Starting phenix.real_space_refine on Sat May 2 15:20:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w0r_65513/05_2026/9w0r_65513.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w0r_65513/05_2026/9w0r_65513.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9w0r_65513/05_2026/9w0r_65513.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w0r_65513/05_2026/9w0r_65513.map" model { file = "/net/cci-nas-00/data/ceres_data/9w0r_65513/05_2026/9w0r_65513.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w0r_65513/05_2026/9w0r_65513.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.004 sd= 0.113 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 46 5.16 5 C 4266 2.51 5 N 1136 2.21 5 O 1202 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6650 Number of models: 1 Model: "" Number of chains: 4 Chain: "R" Number of atoms: 2086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2086 Classifications: {'peptide': 271} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 6, 'TRANS': 264} Chain breaks: 2 Unresolved non-hydrogen bonds: 123 Unresolved non-hydrogen angles: 154 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 6, 'ARG:plan': 3, 'GLN:plan1': 2, 'ASN:plan1': 4, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 85 Chain: "A" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1673 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 19} Link IDs: {'PTRANS': 2, 'TRANS': 212} Chain breaks: 2 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 5} Unresolved non-hydrogen planarities: 38 Chain: "B" Number of atoms: 2506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2506 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 5, 'TRANS': 328} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 49 Planarities with less than four sites: {'ARG:plan': 4, 'GLN:plan1': 2, 'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "C" Number of atoms: 385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 385 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 49} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Time building chain proxies: 1.77, per 1000 atoms: 0.27 Number of scatterers: 6650 At special positions: 0 Unit cell: (74.97, 100.674, 122.094, 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 46 16.00 O 1202 8.00 N 1136 7.00 C 4266 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.56 Conformation dependent library (CDL) restraints added in 436.3 milliseconds 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1662 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 8 sheets defined 45.8% alpha, 19.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'R' and resid 8 through 38 removed outlier: 3.618A pdb=" N PHE R 22 " --> pdb=" O VAL R 18 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE R 27 " --> pdb=" O ALA R 23 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN R 31 " --> pdb=" O ILE R 27 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N SER R 32 " --> pdb=" O ALA R 28 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ILE R 33 " --> pdb=" O LEU R 29 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N GLU R 34 " --> pdb=" O VAL R 30 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TRP R 35 " --> pdb=" O ASN R 31 " (cutoff:3.500A) Processing helix chain 'R' and resid 42 through 71 Processing helix chain 'R' and resid 77 through 111 removed outlier: 3.575A pdb=" N ALA R 99 " --> pdb=" O SER R 95 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR R 100 " --> pdb=" O ASN R 96 " (cutoff:3.500A) Processing helix chain 'R' and resid 115 through 124 Processing helix chain 'R' and resid 124 through 150 Proline residue: R 136 - end of helix removed outlier: 4.106A pdb=" N PHE R 145 " --> pdb=" O VAL R 141 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N VAL R 146 " --> pdb=" O CYS R 142 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE R 147 " --> pdb=" O HIS R 143 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASN R 150 " --> pdb=" O VAL R 146 " (cutoff:3.500A) Processing helix chain 'R' and resid 170 through 176 Processing helix chain 'R' and resid 177 through 212 removed outlier: 3.632A pdb=" N ILE R 181 " --> pdb=" O THR R 177 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA R 183 " --> pdb=" O VAL R 179 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASN R 184 " --> pdb=" O THR R 180 " (cutoff:3.500A) Proline residue: R 187 - end of helix removed outlier: 3.808A pdb=" N HIS R 212 " --> pdb=" O LYS R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 224 through 247 removed outlier: 3.514A pdb=" N MET R 247 " --> pdb=" O LEU R 243 " (cutoff:3.500A) Processing helix chain 'R' and resid 261 through 270 Processing helix chain 'R' and resid 270 through 283 removed outlier: 3.501A pdb=" N THR R 274 " --> pdb=" O SER R 270 " (cutoff:3.500A) Proline residue: R 276 - end of helix removed outlier: 3.628A pdb=" N LEU R 279 " --> pdb=" O HIS R 275 " (cutoff:3.500A) Processing helix chain 'R' and resid 283 through 302 Processing helix chain 'A' and resid 7 through 31 removed outlier: 4.206A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N VAL A 13 " --> pdb=" O ASP A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.592A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.622A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 330 through 351 removed outlier: 3.620A pdb=" N VAL A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 26 removed outlier: 3.596A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 33 Processing helix chain 'C' and resid 10 through 24 removed outlier: 3.930A pdb=" N GLN C 18 " --> pdb=" O LYS C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.465A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.388A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.922A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.080A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.044A 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 151 removed outlier: 4.018A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.887A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.631A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP B 254 " --> pdb=" O GLN B 259 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.539A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 365 hydrogen bonds defined for protein. 1056 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.07 Time building geometry restraints manager: 0.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2131 1.34 - 1.46: 1530 1.46 - 1.58: 3057 1.58 - 1.69: 0 1.69 - 1.81: 65 Bond restraints: 6783 Sorted by residual: bond pdb=" C ASP R 218 " pdb=" N PRO R 219 " ideal model delta sigma weight residual 1.336 1.353 -0.017 9.80e-03 1.04e+04 3.03e+00 bond pdb=" CA THR R 177 " pdb=" C THR R 177 " ideal model delta sigma weight residual 1.520 1.531 -0.011 1.20e-02 6.94e+03 7.80e-01 bond pdb=" N THR R 177 " pdb=" CA THR R 177 " ideal model delta sigma weight residual 1.457 1.466 -0.009 1.26e-02 6.30e+03 5.54e-01 bond pdb=" CA VAL B 307 " pdb=" CB VAL B 307 " ideal model delta sigma weight residual 1.541 1.550 -0.009 1.28e-02 6.10e+03 5.03e-01 bond pdb=" CA THR A 202 " pdb=" C THR A 202 " ideal model delta sigma weight residual 1.522 1.513 0.009 1.40e-02 5.10e+03 4.60e-01 ... (remaining 6778 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 9029 1.45 - 2.90: 153 2.90 - 4.35: 27 4.35 - 5.79: 5 5.79 - 7.24: 2 Bond angle restraints: 9216 Sorted by residual: angle pdb=" C MET R 221 " pdb=" N LYS R 222 " pdb=" CA LYS R 222 " ideal model delta sigma weight residual 121.54 128.12 -6.58 1.91e+00 2.74e-01 1.19e+01 angle pdb=" CA GLY A 40 " pdb=" C GLY A 40 " pdb=" N ALA A 41 " ideal model delta sigma weight residual 114.58 117.14 -2.56 8.60e-01 1.35e+00 8.86e+00 angle pdb=" C CYS R 264 " pdb=" N GLU R 265 " pdb=" CA GLU R 265 " ideal model delta sigma weight residual 120.72 115.94 4.78 1.67e+00 3.59e-01 8.20e+00 angle pdb=" C LEU R 71 " pdb=" N ASN R 72 " pdb=" CA ASN R 72 " ideal model delta sigma weight residual 123.16 119.95 3.21 1.23e+00 6.61e-01 6.79e+00 angle pdb=" N THR B 87 " pdb=" CA THR B 87 " pdb=" C THR B 87 " ideal model delta sigma weight residual 113.38 110.62 2.76 1.17e+00 7.31e-01 5.56e+00 ... (remaining 9211 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 3710 17.81 - 35.61: 238 35.61 - 53.42: 29 53.42 - 71.22: 11 71.22 - 89.03: 4 Dihedral angle restraints: 3992 sinusoidal: 1444 harmonic: 2548 Sorted by