Starting phenix.real_space_refine on Sat Dec 28 00:31:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jpp_36486/12_2024/8jpp_36486.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jpp_36486/12_2024/8jpp_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_36486/12_2024/8jpp_36486.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jpp_36486/12_2024/8jpp_36486.map" model { file = "/net/cci-nas-00/data/ceres_data/8jpp_36486/12_2024/8jpp_36486.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jpp_36486/12_2024/8jpp_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-5532/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: 5.05, per 1000 atoms: 0.71 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 1.0 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: 0.82 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: 2.10 Time building geometry restraints manager: 2.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 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: 0.010 Normalize map: mean=0, sd=1: 2.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.500 Find NCS groups from input model: 0.090 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.530 ------------------------------------------------------------------------------- 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 : 0.805 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: 0.2369 time to fit residues: 45.2180 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 : 0.841 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 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 : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 292 PHE cc_start: 0.8782 (m-10) cc_final: 0.8424 (m-80) REVERT: R 33 GLU cc_start: 0.8369 (mm-30) cc_final: 0.7994 (mt-10) REVERT: R 186 ILE cc_start: 0.8119 (pt) cc_final: 0.7278 (mm) REVERT: R 190 CYS cc_start: 0.7926 (m) cc_final: 0.7643 (m) outliers start: 28 outliers final: 16 residues processed: 146 average time/residue: 0.2157 time to fit residues: 41.8132 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 : 0.951 ------------------------------------------------------------------------------- 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 45 optimal weight: 0.0870 chunk 25 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 27 optimal weight: 0.4980 chunk 65 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7289 Z= 0.231 Angle : 0.549 5.986 9913 Z= 0.288 Chirality : 0.044 0.214 1139 Planarity : 0.004 0.035 1265 Dihedral : 4.478 50.732 1008 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.93 % Allowed : 16.28 % 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: 0.40 (0.28), residues: 910 helix: 1.87 (0.26), residues: 406 sheet: -1.72 (0.35), residues: 173 loop : -0.54 (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 A 212 TYR 0.018 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 152 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 123 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 292 PHE cc_start: 0.8796 (m-10) cc_final: 0.8556 (m-80) REVERT: B 329 THR cc_start: 0.9023 (m) cc_final: 0.8505 (p) REVERT: B 337 LYS cc_start: 0.8717 (mttp) cc_final: 0.8368 (mttp) REVERT: R 33 GLU cc_start: 0.8369 (mm-30) cc_final: 0.8032 (mt-10) REVERT: R 41 ASN cc_start: 0.8544 (m-40) cc_final: 0.8286 (m110) outliers start: 29 outliers final: 18 residues processed: 140 average time/residue: 0.1946 time to fit residues: 36.6468 Evaluate side-chains 134 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 0.863 ------------------------------------------------------------------------------- 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 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 124 ILE Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 203 MET Chi-restraints excluded: chain R residue 204 CYS Chi-restraints excluded: chain R residue 243 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 72 optimal weight: 0.2980 chunk 49 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1727 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= 0.243 Angle : 0.545 6.924 9913 Z= 0.287 Chirality : 0.044 0.202 1139 Planarity : 0.004 0.038 1265 Dihedral : 4.462 51.647 1008 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 4.21 % Allowed : 17.37 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.28), residues: 910 helix: 1.99 (0.26), residues: 406 sheet: -1.78 (0.36), residues: 173 loop : -0.55 (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 0.016 0.001 PHE A 222 TYR 0.020 0.001 TYR R 187 ARG 0.004 0.000 ARG A 346 *********************** 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 157 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 126 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 198 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8426 (pp) REVERT: B 262 MET cc_start: 0.8021 (tpp) cc_final: 0.7321 (mmt) REVERT: B 329 THR cc_start: 0.9005 (m) cc_final: 0.8488 (p) REVERT: B 337 LYS cc_start: 0.8701 (mttp) cc_final: 0.8358 (mttp) REVERT: R 33 GLU cc_start: 0.8475 (mm-30) cc_final: 0.8145 (mt-10) REVERT: R 41 ASN cc_start: 0.8506 (m-40) cc_final: 0.8251 (m110) outliers start: 31 outliers final: 22 residues processed: 143 average time/residue: 0.2160 time to fit residues: 40.9408 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 : 0.877 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 44 optimal weight: 0.9990 chunk 78 optimal weight: 0.7980 chunk 21 optimal weight: 0.1980 chunk 29 optimal weight: 0.8980 chunk 17 optimal weight: 0.2980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7289 Z= 0.208 Angle : 0.527 5.846 9913 Z= 0.277 Chirality : 0.043 0.196 1139 Planarity : 0.004 0.038 1265 Dihedral : 4.429 53.592 1008 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.93 % Allowed : 18.32 % 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: 0.51 (0.29), residues: 910 helix: 2.08 (0.26), residues: 406 sheet: -1.80 (0.36), residues: 173 loop : -0.57 (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 A 347 PHE 0.014 0.001 PHE B 292 TYR 0.019 0.001 TYR R 187 ARG 0.004 0.000 ARG A 38 *********************** 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 153 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 124 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 198 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8462 (pp) REVERT: B 262 MET cc_start: 0.8023 (tpp) cc_final: 0.7287 (mmt) REVERT: B 292 PHE cc_start: 0.8619 (m-80) cc_final: 0.8251 (m-80) REVERT: B 329 THR cc_start: 0.9017 (m) cc_final: 0.8505 (p) REVERT: B 337 LYS cc_start: 0.8696 (mttp) cc_final: 0.8375 (mttp) REVERT: R 33 GLU cc_start: 0.8517 (mm-30) cc_final: 0.8220 (mt-10) REVERT: R 41 ASN cc_start: 0.8408 (m-40) cc_final: 0.8160 (m110) outliers start: 29 outliers final: 21 residues processed: 139 average time/residue: 0.2157 time to fit residues: 39.9962 Evaluate side-chains 138 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 0.838 ------------------------------------------------------------------------------- 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 59 GLN Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain B residue 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 124 ILE Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 203 MET Chi-restraints excluded: chain R residue 204 CYS Chi-restraints excluded: chain R residue 239 VAL Chi-restraints excluded: chain R residue 243 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7289 Z= 0.250 Angle : 0.542 5.982 9913 Z= 0.284 Chirality : 0.044 0.203 1139 Planarity : 0.004 0.038 1265 Dihedral : 4.494 54.487 1008 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 4.07 % Allowed : 18.86 % 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: 0.47 (0.29), residues: 910 helix: 2.00 (0.26), residues: 411 sheet: -1.85 (0.36), residues: 172 loop : -0.54 (0.35), residues: 327 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 0.015 0.002 PHE R 294 TYR 0.018 0.001 TYR R 187 ARG 0.006 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 152 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 122 time to evaluate : 0.870 Fit side-chains revert: symmetry clash REVERT: A 220 HIS cc_start: 0.7697 (t-170) cc_final: 0.6942 (t-170) REVERT: B 198 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8425 (pp) REVERT: B 262 MET cc_start: 0.7991 (tpp) cc_final: 0.7530 (mmt) REVERT: B 292 PHE cc_start: 0.8627 (m-80) cc_final: 0.8303 (m-80) REVERT: B 329 THR cc_start: 0.9032 (m) cc_final: 0.8506 (p) REVERT: B 337 LYS cc_start: 0.8684 (mttp) cc_final: 0.8376 (mttp) REVERT: R 33 GLU cc_start: 0.8550 (mm-30) cc_final: 0.8228 (mt-10) REVERT: R 41 ASN cc_start: 0.8434 (m-40) cc_final: 0.8208 (m110) outliers start: 30 outliers final: 21 residues processed: 142 average time/residue: 0.1968 time to fit residues: 37.4824 Evaluate side-chains 138 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 0.818 ------------------------------------------------------------------------------- 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 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 G residue 16 