Starting phenix.real_space_refine on Mon Apr 28 06:59:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jpp_36486/04_2025/8jpp_36486.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jpp_36486/04_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8jpp_36486/04_2025/8jpp_36486.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jpp_36486/04_2025/8jpp_36486.map" model { file = "/net/cci-nas-00/data/ceres_data/8jpp_36486/04_2025/8jpp_36486.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jpp_36486/04_2025/8jpp_36486.cif" } resolution = 3.2 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= 0.047 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1, 'ARG:plan': 4} 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: {'GLU:plan': 3, 'ASP:plan': 2} 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: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 2} 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: 5.73, per 1000 atoms: 0.80 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: 1.98 Conformation dependent library (CDL) restraints added in 970.9 milliseconds 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: 0.74 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: 2.03 Time building geometry restraints manager: 2.27 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: 1.920 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.430 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.900 ------------------------------------------------------------------------------- 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 (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: -0.08 (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 TRP 0.010 0.001 TRP R 263 HIS 0.004 0.001 HIS A 220 PHE 0.025 0.002 PHE A 208 TYR 0.012 0.001 TYR R 107 ARG 0.009 0.000 ARG A 38 Details of bonding type rmsd hydrogen bonds : bond 0.17445 ( 390) hydrogen bonds : angle 7.34456 ( 1131) SS BOND : bond 0.00334 ( 2) SS BOND : angle 0.62662 ( 4) covalent geometry : bond 0.00390 ( 7289) covalent geometry : angle 0.65238 ( 9913) *********************** 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 : 0.750 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: 0.2215 time to fit residues: 42.6103 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 : 0.725 ------------------------------------------------------------------------------- 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 75 optimal weight: 0.9990 chunk 68 optimal weight: 0.0070 chunk 37 optimal weight: 0.8980 chunk 23 optimal weight: 9.9990 chunk 46 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 52 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 overall best weight: 0.7600 ------------------------------------------------------------------------------- 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 = 0.4048 r_free = 0.4048 target = 0.163033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.127251 restraints weight = 9353.281| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 2.70 r_work: 0.3452 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7291 Z= 0.165 Angle : 0.576 6.951 9917 Z= 0.304 Chirality : 0.045 0.208 1139 Planarity : 0.004 0.037 1265 Dihedral : 4.949 50.056 1012 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.66 % Allowed : 14.11 % Favored : 82.23 % 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: 0.28 (0.28), residues: 910 helix: 1.73 (0.26), residues: 406 sheet: -1.77 (0.35), residues: 171 loop : -0.54 (0.35), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 263 HIS 0.004 0.001 HIS A 220 PHE 0.013 0.001 PHE A 212 TYR 0.024 0.001 TYR R 187 ARG 0.006 0.000 ARG A 38 Details of bonding type rmsd hydrogen bonds : bond 0.04714 ( 390) hydrogen bonds : angle 4.87033 ( 1131) SS BOND : bond 0.00384 ( 2) SS BOND : angle 0.62293 ( 4) covalent geometry : bond 0.00380 ( 7289) covalent geometry : angle 0.57561 ( 9913) *********************** 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 157 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 292 PHE cc_start: 0.8804 (m-10) cc_final: 0.8486 (m-80) REVERT: R 33 GLU cc_start: 0.8316 (mm-30) cc_final: 0.7961 (mt-10) REVERT: R 41 ASN cc_start: 0.8611 (m-40) cc_final: 0.8288 (m110) REVERT: R 186 ILE cc_start: 0.8053 (pt) cc_final: 0.7813 (mm) outliers start: 27 outliers final: 15 