Starting phenix.real_space_refine on Wed Apr 30 05:42:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k27_61992/04_2025/9k27_61992_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k27_61992/04_2025/9k27_61992.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9k27_61992/04_2025/9k27_61992.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k27_61992/04_2025/9k27_61992.map" model { file = "/net/cci-nas-00/data/ceres_data/9k27_61992/04_2025/9k27_61992_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k27_61992/04_2025/9k27_61992_neut_trim.cif" } resolution = 2.68 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= -0.001 sd= 0.013 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 55 5.16 5 C 5872 2.51 5 N 1600 2.21 5 O 1686 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 9213 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2417 Classifications: {'peptide': 301} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 288} Chain: "B" Number of atoms: 2559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2559 Classifications: {'peptide': 333} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 327} Chain: "C" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 418 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "D" Number of atoms: 1791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1791 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 1 Chain: "E" Number of atoms: 1880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1880 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 5, 'TRANS': 222} Chain breaks: 1 Chain: "F" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 147 Classifications: {'peptide': 18} Link IDs: {'PTRANS': 2, 'TRANS': 15} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.92, per 1000 atoms: 0.64 Number of scatterers: 9213 At special positions: 0 Unit cell: (87.98, 124.5, 127.82, 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 55 16.00 O 1686 8.00 N 1600 7.00 C 5872 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 134 " - pdb=" SG CYS A 211 " distance=2.03 Simple disulfide: pdb=" SG CYS D 39 " - pdb=" SG CYS D 113 " distance=2.04 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.26 Conformation dependent library (CDL) restraints added in 865.5 milliseconds 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2188 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 14 sheets defined 36.2% alpha, 20.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'A' and resid 56 through 58 No H-bonds generated for 'chain 'A' and resid 56 through 58' Processing helix chain 'A' and resid 59 through 88 removed outlier: 4.214A pdb=" N CYS A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 121 Proline residue: A 115 - end of helix removed outlier: 3.610A pdb=" N ALA A 121 " --> pdb=" O THR A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 164 removed outlier: 3.609A pdb=" N HIS A 135 " --> pdb=" O GLY A 131 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU A 136 " --> pdb=" O GLY A 132 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N PHE A 138 " --> pdb=" O CYS A 134 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N PHE A 139 " --> pdb=" O HIS A 135 " (cutoff:3.500A) Proline residue: A 142 - end of helix removed outlier: 4.304A pdb=" N VAL A 149 " --> pdb=" O VAL A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 196 Proline residue: A 193 - end of helix removed outlier: 3.950A pdb=" N VAL A 196 " --> pdb=" O LEU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 234 removed outlier: 3.594A pdb=" N GLN A 223 " --> pdb=" O GLU A 219 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA A 226 " --> pdb=" O ARG A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 254 Processing helix chain 'A' and resid 262 through 304 removed outlier: 3.638A pdb=" N ALA A 266 " --> pdb=" O THR A 262 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ASP A 267 " --> pdb=" O GLN A 263 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N TRP A 268 " --> pdb=" O SER A 264 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N CYS A 290 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N TRP A 291 " --> pdb=" O PHE A 287 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU A 292 " --> pdb=" O ALA A 288 " (cutoff:3.500A) Proline residue: A 293 - end of helix Processing helix chain 'A' and resid 312 through 336 Proline residue: A 332 - end of helix removed outlier: 3.987A pdb=" N TYR A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 352 removed outlier: 3.527A pdb=" N ARG A 343 " --> pdb=" O HIS A 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 25 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'C' and resid 10 through 23 Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.500A pdb=" N HIS C 44 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 49 removed outlier: 3.516A pdb=" N PHE D 49 " --> pdb=" O PHE D 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 30 Processing helix chain 'E' and resid 45 through 57 Processing helix chain 'E' and resid 206 through 215 removed outlier: 3.594A pdb=" N LYS E 209 " --> pdb=" O GLU E 206 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ILE E 211 " --> pdb=" O ARG E 208 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N HIS E 212 " --> pdb=" O LYS E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 