VAL Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain R residue 114 THR Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 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 63 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 73 optimal weight: 0.7980 chunk 48 optimal weight: 0.0370 chunk 86 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 51 optimal weight: 0.2980 overall best weight: 0.4858 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2137 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= 0.183 Angle : 0.531 8.022 9913 Z= 0.277 Chirality : 0.043 0.192 1139 Planarity : 0.004 0.039 1265 Dihedral : 4.421 55.379 1008 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.53 % Allowed : 19.67 % 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: 0.52 (0.29), residues: 910 helix: 2.11 (0.26), residues: 411 sheet: -1.92 (0.37), residues: 166 loop : -0.61 (0.34), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 263 HIS 0.003 0.001 HIS R 131 PHE 0.015 0.001 PHE R 294 TYR 0.021 0.001 TYR R 187 ARG 0.006 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 151 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 125 time to evaluate : 0.875 Fit side-chains revert: symmetry clash REVERT: A 220 HIS cc_start: 0.7677 (t-170) cc_final: 0.6902 (t-170) REVERT: A 300 ASP cc_start: 0.6841 (m-30) cc_final: 0.6561 (t0) REVERT: B 198 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8451 (pp) REVERT: B 262 MET cc_start: 0.7960 (tpp) cc_final: 0.7496 (mmt) REVERT: B 292 PHE cc_start: 0.8610 (m-80) cc_final: 0.8279 (m-80) REVERT: B 329 THR cc_start: 0.9007 (m) cc_final: 0.8500 (p) REVERT: B 337 LYS cc_start: 0.8679 (mttp) cc_final: 0.8343 (mttp) REVERT: G 21 MET cc_start: 0.7561 (ptm) cc_final: 0.7298 (ppp) REVERT: R 33 GLU cc_start: 0.8491 (mm-30) cc_final: 0.8247 (mt-10) REVERT: R 41 ASN cc_start: 0.8409 (m-40) cc_final: 0.8141 (m110) outliers start: 26 outliers final: 20 residues processed: 144 average time/residue: 0.1932 time to fit residues: 37.8816 Evaluate side-chains 136 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 0.867 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 59 optimal weight: 0.3980 chunk 42 optimal weight: 0.9990 chunk 8 optimal weight: 0.3980 chunk 68 optimal weight: 0.6980 chunk 78 optimal weight: 0.0070 chunk 83 optimal weight: 0.5980 chunk 75 optimal weight: 0.0010 overall best weight: 0.2804 ------------------------------------------------------------------------------- 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** B 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 7289 Z= 0.155 Angle : 0.535 8.685 9913 Z= 0.276 Chirality : 0.043 0.222 1139 Planarity : 0.003 0.039 1265 Dihedral : 4.292 55.829 1008 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.58 % Allowed : 21.17 % 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: 0.59 (0.29), residues: 910 helix: 2.16 (0.26), residues: 410 sheet: -1.81 (0.37), residues: 169 loop : -0.59 (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 0.017 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 145 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 0.855 Fit side-chains revert: symmetry clash REVERT: A 220 HIS cc_start: 0.7647 (t-170) cc_final: 0.6910 (t-170) REVERT: B 198 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8453 (pp) REVERT: B 262 MET cc_start: 0.7905 (tpp) cc_final: 0.7465 (mmt) REVERT: B 292 PHE cc_start: 0.8506 (m-80) cc_final: 0.8171 (m-80) REVERT: B 329 THR cc_start: 0.8979 (m) cc_final: 0.8526 (p) REVERT: B 337 LYS cc_start: 0.8658 (mttp) cc_final: 0.8290 (mttp) REVERT: G 21 MET cc_start: 0.7555 (ptm) cc_final: 0.7296 (ppp) REVERT: R 33 GLU cc_start: 0.8461 (mm-30) cc_final: 0.8200 (mt-10) REVERT: R 41 ASN cc_start: 0.8260 (m-40) cc_final: 0.8043 (m110) outliers start: 19 outliers final: 15 residues processed: 141 average time/residue: 0.2030 time to fit residues: 38.7214 Evaluate side-chains 131 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 0.998 ------------------------------------------------------------------------------- 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 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 73 optimal weight: 1.9990 chunk 76 optimal weight: 0.0020 chunk 53 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 overall best weight: 1.