 0.197384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.155671 restraints weight = 12684.925| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 2.82 r_work: 0.3572 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.3514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10912 Z= 0.241 Angle : 0.564 8.022 14818 Z= 0.298 Chirality : 0.043 0.278 1749 Planarity : 0.005 0.065 1829 Dihedral : 7.925 70.669 1572 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.81 % Allowed : 14.57 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.24), residues: 1374 helix: 2.39 (0.22), residues: 549 sheet: -0.50 (0.32), residues: 292 loop : -1.50 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 211 HIS 0.003 0.001 HIS C 73 PHE 0.017 0.001 PHE A 70 TYR 0.024 0.002 TYR N 223 ARG 0.006 0.000 ARG B 327 *********************** 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 214 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 182 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 MET cc_start: 0.7741 (ptm) cc_final: 0.7177 (ppp) REVERT: A 199 MET cc_start: 0.7009 (ttm) cc_final: 0.6748 (mmm) REVERT: B 62 LEU cc_start: 0.7244 (mt) cc_final: 0.6627 (tt) REVERT: B 81 LYS cc_start: 0.7556 (ttmm) cc_final: 0.6764 (ttpt) REVERT: B 199 MET cc_start: 0.7697 (tmm) cc_final: 0.7224 (mtt) REVERT: B 200 THR cc_start: 0.6050 (OUTLIER) cc_final: 0.5807 (p) REVERT: C 35 LYS cc_start: 0.7826 (mtmm) cc_final: 0.7620 (mttp) REVERT: C 124 LEU cc_start: 0.7881 (tp) cc_final: 0.7597 (tp) REVERT: C 136 ASP cc_start: 0.8312 (t70) cc_final: 0.7950 (t0) REVERT: C 169 ASN cc_start: 0.7427 (m-40) cc_final: 0.6687 (t0) REVERT: D 127 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7889 (mmtt) REVERT: D 130 GLU cc_start: 0.7668 (mt-10) cc_final: 0.7176 (mp0) REVERT: D 155 ASN cc_start: 0.7902 (t0) cc_final: 0.7639 (t0) REVERT: D 175 GLN cc_start: 0.6779 (mm-40) cc_final: 0.6416 (mm110) REVERT: D 243 THR cc_start: 0.6854 (OUTLIER) cc_final: 0.6617 (m) REVERT: D 260 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7629 (tt0) REVERT: D 262 MET cc_start: 0.5101 (tpp) cc_final: 0.4493 (tpp) REVERT: D 289 TYR cc_start: 0.6684 (m-80) cc_final: 0.6423 (m-80) REVERT: D 339 TRP cc_start: 0.6935 (m100) cc_final: 0.5755 (m100) REVERT: N 219 GLN cc_start: 0.7460 (pp30) cc_final: 0.6912 (pp30) REVERT: Y 21 MET cc_start: 0.6493 (tpp) cc_final: 0.6054 (tmm) REVERT: Y 38 MET cc_start: 0.6020 (mmm) cc_final: 0.5691 (ptt) outliers start: 32 outliers final: 20 residues processed: 201 average time/residue: 0.2295 time to fit residues: 66.4623 Evaluate side-chains 196 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 172 time to evaluate : 1.346 ------------------------------------------------------------------------------- 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 104 LEU 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 D residue 74 SER Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 260 GLU Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 126 ILE Chi-restraints excluded: chain N residue 129 THR Chi-restraints excluded: chain N residue 135 VAL Chi-restraints excluded: chain N residue 190 ARG Chi-restraints excluded: chain N residue 192 SER Chi-restraints excluded: chain N residue 212 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 22 optimal weight: 0.3980 chunk 30 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 128 optimal weight: 0.0570 chunk 29 optimal weight: 0.7980 chunk 64 optimal weight: 8.9990 chunk 110 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 26 optimal weight: 5.9990 chunk 54 optimal weight: 0.5980 chunk 135 optimal weight: 2.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN ** C 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.200345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.157669 restraints weight = 12613.424| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 2.89 r_work: 0.3606 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10912 Z= 0.186 Angle : 0.530 7.681 14818 Z= 0.282 Chirality : 0.042 0.242 1749 Planarity : 0.004 0.064 1829 Dihedral : 7.538 70.269 1572 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.34 % Allowed : 14.57 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.24), residues: 1374 helix: 2.43 (0.22), residues: 552 sheet: -0.42 (0.32), residues: 291 loop : -1.44 (0.28), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 169 HIS 0.003 0.001 HIS C 73 PHE 0.019 0.001 PHE A 70 TYR 0.023 0.001 TYR N 223 ARG 0.006 0.000 ARG B 75 *********************** 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 221 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 183 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 174 MET cc_start: 0.7681 (ptm) cc_final: 0.7123 (ppp) REVERT: A 197 VAL cc_start: 0.8872 (OUTLIER) cc_final: 0.8527 (p) REVERT: A 199 MET cc_start: 0.6992 (ttm) cc_final: 0.6606 (mmm) REVERT: B 81 LYS cc_start: 0.7564 (ttmm) cc_final: 0.6786 (ttpt) REVERT: C 136 ASP cc_start: 0.8334 (t70) cc_final: 0.7966 (t0) REVERT: C 169 ASN cc_start: 0.7412 (m-40) cc_final: 0.6580 (t0) REVERT: C 202 ASP cc_start: 0.7686 (t0) cc_final: 0.7426 (t0) REVERT: D 17 GLN cc_start: 0.8539 (tm-30) cc_final: 0.7917 (pt0) REVERT: D 127 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7966 (mmtt) REVERT: D 130 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7203 (mp0) REVERT: D 175 GLN cc_start: 0.6800 (mm-40) cc_final: 0.6429 (mm110) REVERT: D 260 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7273 (tp30) REVERT: D 289 TYR cc_start: 0.6613 (m-80) cc_final: 0.6402 (m-80) REVERT: D 329 THR cc_start: 0.8062 (m) cc_final: 0.7847 (p) REVERT: D 339 TRP cc_start: 0.6950 (m100) cc_final: 0.5625 (m100) REVERT: N 130 GLN cc_start: 0.7160 (OUTLIER) cc_final: 0.5954 (pt0) REVERT: N 219 GLN cc_start: 0.7473 (pp30) cc_final: 0.6932 (pp30) REVERT: Y 21 MET cc_start: 0.6492 (tpp) cc_final: 0.6043 (tmm) REVERT: Y 38 MET cc_start: 0.6038 (mmm) cc_final: 0.5675 (ptt) outliers start: 38 outliers final: 24 residues processed: 205 average time/residue: 0.2214 time to fit residues: 64.8701 Evaluate side-chains 204 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 176 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 57 LEU Chi-restraints excluded: chain B residue 197 VAL 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 102 ASP Chi-restraints excluded: chain C residue 165 TYR Chi-restraints excluded: chain C residue 228 TYR Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 127 LYS 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 260 GLU Chi-restraints excluded: chain D residue 264 TYR Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain N residue 69 THR 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 135 VAL Chi-restraints excluded: chain N residue 190 ARG Chi-restraints excluded: chain N residue 192 SER Chi-restraints excluded: chain N residue 212 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 108 optimal weight: 2.9990 chunk 68 optimal weight: 0.0010 chunk 32 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 76 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 overall best weight: 1.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 77 ASN ** C 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 155 ASN D 225 HIS N 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.191817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.149568 restraints weight = 13153.943| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 2.81 r_work: 0.3558 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 10912 Z= 0.347 Angle : 0.617 7.404 14818 Z= 0.326 Chirality : 0.045 0.290 1749 Planarity : 0.005 0.061 1829 Dihedral : 7.882 71.331 1572 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 4.04 % Allowed : 14.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.24), residues: 1374 helix: 2.23 (0.22), residues: 546 sheet: -0.44 (0.30), residues: 313 loop : -1.53 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 211 HIS 0.004 0.001 HIS D 91 PHE 0.025 0.002 PHE C 74 TYR 0.025 0.002 TYR N 223 ARG 0.004 0.001 ARG A 219 *********************** 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 224 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 178 time to evaluate : 1.130 Fit side-chains revert: symmetry clash REVERT: A 174 MET cc_start: 0.7777 (ptm) cc_final: 0.7201 (ppp) REVERT: A 197 VAL cc_start: 0.8873 (OUTLIER) cc_final: 0.8633 (p) REVERT: B 62 LEU cc_start: 0.7327 (mt) cc_final: 0.6683 (tt) REVERT: B 81 LYS cc_start: 0.7545 (ttmm) cc_final: 0.6771 (tttt) REVERT: C 136 ASP cc_start: 0.8462 (t70) cc_final: 0.8107 (t0) REVERT: C 169 ASN cc_start: 0.7422 (m-40) cc_final: 