Starting phenix.real_space_refine on Wed Feb 12 03:26:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jpp_36486/02_2025/8jpp_36486.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jpp_36486/02_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_36486/02_2025/8jpp_36486.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jpp_36486/02_2025/8jpp_36486.map" model { file = "/net/cci-nas-00/data/ceres_data/8jpp_36486/02_2025/8jpp_36486.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jpp_36486/02_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 4.86, per 1000 atoms: 0.68 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: 1.74 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.76 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: 2.08 Time building geometry restraints manager: 1.99 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: 2.190 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.850 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.390 ------------------------------------------------------------------------------- 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 7289 Z= 0.257 Angle : 0.652 7.764 9913 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 *********************** 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 : 0.817 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: 0.2307 time to fit residues: 44.2842 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 : 0.846 ------------------------------------------------------------------------------- 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: 0.9980 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: 0.9582 ------------------------------------------------------------------------------- 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 = 0.4041 r_free = 0.4041 target = 0.162322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.126278 restraints weight = 9355.347| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 2.72 r_work: 0.3437 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7289 Z= 0.289 Angle : 0.586 7.106 9913 Z= 0.309 Chirality : 0.045 0.214 1139 Planarity : 0.004 0.039 1265 Dihedral : 4.975 49.908 1012 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.80 % Allowed : 14.65 % Favored : 81.55 % 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: 0.23 (0.28), residues: 910 helix: 1.70 (0.26), residues: 405 sheet: -1.80 (0.35), residues: 171 loop : -0.59 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 263 HIS 0.004 0.001 HIS A 220 PHE 0.014 0.002 PHE R 115 TYR 0.022 0.002 TYR R 187 ARG 0.005 0.000 ARG A 38 *********************** 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 156 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 128 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 292 PHE cc_start: 0.8825 (m-10) cc_final: 0.8511 (m-80) REVERT: R 33 GLU cc_start: 0.8342 (mm-30) cc_final: 0.7960 (mt-10) REVERT: R 186 ILE cc_start: 0.8066 (pt) cc_final: 0.7293 (mm) REVERT: R 190 CYS cc_start: 0.8267 (m) cc_final: 0.7921 (m) outliers start: 28 outliers final: 16 residues processed: 146 average time/residue: 0.2093 time to fit residues: 40.4677 Evaluate side-chains 125 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.779 ------------------------------------------------------------------------------- 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 289 GLU 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: 1.9990 chunk 3 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 57 optimal weight: 9.9990 chunk 29 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 268 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 = 0.4063 r_free = 0.4063 target = 0.163365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.128552 restraints weight = 9310.752| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 2.59 r_work: 0.3492 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7289 Z= 0.251 Angle : 0.556 5.887 9913 Z= 0.291 Chirality : 0.044 0.212 1139 Planarity : 0.004 0.035 1265 Dihedral : 4.498 50.868 1008 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 4.07 % Allowed : 16.15 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.28), residues: 910 helix: 1.85 (0.26), residues: 406 sheet: -1.74 (0.35), 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 0.013 0.001 PHE R 115 TYR 0.017 0.001 TYR R 187 ARG 0.004 0.000 ARG A 38 *********************** 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 154 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 124 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 33 GLU cc_start: 0.8425 (mm-30) cc_final: 0.8063 (mt-10) REVERT: R 41 ASN cc_start: 0.8500 (m-40) cc_final: 0.8182 (m110) outliers start: 30 outliers final: 18 residues processed: 141 average time/residue: 0.1971 time to fit residues: 37.0738 Evaluate side-chains 132 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 0.819 ------------------------------------------------------------------------------- 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 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 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 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: 3.9990 chunk 69 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.163265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.127280 restraints weight = 