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 7289 Z= 0.371 Angle : 0.646 12.508 9913 Z= 0.328 Chirality : 0.046 0.260 1139 Planarity : 0.004 0.039 1265 Dihedral : 4.656 54.481 1008 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.39 % Allowed : 19.54 % 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: 0.34 (0.29), residues: 910 helix: 1.87 (0.26), residues: 410 sheet: -1.93 (0.35), residues: 175 loop : -0.55 (0.34), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 263 HIS 0.003 0.001 HIS R 131 PHE 0.016 0.002 PHE R 285 TYR 0.021 0.002 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 139 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 114 time to evaluate : 1.004 Fit side-chains revert: symmetry clash REVERT: A 220 HIS cc_start: 0.7753 (t-170) cc_final: 0.6944 (t-170) REVERT: A 346 ARG cc_start: 0.7478 (mtm-85) cc_final: 0.7189 (mtm-85) REVERT: B 262 MET cc_start: 0.7970 (tpp) cc_final: 0.7530 (mmt) REVERT: B 292 PHE cc_start: 0.8717 (m-80) cc_final: 0.8351 (m-80) REVERT: G 21 MET cc_start: 0.7619 (ptm) cc_final: 0.7337 (ppp) REVERT: R 33 GLU cc_start: 0.8575 (mm-30) cc_final: 0.8274 (mt-10) REVERT: R 41 ASN cc_start: 0.8511 (m-40) cc_final: 0.8254 (m110) outliers start: 25 outliers final: 19 residues processed: 127 average time/residue: 0.2163 time to fit residues: 36.8854 Evaluate side-chains 130 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 0.820 ------------------------------------------------------------------------------- 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 90 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 114 THR Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 203 MET Chi-restraints excluded: chain R residue 204 CYS Chi-restraints excluded: chain R residue 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 40 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 89 optimal weight: 8.9990 chunk 82 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 55 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 56 optimal weight: 0.1980 chunk 76 optimal weight: 0.8980 chunk 21 optimal weight: 0.0980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2314 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= 0.192 Angle : 0.554 8.567 9913 Z= 0.286 Chirality : 0.043 0.220 1139 Planarity : 0.004 0.040 1265 Dihedral : 4.508 55.761 1008 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.17 % Allowed : 20.62 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.29), residues: 910 helix: 2.02 (0.26), residues: 410 sheet: -1.98 (0.36), residues: 173 loop : -0.53 (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 R 115 TYR 0.022 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 129 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.824 Fit side-chains REVERT: A 220 HIS cc_start: 0.7680 (t-170) cc_final: 0.6896 (t-170) REVERT: A 346 ARG cc_start: 0.7406 (mtm-85) cc_final: 0.7150 (mtm-85) REVERT: B 262 MET cc_start: 0.7880 (tpp) cc_final: 0.7443 (mmt) REVERT: B 292 PHE cc_start: 0.8620 (m-80) cc_final: 0.8266 (m-80) REVERT: B 329 THR cc_start: 0.9010 (m) cc_final: 0.8517 (p) REVERT: G 21 MET cc_start: 0.7598 (ptm) cc_final: 0.7327 (ppp) REVERT: R 33 GLU cc_start: 0.8490 (mm-30) cc_final: 0.8268 (mt-10) REVERT: R 41 ASN cc_start: 0.8393 (m-40) cc_final: 0.8158 (m110) outliers start: 16 outliers final: 15 residues processed: 122 average time/residue: 0.2001 time to fit residues: 32.5379 Evaluate side-chains 124 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 0.838 ------------------------------------------------------------------------------- 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 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 114 THR Chi-restraints excluded: chain R residue 124 ILE Chi-restraints excluded: chain R residue 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 71 optimal weight: 0.4980 chunk 29 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 9 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.163894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.127400 restraints weight = 9270.920| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 2.51 r_work: 0.3468 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7289 Z= 0.218 Angle : 0.564 7.979 9913 Z= 0.290 Chirality : 0.044 0.225 1139 Planarity : 0.004 0.041 1265 Dihedral : 4.495 55.514 1008 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.85 % Allowed : 20.49 % 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: 0.46 (0.29), residues: 910 helix: 2.03 (0.26), residues: 410 sheet: -1.96 (0.36), residues: 172 loop : -0.53 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 263 HIS 0.003 0.001 HIS R 131 PHE 0.013 0.001 PHE R 115 TYR 0.020 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: 1954.10 seconds wall clock time: 37 minutes 23.47 seconds (2243.47 seconds total)