0.6550 (t0) REVERT: C 202 ASP cc_start: 0.7839 (t0) cc_final: 0.7581 (t0) REVERT: D 127 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7944 (mmtt) REVERT: D 130 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7307 (mp0) REVERT: D 183 HIS cc_start: 0.4741 (OUTLIER) cc_final: 0.4192 (m-70) REVERT: D 289 TYR cc_start: 0.6595 (m-80) cc_final: 0.6007 (m-80) REVERT: D 339 TRP cc_start: 0.7027 (m100) cc_final: 0.5970 (m-10) REVERT: N 130 GLN cc_start: 0.7564 (OUTLIER) cc_final: 0.6488 (pt0) REVERT: N 218 MET cc_start: 0.7827 (ttp) cc_final: 0.7614 (ttp) REVERT: N 219 GLN cc_start: 0.7358 (pp30) cc_final: 0.6796 (pp30) REVERT: Y 21 MET cc_start: 0.6581 (tpp) cc_final: 0.6134 (tmm) REVERT: Y 38 MET cc_start: 0.6051 (mmm) cc_final: 0.5709 (ptt) outliers start: 46 outliers final: 29 residues processed: 209 average time/residue: 0.2100 time to fit residues: 63.8894 Evaluate side-chains 197 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 164 time to evaluate : 1.207 ------------------------------------------------------------------------------- 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 52 ILE Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 197 VAL 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 38 LEU Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 165 TYR Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 127 LYS 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 264 TYR Chi-restraints excluded: chain D residue 292 PHE Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 69 THR 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 135 VAL Chi-restraints excluded: chain N residue 146 SER Chi-restraints excluded: chain N residue 190 ARG Chi-restraints excluded: chain N residue 192 SER Chi-restraints excluded: chain N residue 212 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 29 optimal weight: 0.0770 chunk 72 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 126 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 105 optimal weight: 8.9990 chunk 79 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 overall best weight: 0.7338 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.196964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.154379 restraints weight = 12717.082| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 2.89 r_work: 0.3657 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.4140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10912 Z= 0.233 Angle : 0.568 8.138 14818 Z= 0.300 Chirality : 0.043 0.248 1749 Planarity : 0.004 0.062 1829 Dihedral : 7.607 72.665 1572 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.90 % Allowed : 16.77 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.24), residues: 1374 helix: 2.35 (0.22), residues: 548 sheet: -0.40 (0.31), residues: 314 loop : -1.54 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 63 HIS 0.003 0.001 HIS C 80 PHE 0.021 0.001 PHE C 74 TYR 0.025 0.001 TYR N 223 ARG 0.003 0.000 ARG A 219 *********************** 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 210 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 177 time to evaluate : 1.105 Fit side-chains revert: symmetry clash REVERT: A 174 MET cc_start: 0.7801 (ptm) cc_final: 0.7200 (ppp) REVERT: A 197 VAL cc_start: 0.8883 (OUTLIER) cc_final: 0.8572 (p) REVERT: A 199 MET cc_start: 0.6939 (ttm) cc_final: 0.6496 (mmm) REVERT: B 81 LYS cc_start: 0.7535 (ttmm) cc_final: 0.6774 (ttpt) REVERT: C 136 ASP cc_start: 0.8472 (t70) cc_final: 0.8127 (t0) REVERT: C 169 ASN cc_start: 0.7394 (m-40) cc_final: 0.6536 (t0) REVERT: D 97 SER cc_start: 0.8899 (OUTLIER) cc_final: 0.8640 (p) REVERT: D 130 GLU cc_start: 0.7705 (mt-10) cc_final: 0.7258 (mp0) REVERT: D 289 TYR cc_start: 0.6645 (m-80) cc_final: 0.6189 (m-80) REVERT: D 339 TRP cc_start: 0.6940 (m100) cc_final: 0.5792 (m-10) REVERT: N 130 GLN cc_start: 0.7261 (OUTLIER) cc_final: 0.6097 (pt0) REVERT: N 219 GLN cc_start: 0.7401 (pp30) cc_final: 0.6870 (pp30) REVERT: Y 21 MET cc_start: 0.6553 (tpp) cc_final: 0.6145 (tmm) REVERT: Y 38 MET cc_start: 0.5988 (mmm) cc_final: 0.5715 (ptt) outliers start: 33 outliers final: 26 residues processed: 197 average time/residue: 0.2243 time to fit residues: 63.2048 Evaluate side-chains 196 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 167 time to evaluate : 