residual: dihedral pdb=" CB GLU A 318 " pdb=" CG GLU A 318 " pdb=" CD GLU A 318 " pdb=" OE1 GLU A 318 " ideal model delta sinusoidal sigma weight residual 0.00 -88.32 88.32 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CB GLU B 172 " pdb=" CG GLU B 172 " pdb=" CD GLU B 172 " pdb=" OE1 GLU B 172 " ideal model delta sinusoidal sigma weight residual 0.00 85.65 -85.65 1 3.00e+01 1.11e-03 9.86e+00 dihedral pdb=" CA ASN A 241 " pdb=" CB ASN A 241 " pdb=" CG ASN A 241 " pdb=" OD1 ASN A 241 " ideal model delta sinusoidal sigma weight residual 120.00 -176.29 -63.71 2 2.00e+01 2.50e-03 9.65e+00 ... (remaining 3989 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 669 0.027 - 0.054: 271 0.054 - 0.081: 98 0.081 - 0.108: 37 0.108 - 0.135: 20 Chirality restraints: 1095 Sorted by residual: chirality pdb=" CA ILE B 123 " pdb=" N ILE B 123 " pdb=" C ILE B 123 " pdb=" CB ILE B 123 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.56e-01 chirality pdb=" CA ILE B 229 " pdb=" N ILE B 229 " pdb=" C ILE B 229 " pdb=" CB ILE B 229 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.67e-01 chirality pdb=" CA ILE A 265 " pdb=" N ILE A 265 " pdb=" C ILE A 265 " pdb=" CB ILE A 265 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.64e-01 ... (remaining 1092 not shown) Planarity restraints: 1147 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 52 " -0.056 5.00e-02 4.00e+02 8.56e-02 1.17e+01 pdb=" N PRO C 53 " 0.148 5.00e-02 4.00e+02 pdb=" CA PRO C 53 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO C 53 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.024 5.00e-02 4.00e+02 3.57e-02 2.03e+00 pdb=" N PRO B 236 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY R 135 " 0.021 5.00e-02 4.00e+02 3.10e-02 1.54e+00 pdb=" N PRO R 136 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO R 136 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO R 136 " 0.017 5.00e-02 4.00e+02 ... (remaining 1144 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1482 2.79 - 3.32: 6369 3.32 - 3.84: 11142 3.84 - 4.37: 13063 4.37 - 4.90: 22419 Nonbonded interactions: 54475 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.260 3.040 nonbonded pdb=" O LEU R 108 " pdb=" NZ LYS R 122 " model vdw 2.268 3.120 nonbonded pdb=" OE2 GLU B 260 " pdb=" OG1 THR B 263 " model vdw 2.278 3.040 nonbonded pdb=" NZ LYS A 209 " pdb=" OD2 ASP B 228 " model vdw 2.323 3.120 nonbonded pdb=" OD1 ASP A 251 " pdb=" ND2 ASN A 255 " model vdw 2.324 3.120 ... (remaining 54470 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.150 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.040 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 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 : 0.002 0.032 6783 Z= 0.100 Angle : 0.492 7.243 9216 Z= 0.283 Chirality : 0.038 0.135 1095 Planarity : 0.004 0.086 1147 Dihedral : 12.615 89.029 2330 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.29 % Allowed : 0.58 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.29), residues: 858 helix: 1.77 (0.28), residues: 376 sheet: 0.67 (0.37), residues: 182 loop : -0.71 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 219 TYR 0.008 0.001 TYR B 59 PHE 0.012 0.001 PHE R 17 TRP 0.021 0.001 TRP B 211 HIS 0.004 0.001 HIS R 224 Details of bonding type rmsd covalent geometry : bond 0.00180 ( 6783) covalent geometry : angle 0.49170 ( 9216) hydrogen bonds : bond 0.13026 ( 365) hydrogen bonds : angle 5.01166 ( 1056) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 138 time to evaluate : 0.289 Fit side-chains REVERT: A 337 ASP cc_start: 0.7700 (m-30) cc_final: 0.7404 (m-30) outliers start: 2 outliers final: 0 residues processed: 139 average time/residue: 0.5542 time to fit residues: 80.9419 Evaluate side-chains 103 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 49 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.4980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.0870 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.0362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 112 ASN A 241 ASN B 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.199726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.137114 restraints weight = 6954.459| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 