9461.951| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 2.83 r_work: 0.3467 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7289 Z= 0.248 Angle : 0.550 7.515 9913 Z= 0.290 Chirality : 0.044 0.203 1139 Planarity : 0.004 0.040 1265 Dihedral : 4.485 51.848 1008 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.93 % Allowed : 17.77 % 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 (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: 0.42 (0.28), residues: 910 helix: 1.96 (0.26), residues: 406 sheet: -1.81 (0.36), residues: 173 loop : -0.57 (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 0.018 0.002 PHE B 292 TYR 0.020 0.001 TYR R 187 ARG 0.004 0.000 ARG A 38 *********************** 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 152 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 123 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 198 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8495 (pp) REVERT: B 262 MET cc_start: 0.8167 (tpp) cc_final: 0.7593 (mmt) REVERT: B 292 PHE cc_start: 0.8668 (m-80) cc_final: 0.8349 (m-80) REVERT: B 329 THR cc_start: 0.9032 (m) cc_final: 0.8664 (p) REVERT: R 33 GLU cc_start: 0.8470 (mm-30) cc_final: 0.8124 (mt-10) REVERT: R 41 ASN cc_start: 0.8446 (m-40) cc_final: 0.8153 (m110) outliers start: 29 outliers final: 19 residues processed: 139 average time/residue: 0.1994 time to fit residues: 37.4812 Evaluate side-chains 135 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 115 time to evaluate : 0.750 ------------------------------------------------------------------------------- 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 41 optimal weight: 0.0010 chunk 18 optimal weight: 0.5980 chunk 78 optimal weight: 0.0470 chunk 62 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 71 optimal weight: 0.5980 overall best weight: 0.3684 ------------------------------------------------------------------------------- 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 = 0.4076 r_free = 0.4076 target = 0.165674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.129202 restraints weight = 9350.566| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.79 r_work: 0.3491 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7289 Z= 0.164 Angle : 0.512 5.588 9913 Z= 0.269 Chirality : 0.042 0.182 1139 Planarity : 0.004 0.037 1265 Dihedral : 4.331 51.692 1008 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.26 % Allowed : 19.13 % 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 (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: 2.08 (0.26), residues: 412 sheet: -1.80 (0.35), residues: 175 loop : -0.45 (0.35), residues: 323 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 0.019 0.001 PHE A 222 TYR 0.019 0.001 TYR R 187 ARG 0.006 0.000 ARG A 346 *********************** 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 151 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.8653 (mmm-85) cc_final: 0.8392 (mtp85) REVERT: B 198 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8483 (pp) REVERT: B 262 MET cc_start: 0.8123 (tpp) cc_final: 0.7482 (mmt) REVERT: B 292 PHE cc_start: 0.8547 (m-80) cc_final: 0.8232 (m-80) REVERT: B 329 THR cc_start: 0.9039 (m) cc_final: 0.8676 (p) REVERT: R 33 GLU cc_start: 0.8414 (mm-30) cc_final: 0.8135 (mt-10) REVERT: R 41 ASN cc_start: 0.8292 (m-40) cc_final: 0.7954 (m110) REVERT: R 125 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8400 (tttp) outliers start: 24 outliers final: 13 residues processed: 140 average time/residue: 0.1924 time to fit residues: 36.2020 Evaluate side-chains 134 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LYS Chi-restraints excluded: chain A residue 59 GLN 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 198 LEU 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 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 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: 0.9980 chunk 11 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.4047 r_free = 0.4047 target = 0.163187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.127617 restraints weight = 9322.225| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 2.66 r_work: 0.3454 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7289 Z= 0.244 Angle : 0.539 6.038 9913 Z= 0.281 Chirality : 0.044 0.209 1139 Planarity : 0.004 0.037 1265 Dihedral : 4.423 53.720 1008 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.80 % Allowed : 19.27 % 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: 0.52 (0.28), residues: 910 helix: 2.04 (0.26), residues: 411 sheet: -1.85 (0.35), residues: 174 loop : -0.49 (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 0.013 0.001 PHE A 222 TYR 0.018 0.001 TYR R 187 ARG 0.007 0.000 ARG A 346 *********************** 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 145 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 117 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 198 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8488 (pp) REVERT: B 262 MET cc_start: 0.8137 (tpp) cc_final: 0.7733 (mmt) REVERT: B 292 PHE cc_start: 0.8608 (m-80) cc_final: 0.8328 (m-80) REVERT: B 329 THR cc_start: 0.9075 (m) cc_final: 0.8694 (p) REVERT: R 33 GLU cc_start: 0.8508 (mm-30) cc_final: 0.8221 (mt-10) REVERT: R 41 ASN cc_start: 0.8361 (m-40) cc_final: 0.8047 (m110) REVERT: R 125 LYS cc_start: 0.8650 (OUTLIER) cc_final: 0.8359 (tttp) outliers start: 28 outliers final: 