229 No H-bonds generated for 'chain 'E' and resid 227 through 229' Processing helix chain 'E' and resid 233 through 238 Processing helix chain 'E' and resid 240 through 247 Processing helix chain 'E' and resid 269 through 277 Processing helix chain 'E' and resid 281 through 286 removed outlier: 3.990A pdb=" N TYR E 285 " --> pdb=" O HIS E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 309 Processing helix chain 'E' and resid 329 through 350 Processing helix chain 'F' and resid 17 through 23 removed outlier: 3.586A pdb=" N TYR F 20 " --> pdb=" O PRO F 17 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 198 through 199 removed outlier: 3.680A pdb=" N GLU A 212 " --> pdb=" O TYR A 199 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 52 removed outlier: 6.749A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.980A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.490A 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: 6.865A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.503A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 4.025A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.195A 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: 6.629A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP B 254 " --> pdb=" O GLN B 259 " (cutoff:3.500A) removed outlier: 3.524A 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: 3.610A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 20 through 24 removed outlier: 5.879A pdb=" N GLY D 33 " --> pdb=" O SER D 102 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 27 through 29 Processing sheet with id=AB2, first strand: chain 'D' and resid 67 through 68 Processing sheet with id=AB3, first strand: chain 'D' and resid 163 through 165 removed outlier: 6.496A pdb=" N LEU D 191 " --> pdb=" O TYR D 207 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N TYR D 207 " --> pdb=" O LEU D 191 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N TRP D 193 " --> pdb=" O LEU D 205 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 173 through 177 Processing sheet with id=AB5, first strand: chain 'E' and resid 184 through 189 removed outlier: 7.030A pdb=" N LEU E 36 " --> pdb=" O VAL E 198 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER E 219 " --> pdb=" O LYS E 35 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ILE E 220 " --> pdb=" O ILE E 264 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N PHE E 266 " --> pdb=" O ILE E 220 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N PHE E 222 " --> pdb=" O PHE E 266 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ASN E 268 " --> pdb=" O PHE E 222 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N VAL E 224 " --> pdb=" O ASN E 268 " (cutoff:3.500A) 419 hydrogen bonds defined for protein. 1167 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: 2.50 Time building geometry restraints manager: 2.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2935 1.34 - 1.46: 1474 1.46 - 1.57: 4923 1.57 - 1.69: 0 1.69 - 1.81: 79 Bond restraints: 9411 Sorted by residual: bond pdb=" N TYR E 350 " pdb=" CA TYR E 350 " ideal model delta sigma weight residual 1.456 1.484 -0.028 1.18e-02 7.18e+03 5.55e+00 bond pdb=" N ARG A 170 " pdb=" CA ARG A 170 " ideal model delta sigma weight residual 1.455 1.482 -0.027 1.27e-02 6.20e+03 4.51e+00 bond pdb=" N TYR A 225 " pdb=" CA TYR A 225 " ideal model delta sigma weight residual 1.459 1.483 -0.024 1.19e-02 7.06e+03 3.95e+00 bond pdb=" N THR A 95 " pdb=" CA THR A 95 " ideal model delta sigma weight residual 1.459 1.480 -0.022 1.16e-02 7.43e+03 3.45e+00 bond pdb=" CA TYR A 146 " pdb=" C TYR A 146 " ideal model delta sigma weight residual 1.521 1.497 0.023 1.27e-02 6.20e+03 3.41e+00 ... (remaining 9406 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 12546 2.17 - 4.33: 191 4.33 - 6.50: 26 6.50 - 8.66: 4 8.66 - 10.83: 3 Bond angle restraints: 12770 Sorted by residual: angle pdb=" CA GLN B 13 " pdb=" CB GLN B 13 " pdb=" CG GLN B 13 " ideal model delta sigma weight residual 114.10 121.91 -7.81 2.00e+00 2.50e-01 1.53e+01 angle pdb=" CB MET E 53 " pdb=" CG MET E 53 " pdb=" SD MET E 53 " ideal model delta sigma weight residual 112.70 101.87 10.83 3.00e+00 1.11e-01 1.30e+01 angle pdb=" N THR B 184 " pdb=" CA THR B 184 " pdb=" C THR B 184 " ideal model delta sigma weight residual 114.31 109.96 4.35 1.29e+00 6.01e-01 1.14e+01 angle pdb=" N VAL A 147 " pdb=" CA VAL A 147 " pdb=" C VAL A 147 " ideal model delta sigma weight residual 112.50 108.01 4.49 1.39e+00 5.18e-01 1.04e+01 angle pdb=" C GLU B 12 " pdb=" N GLN B 13 " pdb=" CA GLN B 13 " ideal model delta sigma weight residual 120.68 115.80 4.88 1.70e+00 3.46e-01 8.24e+00 ... (remaining 12765 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 5023 17.80 - 35.60: 460 35.60 - 53.41: 80 53.41 - 71.21: 16 71.21 - 89.01: 4 Dihedral angle restraints: 5583 sinusoidal: 2192 harmonic: 3391 Sorted by residual: dihedral pdb=" CA HIS A 206 " pdb=" C HIS A 206 " pdb=" N ASP A 207 " pdb=" CA ASP A 207 " ideal model delta harmonic sigma weight residual 180.00 159.72 20.28 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 161.60 18.40 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA ASP E 313 " pdb=" C ASP E 313 " pdb=" N SER E 314 " pdb=" CA SER E 314 " ideal model delta harmonic sigma weight residual 180.00 161.83 18.17 