1.96 r_work: 0.3254 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6783 Z= 0.178 Angle : 0.599 11.316 9216 Z= 0.312 Chirality : 0.042 0.164 1095 Planarity : 0.004 0.062 1147 Dihedral : 4.302 45.811 920 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.33 % Allowed : 11.00 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.29), residues: 858 helix: 1.74 (0.28), residues: 378 sheet: 0.83 (0.37), residues: 180 loop : -0.92 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 150 TYR 0.012 0.002 TYR R 271 PHE 0.024 0.002 PHE R 139 TRP 0.015 0.002 TRP B 82 HIS 0.004 0.001 HIS R 205 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 6783) covalent geometry : angle 0.59916 ( 9216) hydrogen bonds : bond 0.04004 ( 365) hydrogen bonds : angle 4.38139 ( 1056) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 0.212 Fit side-chains REVERT: R 115 ASN cc_start: 0.7683 (t0) cc_final: 0.7349 (t0) REVERT: R 262 MET cc_start: 0.4573 (tpp) cc_final: 0.2766 (tmm) REVERT: B 46 ARG cc_start: 0.8147 (OUTLIER) cc_final: 0.7447 (mmt180) REVERT: B 258 ASP cc_start: 0.6862 (t70) cc_final: 0.6281 (t70) outliers start: 23 outliers final: 8 residues processed: 120 average time/residue: 0.6541 time to fit residues: 81.9581 Evaluate side-chains 110 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 189 THR Chi-restraints excluded: chain R residue 232 THR Chi-restraints excluded: chain R residue 273 SER Chi-restraints excluded: chain R residue 274 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain C residue 52 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 65 optimal weight: 0.0970 chunk 46 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 49 optimal weight: 6.9990 chunk 16 optimal weight: 0.0270 chunk 4 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.5636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 112 ASN A 244 HIS B 176 GLN B 259 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.201039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.139368 restraints weight = 6901.048| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.10 r_work: 0.3302 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6783 Z= 0.118 Angle : 0.506 8.933 9216 Z= 0.264 Chirality : 0.039 0.146 1095 Planarity : 0.003 0.054 1147 Dihedral : 4.084 43.899 920 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.60 % Allowed : 13.75 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.29), residues: 858 helix: 1.94 (0.28), residues: 375 sheet: 0.83 (0.38), residues: 173 loop : -0.89 (0.33), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 150 TYR 0.017 0.001 TYR R 241 PHE 0.025 0.002 PHE R 17 TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS R 205 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 6783) covalent geometry : angle 0.50617 ( 9216) hydrogen bonds : bond 0.03526 ( 365) hydrogen bonds : angle 4.09892 ( 1056) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.255 Fit side-chains REVERT: R 115 ASN cc_start: 0.7659 (t0) cc_final: 0.7342 (t0) REVERT: R 262 MET cc_start: 0.4551 (tpp) cc_final: 0.3847 (mtp) REVERT: B 134 ARG cc_start: 0.7885 (mtm-85) cc_final: 0.6717 (mmm160) REVERT: B 258 ASP cc_start: 0.6742 (t70) cc_final: 0.6335 (t70) REVERT: B 269 ILE cc_start: 0.8004 (OUTLIER) cc_final: 0.7526 (mt) outliers start: 18 outliers final: 9 residues processed: 117 average time/residue: 0.5964 time to fit residues: 73.0475 Evaluate side-chains 113 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 103 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 149 MET Chi-restraints excluded: chain R residue 189 THR Chi-restraints excluded: chain R residue 273 SER Chi-restraints excluded: chain R residue 274 THR Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 269 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 47 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 7 optimal weight: 8.9990 chunk 75 optimal weight: 1.9990 chunk 82 optimal weight: 7.9990 chunk 42 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 63 optimal weight: 0.4980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 112 ASN ** R 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN B 