18 residues processed: 133 average time/residue: 0.1865 time to fit residues: 33.8501 Evaluate side-chains 133 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.752 ------------------------------------------------------------------------------- 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 R residue 73 LEU Chi-restraints excluded: chain R residue 114 THR 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 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: 1.9990 chunk 40 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 43 optimal weight: 0.0040 chunk 39 optimal weight: 0.8980 overall best weight: 0.6792 ------------------------------------------------------------------------------- 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 = 0.4054 r_free = 0.4054 target = 0.163786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.128080 restraints weight = 9288.104| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 2.70 r_work: 0.3450 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7289 Z= 0.218 Angle : 0.540 8.204 9913 Z= 0.281 Chirality : 0.044 0.212 1139 Planarity : 0.004 0.038 1265 Dihedral : 4.421 54.542 1008 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.53 % Allowed : 19.95 % Favored : 76.53 % 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: 0.48 (0.28), residues: 910 helix: 2.03 (0.26), residues: 411 sheet: -1.92 (0.36), residues: 172 loop : -0.54 (0.34), residues: 327 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 0.013 0.001 PHE A 222 TYR 0.021 0.001 TYR R 187 ARG 0.007 0.000 ARG A 346 *********************** 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 142 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 116 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.8693 (mmm-85) cc_final: 0.8465 (mtp85) REVERT: B 198 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8490 (pp) REVERT: B 262 MET cc_start: 0.8174 (tpp) cc_final: 0.7773 (mmt) REVERT: B 292 PHE cc_start: 0.8642 (m-80) cc_final: 0.8349 (m-80) REVERT: B 329 THR cc_start: 0.9075 (m) cc_final: 0.8687 (p) REVERT: G 21 MET cc_start: 0.7650 (ptm) cc_final: 0.7307 (ppp) REVERT: R 33 GLU cc_start: 0.8497 (mm-30) cc_final: 0.8203 (mt-10) REVERT: R 41 ASN cc_start: 0.8340 (m-40) cc_final: 0.8055 (m110) REVERT: R 125 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.8349 (tttp) outliers start: 26 outliers final: 21 residues processed: 134 average time/residue: 0.1966 time to fit residues: 35.4732 Evaluate side-chains 134 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LYS 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 66 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 75 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 41 optimal weight: 0.1980 chunk 55 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 chunk 67 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4052 r_free = 0.4052 target = 0.163678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.127678 restraints weight = 9363.048| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 2.76 r_work: 0.3460 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 7289 Z= 0.222 Angle : 0.560 11.191 9913 Z= 0.287 Chirality : 0.044 0.220 1139 Planarity : 0.004 0.038 1265 Dihedral : 4.418 54.886 1008 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.80 % Allowed : 19.67 % Favored : 76.53 % 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: 0.44 (0.28), residues: 910 helix: 1.99 (0.26), residues: 411 sheet: -1.85 (0.36), residues: 168 loop : -0.62 (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 R 131 PHE 0.013 0.001 PHE R 115 TYR 0.019 0.001 TYR R 187 ARG 0.006 0.000 ARG A 346 *********************** 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 142 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 114 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.8680 (mmm-85) cc_final: 0.8450 (mtp85) REVERT: B 198 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8490 (pp) REVERT: B 262 MET cc_start: 0.8152 (tpp) cc_final: 0.7758 (mmt) REVERT: B 292 PHE cc_start: 0.8667 (m-80) cc_final: 0.8374 (m-80) REVERT: B 329 THR cc_start: 0.9084 (m) cc_final: 0.8694 (p) REVERT: G 21 MET cc_start: 0.7693 (ptm) cc_final: 0.7336 (ppp) REVERT: R 33 GLU cc_start: 0.8494 (mm-30) cc_final: 0.8227 (mt-10) REVERT: R 41 ASN cc_start: 0.8321 (m-40) cc_final: 0.8022 (m110) outliers start: 28 outliers final: 21 residues processed: 132 average time/residue: 0.1862 time to fit residues: 33.1040 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 : 0.755 ------------------------------------------------------------------------------- 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 227 SER 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 30 optimal weight: 0.7980 chunk 41 optimal weight: 0.1980 chunk 34 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 88 optimal weight: 0.8980 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 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 = 0.4056 r_free = 0.4056 target = 0.163987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.127878 restraints weight = 9418.986| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 2.83 r_work: 0.3468 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 7289 Z= 0.219 Angle : 0.574 10.795 9913 Z= 0.291 Chirality : 0.043 0.215 1139 Planarity : 0.004 0.038 1265 Dihedral : 4.401 54.993 1008 