Starting phenix.real_space_refine on Fri Aug 22 19:13:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jpp_36486/08_2025/8jpp_36486.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jpp_36486/08_2025/8jpp_36486.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jpp_36486/08_2025/8jpp_36486.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jpp_36486/08_2025/8jpp_36486.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jpp_36486/08_2025/8jpp_36486.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jpp_36486/08_2025/8jpp_36486.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.047 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 41 5.16 5 C 4565 2.51 5 N 1228 2.21 5 O 1303 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7137 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1897 Classifications: {'peptide': 237} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 6, 'TRANS': 230} Chain breaks: 1 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 2, 'ARG:plan': 4, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "B" Number of atoms: 2511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2511 Classifications: {'peptide': 331} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 5, 'TRANS': 325} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 18 Chain: "G" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 376 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 44} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "R" Number of atoms: 2345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2345 Classifications: {'peptide': 305} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 12, 'TRANS': 292} Chain breaks: 1 Unresolved non-hydrogen bonds: 154 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 130 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'PHE:plan': 3, 'ASN:plan1': 3, 'ASP:plan': 3, 'GLU:plan': 3, 'GLN:plan1': 4, 'ARG:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 81 Chain: "R" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SIN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.83, per 1000 atoms: 0.26 Number of scatterers: 7137 At special positions: 0 Unit cell: (74.048, 99.84, 132.288, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 41 16.00 O 1303 8.00 N 1228 7.00 C 4565 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 11 " - pdb=" SG CYS R 268 " distance=2.03 Simple disulfide: pdb=" SG CYS R 95 " - pdb=" SG CYS R 172 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 507.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1748 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 8 sheets defined 47.0% alpha, 16.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 12 through 40 removed outlier: 3.591A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 62 Processing helix chain 'A' and resid 233 through 241 removed outlier: 4.477A pdb=" N ASP A 240 " --> pdb=" O CYS A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 268 Processing helix chain 'A' and resid 283 through 293 Processing helix chain 'A' and resid 297 through 302 removed outlier: 4.024A pdb=" N TYR A 301 " --> pdb=" O LYS A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 306 Processing helix chain 'A' and resid 321 through 341 Processing helix chain 'A' and resid 360 through 381 Processing helix chain 'B' and resid 11 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 15 through 24 removed outlier: 3.742A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'R' and resid 11 through 50 removed outlier: 4.260A pdb=" N LEU R 26 " --> pdb=" O GLU R 22 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N SER R 27 " --> pdb=" O LYS R 23 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU R 39 " --> pdb=" O VAL R 35 " (cutoff:3.500A) Processing helix chain 'R' and resid 56 through 75 removed outlier: 3.507A pdb=" N THR R 75 " --> pdb=" O ALA R 71 " (cutoff:3.500A) Processing helix chain 'R' and resid 75 through 86 removed outlier: 4.541A pdb=" N LEU R 79 " --> pdb=" O THR R 75 " (cutoff:3.500A) Processing helix chain 'R' and resid 90 through 126 removed outlier: 4.173A pdb=" N LEU R 94 " --> pdb=" O TYR R 90 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N CYS R 95 " --> pdb=" O GLY R 91 " (cutoff:3.500A) Processing helix chain 'R' and resid 135 through 154 Processing helix chain 'R' and resid 157 through 162 Processing helix chain 'R' and resid 180 through 196 removed outlier: 3.510A pdb=" N TYR R 187 " --> pdb=" O TYR R 183 " (cutoff:3.500A) Processing