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.196687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.139571 restraints weight = 6907.785| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 1.89 r_work: 0.3255 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6783 Z= 0.172 Angle : 0.585 12.948 9216 Z= 0.301 Chirality : 0.042 0.156 1095 Planarity : 0.004 0.050 1147 Dihedral : 4.380 42.452 920 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 4.34 % Allowed : 13.46 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.28), residues: 858 helix: 1.77 (0.27), residues: 377 sheet: 0.77 (0.38), residues: 179 loop : -1.02 (0.32), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 150 TYR 0.020 0.001 TYR R 241 PHE 0.023 0.002 PHE R 139 TRP 0.018 0.002 TRP B 82 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 6783) covalent geometry : angle 0.58532 ( 9216) hydrogen bonds : bond 0.03998 ( 365) hydrogen bonds : angle 4.30904 ( 1056) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 97 time to evaluate : 0.270 Fit side-chains REVERT: R 115 ASN cc_start: 0.7675 (t0) cc_final: 0.7329 (t0) REVERT: R 262 MET cc_start: 0.5018 (tpp) cc_final: 0.4147 (mtm) REVERT: R 265 GLU cc_start: 0.6500 (OUTLIER) cc_final: 0.6043 (pm20) REVERT: A 21 ARG cc_start: 0.7705 (ptp-110) cc_final: 0.7443 (ptp-110) REVERT: B 46 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.7693 (mmt180) REVERT: B 227 SER cc_start: 0.8951 (t) cc_final: 0.8616 (m) REVERT: B 258 ASP cc_start: 0.7024 (t70) cc_final: 0.6568 (t70) outliers start: 30 outliers final: 11 residues processed: 114 average time/residue: 0.6489 time to fit residues: 77.4267 Evaluate side-chains 107 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 189 THR Chi-restraints excluded: chain R residue 232 THR Chi-restraints excluded: chain R residue 265 GLU Chi-restraints excluded: chain R residue 273 SER Chi-restraints excluded: chain R residue 274 THR Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 52 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 77 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 55 optimal weight: 0.0370 chunk 78 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 112 ASN ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN B 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.197952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.134972 restraints weight = 6973.437| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.12 r_work: 0.3270 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6783 Z= 0.127 Angle : 0.518 10.230 9216 Z= 0.271 Chirality : 0.040 0.148 1095 Planarity : 0.003 0.048 1147 Dihedral : 4.221 42.547 920 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.47 % Allowed : 14.47 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.29), residues: 858 helix: 1.86 (0.27), residues: 377 sheet: 0.76 (0.38), residues: 177 loop : -1.01 (0.32), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 150 TYR 0.021 0.001 TYR R 241 PHE 0.020 0.002 PHE R 139 TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS R 205 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 6783) covalent geometry : angle 0.51847 ( 9216) hydrogen bonds : bond 0.03555 ( 365) hydrogen bonds : angle 4.16888 ( 1056) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 0.270 Fit side-chains REVERT: R 115 ASN cc_start: 0.7634 (t0) cc_final: 0.7279 (t0) REVERT: R 262 MET cc_start: 0.4865 (tpp) cc_final: 0.3955 (mtm) REVERT: R 265 GLU cc_start: 0.6459 (OUTLIER) cc_final: 0.6041 (pm20) REVERT: A 21 ARG cc_start: 0.7707 (ptp-110) cc_final: 0.7454 (ptp-110) REVERT: B 227 SER cc_start: 0.9005 (t) cc_final: 0.8685 (m) REVERT: B 258 ASP cc_start: 0.6950 (t70) cc_final: 0.6489 (t70) outliers start: 24 outliers final: 15 residues processed: 116 average time/residue: 0.6164 time to fit residues: 74.8763 Evaluate side-chains 113 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 149 MET Chi-restraints excluded: chain R residue 232 THR Chi-restraints excluded: chain R residue 246 ILE Chi-restraints excluded: chain R residue 265 GLU Chi-restraints excluded: chain R residue 273 SER Chi-restraints excluded: chain R residue 274 THR Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 52 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 20 