residues processed: 148 average time/residue: 0.2085 time to fit residues: 40.7926 Evaluate side-chains 125 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.822 ------------------------------------------------------------------------------- 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 57 LYS 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 35 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 57 optimal weight: 0.0980 chunk 29 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 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 59 GLN R 98 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.163732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.128015 restraints weight = 9322.014| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 2.69 r_work: 0.3461 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7291 Z= 0.146 Angle : 0.543 6.129 9917 Z= 0.285 Chirality : 0.044 0.207 1139 Planarity : 0.004 0.035 1265 Dihedral : 4.435 50.842 1008 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.93 % Allowed : 16.15 % Favored : 79.92 % 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: 0.45 (0.28), residues: 910 helix: 1.93 (0.26), residues: 406 sheet: -1.69 (0.35), residues: 173 loop : -0.55 (0.34), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 263 HIS 0.003 0.001 HIS R 131 PHE 0.012 0.001 PHE A 212 TYR 0.016 0.001 TYR R 187 ARG 0.004 0.000 ARG A 38 Details of bonding type rmsd hydrogen bonds : bond 0.04363 ( 390) hydrogen bonds : angle 4.61506 ( 1131) SS BOND : bond 0.00353 ( 2) SS BOND : angle 0.60997 ( 4) covalent geometry : bond 0.00335 ( 7289) covalent geometry : angle 0.54291 ( 9913) *********************** 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 153 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 124 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 262 MET cc_start: 0.8118 (tpp) cc_final: 0.7509 (mmt) REVERT: B 292 PHE cc_start: 0.8812 (m-10) cc_final: 0.8567 (m-80) REVERT: B 329 THR cc_start: 0.9081 (m) cc_final: 0.8684 (p) REVERT: R 33 GLU cc_start: 0.8323 (mm-30) cc_final: 0.7986 (mt-10) REVERT: R 41 ASN cc_start: 0.8459 (m-40) cc_final: 0.8137 (m110) outliers start: 29 outliers final: 19 residues processed: 141 average time/residue: 0.1787 time to fit residues: 34.3919 Evaluate side-chains 137 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 0.762 ------------------------------------------------------------------------------- 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 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 124 ILE Chi-restraints excluded: chain R residue 125 LYS 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: 0.8980 chunk 53 optimal weight: 0.7980 chunk 69 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 ASN B 230 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.163023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.126412 restraints weight = 9485.966| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 2.85 r_work: 0.3443 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 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 0.035 7291 Z= 0.168 Angle : 0.548 6.833 9917 Z= 0.288 Chirality : 0.044 0.205 1139 Planarity : 0.004 0.037 1265 Dihedral : 4.469 52.986 1008 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 4.21 % Allowed : 17.23 % Favored : 78.56 % 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 (0.29), residues: 910 helix: 2.00 (0.26), residues: 406 sheet: -1.74 (0.36), residues: 173 loop : -0.56 (0.35), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 263 HIS 0.003 0.001 HIS R 131 PHE 0.015 0.002 PHE A 222 TYR 0.020 0.001 TYR R 187 ARG 0.004 0.000 ARG A 38 Details of bonding type rmsd hydrogen bonds : bond 0.04282 ( 390) hydrogen bonds : angle 4.50984 ( 1131) SS BOND : bond 0.00468 ( 2) SS BOND : angle 0.57675 ( 4) covalent geometry : bond 0.00394 ( 7289) covalent geometry : angle 0.54773 ( 9913) *********************** 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 151 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 120 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 198 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8465 (pp) REVERT: B 262 MET cc_start: 0.8177 (tpp) cc_final: 0.7545 (mmt) REVERT: B 329 THR cc_start: 0.9084 (m) cc_final: 0.8671 (p) REVERT: R 33 GLU cc_start: 0.8459 (mm-30) cc_final: 0.8117 (mt-10) REVERT: R 41 ASN cc_start: 0.8434 (m-40) cc_final: 0.8114 (m110) outliers start: 31 outliers final: 20 residues processed: 138 average time/residue: 0.2251 time to fit residues: 40.9939 Evaluate side-chains 135 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.832 ------------------------------------------------------------------------------- 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 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 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 239 VAL Chi-restraints excluded: chain R residue 243 VAL 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 41 optimal weight: 0.2980 chunk 18 optimal weight: 0.9990 chunk 78 optimal weight: 0.0970 chunk 62 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.165111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.129505 restraints weight = 9368.563| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 2.70 r_work: 0.3473 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7291 Z= 0.127 Angle : 0.518 5.757 9917 Z= 0.273 Chirality : 0.043 0.197 1139 Planarity : 0.004 0.037 1265 Dihedral : 4.386 54.251 1008 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.26 % Allowed : 19.00 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.58 (0.29), residues: 910 helix: 2.07 (0.26), residues: 412 sheet: -1.74 (0.36), residues: 173 loop : -0.50 (0.35), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 263 HIS 0.002 0.001 HIS A 347 PHE 0.014 0.001 PHE R 294 TYR 0.021 0.001 TYR R 187 ARG 0.006 0.000 ARG A 346 Details of bonding type rmsd hydrogen bonds : bond 0.03992 ( 390) hydrogen bonds : angle 4.38564 ( 1131) SS BOND : bond 0.00285 ( 2) SS BOND : angle 0.49051 ( 4) covalent geometry : bond 0.00285 ( 7289) covalent geometry : angle 0.51829 ( 9913) *********************** 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 147 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 300 ASP cc_start: 0.7105 (m-30) cc_final: 0.6660 (t0) REVERT: B 198 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8491 (pp) REVERT: B 262 MET cc_start: 0.8149 (tpp) cc_final: 0.7503 (mmt) REVERT: B 292 PHE cc_start: 0.8578 (m-80) cc_final: 0.8247 (m-80) REVERT: B 329 THR cc_start: 0.9080 (m) cc_final: 0.8704 (p) REVERT: R 33 GLU cc_start: 0.8424 (mm-30) cc_final: 0.8125 (mt-10) REVERT: R 41 ASN cc_start: 0.8328 (m-40) cc_final: 0.8018 (m110) REVERT: R 125 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8431 (tttp) outliers start: 24 outliers final: 16 residues processed: 136 average time/residue: 0.2716 time to fit residues: 50.1146 Evaluate side-chains 131 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 125 LYS 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 243 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 18 optimal weight: 0.5980 chunk 62 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.163675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.127935 restraints weight = 9304.426| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 2.71 r_work: 0.3444 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2020 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= 0.156 Angle : 0.535 5.967 9917 Z= 0.280 Chirality : 0.044 0.203 1139 Planarity : 0.004 0.037 1265 Dihedral : 4.425 54.880 1008 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 4.07 % Allowed : 19.13 % Favored : 76.80 % 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: 0.54 (0.29), residues: 910 helix: 2.05 (0.26), residues: 411 sheet: -1.80 (0.36), residues: 174 loop : -0.51 (0.35), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 263 HIS 0.002 0.001 HIS R 131 PHE 0.014 0.001 PHE B 292 TYR 0.018 0.001 TYR R 187 ARG 0.008 0.000 ARG A 346 Details of bonding type rmsd hydrogen bonds : bond 0.04116 ( 390) hydrogen bonds : angle 4.40439 ( 1131) SS BOND : bond 0.00413 ( 2) SS BOND : angle 0.46284 ( 4) covalent geometry : bond 0.00362 ( 7289) covalent geometry : angle 0.53546 ( 9913) *********************** 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 148 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 118 time to evaluate : 0.896 Fit side-chains revert: symmetry clash REVERT: A 220 HIS cc_start: 0.7869 (t-170) cc_final: 0.6896 (t-170) REVERT: B 198 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8485 (pp) REVERT: B 