helix chain 'R' and resid 196 through 221 Processing helix chain 'R' and resid 227 through 258 removed outlier: 3.560A pdb=" N LEU R 231 " --> pdb=" O LEU R 227 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE R 241 " --> pdb=" O ALA R 237 " (cutoff:3.500A) Proline residue: R 247 - end of helix removed outlier: 3.582A pdb=" N VAL R 254 " --> pdb=" O VAL R 250 " (cutoff:3.500A) Processing helix chain 'R' and resid 266 through 285 removed outlier: 3.558A pdb=" N THR R 280 " --> pdb=" O PHE R 276 " (cutoff:3.500A) Proline residue: R 282 - end of helix Processing helix chain 'R' and resid 286 through 296 Proline residue: R 292 - end of helix Processing helix chain 'R' and resid 301 through 317 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 3.525A pdb=" N LEU A 45 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N ASP A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE A 244 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N PHE A 280 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N PHE A 246 " --> pdb=" O PHE A 280 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ASN A 282 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N VAL A 248 " --> pdb=" O ASN A 282 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 50 removed outlier: 6.841A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.612A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 103 through 105 removed outlier: 6.278A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.317A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.584A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N MET B 217 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 232 removed outlier: 6.572A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.720A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 390 hydrogen bonds defined for protein. 1131 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.21 Time building geometry restraints manager: 0.97 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: 1162 1.32 - 1.44: 2021 1.44 - 1.56: 4049 1.56 - 1.69: 0 1.69 - 1.81: 57 Bond restraints: 7289 Sorted by residual: bond pdb=" C LEU R 185 " pdb=" O LEU R 185 " ideal model delta sigma weight residual 1.234 1.195 0.040 1.17e-02 7.31e+03 1.17e+01 bond pdb=" C PRO R 181 " pdb=" O PRO R 181 " ideal model delta sigma weight residual 1.237 1.199 0.038 1.29e-02 6.01e+03 8.54e+00 bond pdb=" N ILE R 118 " pdb=" CA ILE R 118 " ideal model delta sigma weight residual 1.458 1.498 -0.040 1.41e-02 5.03e+03 8.10e+00 bond pdb=" CA SER A 250 " pdb=" CB SER A 250 " ideal model delta sigma weight residual 1.530 1.482 0.048 1.75e-02 3.27e+03 7.61e+00 bond pdb=" N ILE R 89 " pdb=" CA ILE R 89 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.25e-02 6.40e+03 7.03e+00 ... (remaining 7284 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 9535 1.55 - 3.11: 306 3.11 - 4.66: 60 4.66 - 6.21: 9 6.21 - 7.76: 3 Bond angle restraints: 9913 Sorted by residual: angle pdb=" N LEU A 262 " pdb=" CA LEU A 262 " pdb=" C LEU A 262 " ideal model delta sigma weight residual 112.23 104.47 7.76 1.26e+00 6.30e-01 3.80e+01 angle pdb=" N ASN R 184 " pdb=" CA ASN R 184 " pdb=" C ASN R 184 " ideal model delta sigma weight residual 113.18 106.47 6.71 1.21e+00 6.83e-01 3.08e+01 angle pdb=" N ARG R 120 " pdb=" CA ARG R 120 " pdb=" C ARG R 120 " ideal model delta sigma weight residual 112.23 106.54 5.69 1.26e+00 6.30e-01 2.04e+01 angle pdb=" CA PHE A 208 " pdb=" CB PHE A 208 " pdb=" CG PHE A 208 " ideal model delta sigma weight residual 113.80 117.96 -4.16 1.00e+00 1.00e+00 1.73e+01 angle pdb=" N LEU A 260 " pdb=" CA LEU A 260 " pdb=" C LEU A 260 " ideal model delta sigma weight residual 112.54 107.55 4.99 1.22e+00 6.72e-01 1.68e+01 ... (remaining 9908 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.36: 3801 17.36 - 34.71: 388 34.71 - 52.06: 99 52.06 - 69.42: 10 69.42 - 86.77: 8 Dihedral angle restraints: 4306 sinusoidal: 1606 harmonic: 2700 Sorted by residual: dihedral pdb=" CD ARG A 61 " pdb=" NE ARG A 61 " pdb=" CZ ARG A 61 " pdb=" NH1 ARG A 61 " ideal model delta sinusoidal sigma weight residual 0.00 -28.40 28.40 1 1.00e+01 1.00e-02 1.16e+01 dihedral pdb=" CA ASP R 119 " pdb=" CB ASP R 119 " pdb=" CG ASP R 119 " pdb=" OD1 ASP R 119 " ideal model delta sinusoidal sigma weight residual -30.00 -85.50 55.50 1 2.00e+01 2.50e-03 1.04e+01 dihedral pdb=" CG ARG R 303 " pdb=" CD ARG R 303 " pdb=" NE ARG R 303 " pdb=" CZ ARG R 303 " ideal model delta sinusoidal sigma weight residual -90.00 -133.94 43.94 2 1.50e+01 4.44e-03 1.03e+01 ... (remaining 4303 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 822 0.038 - 0.076: 206 0.076 - 0.114: 81 0.114 - 0.152: 27 0.152 - 0.190: 3 Chirality restraints: 1139 Sorted by residual: chirality pdb=" CA ILE R 186 " pdb=" N ILE R 186 " pdb=" C ILE R 186 " pdb=" CB ILE R 186 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 9.03e-01 chirality pdb=" CB VAL R 38 " pdb=" CA VAL R 38 " pdb=" CG1 VAL R 38 " pdb=" CG2 VAL R 38 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.30e-01 chirality pdb=" CA ILE R 89 " pdb=" N ILE R 89 " pdb=" C ILE R 89 " pdb=" CB ILE R 89 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.66e-01 ... (remaining 1136 not shown) Planarity restraints: 1265 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 61 " -0.519 9.50e-02 1.11e+02 2.33e-01 3.30e+01 pdb=" NE ARG A 61 " 0.030 2.00e-02 2.50e+03 pdb=" CZ ARG A 61 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 61 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 61 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG R 120 " 0.260 9.50e-02 1.11e+02 1.17e-01 8.34e+00 pdb=" NE ARG R 120 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG R 120 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG R 120 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG R 120 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 232 " -0.009 2.00e-02 2.50e+03 1.80e-02 3.24e+00 pdb=" C ILE B 232 " 0.031 2.00e-02 2.50e+03 pdb=" O ILE B 232 " -0.012 2.00e-02 2.50e+03 pdb=" N CYS B 233 " -0.010 2.00e-02 2.50e+03 ... (remaining 1262 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1255 2.76 - 3.29: 7449 3.29 - 3.83: 12170 3.83 - 4.36: 14863 4.36 - 4.90: 25806 Nonbonded interactions: 61543 Sorted by model distance: nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.223 3.040 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.232 3.040 nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.233 3.040 nonbonded pdb=" N GLU G 47 " pdb=" OE1 GLU G 47 " model vdw 2.236 3.120 nonbonded pdb=" O LEU R 39 " pdb=" OG1 THR R 42 " model vdw 2.257 3.040 ... (remaining 61538 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.320 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.900 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7291 Z= 0.233 Angle : 0.652 7.764 9917 Z= 0.418 Chirality : 0.043 0.190 1139 Planarity : 0.008 0.233 1265 Dihedral : 15.093 86.773 2552 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.68 % Allowed : 16.01 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.29), residues: 910 helix: 1.32 (0.28), residues: 407 sheet: -1.88 (0.35), residues: 173 loop : -0.60 (0.35), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 38 TYR 0.012 0.001 TYR R 107 PHE 0.025 0.002 PHE A 208 TRP 0.010 0.001 TRP R 263 HIS 0.004 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 7289) covalent geometry : angle 0.65238 ( 9913) SS BOND : bond 0.00334 ( 2) SS BOND : angle 0.62662 ( 4) hydrogen bonds : bond 0.17445 ( 390) hydrogen bonds : angle 7.34456 ( 1131) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 145 time to evaluate : 0.277 Fit side-chains revert: symmetry clash REVERT: A 13 ARG cc_start: 0.7411 (mpt180) cc_final: 0.6551 (mtm-85) REVERT: A 21 GLU cc_start: 0.7540 (tm-30) cc_final: 0.7157 (tm-30) REVERT: A 220 HIS cc_start: 0.7716 (t-170) cc_final: 0.6985 (t-170) REVERT: A 376 MET cc_start: 0.7941 (ttm) cc_final: 0.7645 (ttt) REVERT: B 292 PHE cc_start: 0.8634 (m-10) cc_final: 0.8272 (m-80) REVERT: B 329 THR cc_start: 0.9005 (m) cc_final: 0.8545 (p) outliers start: 5 outliers final: 2 residues processed: 149 average time/residue: 0.1093 time to fit residues: 21.0347 Evaluate side-chains 123 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 121 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ARG Chi-restraints excluded: chain B residue 234 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.0670 chunk 33 optimal weight: 0.0980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 0.0470 overall best weight: 0.4016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN R 270 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.165561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.129869 restraints weight = 9448.430| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 2.74 r_work: 0.3507 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7291 Z= 0.133 Angle : 0.556 6.864 9917 Z= 0.294 Chirality : 0.044 0.207 1139 Planarity : 0.004 0.033 1265 