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 5580 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1028 0.042 - 0.084: 308 0.084 - 0.126: 101 0.126 - 0.169: 12 0.169 - 0.211: 3 Chirality restraints: 1452 Sorted by residual: chirality pdb=" CB ILE A 308 " pdb=" CA ILE A 308 " pdb=" CG1 ILE A 308 " pdb=" CG2 ILE A 308 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CB ILE D 75 " pdb=" CA ILE D 75 " pdb=" CG1 ILE D 75 " pdb=" CG2 ILE D 75 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.19 2.00e-01 2.50e+01 9.44e-01 chirality pdb=" CB VAL E 200 " pdb=" CA VAL E 200 " pdb=" CG1 VAL E 200 " pdb=" CG2 VAL E 200 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.83e-01 ... (remaining 1449 not shown) Planarity restraints: 1618 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 215 " -0.018 2.00e-02 2.50e+03 1.49e-02 5.53e+00 pdb=" CG TRP A 215 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP A 215 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP A 215 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 215 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 215 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 215 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 215 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 215 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 215 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 49 " -0.018 2.00e-02 2.50e+03 1.62e-02 4.57e+00 pdb=" CG PHE E 49 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE E 49 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE E 49 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE E 49 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE E 49 " -0.013 2.00e-02 2.50e+03 pdb=" CZ PHE E 49 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 309 " 0.030 5.00e-02 4.00e+02 4.58e-02 3.36e+00 pdb=" N PRO A 310 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 310 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 310 " 0.025 5.00e-02 4.00e+02 ... (remaining 1615 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.45: 49 2.45 - 3.06: 6077 3.06 - 3.67: 13546 3.67 - 4.29: 19622 4.29 - 4.90: 34260 Nonbonded interactions: 73554 Sorted by model distance: nonbonded pdb=" NE2 HIS A 321 " pdb=" O PHE F 31 " model vdw 1.835 3.120 nonbonded pdb=" OE1 GLN A 141 " pdb=" N NH2 F 33 " model vdw 2.124 3.120 nonbonded pdb=" OG1 THR B 86 " pdb=" OD1 ASN B 88 " model vdw 2.147 3.040 nonbonded pdb=" OH TYR E 229 " pdb=" OG SER E 280 " model vdw 2.170 3.040 nonbonded pdb=" OG SER A 217 " pdb=" OE1 GLN A 218 " model vdw 2.189 3.040 ... (remaining 73549 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: 1.900 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: 0.000 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.800 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 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:13.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 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 0.140 9414 Z= 0.243 Angle : 0.684 10.826 12774 Z= 0.381 Chirality : 0.044 0.211 1452 Planarity : 0.004 0.046 1618 Dihedral : 13.891 89.009 3389 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 0.10 % Allowed : 0.40 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.25), residues: 1151 helix: 1.58 (0.28), residues: 388 sheet: -0.93 (0.31), residues: 283 loop : -1.62 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 215 HIS 0.006 0.001 HIS A 206 PHE 0.035 0.001 PHE E 49 TYR 0.016 0.001 TYR A 311 ARG 0.007 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.14830 ( 419) hydrogen bonds : angle 5.24653 ( 1167) SS BOND : bond 0.00353 ( 2) SS BOND : angle 0.81685 ( 4) covalent geometry : bond 0.00413 ( 9411) covalent geometry : angle 0.68399 (12770) Misc. bond : bond 0.13970 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 195 time to evaluate : 1.509 Fit side-chains REVERT: A 79 CYS cc_start: 0.9285 (m) cc_final: 0.9034 (m) REVERT: A 219 GLU cc_start: 0.8488 (tp30) cc_final: 0.7867 (tp30) REVERT: A 223 GLN cc_start: 0.8400 (mp10) cc_final: 0.7869 (mp10) REVERT: A 251 LYS cc_start: 0.8709 (tptp) cc_final: 0.8337 (tptp) REVERT: B 10 GLU cc_start: 0.7689 (pm20) cc_final: 0.7033 (mp0) REVERT: B 15 LYS cc_start: 0.9521 (tppp) cc_final: 0.9274 (tmmt) REVERT: B 17 GLN cc_start: 0.9316 (tm-30) cc_final: 0.9061 (tm-30) REVERT: B 20 ASP cc_start: 0.9164 (m-30) cc_final: 0.8899 (m-30) REVERT: B 32 GLN cc_start: 0.9019 (pt0) cc_final: 0.8367 (pp30) REVERT: C 18 GLN cc_start: 0.8626 (tp40) cc_final: 0.8408 (tp40) REVERT: D 82 LYS cc_start: 0.8847 (tppt) cc_final: 0.8611 (tptp) REVERT: E 20 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7643 (mt-10) REVERT: E 289 TYR cc_start: 0.9073 (t80) cc_final: 0.8855 (t80) outliers start: 1 outliers final: 0 residues processed: 196 average time/residue: 1.6859 time to fit residues: 350.0110 Evaluate side-chains 149 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 29 optimal weight: 0.3980 chunk 58 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 103 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN A 331 ASN B 44 GLN B 75 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.094889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.067775 restraints weight = 18555.003| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 3.72 r_work: 0.2788 