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 112 ASN ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN B 176 GLN B 259 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.197144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.138392 restraints weight = 6999.099| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 1.89 r_work: 0.3296 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6783 Z= 0.144 Angle : 0.539 11.586 9216 Z= 0.280 Chirality : 0.040 0.150 1095 Planarity : 0.003 0.046 1147 Dihedral : 4.260 42.398 920 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 4.92 % Allowed : 13.60 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.28), residues: 858 helix: 1.82 (0.27), residues: 377 sheet: 0.67 (0.39), residues: 172 loop : -1.01 (0.32), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 150 TYR 0.021 0.001 TYR R 241 PHE 0.021 0.002 PHE R 139 TRP 0.016 0.002 TRP B 82 HIS 0.003 0.001 HIS R 205 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 6783) covalent geometry : angle 0.53881 ( 9216) hydrogen bonds : bond 0.03694 ( 365) hydrogen bonds : angle 4.21974 ( 1056) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 101 time to evaluate : 0.200 Fit side-chains REVERT: R 115 ASN cc_start: 0.7572 (t0) cc_final: 0.7363 (m-40) REVERT: R 262 MET cc_start: 0.4828 (tpp) cc_final: 0.4000 (mtm) REVERT: R 265 GLU cc_start: 0.6609 (OUTLIER) cc_final: 0.6138 (pm20) REVERT: B 217 MET cc_start: 0.8363 (OUTLIER) cc_final: 0.8055 (ptp) REVERT: B 227 SER cc_start: 0.8955 (t) cc_final: 0.8658 (m) REVERT: B 258 ASP cc_start: 0.6937 (t70) cc_final: 0.6441 (t70) outliers start: 34 outliers final: 19 residues processed: 122 average time/residue: 0.5862 time to fit residues: 75.0400 Evaluate side-chains 118 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 232 THR Chi-restraints excluded: chain R residue 246 ILE Chi-restraints excluded: chain R residue 265 GLU Chi-restraints excluded: chain R residue 273 SER Chi-restraints excluded: chain R residue 274 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 52 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 26 optimal weight: 6.9990 chunk 9 optimal weight: 0.6980 chunk 71 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 81 optimal weight: 20.0000 chunk 45 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 74 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 112 ASN ** R 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN B 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.196168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.133060 restraints weight = 6898.815| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 1.83 r_work: 0.3289 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6783 Z= 0.164 Angle : 0.584 13.405 9216 Z= 0.296 Chirality : 0.041 0.153 1095 Planarity : 0.003 0.045 1147 Dihedral : 4.377 42.848 920 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.76 % Allowed : 15.63 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.28), residues: 858 helix: 1.72 (0.27), residues: 377 sheet: 0.61 (0.39), residues: 174 loop : -1.04 (0.32), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 150 TYR 0.006 0.001 TYR A 302 PHE 0.020 0.002 PHE R 139 TRP 0.017 0.002 TRP B 82 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 6783) covalent geometry : angle 0.58383 ( 9216) hydrogen bonds : bond 0.03889 ( 365) hydrogen bonds : angle 4.29416 ( 1056) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 103 time to evaluate : 0.274 Fit side-chains REVERT: R 115 ASN cc_start: 0.7579 (t0) cc_final: 0.7334 (m-40) REVERT: R 182 LEU cc_start: 0.7656 (tp) cc_final: 0.7239 (tt) REVERT: R 262 MET cc_start: 0.5051 (tpp) cc_final: 0.4243 (mtm) REVERT: R 265 GLU cc_start: 0.6704 (OUTLIER) cc_final: 0.6202 (pm20) REVERT: B 217 MET cc_start: 0.8339 (OUTLIER) cc_final: 0.8023 (ptp) REVERT: B 227 SER cc_start: 0.9018 (t) cc_final: 0.8702 (m) REVERT: B 258 ASP cc_start: 0.7023 (t70) cc_final: 0.6468 (t70) REVERT: B 269 ILE cc_start: 0.8011 (mt) cc_final: 0.7495 (mt) outliers start: 26 outliers final: 18 residues processed: 119 average time/residue: 0.6250 time to fit residues: 77.9006 Evaluate side-chains 122 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 102 