Dihedral : 4.875 49.792 1012 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.39 % Allowed : 14.11 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.28), residues: 910 helix: 1.83 (0.26), residues: 406 sheet: -1.61 (0.36), residues: 166 loop : -0.54 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 38 TYR 0.022 0.001 TYR R 187 PHE 0.014 0.001 PHE A 212 TRP 0.012 0.001 TRP R 263 HIS 0.003 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 7289) covalent geometry : angle 0.55549 ( 9913) SS BOND : bond 0.00231 ( 2) SS BOND : angle 0.60751 ( 4) hydrogen bonds : bond 0.04563 ( 390) hydrogen bonds : angle 4.82035 ( 1131) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 292 PHE cc_start: 0.8740 (m-10) cc_final: 0.8440 (m-80) REVERT: R 33 GLU cc_start: 0.8251 (mm-30) cc_final: 0.7938 (mt-10) REVERT: R 41 ASN cc_start: 0.8557 (m-40) cc_final: 0.8253 (m110) REVERT: R 186 ILE cc_start: 0.8012 (pt) cc_final: 0.7789 (mm) outliers start: 25 outliers final: 14 residues processed: 151 average time/residue: 0.0971 time to fit residues: 19.3053 Evaluate side-chains 131 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain R residue 114 THR Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 125 LYS Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 243 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 25 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 35 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN B 230 ASN R 98 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.162765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.126594 restraints weight = 9320.558| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.76 r_work: 0.3433 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7291 Z= 0.174 Angle : 0.553 5.805 9917 Z= 0.291 Chirality : 0.044 0.212 1139 Planarity : 0.004 0.036 1265 Dihedral : 4.466 50.824 1008 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 4.34 % Allowed : 16.01 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.28), residues: 910 helix: 1.93 (0.26), residues: 406 sheet: -1.69 (0.35), residues: 173 loop : -0.55 (0.35), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 38 TYR 0.016 0.001 TYR R 187 PHE 0.014 0.002 PHE A 222 TRP 0.013 0.001 TRP R 263 HIS 0.003 0.001 HIS R 131 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 7289) covalent geometry : angle 0.55321 ( 9913) SS BOND : bond 0.00467 ( 2) SS BOND : angle 0.59093 ( 4) hydrogen bonds : bond 0.04423 ( 390) hydrogen bonds : angle 4.61083 ( 1131) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 129 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 262 MET cc_start: 0.8171 (tpp) cc_final: 0.7556 (mmt) REVERT: B 292 PHE cc_start: 0.8832 (m-10) cc_final: 0.8583 (m-80) REVERT: B 329 THR cc_start: 0.9094 (m) cc_final: 0.8681 (p) REVERT: R 33 GLU cc_start: 0.8329 (mm-30) cc_final: 0.7973 (mt-10) REVERT: R 41 ASN cc_start: 0.8466 (m-40) cc_final: 0.8139 (m110) outliers start: 32 outliers final: 20 residues processed: 148 average time/residue: 0.0753 time to fit residues: 15.1579 Evaluate side-chains 137 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain R residue 114 THR Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 203 MET Chi-restraints excluded: chain R residue 204 CYS Chi-restraints excluded: chain R residue 243 VAL Chi-restraints excluded: chain R residue 250 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 29 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 32 optimal weight: 0.2980 chunk 20 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.163482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.127058 restraints weight = 9415.264| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.80 r_work: 0.3449 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7291 Z= 0.154 Angle : 0.542 7.182 9917 Z= 0.284 Chirality : 0.044 0.201 1139 Planarity : 0.004 0.039 1265 Dihedral : 4.433 51.762 1008 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 4.07 % Allowed : 17.23 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.28), residues: 910 helix: 2.01 (0.26), residues: 406 sheet: -1.69 (0.36), residues: 173 loop : -0.53 (0.35), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 38 TYR 0.020 0.001 TYR R 187 PHE 0.013 0.001 PHE A 212 TRP 0.012 0.001 TRP R 263 HIS 0.003 0.001 HIS R 131 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 7289) covalent geometry : angle 0.54191 ( 9913) SS BOND : bond 0.00402 ( 2) SS BOND : angle 0.58281 ( 4) hydrogen bonds : bond 0.04204 ( 390) hydrogen