1.243 ------------------------------------------------------------------------------- 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 179 LEU Chi-restraints excluded: chain B residue 197 VAL 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 D residue 74 SER Chi-restraints excluded: chain D residue 97 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 264 TYR Chi-restraints excluded: chain D residue 292 PHE Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain N residue 69 THR 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 174 GLN Chi-restraints excluded: chain N residue 190 ARG Chi-restraints excluded: chain N residue 192 SER Chi-restraints excluded: chain N residue 212 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 0.5980 chunk 26 optimal weight: 4.9990 chunk 123 optimal weight: 0.0970 chunk 106 optimal weight: 0.5980 chunk 134 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 118 optimal weight: 0.2980 chunk 52 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 HIS ** C 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.199112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.156350 restraints weight = 12697.876| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 2.97 r_work: 0.3608 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.4254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10912 Z= 0.187 Angle : 0.556 8.175 14818 Z= 0.291 Chirality : 0.043 0.271 1749 Planarity : 0.004 0.062 1829 Dihedral : 7.351 72.888 1572 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.55 % Allowed : 17.47 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.24), residues: 1374 helix: 2.42 (0.22), residues: 549 sheet: -0.32 (0.31), residues: 314 loop : -1.51 (0.28), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 63 HIS 0.011 0.001 HIS A 248 PHE 0.019 0.001 PHE A 70 TYR 0.025 0.001 TYR N 223 ARG 0.004 0.000 ARG A 219 *********************** 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 209 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 180 time to evaluate : 1.105 Fit side-chains revert: symmetry clash REVERT: A 174 MET cc_start: 0.7773 (ptm) cc_final: 0.7180 (ppp) REVERT: A 197 VAL cc_start: 0.8863 (OUTLIER) cc_final: 0.8552 (p) REVERT: A 199 MET cc_start: 0.6948 (ttm) cc_final: 0.6449 (mmm) REVERT: B 62 LEU cc_start: 0.7176 (mt) cc_final: 0.6622 (tt) REVERT: B 81 LYS cc_start: 0.7433 (ttmm) cc_final: 0.6668 (tttt) REVERT: B 108 GLN cc_start: 0.6417 (pm20) cc_final: 0.6195 (pm20) REVERT: C 136 ASP cc_start: 0.8449 (t70) cc_final: 0.8104 (t0) REVERT: C 169 ASN cc_start: 0.7361 (m-40) cc_final: 0.6524 (t0) REVERT: D 17 GLN cc_start: 0.8542 (tm-30) cc_final: 0.7859 (pm20) REVERT: D 97 SER cc_start: 0.8899 (OUTLIER) cc_final: 0.8642 (p) REVERT: D 130 GLU cc_start: 0.7700 (mt-10) cc_final: 0.7260 (mp0) REVERT: D 289 TYR cc_start: 0.6686 (m-80) cc_final: 0.6264 (m-80) REVERT: D 339 TRP cc_start: 0.6960 (m100) cc_final: 0.5503 (m-10) REVERT: N 69 THR cc_start: 0.5562 (OUTLIER) cc_final: 0.5317 (t) REVERT: N 130 GLN cc_start: 0.7012 (OUTLIER) cc_final: 0.5805 (pt0) REVERT: N 219 GLN cc_start: 0.7544 (pp30) cc_final: 0.7010 (pp30) REVERT: Y 21 MET cc_start: 0.6548 (tpp) cc_final: 0.6155 (tmm) REVERT: Y 38 MET cc_start: 0.6096 (mmm) cc_final: 0.5689 (ptt) outliers start: 29 outliers final: 20 residues processed: 197 average time/residue: 0.2224 time to fit residues: 62.6447 Evaluate side-chains 194 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 170 time to evaluate : 1.106 ------------------------------------------------------------------------------- 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 166 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 227 LEU 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 D residue 97 SER Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 264 TYR Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain N residue 69 THR 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 190 ARG Chi-restraints excluded: chain N residue 212 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 117 optimal weight: 0.8980 chunk 84 optimal weight: 0.1980 chunk 15 optimal weight: 6.9990 chunk 86 optimal weight: 0.7980 chunk 96 optimal weight: 3.9990 chunk 85 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 HIS ** C 