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 232 THR Chi-restraints excluded: chain R residue 246 ILE Chi-restraints excluded: chain R residue 265 GLU Chi-restraints excluded: chain R residue 273 SER Chi-restraints excluded: chain R residue 274 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 52 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 11 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 75 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 84 optimal weight: 0.0050 chunk 46 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 36 optimal weight: 0.1980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 112 ASN ** R 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.198284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.142870 restraints weight = 6925.452| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.03 r_work: 0.3383 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6783 Z= 0.115 Angle : 0.509 9.501 9216 Z= 0.265 Chirality : 0.039 0.144 1095 Planarity : 0.003 0.043 1147 Dihedral : 4.157 43.326 920 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.46 % Allowed : 17.37 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.29), residues: 858 helix: 1.76 (0.27), residues: 377 sheet: 0.57 (0.39), residues: 172 loop : -0.90 (0.33), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 150 TYR 0.016 0.001 TYR R 241 PHE 0.019 0.002 PHE R 269 TRP 0.014 0.001 TRP B 82 HIS 0.002 0.001 HIS R 275 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 6783) covalent geometry : angle 0.50922 ( 9216) hydrogen bonds : bond 0.03383 ( 365) hydrogen bonds : angle 4.08636 ( 1056) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 0.204 Fit side-chains REVERT: R 116 LEU cc_start: 0.8053 (mp) cc_final: 0.7609 (tm) REVERT: R 262 MET cc_start: 0.5102 (tpp) cc_final: 0.4261 (mtm) REVERT: R 265 GLU cc_start: 0.6752 (OUTLIER) cc_final: 0.6263 (pm20) REVERT: B 217 MET cc_start: 0.8287 (OUTLIER) cc_final: 0.8003 (ptp) REVERT: B 227 SER cc_start: 0.8940 (t) cc_final: 0.8646 (m) REVERT: B 258 ASP cc_start: 0.6820 (t70) cc_final: 0.6263 (t70) REVERT: B 269 ILE cc_start: 0.7931 (mt) cc_final: 0.7507 (mt) outliers start: 17 outliers final: 12 residues processed: 118 average time/residue: 0.6398 time to fit residues: 78.9624 Evaluate side-chains 119 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 246 ILE Chi-restraints excluded: chain R residue 265 GLU Chi-restraints excluded: chain R residue 273 SER Chi-restraints excluded: chain R residue 274 THR Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 52 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 11 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 45 optimal weight: 0.4980 chunk 44 optimal weight: 0.0670 chunk 13 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 96 ASN R 112 ASN ** R 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.198812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.142543 restraints weight = 7008.831| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 2.05 r_work: 0.3400 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6783 Z= 0.122 Angle : 0.531 12.247 9216 Z= 0.273 Chirality : 0.040 0.218 1095 Planarity : 0.003 0.043 1147 Dihedral : 4.170 43.256 920 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.89 % Allowed : 17.51 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.29), residues: 858 helix: 1.82 (0.27), residues: 378 sheet: 0.53 (0.39), residues: 172 loop : -0.92 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 21 TYR 0.019 0.001 TYR R 241 PHE 0.020 0.001 PHE R 139 TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 6783) covalent geometry : angle 0.53114 ( 9216) hydrogen bonds : bond 0.03435 ( 365) hydrogen bonds : angle 4.10283 ( 1056) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 0.166 Fit side-chains REVERT: R 62 LEU cc_start: 0.7196 (OUTLIER) cc_final: 0.6976 (pp) REVERT: R 262 MET cc_start: 0.5078 (tpp) cc_final: 0.4218 (mtm) REVERT: R 265 GLU cc_start: 0.6659 (OUTLIER) cc_final: 0.6222 (pm20) REVERT: B 217 MET cc_start: 0.8258 (OUTLIER) cc_final: 0.7959 (ptp) REVERT: B 227 SER cc_start: 0.8922 (t) cc_final: 0.8609 (m) REVERT: B 269 ILE cc_start: 0.8008 (mt) cc_final: 0.7506 (mt) outliers