bonds : angle 4.51080 ( 1131) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 126 time to evaluate : 0.213 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 262 MET cc_start: 0.8241 (tpp) cc_final: 0.7620 (mmt) REVERT: B 329 THR cc_start: 0.9106 (m) cc_final: 0.8698 (p) REVERT: R 33 GLU cc_start: 0.8419 (mm-30) cc_final: 0.8071 (mt-10) REVERT: R 41 ASN cc_start: 0.8417 (m-40) cc_final: 0.8091 (m110) REVERT: R 251 MET cc_start: 0.6986 (tpt) cc_final: 0.6386 (tmm) outliers start: 30 outliers final: 20 residues processed: 140 average time/residue: 0.0811 time to fit residues: 15.4640 Evaluate side-chains 136 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain R residue 73 LEU Chi-restraints excluded: chain R residue 114 THR Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 203 MET Chi-restraints excluded: chain R residue 204 CYS Chi-restraints excluded: chain R residue 239 VAL Chi-restraints excluded: chain R residue 243 VAL Chi-restraints excluded: chain R residue 246 THR Chi-restraints excluded: chain R residue 250 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 27 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 88 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 23 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.163066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.126538 restraints weight = 9425.604| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.81 r_work: 0.3438 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7291 Z= 0.161 Angle : 0.535 6.398 9917 Z= 0.281 Chirality : 0.044 0.201 1139 Planarity : 0.004 0.037 1265 Dihedral : 4.432 52.116 1008 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 4.48 % Allowed : 17.23 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.28), residues: 910 helix: 2.05 (0.26), residues: 406 sheet: -1.71 (0.36), residues: 172 loop : -0.59 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 38 TYR 0.020 0.001 TYR R 187 PHE 0.015 0.002 PHE A 222 TRP 0.013 0.001 TRP R 263 HIS 0.003 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 7289) covalent geometry : angle 0.53519 ( 9913) SS BOND : bond 0.00433 ( 2) SS BOND : angle 0.56434 ( 4) hydrogen bonds : bond 0.04161 ( 390) hydrogen bonds : angle 4.45112 ( 1131) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 119 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 198 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8455 (pp) REVERT: B 262 MET cc_start: 0.8214 (tpp) cc_final: 0.7586 (mmt) REVERT: B 292 PHE cc_start: 0.8622 (m-80) cc_final: 0.8254 (m-80) REVERT: R 33 GLU cc_start: 0.8516 (mm-30) cc_final: 0.8200 (mt-10) REVERT: R 41 ASN cc_start: 0.8362 (m-40) cc_final: 0.8063 (m110) REVERT: R 251 MET cc_start: 0.7039 (tpt) cc_final: 0.6435 (tmm) outliers start: 33 outliers final: 22 residues processed: 139 average time/residue: 0.0888 time to fit residues: 16.6572 Evaluate side-chains 135 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 112 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain R residue 114 THR Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 203 MET Chi-restraints excluded: chain R residue 204 CYS Chi-restraints excluded: chain R residue 239 VAL Chi-restraints excluded: chain R residue 243 VAL Chi-restraints excluded: chain R residue 250 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 9 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 63 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 268 ASN ** A 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 184 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.159699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.124001 restraints weight = 9486.523| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 2.70 r_work: 0.3409 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 7291 Z= 0.280 Angle : 0.626 6.916 9917 Z= 0.327 Chirality : 0.047 0.245 1139 Planarity : 0.004 0.039 1265 Dihedral : 4.856 54.901 1008 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 4.61 % Allowed : 17.77 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.28), residues: 910 helix: 1.75 (0.26), residues: 404 sheet: -1.94 (0.35), residues: 176 loop : -0.70 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 346 TYR 0.021 0.002 TYR R 187 PHE 0.018 0.002 PHE B 292 TRP 0.016 0.002 TRP R 263 HIS 0.004 0.001 HIS R 131 Details of bonding type rmsd covalent geometry : bond 0.00666 ( 7289) covalent geometry : angle 0.62633 ( 9913) SS BOND : bond 0.00709 ( 2) SS BOND : angle 0.65006 ( 4) hydrogen bonds : bond 0.04675 ( 390) hydrogen bonds : angle 4.68676 ( 1131) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 115 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: A 220 HIS cc_start: 0.7886 (t-170) cc_final: 0.6943 (t-170) REVERT: A 300 ASP cc_start: 0.7328 (m-30) cc_final: 0.6768 (t0) REVERT: B 198 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8448 (pp) REVERT: B 262 MET cc_start: 0.8212 (tpp) cc_final: 0.7862 (mmt) REVERT: B 292 PHE cc_start: 0.8791 (m-80) cc_final: 0.8499 (m-80) REVERT: R 33 GLU cc_start: 0.8574 (mm-30) cc_final: 0.8219 (mt-10) REVERT: R 41 ASN cc_start: 0.8535 (m-40) cc_final: 0.8057 (m110) REVERT: R 251 MET cc_start: 0.7120 (tpt) cc_final: 0.6466 (tmm) outliers start: 34 outliers final: 26 residues processed: 137 average time/residue: 0.0886 time to fit residues: 16.5263 Evaluate side-chains 140 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 113 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 253 TYR Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain R residue 60 ILE Chi-restraints excluded: chain R residue 114 THR Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 203 MET Chi-restraints excluded: chain R residue 204 CYS Chi-restraints excluded: chain R residue 239 VAL Chi-restraints excluded: chain R residue 243 VAL Chi-restraints excluded: chain R residue 250 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 46 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 83 optimal weight: 0.5980 chunk 74 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.162601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.127840 restraints weight = 9380.604| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 2.57 r_work: 0.3474 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7291 Z= 0.161 Angle : 0.557 8.090 9917 Z= 0.291 Chirality : 0.045 0.269 1139 Planarity : 0.004 0.041 1265 Dihedral : 4.608 55.567 1008 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.93 % Allowed : 19.95 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.28), residues: 910 helix: 1.76 (0.26), residues: 411 sheet: -1.88 (0.36), residues: 172 loop : -0.62 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 346 TYR 0.023 0.001 TYR R 187 PHE 0.015 0.002 PHE R 294 TRP 0.013 0.001 TRP R 263 HIS 0.003 0.001 HIS R 131 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 7289) covalent geometry : angle 0.55658 ( 9913) SS BOND : bond 0.00105 ( 2) SS BOND : angle 0.91498 ( 4) hydrogen bonds : bond 0.04233 ( 390) hydrogen bonds : angle 4.56983 ( 1131) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 120 time to evaluate : 0.305 Fit side-chains revert: symmetry clash REVERT: A 38 ARG cc_start: 0.8665 (mmm-85) cc_final: 0.8406 (mtp85) REVERT: A 220 HIS cc_start: 0.7801 (t-170) cc_final: 0.6835 (t-170) REVERT: A 300 ASP cc_start: 0.7271 (m-30) cc_final: 0.6721 (t0) REVERT: B 198 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8484 (pp) REVERT: B 262 MET cc_start: 0.8109 (tpp) cc_final: 0.7549 (mmt) REVERT: B 292 PHE cc_start: 0.8698 (m-80) cc_final: 0.8410 (m-80) REVERT: G 21 MET cc_start: 0.7622 (ptm) cc_final: 0.7280 (ppp) REVERT: R 33 GLU cc_start: 0.8489 (mm-30) cc_final: 0.8195 (mt-10) REVERT: R 41 ASN cc_start: 0.8437 (m-40) cc_final: 0.8141 (m110) REVERT: R 251 MET cc_start: 0.7020 (tpt) cc_final: 0.6306 (tmm) outliers start: 29 outliers final: 18 residues processed: 137 average time/residue: 0.0938 time to fit residues: 17.2014 Evaluate side-chains 134 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 114 THR Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 190 CYS Chi-restraints excluded: chain R residue 203 MET Chi-restraints excluded: chain R residue 204 CYS Chi-restraints excluded: chain R residue 239 VAL Chi-restraints excluded: chain R residue 243 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 43 optimal weight: 0.0980 chunk 5 optimal weight: 6.9990 chunk 21 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 6 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN ** A 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 184 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.163250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.129016 restraints weight = 9377.597| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 2.46 r_work: 0.3490 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7291 Z= 0.156 Angle : 0.560 7.008 9917 Z= 0.292 Chirality : 0.045 0.249 1139 Planarity : 0.004 0.041 1265 Dihedral : 4.550 55.786 1008 