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.39 % Allowed : 20.49 % 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 (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: 0.43 (0.29), residues: 910 helix: 2.00 (0.26), residues: 410 sheet: -1.85 (0.37), residues: 168 loop : -0.64 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 263 HIS 0.004 0.001 HIS A 220 PHE 0.022 0.001 PHE A 222 TYR 0.018 0.001 TYR R 187 ARG 0.006 0.000 ARG A 346 *********************** 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 143 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 118 time to evaluate : 0.789 Fit side-chains revert: symmetry clash REVERT: A 38 ARG cc_start: 0.8669 (mmm-85) cc_final: 0.8433 (mtp85) REVERT: A 220 HIS cc_start: 0.7869 (t-170) cc_final: 0.6874 (t-170) REVERT: B 198 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8489 (pp) REVERT: B 262 MET cc_start: 0.8118 (tpp) cc_final: 0.7719 (mmt) REVERT: B 292 PHE cc_start: 0.8656 (m-80) cc_final: 0.8365 (m-80) REVERT: B 329 THR cc_start: 0.9093 (m) cc_final: 0.8703 (p) REVERT: G 21 MET cc_start: 0.7701 (ptm) cc_final: 0.7333 (ppp) REVERT: R 33 GLU cc_start: 0.8489 (mm-30) cc_final: 0.8220 (mt-10) REVERT: R 41 ASN cc_start: 0.8312 (m-40) cc_final: 0.8019 (m110) outliers start: 25 outliers final: 22 residues processed: 134 average time/residue: 0.1839 time to fit residues: 33.4547 Evaluate side-chains 137 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LYS 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 227 SER 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 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 236 MET 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 28 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 16 optimal weight: 0.0040 chunk 70 optimal weight: 0.1980 chunk 71 optimal weight: 0.2980 chunk 79 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 overall best weight: 0.3792 ------------------------------------------------------------------------------- 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 = 0.4077 r_free = 0.4077 target = 0.165765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.129062 restraints weight = 9517.069| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 2.98 r_work: 0.3494 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7289 Z= 0.173 Angle : 0.533 7.805 9913 Z= 0.276 Chirality : 0.043 0.199 1139 Planarity : 0.003 0.038 1265 Dihedral : 4.306 55.157 1008 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.26 % Allowed : 20.49 % Favored : 76.26 % 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: 2.14 (0.26), residues: 410 sheet: -1.84 (0.37), residues: 169 loop : -0.63 (0.34), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.003 0.001 HIS A 220 PHE 0.017 0.001 PHE A 222 TYR 0.016 0.001 TYR R 187 ARG 0.006 0.000 ARG A 346 ********************** 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 151 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 0.833 Fit side-chains revert: symmetry clash REVERT: B 262 MET cc_start: 0.8080 (tpp) cc_final: 0.7691 (mmt) REVERT: B 292 PHE cc_start: 0.8575 (m-80) cc_final: 0.8309 (m-80) REVERT: B 329 THR cc_start: 0.9065 (m) cc_final: 0.8732 (p) REVERT: B 339 TRP cc_start: 0.8815 (m100) cc_final: 0.8488 (m100) REVERT: R 22 GLU cc_start: 0.7427 (tt0) cc_final: 0.6949 (tp30) REVERT: R 26 LEU cc_start: 0.8633 (mt) cc_final: 0.8395 (mp) REVERT: R 33 GLU cc_start: 0.8444 (mm-30) cc_final: 0.8198 (mt-10) REVERT: R 41 ASN cc_start: 0.8217 (m-40) cc_final: 0.7916 (m110) outliers start: 24 outliers final: 22 residues processed: 144 average time/residue: 0.2001 time to fit residues: 39.0017 Evaluate side-chains 140 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LYS 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 155 ASN Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 227 SER 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 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 236 MET 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: 0.4980 chunk 45 optimal weight: 0.5980 chunk 87 optimal weight: 0.9980 chunk 41 optimal weight: 0.1980 chunk 65 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 81 optimal weight: 0.0270 chunk 19 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 83 optimal weight: 0.6980 overall best weight: 0.3838 ------------------------------------------------------------------------------- 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 = 0.4082 r_free = 0.4082 target = 0.166242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.129780 restraints weight = 9316.479| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 2.54 r_work: 0.3501 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7289 Z= 0.174 Angle : 0.548 8.193 9913 Z= 0.280 Chirality : 0.043 0.194 1139 Planarity : 0.003 0.038 1265 Dihedral : 4.300 54.834 1008 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.99 % Allowed : 20.90 % 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 (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: 2.18 (0.26), residues: 410 sheet: -1.93 (0.36), residues: 173 loop : -0.60 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.002 0.001 HIS A 220 PHE 0.015 0.001 PHE A 222 TYR 0.015 0.001 TYR R 187 ARG 0.006 0.000 ARG A 346 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3665.61 seconds wall clock time: 66 minutes 0.10 seconds (3960.10 seconds total)