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9414 Z= 0.134 Angle : 0.640 10.447 12774 Z= 0.327 Chirality : 0.043 0.170 1452 Planarity : 0.005 0.057 1618 Dihedral : 4.433 20.824 1282 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 1.79 % Allowed : 10.85 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -0.31 (0.25), residues: 1151 helix: 1.69 (0.28), residues: 398 sheet: -0.68 (0.32), residues: 259 loop : -1.55 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 211 HIS 0.005 0.001 HIS A 339 PHE 0.027 0.001 PHE E 49 TYR 0.019 0.001 TYR D 207 ARG 0.008 0.001 ARG E 204 Details of bonding type rmsd hydrogen bonds : bond 0.04147 ( 419) hydrogen bonds : angle 4.22032 ( 1167) SS BOND : bond 0.00530 ( 2) SS BOND : angle 0.67920 ( 4) covalent geometry : bond 0.00302 ( 9411) covalent geometry : angle 0.64002 (12770) Misc. bond : bond 0.00069 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 165 time to evaluate : 1.026 Fit side-chains revert: symmetry clash REVERT: A 60 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.8274 (tppp) REVERT: A 79 CYS cc_start: 0.9408 (m) cc_final: 0.9083 (m) REVERT: A 251 LYS cc_start: 0.8442 (tptp) cc_final: 0.8136 (tptp) REVERT: B 15 LYS cc_start: 0.9439 (tppp) cc_final: 0.9108 (tmmt) REVERT: B 217 MET cc_start: 0.8894 (OUTLIER) cc_final: 0.8280 (pmm) REVERT: C 20 LYS cc_start: 0.8850 (pttm) cc_final: 0.8587 (pttm) REVERT: C 47 GLU cc_start: 0.8319 (tm-30) cc_final: 0.8047 (tm-30) REVERT: D 82 LYS cc_start: 0.8295 (tppt) cc_final: 0.7750 (tptp) REVERT: D 261 LYS cc_start: 0.8027 (ttmm) cc_final: 0.7561 (ttmm) REVERT: E 20 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7644 (mt-10) REVERT: E 289 TYR cc_start: 0.8713 (t80) cc_final: 0.8505 (t80) outliers start: 18 outliers final: 6 residues processed: 172 average time/residue: 1.1572 time to fit residues: 213.0511 Evaluate side-chains 155 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 147 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 206 HIS Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain C residue 62 PHE Chi-restraints excluded: chain F residue 19 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 42 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 71 optimal weight: 0.5980 chunk 94 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN B 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.092378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.065501 restraints weight = 18975.527| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 3.71 r_work: 0.2742 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9414 Z= 0.182 Angle : 0.645 10.085 12774 Z= 0.330 Chirality : 0.044 0.174 1452 Planarity : 0.004 0.051 1618 Dihedral : 4.365 19.294 1282 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 1.59 % Allowed : 14.73 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -0.29 (0.25), residues: 1151 helix: 1.69 (0.28), residues: 401 sheet: -0.69 (0.32), residues: 258 loop : -1.51 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.005 0.001 HIS A 339 PHE 0.029 0.001 PHE E 49 TYR 0.014 0.001 TYR D 207 ARG 0.006 0.000 ARG E 204 Details of bonding type rmsd hydrogen bonds : bond 0.04534 ( 419) hydrogen bonds : angle 4.15058 ( 1167) SS BOND : bond 0.00509 ( 2) SS BOND : angle 0.53696 ( 4) covalent geometry : bond 0.00423 ( 9411) covalent geometry : angle 0.64546 (12770) Misc. bond : bond 0.00022 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 156 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 CYS cc_start: 0.9424 (m) cc_final: 0.9068 (m) REVERT: A 219 GLU cc_start: 0.9058 (tp30) cc_final: 0.8592 (tm-30) REVERT: A 251 LYS cc_start: 0.8495 (tptp) cc_final: 0.8197 (tptp) REVERT: B 15 LYS cc_start: 0.9442 (tppp) cc_final: 0.9116 (tmmt) REVERT: B 30 LEU cc_start: 0.6475 (tt) cc_final: 0.6206 (tt) REVERT: C 20 LYS cc_start: 0.8761 (pttm) cc_final: 0.8502 (pttm) REVERT: C 47 GLU cc_start: 0.8380 (tm-30) cc_final: 0.8114 (tm-30) REVERT: C 62 PHE cc_start: 0.7130 (OUTLIER) cc_final: 0.6913 (m-10) REVERT: D 82 LYS cc_start: 0.8396 (tppt) cc_final: 0.7809 (tptp) REVERT: D 218 ASP cc_start: 0.8715 (p0) cc_final: 0.8472 (p0) REVERT: D 247 MET cc_start: 0.9103 (ttp) cc_final: 0.8845 (ttp) REVERT: D 251 GLU cc_start: 0.8650 (mt-10) cc_final: 0.8434 (mt-10) REVERT: E 20 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7699 (mt-10) REVERT: E 289 TYR cc_start: 0.8733 (t80) cc_final: 0.8526 (t80) REVERT: E 351 ASN cc_start: 0.9005 (m110) cc_final: 0.8777 (m-40) outliers start: 16 outliers final: 9 residues processed: 165 average time/residue: 1.3644 time to fit residues: 239.5591 Evaluate side-chains 158 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 148 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 HIS Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 62 PHE Chi-restraints excluded: chain F residue 19 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 67 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN B 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.093876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.067101 restraints weight = 18556.280| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 3.70 r_work: 0.2772 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9414 Z= 0.138 Angle : 0.628 11.792 12774 Z= 0.318 Chirality : 0.042 0.148 1452 Planarity : 0.004 0.046 1618 Dihedral : 4.233 18.170 1282 