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.53 % Allowed : 19.40 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.28), residues: 910 helix: 1.84 (0.26), residues: 410 sheet: -1.87 (0.36), residues: 174 loop : -0.55 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 346 TYR 0.020 0.001 TYR R 187 PHE 0.015 0.001 PHE R 294 TRP 0.012 0.001 TRP R 263 HIS 0.003 0.001 HIS R 131 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 7289) covalent geometry : angle 0.56041 ( 9913) SS BOND : bond 0.00298 ( 2) SS BOND : angle 0.47390 ( 4) hydrogen bonds : bond 0.04204 ( 390) hydrogen bonds : angle 4.54877 ( 1131) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 114 time to evaluate : 0.240 Fit side-chains revert: symmetry clash REVERT: A 38 ARG cc_start: 0.8587 (mmm-85) cc_final: 0.8369 (mtp85) REVERT: A 220 HIS cc_start: 0.7809 (t-170) cc_final: 0.6876 (t-170) REVERT: A 346 ARG cc_start: 0.7569 (mtm-85) cc_final: 0.7291 (mtm-85) REVERT: B 198 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8476 (pp) REVERT: B 246 ASP cc_start: 0.8079 (m-30) cc_final: 0.7806 (m-30) REVERT: B 262 MET cc_start: 0.8047 (tpp) cc_final: 0.7498 (mmt) REVERT: B 292 PHE cc_start: 0.8663 (m-80) cc_final: 0.8397 (m-80) REVERT: B 329 THR cc_start: 0.8990 (m) cc_final: 0.8647 (p) REVERT: G 21 MET cc_start: 0.7643 (ptm) cc_final: 0.7288 (ppp) REVERT: R 33 GLU cc_start: 0.8499 (mm-30) cc_final: 0.8208 (mt-10) REVERT: R 41 ASN cc_start: 0.8371 (m-40) cc_final: 0.8097 (m110) outliers start: 26 outliers final: 20 residues processed: 133 average time/residue: 0.0837 time to fit residues: 15.0307 Evaluate side-chains 133 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain R residue 114 THR Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 190 CYS Chi-restraints excluded: chain R residue 203 MET Chi-restraints excluded: chain R residue 204 CYS Chi-restraints excluded: chain R residue 239 VAL Chi-restraints excluded: chain R residue 243 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 58 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 36 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.162885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.127276 restraints weight = 9301.675| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 2.68 r_work: 0.3445 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7291 Z= 0.147 Angle : 0.549 6.655 9917 Z= 0.286 Chirality : 0.044 0.240 1139 Planarity : 0.004 0.040 1265 Dihedral : 4.490 55.740 1008 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.66 % Allowed : 19.13 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.28), residues: 910 helix: 1.88 (0.26), residues: 410 sheet: -1.87 (0.36), residues: 174 loop : -0.55 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 346 TYR 0.018 0.001 TYR R 187 PHE 0.013 0.001 PHE A 212 TRP 0.012 0.001 TRP R 263 HIS 0.003 0.001 HIS R 131 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 7289) covalent geometry : angle 0.54918 ( 9913) SS BOND : bond 0.00257 ( 2) SS BOND : angle 0.38478 ( 4) hydrogen bonds : bond 0.04118 ( 390) hydrogen bonds : angle 4.54681 ( 1131) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 121 time to evaluate : 0.209 Fit side-chains revert: symmetry clash REVERT: A 38 ARG cc_start: 0.8673 (mmm-85) cc_final: 0.8444 (mtp85) REVERT: A 220 HIS cc_start: 0.7830 (t-170) cc_final: 0.6873 (t-170) REVERT: A 346 ARG cc_start: 0.7629 (mtm-85) cc_final: 0.7339 (mtm-85) REVERT: B 198 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8504 (pp) REVERT: B 246 ASP cc_start: 0.8126 (m-30) cc_final: 0.7809 (m-30) REVERT: B 262 MET cc_start: 0.8101 (tpp) cc_final: 0.7527 (mmt) REVERT: B 292 PHE cc_start: 0.8666 (m-80) cc_final: 0.8366 (m-80) REVERT: B 329 THR cc_start: 0.9004 (m) cc_final: 0.8662 (p) REVERT: G 21 MET cc_start: 0.7679 (ptm) cc_final: 0.7322 (ppp) REVERT: R 33 GLU cc_start: 0.8495 (mm-30) cc_final: 0.8211 (mt-10) REVERT: R 41 ASN cc_start: 0.8383 (m-40) cc_final: 0.8092 (m110) REVERT: R 99 ARG cc_start: 0.7696 (OUTLIER) cc_final: 0.7327 (mmt90) outliers start: 27 outliers final: 22 residues processed: 141 average time/residue: 0.0778 time to fit residues: 15.0220 Evaluate side-chains 138 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 114 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain R residue 99 ARG Chi-restraints excluded: chain R residue 114 THR Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 190 CYS Chi-restraints excluded: chain R residue 203 MET Chi-restraints excluded: chain R residue 204 CYS Chi-restraints