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.191605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.148827 restraints weight = 12985.373| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 2.88 r_work: 0.3600 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.4348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10912 Z= 0.213 Angle : 0.572 7.873 14818 Z= 0.298 Chirality : 0.043 0.262 1749 Planarity : 0.004 0.061 1829 Dihedral : 7.298 72.790 1572 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.55 % Allowed : 17.82 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.24), residues: 1374 helix: 2.40 (0.22), residues: 549 sheet: -0.28 (0.31), residues: 312 loop : -1.52 (0.28), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 63 HIS 0.009 0.001 HIS A 248 PHE 0.018 0.001 PHE A 70 TYR 0.024 0.001 TYR N 223 ARG 0.004 0.000 ARG A 219 ********************** 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 202 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 173 time to evaluate : 1.216 Fit side-chains revert: symmetry clash REVERT: A 174 MET cc_start: 0.7779 (ptm) cc_final: 0.7181 (ppp) REVERT: A 197 VAL cc_start: 0.8864 (OUTLIER) cc_final: 0.8556 (p) REVERT: A 199 MET cc_start: 0.6920 (ttm) cc_final: 0.6448 (mmm) REVERT: B 62 LEU cc_start: 0.7147 (mt) cc_final: 0.6620 (tt) REVERT: B 81 LYS cc_start: 0.7474 (ttmm) cc_final: 0.6692 (ttpt) REVERT: B 108 GLN cc_start: 0.6317 (pm20) cc_final: 0.6094 (pm20) REVERT: C 136 ASP cc_start: 0.8440 (t70) cc_final: 0.8091 (t0) REVERT: C 169 ASN cc_start: 0.7308 (m-40) cc_final: 0.6438 (t0) REVERT: D 17 GLN cc_start: 0.8540 (tm-30) cc_final: 0.7837 (pt0) REVERT: D 97 SER cc_start: 0.8895 (OUTLIER) cc_final: 0.8623 (p) REVERT: D 130 GLU cc_start: 0.7685 (mt-10) cc_final: 0.7234 (mp0) REVERT: D 289 TYR cc_start: 0.6676 (m-80) cc_final: 0.6263 (m-80) REVERT: D 339 TRP cc_start: 0.6969 (m100) cc_final: 0.5542 (m-10) REVERT: N 130 GLN cc_start: 0.7192 (OUTLIER) cc_final: 0.6051 (pt0) REVERT: N 219 GLN cc_start: 0.7417 (pp30) cc_final: 0.6918 (pp30) REVERT: Y 38 MET cc_start: 0.6120 (mmm) cc_final: 0.5711 (ptt) outliers start: 29 outliers final: 25 residues processed: 190 average time/residue: 0.2283 time to fit residues: 61.7918 Evaluate side-chains 196 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 168 time to evaluate : 1.121 ------------------------------------------------------------------------------- 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 166 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 227 LEU 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 228 TYR Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 264 TYR Chi-restraints excluded: chain D residue 292 PHE Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain N residue 69 THR 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 190 ARG Chi-restraints excluded: chain N residue 212 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 7 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 97 optimal weight: 0.0970 chunk 65 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 129 optimal weight: 0.9980 chunk 10 optimal weight: 0.0870 chunk 8 optimal weight: 0.5980 overall best weight: 0.4956 ------------------------------------------------------------------------------- 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** D 155 ASN ** D 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.198565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.156620 restraints weight = 12603.812| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 2.85 r_work: 0.3625 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.4416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10912 Z= 0.193 Angle : 0.559 9.019 14818 Z= 0.292 Chirality : 0.043 0.264 1749 Planarity : 0.004 0.062 1829 Dihedral : 7.165 72.847 1572 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 2.19 % Allowed : 18.00 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.24), residues: 1374 helix: 2.46 (0.22), residues: 549 sheet: -0.29 (0.31), residues: 313 loop : -1.47 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 63 HIS 0.007 0.001 HIS D 183 PHE 0.019 0.001 PHE C 74 TYR 0.022 0.001 TYR N 223 ARG 0.004 0.000 ARG A 219 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5170.59 seconds wall clock time: 92 minutes 51.23 seconds (5571.23 seconds total)