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 2.09 % Allowed : 17.21 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -0.09 (0.26), residues: 1151 helix: 1.74 (0.27), residues: 402 sheet: -0.37 (0.32), residues: 259 loop : -1.44 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.004 0.001 HIS A 339 PHE 0.030 0.001 PHE E 49 TYR 0.014 0.001 TYR D 207 ARG 0.008 0.000 ARG E 24 Details of bonding type rmsd hydrogen bonds : bond 0.03959 ( 419) hydrogen bonds : angle 3.98860 ( 1167) SS BOND : bond 0.00492 ( 2) SS BOND : angle 0.56157 ( 4) covalent geometry : bond 0.00318 ( 9411) covalent geometry : angle 0.62806 (12770) Misc. bond : bond 0.00037 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 159 time to evaluate : 0.998 Fit side-chains revert: symmetry clash REVERT: A 79 CYS cc_start: 0.9450 (m) cc_final: 0.9044 (m) REVERT: A 212 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7095 (pp20) REVERT: A 219 GLU cc_start: 0.9012 (tp30) cc_final: 0.8425 (tp30) REVERT: A 223 GLN cc_start: 0.8104 (mp10) cc_final: 0.7680 (mp10) REVERT: A 251 LYS cc_start: 0.8478 (tptp) cc_final: 0.8198 (tptp) REVERT: B 15 LYS cc_start: 0.9445 (tppp) cc_final: 0.9108 (tmmt) REVERT: C 20 LYS cc_start: 0.8798 (pttm) cc_final: 0.8495 (ptpp) REVERT: C 32 LYS cc_start: 0.8851 (mtpp) cc_final: 0.8633 (tppp) REVERT: C 46 LYS cc_start: 0.9342 (mmmm) cc_final: 0.9057 (mmmm) REVERT: C 47 GLU cc_start: 0.8533 (tm-30) cc_final: 0.8314 (tm-30) REVERT: D 60 LYS cc_start: 0.7894 (mmtm) cc_final: 0.7618 (mmpt) REVERT: D 82 LYS cc_start: 0.8348 (tppt) cc_final: 0.7785 (tptp) REVERT: D 93 LYS cc_start: 0.8986 (mtmm) cc_final: 0.8432 (pmmt) REVERT: D 110 MET cc_start: 0.7808 (mmm) cc_final: 0.7431 (mmm) REVERT: D 157 MET cc_start: 0.9027 (OUTLIER) cc_final: 0.7832 (mtp) REVERT: D 218 ASP cc_start: 0.8661 (p0) cc_final: 0.8417 (p0) REVERT: D 247 MET cc_start: 0.9110 (ttp) cc_final: 0.8797 (ttp) REVERT: D 248 GLN cc_start: 0.8833 (pp30) cc_final: 0.8403 (pp30) REVERT: D 251 GLU cc_start: 0.8629 (mt-10) cc_final: 0.8426 (mt-10) REVERT: D 261 LYS cc_start: 0.8076 (ttmm) cc_final: 0.7801 (ttmm) REVERT: E 20 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7619 (mt-10) REVERT: E 289 TYR cc_start: 0.8727 (t80) cc_final: 0.8518 (t80) REVERT: E 351 ASN cc_start: 0.8939 (m110) cc_final: 0.8736 (m-40) outliers start: 21 outliers final: 9 residues processed: 170 average time/residue: 1.2650 time to fit residues: 229.0057 Evaluate side-chains 155 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 144 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 HIS Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain C residue 62 PHE Chi-restraints excluded: chain D residue 157 MET Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain F residue 19 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 88 optimal weight: 7.9990 chunk 91 optimal weight: 0.6980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN B 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.093437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.066661 restraints weight = 18559.758| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 3.70 r_work: 0.2769 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9414 Z= 0.142 Angle : 0.636 10.697 12774 Z= 0.319 Chirality : 0.042 0.154 1452 Planarity : 0.004 0.045 1618 Dihedral : 4.158 17.790 1282 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 2.49 % Allowed : 18.61 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -0.03 (0.26), residues: 1151 helix: 1.78 (0.27), residues: 402 sheet: -0.31 (0.33), residues: 259 loop : -1.41 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.003 0.001 HIS A 339 PHE 0.027 0.001 PHE E 49 TYR 0.013 0.001 TYR D 207 ARG 0.008 0.000 ARG E 204 Details of bonding type rmsd hydrogen bonds : bond 0.03948 ( 419) hydrogen bonds : angle 3.96342 ( 1167) SS BOND : bond 0.00488 ( 2) SS BOND : angle 0.54310 ( 4) covalent geometry : bond 0.00331 ( 9411) covalent geometry : angle 0.63616 (12770) Misc. bond : bond 0.00035 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 152 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 CYS cc_start: 0.9452 (m) cc_final: 0.9077 (m) REVERT: A 219 GLU cc_start: 0.9010 (tp30) cc_final: 0.8544 (tm-30) REVERT: A 251 LYS cc_start: 0.8497 (tptp) cc_final: 0.8222 (tptp) REVERT: B 15 LYS cc_start: 0.9451 (tppp) cc_final: 0.9126 (tmmt) REVERT: C 20 LYS cc_start: 0.8835 (pttm) cc_final: 0.8503 (pttm) REVERT: C 32 LYS cc_start: 0.8841 (mtpp) cc_final: 0.8630 (tppp) REVERT: C 46 LYS cc_start: 0.9343 (mmmm) cc_final: 0.9064 (mmmm) REVERT: C 47 GLU cc_start: 0.8577 (tm-30) cc_final: 0.8315 (tm-30) REVERT: D 60 LYS cc_start: 0.7899 (mmtm) cc_final: 0.7615 (mmpt) REVERT: D 82 LYS cc_start: 0.8341 (tppt) cc_final: 0.7770 (tptp) REVERT: D 93 LYS cc_start: 0.8963 (mtmm) cc_final: 0.8359 (pmmt) REVERT: D 110 MET cc_start: 0.7784 (mmm) cc_final: 0.7470 (mmm) REVERT: D 157 MET cc_start: 0.8815 (OUTLIER) cc_final: 0.7946 (mtp) REVERT: D 240 ASP cc_start: 0.8206 (m-30) cc_final: 0.7906 (m-30) REVERT: D 248 GLN cc_start: 0.8812 (pp30) cc_final: 0.8289 (pp30) REVERT: E 20 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7608 (mt-10) REVERT: E 289 TYR cc_start: 0.8698 (t80) cc_final: 0.8481 (t80) outliers start: 25 outliers final: 14 residues processed: 167 average time/residue: 1.3289 time to fit residues: 235.9713 Evaluate side-chains 