start: 20 outliers final: 16 residues processed: 121 average time/residue: 0.6270 time to fit residues: 79.4433 Evaluate side-chains 121 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 62 LEU Chi-restraints excluded: chain R residue 246 ILE Chi-restraints excluded: chain R residue 265 GLU Chi-restraints excluded: chain R residue 273 SER Chi-restraints excluded: chain R residue 274 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 52 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 38 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 49 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 112 ASN ** R 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 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 = 0.4170 r_free = 0.4170 target = 0.195659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.138619 restraints weight = 6912.830| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.02 r_work: 0.3291 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6783 Z= 0.178 Angle : 0.599 13.111 9216 Z= 0.306 Chirality : 0.042 0.197 1095 Planarity : 0.004 0.043 1147 Dihedral : 4.455 43.571 920 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.47 % Allowed : 17.08 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.29), residues: 858 helix: 1.72 (0.27), residues: 380 sheet: 0.55 (0.39), residues: 174 loop : -1.01 (0.33), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 150 TYR 0.026 0.002 TYR R 241 PHE 0.020 0.002 PHE R 139 TRP 0.019 0.002 TRP B 82 HIS 0.005 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 6783) covalent geometry : angle 0.59939 ( 9216) hydrogen bonds : bond 0.03897 ( 365) hydrogen bonds : angle 4.32890 ( 1056) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1716 Ramachandran restraints generated. 858 Oldfield, 0 Emsley, 858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 0.264 Fit side-chains REVERT: R 182 LEU cc_start: 0.7697 (tp) cc_final: 0.7267 (tt) REVERT: R 262 MET cc_start: 0.4713 (tpp) cc_final: 0.3798 (mtm) REVERT: R 265 GLU cc_start: 0.6696 (OUTLIER) cc_final: 0.6181 (pm20) REVERT: B 46 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.7647 (mmt180) REVERT: B 217 MET cc_start: 0.8377 (OUTLIER) cc_final: 0.8052 (ptp) REVERT: B 227 SER cc_start: 0.9002 (t) cc_final: 0.8675 (m) REVERT: B 258 ASP cc_start: 0.7164 (t70) cc_final: 0.6524 (t70) REVERT: B 269 ILE cc_start: 0.8031 (mt) cc_final: 0.7513 (mt) outliers start: 24 outliers final: 17 residues processed: 116 average time/residue: 0.6394 time to fit residues: 77.6209 Evaluate side-chains 118 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 181 ILE Chi-restraints excluded: chain R residue 232 THR Chi-restraints excluded: chain R residue 246 ILE Chi-restraints excluded: chain R residue 265 GLU Chi-restraints excluded: chain R residue 273 SER Chi-restraints excluded: chain R residue 274 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 52 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 21 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 84 optimal weight: 0.4980 chunk 76 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 24 ASN R 112 ASN ** R 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.197674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.135043 restraints weight = 6935.734| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.08 r_work: 0.3272 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6783 Z= 0.146 Angle : 0.555 11.649 9216 Z= 0.287 Chirality : 0.041 0.150 1095 Planarity : 0.003 0.043 1147 Dihedral : 4.359 44.196 920 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.76 % Allowed : 16.79 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.29), residues: 858 helix: 1.75 (0.27), residues: 378 sheet: 0.54 (0.38), residues: 179 loop : -0.95 (0.33), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 150 TYR 0.024 0.001 TYR R 241 PHE 0.014 0.001 PHE B 151 TRP 0.017 0.002 TRP B 82 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 6783) covalent geometry : angle 0.55545 ( 9216) hydrogen bonds : bond 0.03672 ( 365) hydrogen bonds : angle 4.23302 ( 1056) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3136.44 seconds wall clock time: 54 minutes 9.65 seconds (3249.65 seconds total)