262 MET cc_start: 0.8169 (tpp) cc_final: 0.7527 (mmt) REVERT: B 292 PHE cc_start: 0.8623 (m-80) cc_final: 0.8332 (m-80) REVERT: B 329 THR cc_start: 0.9112 (m) cc_final: 0.8713 (p) REVERT: R 33 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8198 (mt-10) REVERT: R 41 ASN cc_start: 0.8334 (m-40) cc_final: 0.8048 (m110) REVERT: R 125 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8407 (tttp) outliers start: 30 outliers final: 20 residues processed: 137 average time/residue: 0.2231 time to fit residues: 41.9353 Evaluate side-chains 136 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 0.904 ------------------------------------------------------------------------------- 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 359 THR Chi-restraints excluded: chain A residue 376 MET 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 125 LYS 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 71 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 59 optimal weight: 0.4980 chunk 56 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 43 optimal weight: 0.0000 chunk 39 optimal weight: 1.9990 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4058 r_free = 0.4058 target = 0.164216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.128593 restraints weight = 9276.401| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 2.67 r_work: 0.3462 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7291 Z= 0.144 Angle : 0.537 7.765 9917 Z= 0.280 Chirality : 0.044 0.212 1139 Planarity : 0.004 0.038 1265 Dihedral : 4.413 55.526 1008 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.93 % Allowed : 19.13 % 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 (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: 0.53 (0.29), residues: 910 helix: 2.09 (0.26), residues: 411 sheet: -1.88 (0.37), residues: 166 loop : -0.58 (0.34), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 263 HIS 0.002 0.001 HIS A 347 PHE 0.014 0.001 PHE R 115 TYR 0.022 0.001 TYR R 187 ARG 0.007 0.000 ARG A 346 Details of bonding type rmsd hydrogen bonds : bond 0.04049 ( 390) hydrogen bonds : angle 4.40203 ( 1131) SS BOND : bond 0.00329 ( 2) SS BOND : angle 0.42300 ( 4) covalent geometry : bond 0.00330 ( 7289) covalent geometry : angle 0.53747 ( 9913) *********************** 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 148 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 119 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.8637 (mmm-85) cc_final: 0.8427 (mtp85) REVERT: B 198 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8497 (pp) REVERT: B 262 MET cc_start: 0.8128 (tpp) cc_final: 0.7735 (mmt) REVERT: B 292 PHE cc_start: 0.8619 (m-80) cc_final: 0.8316 (m-80) REVERT: B 329 THR cc_start: 0.9097 (m) cc_final: 0.8683 (p) REVERT: G 21 MET cc_start: 0.7674 (ptm) cc_final: 0.7307 (ppp) REVERT: R 33 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8203 (mt-10) REVERT: R 41 ASN cc_start: 0.8311 (m-40) cc_final: 0.8014 (m110) REVERT: R 125 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.8373 (tttp) outliers start: 29 outliers final: 20 residues processed: 138 average time/residue: 0.2261 time to fit residues: 43.1271 Evaluate side-chains 135 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 0.851 ------------------------------------------------------------------------------- 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 B residue 294 CYS 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 125 LYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 66 optimal weight: 2.9990 chunk 17 optimal weight: 0.0370 chunk 46 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 43 optimal weight: 0.3980 chunk 41 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 67 optimal weight: 0.8980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN ** A 375 GLN ** 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 = 0.4067 r_free = 0.4067 target = 0.164854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.128210 restraints weight = 9355.169| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 2.52 r_work: 0.3481 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 7291 Z= 0.138 Angle : 0.556 11.598 9917 Z= 0.285 Chirality : 0.043 0.187 1139 Planarity : 0.004 0.037 1265 Dihedral : 4.384 55.458 1008 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.93 % Allowed : 19.00 % 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 (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: 0.52 (0.29), residues: 910 helix: 2.06 (0.26), residues: 411 sheet: -1.80 (0.37), residues: 168 loop : -0.59 (0.34), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 263 HIS 0.002 0.001 HIS A 347 PHE 0.013 0.001 PHE R 115 TYR 0.018 0.001 TYR R 187 ARG 0.006 0.000 ARG A 346 Details of bonding type rmsd hydrogen bonds : bond 0.04009 ( 390) hydrogen bonds : angle 4.43199 ( 1131) SS BOND : bond 0.00121 ( 2) SS BOND : angle 0.77179 ( 4) covalent geometry : bond 0.00322 ( 7289) covalent geometry : angle 0.55561 ( 9913) *********************** 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 148 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 119 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.8658 (mmm-85) cc_final: 0.8443 (mtp85) REVERT: B 262 MET cc_start: 0.8119 (tpp) cc_final: 0.7725 (mmt) REVERT: B 292 PHE cc_start: 0.8613 (m-80) cc_final: 0.8322 (m-80) REVERT: B 329 THR cc_start: 0.9083 (m) cc_final: 0.8671 (p) REVERT: G 21 MET cc_start: 0.7670 (ptm) cc_final: 0.7318 (ppp) REVERT: R 33 GLU cc_start: 0.8446 (mm-30) cc_final: 0.8219 (mt-10) REVERT: R 41 ASN cc_start: 0.8295 (m-40) cc_final: 0.7953 (m110) REVERT: R 125 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8382 (tttp) outliers start: 29 outliers final: 22 residues processed: 137 average time/residue: 0.1828 time to fit residues: 33.9415 Evaluate side-chains 140 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER 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 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 B residue 294 CYS 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 125 LYS 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 236 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 30 optimal weight: 0.8980 chunk 41 optimal weight: 0.2980 chunk 34 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 8 optimal weight: 0.0980 chunk 47 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 88 optimal weight: 0.4980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4074 r_free = 0.4074 target = 0.165590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.129092 restraints weight = 9406.837| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 2.52 r_work: 0.3497 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2299 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= 0.127 Angle : 0.564 10.284 9917 Z= 0.286 Chirality : 0.043 0.214 1139 Planarity : 0.004 0.038 1265 Dihedral : 4.296 55.404 1008 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.26 % Allowed : 19.95 % Favored : 76.80 % 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: 0.54 (0.29), residues: 910 helix: 2.06 (0.26), residues: 411 sheet: -1.75 (0.37), residues: 168 loop : -0.58 (0.34), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.002 0.001 HIS A 347 PHE 0.012 0.001 PHE A 212 TYR 0.017 0.001 TYR R 187 ARG 0.006 0.000 ARG A 346 Details of bonding type rmsd hydrogen bonds : bond 0.03965 ( 390) hydrogen bonds : angle 4.43684 ( 1131) SS BOND : bond 0.00203 ( 2) SS BOND : angle 0.43729 ( 4) covalent geometry : bond 0.00292 ( 7289) covalent geometry : angle 0.56422 ( 9913) *********************** 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 144 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 0.753 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8158 (OUTLIER) cc_final: 0.7927 (pttm) REVERT: A 38 ARG cc_start: 0.8682 (mmm-85) cc_final: 0.8453 (mtp85) REVERT: A 220 HIS cc_start: 0.7804 (t-170) cc_final: 0.6826 (t-170) REVERT: B 262 MET cc_start: 0.8065 (tpp) cc_final: 0.7674 (mmt) REVERT: B 292 PHE cc_start: 0.8559 (m-80) cc_final: 0.8274 (m-80) REVERT: B 329 THR cc_start: 0.9077 (m) cc_final: 0.8699 (p) REVERT: G 21 MET cc_start: 0.7675 (ptm) cc_final: 0.7328 (ppp) REVERT: R 33 GLU cc_start: 0.8435 (mm-30) cc_final: 0.8209 (mt-10) REVERT: R 41 ASN cc_start: 0.8221 (m-40) cc_final: 0.7950 (m110) REVERT: R 125 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.8355 (tttp) outliers start: 24 outliers final: 19 residues processed: 135 average time/residue: 0.1881 time to fit residues: 34.2470 Evaluate side-chains 135 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 54 SER 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 