155 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 140 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 206 HIS Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain C residue 62 PHE Chi-restraints excluded: chain D residue 157 MET Chi-restraints excluded: chain D residue 261 LYS Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain F residue 19 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 92 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 106 optimal weight: 0.6980 chunk 104 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 111 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 57 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN B 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.091973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.066300 restraints weight = 18441.841| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 3.61 r_work: 0.2742 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9414 Z= 0.182 Angle : 0.670 10.847 12774 Z= 0.338 Chirality : 0.044 0.159 1452 Planarity : 0.004 0.061 1618 Dihedral : 4.233 17.506 1282 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 3.58 % Allowed : 18.91 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: -0.04 (0.26), residues: 1151 helix: 1.81 (0.27), residues: 401 sheet: -0.35 (0.32), residues: 264 loop : -1.42 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 211 HIS 0.004 0.001 HIS B 225 PHE 0.026 0.001 PHE E 49 TYR 0.013 0.001 TYR D 207 ARG 0.013 0.000 ARG E 204 Details of bonding type rmsd hydrogen bonds : bond 0.04365 ( 419) hydrogen bonds : angle 4.03745 ( 1167) SS BOND : bond 0.00520 ( 2) SS BOND : angle 0.52319 ( 4) covalent geometry : bond 0.00429 ( 9411) covalent geometry : angle 0.67018 (12770) Misc. bond : bond 0.00071 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 148 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 CYS cc_start: 0.9447 (m) cc_final: 0.9038 (m) REVERT: A 219 GLU cc_start: 0.8974 (tp30) cc_final: 0.8387 (tm-30) REVERT: A 223 GLN cc_start: 0.8028 (mp10) cc_final: 0.7665 (mp10) REVERT: A 251 LYS cc_start: 0.8488 (tptp) cc_final: 0.8214 (tptp) REVERT: B 15 LYS cc_start: 0.9431 (tppp) cc_final: 0.9099 (tmmt) REVERT: B 217 MET cc_start: 0.8848 (OUTLIER) cc_final: 0.8222 (pmm) REVERT: C 20 LYS cc_start: 0.8850 (pttm) cc_final: 0.8570 (pttm) REVERT: C 46 LYS cc_start: 0.9351 (mmmm) cc_final: 0.9066 (mmmm) REVERT: C 47 GLU cc_start: 0.8612 (tm-30) cc_final: 0.8329 (tm-30) REVERT: D 60 LYS cc_start: 0.7890 (mmtm) cc_final: 0.7591 (mmpt) REVERT: D 82 LYS cc_start: 0.8432 (tppt) cc_final: 0.7838 (tptp) REVERT: D 90 ASP cc_start: 0.7092 (OUTLIER) cc_final: 0.6746 (t0) REVERT: D 110 MET cc_start: 0.7785 (mmm) cc_final: 0.7410 (mmm) REVERT: D 157 MET cc_start: 0.8802 (OUTLIER) cc_final: 0.7964 (mtp) REVERT: D 240 ASP cc_start: 0.8268 (m-30) cc_final: 0.7863 (m-30) REVERT: D 248 GLN cc_start: 0.8809 (pp30) cc_final: 0.8318 (pp30) REVERT: E 20 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7691 (mt-10) REVERT: E 289 TYR cc_start: 0.8666 (t80) cc_final: 0.8418 (t80) outliers start: 36 outliers final: 18 residues processed: 173 average time/residue: 1.2871 time to fit residues: 237.8100 Evaluate side-chains 164 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 143 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 206 HIS Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 62 PHE Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 113 CYS Chi-restraints excluded: chain D residue 157 MET Chi-restraints excluded: chain D residue 261 LYS Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain F residue 19 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 67 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 74 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 108 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 79 optimal weight: 4.9990 chunk 91 optimal weight: 0.0970 chunk 16 optimal weight: 8.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN B 75 GLN E 22 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.093276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.066851 restraints weight = 18662.720| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 3.68 r_work: 0.2767 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9414 Z= 0.144 Angle : 0.664 11.153 12774 Z= 0.334 Chirality : 0.043 0.166 1452 Planarity : 0.004 0.065 1618 Dihedral : 4.143 17.420 1282 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 3.28 % Allowed : 19.90 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 0.03 (0.26), residues: 1151 helix: 1.82 (0.27), residues: 401 sheet: -0.32 (0.32), residues: 270 loop : -1.35 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 211 HIS 0.002 0.001 HIS B 183 PHE 0.027 0.001 PHE E 49 TYR 0.013 0.001 TYR D 207 ARG 0.015 0.000 ARG E 204 Details of bonding type rmsd hydrogen bonds : bond 0.03984 ( 419) hydrogen bonds : angle 3.96827 ( 1167) SS BOND : bond 0.00491 ( 2) SS BOND : angle 0.54051 ( 4) covalent geometry : bond 0.00337 ( 9411) covalent geometry : angle 0.66372 (12770) Misc. bond : bond 0.00044 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 148 time to evaluate : 1.495 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 CYS cc_start: 0.9455 (m) cc_final: 0.9030 (m) REVERT: A 219 GLU cc_start: 0.8942 (tp30) cc_final: 0.8359 (tm-30) REVERT: A 223 GLN cc_start: 