excluded: chain R residue 239 VAL Chi-restraints excluded: chain R residue 243 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 33 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 chunk 60 optimal weight: 0.2980 chunk 89 optimal weight: 10.0000 chunk 34 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.163437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.128085 restraints weight = 9341.221| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 2.60 r_work: 0.3479 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 7291 Z= 0.147 Angle : 0.572 8.024 9917 Z= 0.295 Chirality : 0.044 0.233 1139 Planarity : 0.004 0.040 1265 Dihedral : 4.490 55.619 1008 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.39 % Allowed : 19.67 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.37 (0.28), residues: 910 helix: 1.89 (0.26), residues: 410 sheet: -1.87 (0.36), residues: 174 loop : -0.56 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 346 TYR 0.018 0.001 TYR R 187 PHE 0.013 0.001 PHE A 212 TRP 0.012 0.001 TRP R 263 HIS 0.003 0.001 HIS R 131 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 7289) covalent geometry : angle 0.57176 ( 9913) SS BOND : bond 0.00271 ( 2) SS BOND : angle 0.32410 ( 4) hydrogen bonds : bond 0.04145 ( 390) hydrogen bonds : angle 4.56462 ( 1131) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1820 Ramachandran restraints generated. 910 Oldfield, 0 Emsley, 910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 115 time to evaluate : 0.262 Fit side-chains revert: symmetry clash REVERT: A 13 ARG cc_start: 0.6748 (mpt180) cc_final: 0.5596 (mtm-85) REVERT: A 21 GLU cc_start: 0.7900 (tm-30) cc_final: 0.7644 (tm-30) REVERT: A 346 ARG cc_start: 0.7570 (mtm-85) cc_final: 0.7316 (mtm-85) REVERT: B 246 ASP cc_start: 0.8107 (m-30) cc_final: 0.7817 (m-30) REVERT: B 262 MET cc_start: 0.8044 (tpp) cc_final: 0.7482 (mmt) REVERT: B 292 PHE cc_start: 0.8642 (m-80) cc_final: 0.8364 (m-80) REVERT: B 329 THR cc_start: 0.8980 (m) cc_final: 0.8639 (p) REVERT: G 21 MET cc_start: 0.7668 (ptm) cc_final: 0.7319 (ppp) REVERT: R 33 GLU cc_start: 0.8475 (mm-30) cc_final: 0.8218 (mt-10) REVERT: R 41 ASN cc_start: 0.8386 (m-40) cc_final: 0.8112 (m110) REVERT: R 99 ARG cc_start: 0.7668 (OUTLIER) cc_final: 0.7306 (mmt90) outliers start: 25 outliers final: 22 residues processed: 134 average time/residue: 0.0840 time to fit residues: 15.1815 Evaluate side-chains 139 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 116 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain R residue 99 ARG Chi-restraints excluded: chain R residue 114 THR Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 190 CYS Chi-restraints excluded: chain R residue 203 MET Chi-restraints excluded: chain R residue 204 CYS Chi-restraints excluded: chain R residue 239 VAL Chi-restraints excluded: chain R residue 243 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 22 optimal weight: 0.5980 chunk 39 optimal weight: 0.2980 chunk 2 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 78 optimal weight: 0.0170 chunk 89 optimal weight: 8.9990 chunk 33 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 68 optimal weight: 0.0000 chunk 48 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 overall best weight: 0.3022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 HIS ** A 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.166559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.130153 restraints weight = 9340.774| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 2.52 r_work: 0.3510 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 7291 Z= 0.117 Angle : 0.561 8.914 9917 Z= 0.288 Chirality : 0.043 0.211 1139 Planarity : 0.004 0.042 1265 Dihedral : 4.326 55.872 1008 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.58 % Allowed : 20.76 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.29), residues: 910 helix: 1.91 (0.26), residues: 417 sheet: -1.80 (0.37), residues: 172 loop : -0.47 (0.35), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 346 TYR 0.015 0.001 TYR R 187 PHE 0.017 0.001 PHE A 222 TRP 0.010 0.001 TRP B 82 HIS 0.002 0.001 HIS R 131 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 7289) covalent geometry : angle 0.56086 ( 9913) SS BOND : bond 0.00125 ( 2) SS BOND : angle 0.25389 ( 4) hydrogen bonds : bond 0.03951 ( 390) hydrogen bonds : angle 4.47972 ( 1131) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1900.22 seconds wall clock time: 33 minutes 21.57 seconds (2001.57 seconds total)