90 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 294 CYS 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 125 LYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 28 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 0 optimal weight: 9.9990 chunk 16 optimal weight: 0.0980 chunk 70 optimal weight: 0.1980 chunk 71 optimal weight: 0.0040 chunk 79 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 66 optimal weight: 0.8980 overall best weight: 0.3192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4091 r_free = 0.4091 target = 0.166990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.130564 restraints weight = 9507.411| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 2.53 r_work: 0.3525 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7291 Z= 0.113 Angle : 0.541 7.657 9917 Z= 0.277 Chirality : 0.043 0.214 1139 Planarity : 0.003 0.038 1265 Dihedral : 4.235 55.353 1008 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.71 % Allowed : 20.62 % 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 (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: 0.59 (0.29), residues: 910 helix: 2.16 (0.26), residues: 411 sheet: -1.78 (0.37), residues: 167 loop : -0.62 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.002 0.001 HIS A 347 PHE 0.012 0.001 PHE A 212 TYR 0.014 0.001 TYR R 187 ARG 0.006 0.000 ARG A 346 Details of bonding type rmsd hydrogen bonds : bond 0.03844 ( 390) hydrogen bonds : angle 4.31733 ( 1131) SS BOND : bond 0.00160 ( 2) SS BOND : angle 0.31180 ( 4) covalent geometry : bond 0.00248 ( 7289) covalent geometry : angle 0.54096 ( 9913) ********************** 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 147 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 0.769 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7965 (pttm) REVERT: A 220 HIS cc_start: 0.7765 (t-170) cc_final: 0.6806 (t-170) REVERT: B 262 MET cc_start: 0.7987 (tpp) cc_final: 0.7627 (mmt) REVERT: B 292 PHE cc_start: 0.8456 (m-80) cc_final: 0.8207 (m-80) REVERT: B 329 THR cc_start: 0.9065 (m) cc_final: 0.8701 (p) REVERT: B 339 TRP cc_start: 0.8800 (m100) cc_final: 0.8464 (m100) REVERT: G 21 MET cc_start: 0.7719 (ptm) cc_final: 0.7355 (ppp) REVERT: R 22 GLU cc_start: 0.7343 (tt0) cc_final: 0.6890 (tp30) REVERT: R 26 LEU cc_start: 0.8511 (mt) cc_final: 0.8286 (mp) REVERT: R 33 GLU cc_start: 0.8428 (mm-30) cc_final: 0.8217 (mt-10) REVERT: R 41 ASN cc_start: 0.8110 (m-40) cc_final: 0.7801 (m110) outliers start: 20 outliers final: 17 residues processed: 140 average time/residue: 0.1834 time to fit residues: 34.8399 Evaluate side-chains 135 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 114 THR 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 59 optimal weight: 0.6980 chunk 45 optimal weight: 0.0970 chunk 87 optimal weight: 0.9990 chunk 41 optimal weight: 0.1980 chunk 65 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 81 optimal weight: 0.0020 chunk 19 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 83 optimal weight: 0.5980 overall best weight: 0.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 131 HIS R 232 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.167311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.130990 restraints weight = 9305.085| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 2.53 r_work: 0.3532 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7291 Z= 0.112 Angle : 0.545 8.063 9917 Z= 0.279 Chirality : 0.043 0.211 1139 Planarity : 0.003 0.038 1265 Dihedral : 4.229 55.325 1008 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % 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 (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: 0.63 (0.29), residues: 910 helix: 2.21 (0.26), residues: 410 sheet: -1.72 (0.37), residues: 169 loop : -0.61 (0.34), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.002 0.001 HIS R 131 PHE 0.012 0.001 PHE A 212 TYR 0.014 0.001 TYR R 187 ARG 0.007 0.000 ARG A 346 Details of bonding type rmsd hydrogen bonds : bond 0.03838 ( 390) hydrogen bonds : angle 4.31779 ( 1131) SS BOND : bond 0.00157 ( 2) SS BOND : angle 0.26943 ( 4) covalent geometry : bond 0.00245 ( 7289) covalent geometry : angle 0.54543 ( 9913) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4086.15 seconds wall clock time: 72 minutes 48.94 seconds (4368.94 seconds total)