0.8058 (mp10) cc_final: 0.7679 (mp10) REVERT: A 251 LYS cc_start: 0.8501 (tptp) cc_final: 0.8228 (tptp) REVERT: B 15 LYS cc_start: 0.9436 (tppp) cc_final: 0.9114 (tmmt) REVERT: B 217 MET cc_start: 0.8889 (OUTLIER) cc_final: 0.8282 (pmm) REVERT: B 259 GLN cc_start: 0.8540 (mm-40) cc_final: 0.7940 (mm110) REVERT: C 20 LYS cc_start: 0.8862 (pttm) cc_final: 0.8533 (pttm) REVERT: C 46 LYS cc_start: 0.9357 (mmmm) cc_final: 0.9076 (mmmm) REVERT: C 47 GLU cc_start: 0.8640 (tm-30) cc_final: 0.8339 (tm-30) REVERT: D 60 LYS cc_start: 0.7895 (mmtm) cc_final: 0.7600 (mmpt) REVERT: D 82 LYS cc_start: 0.8385 (tppt) cc_final: 0.7784 (tptp) REVERT: D 90 ASP cc_start: 0.7120 (OUTLIER) cc_final: 0.6797 (t0) REVERT: D 110 MET cc_start: 0.7813 (mmm) cc_final: 0.7411 (mmm) REVERT: D 113 CYS cc_start: 0.8259 (OUTLIER) cc_final: 0.7590 (p) REVERT: D 157 MET cc_start: 0.8808 (OUTLIER) cc_final: 0.7944 (mtp) REVERT: D 240 ASP cc_start: 0.8249 (m-30) cc_final: 0.7887 (m-30) REVERT: D 248 GLN cc_start: 0.8802 (pp30) cc_final: 0.8364 (pp30) REVERT: E 20 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7657 (mt-10) REVERT: E 289 TYR cc_start: 0.8678 (t80) cc_final: 0.8436 (t80) REVERT: F 16 ASN cc_start: 0.8450 (t0) cc_final: 0.7935 (m-40) outliers start: 33 outliers final: 15 residues processed: 170 average time/residue: 1.3831 time to fit residues: 250.3543 Evaluate side-chains 160 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 141 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 206 HIS Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 62 PHE Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 113 CYS Chi-restraints excluded: chain D residue 157 MET Chi-restraints excluded: chain E residue 306 MET Chi-restraints excluded: chain F residue 19 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 74 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 113 optimal weight: 0.4980 chunk 56 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 111 optimal weight: 0.0970 chunk 78 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 7 optimal weight: 0.0070 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN B 75 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 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 = 0.3455 r_free = 0.3455 target = 0.096444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.069600 restraints weight = 18336.885| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 3.72 r_work: 0.2831 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9414 Z= 0.123 Angle : 0.675 11.455 12774 Z= 0.336 Chirality : 0.042 0.163 1452 Planarity : 0.004 0.064 1618 Dihedral : 3.975 17.008 1282 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.19 % Allowed : 22.19 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 0.12 (0.26), residues: 1151 helix: 1.87 (0.27), residues: 400 sheet: -0.18 (0.32), residues: 270 loop : -1.32 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 211 HIS 0.003 0.000 HIS E 281 PHE 0.027 0.001 PHE E 49 TYR 0.013 0.001 TYR D 207 ARG 0.017 0.000 ARG E 204 Details of bonding type rmsd hydrogen bonds : bond 0.03443 ( 419) hydrogen bonds : angle 3.86898 ( 1167) SS BOND : bond 0.00410 ( 2) SS BOND : angle 0.50161 ( 4) covalent geometry : bond 0.00284 ( 9411) covalent geometry : angle 0.67464 (12770) Misc. bond : bond 0.00022 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 155 time to evaluate : 1.275 Fit side-chains revert: symmetry clash REVERT: A 79 CYS cc_start: 0.9474 (m) cc_final: 0.9055 (m) REVERT: A 219 GLU cc_start: 0.8975 (tp30) cc_final: 0.8388 (tm-30) REVERT: A 223 GLN cc_start: 0.8200 (mp10) cc_final: 0.7731 (mp10) REVERT: A 251 LYS cc_start: 0.8455 (tptp) cc_final: 0.8138 (tptp) REVERT: B 15 LYS cc_start: 0.9427 (tppp) cc_final: 0.9093 (tmmt) REVERT: B 20 ASP cc_start: 0.8942 (m-30) cc_final: 0.8705 (m-30) REVERT: B 217 MET cc_start: 0.8888 (OUTLIER) cc_final: 0.8333 (pmm) REVERT: B 259 GLN cc_start: 0.8564 (mm-40) cc_final: 0.8019 (mm110) REVERT: C 20 LYS cc_start: 0.8905 (pttm) cc_final: 0.8640 (pttm) REVERT: C 22 GLU cc_start: 0.7809 (tt0) cc_final: 0.7601 (tt0) REVERT: C 46 LYS cc_start: 0.9331 (mmmm) cc_final: 0.9056 (mmmm) REVERT: C 47 GLU cc_start: 0.8633 (tm-30) cc_final: 0.8333 (tm-30) REVERT: D 60 LYS cc_start: 0.7879 (mmtm) cc_final: 0.7587 (mmpt) REVERT: D 82 LYS cc_start: 0.8319 (tppt) cc_final: 0.7731 (tptp) REVERT: D 90 ASP cc_start: 0.7138 (OUTLIER) cc_final: 0.6819 (t0) REVERT: D 110 MET cc_start: 0.7813 (mmm) cc_final: 0.7398 (mmm) REVERT: D 157 MET cc_start: 0.8779 (OUTLIER) cc_final: 0.7978 (mtp) REVERT: D 240 ASP cc_start: 0.8176 (m-30) cc_final: 0.7831 (m-30) REVERT: E 20 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7663 (mt-10) REVERT: E 289 TYR cc_start: 0.8719 (t80) cc_final: 0.8492 (t80) REVERT: E 293 GLN cc_start: 0.7384 (tm130) cc_final: 0.7111 (tm-30) REVERT: F 16 ASN cc_start: 0.8398 (t0) cc_final: 0.7870 (m-40) outliers start: 22 outliers final: 8 residues processed: 169 average time/residue: 1.4493 time to fit residues: 261.2132 Evaluate side-chains 148 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 137 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 HIS Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 62 PHE Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 113 CYS Chi-restraints excluded: chain D residue 157 MET Chi-restraints excluded: chain F residue 19 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 27 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 107 optimal weight: 7.9990 chunk 80 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 84 optimal weight: 0.0020 chunk 51 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 95 optimal weight: 0.6980 chunk 111 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN B 75 GLN E 22 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.095602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.068826 restraints weight = 18180.520| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 3.70 r_work: 0.2820 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9414 Z= 0.135 Angle : 0.695 12.096 12774 Z= 0.345 Chirality : 0.043 0.174 1452 Planarity : 0.004 0.076 1618 Dihedral : 3.968 16.867 1282 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 1.99 % Allowed : 22.99 % Favored : 75.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 0.22 (0.26), residues: 1151 helix: 1.85 (0.27), residues: 401 sheet: 0.01 (0.33), residues: 273 loop : -1.28 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.002 0.001 HIS E 281 PHE 0.041 0.001 PHE E 49 TYR 0.012 0.001 TYR D 207 ARG 0.018 0.000 ARG E 204 Details of bonding type rmsd hydrogen bonds : bond 0.03646 ( 419) hydrogen bonds : angle 3.84876 ( 1167) SS BOND : bond 0.00400 ( 2) SS BOND : angle 0.51408 ( 4) covalent geometry : bond 0.00318 ( 9411) covalent geometry : angle 0.69487 (12770) Misc. bond : bond 0.00029 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 145 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 CYS cc_start: 0.9466 (m) cc_final: 0.9039 (m) REVERT: A 219 GLU cc_start: 0.8968 (tp30) cc_final: 0.8369 (tm-30) REVERT: A 223 GLN cc_start: 0.8206 (mp10) cc_final: 0.7754 (mp10) REVERT: A 251 LYS cc_start: 0.8455 (tptp) cc_final: 0.8137 (tptp) REVERT: B 15 LYS cc_start: 0.9424 (tppp) cc_final: 0.9096 (tmmt) REVERT: B 57 LYS cc_start: 0.8206 (mtpp) cc_final: 0.7734 (mtpt) REVERT: B 138 GLU cc_start: 0.9144 (OUTLIER) cc_final: 0.8871 (tp30) REVERT: B 217 MET cc_start: 0.8876 (OUTLIER) cc_final: 0.8277 (pmm) REVERT: C 20 LYS cc_start: 0.8874 (pttm) cc_final: 0.8606 (pttm) REVERT: C 22 GLU cc_start: 0.7780 (tt0) cc_final: 0.7578 (tt0) REVERT: C 46 LYS cc_start: 0.9326 (mmmm) cc_final: 0.9051 (mmmm) REVERT: C 47 GLU cc_start: 0.8634 (tm-30) cc_final: 0.8335 (tm-30) REVERT: D 60 LYS cc_start: 0.7912 (mmtm) cc_final: 0.7619 (mmpt) REVERT: D 82 LYS cc_start: 0.8340 (tppt) cc_final: 0.7738 (tptp) REVERT: D 90 ASP cc_start: 0.7147 (OUTLIER) cc_final: 0.6843 (t0) REVERT: D 110 MET cc_start: 0.7812 (mmm) cc_final: 0.7388 (mmm) REVERT: D 113 CYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7650 (p) REVERT: D 157 MET cc_start: 0.8809 (OUTLIER) cc_final: 0.7928 (mtp) REVERT: D 240 ASP cc_start: 0.8079 (m-30) cc_final: 0.7768 (m-30) REVERT: D 248 GLN cc_start: 0.8825 (pp30) cc_final: 0.8288 (pp30) REVERT: E 20 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7673 (mt-10) REVERT: E 53 MET cc_start: 0.8750 (mtt) cc_final: 0.8344 (mtt) REVERT: E 289 TYR cc_start: 0.8697 (t80) cc_final: 0.8475 (t80) REVERT: F 16 ASN cc_start: 0.8437 (t0) cc_final: 0.7962 (m-40) outliers start: 20 outliers final: 8 residues processed: 156 average time/residue: 1.4529 time to fit residues: 241.2407 Evaluate side-chains 155 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 142 time to evaluate : 2.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 206 HIS Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 62 PHE Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 113 CYS Chi-restraints excluded: chain D residue 157 MET Chi-restraints excluded: chain F residue 19 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 9 optimal weight: 0.5980 chunk 31 optimal weight: 8.9990 chunk 22 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 112 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN B 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.095686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.069892 restraints weight = 18532.024| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 3.66 r_work: 0.2817 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9414 Z= 0.140 Angle : 0.715 12.531 12774 Z= 0.355 Chirality : 0.043 0.200 1452 Planarity : 0.004 0.081 1618 Dihedral : 3.973 16.499 1282 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.49 % Allowed : 23.88 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 0.18 (0.26), residues: 1151 helix: 1.83 (0.27), residues: 401 sheet: 0.02 (0.33), residues: 263 loop : -1.30 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.002 0.000 HIS A 321 PHE 0.038 0.001 PHE E 49 TYR 0.012 0.001 TYR D 207 ARG 0.019 0.000 ARG E 204 Details of bonding type rmsd hydrogen bonds : bond 0.03706 ( 419) hydrogen bonds : angle 3.85967 ( 1167) SS BOND : bond 0.00429 ( 2) SS BOND : angle 0.54289 ( 4) covalent geometry : bond 0.00331 ( 9411) covalent geometry : angle 0.71528 (12770) Misc. bond : bond 0.00032 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2302 Ramachandran restraints generated. 1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 141 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 CYS cc_start: 0.9451 (m) cc_final: 0.8988 (m) REVERT: A 219 GLU cc_start: 0.8941 (tp30) cc_final: 0.8536 (tm-30) REVERT: A 251 LYS cc_start: 0.8454 (tptp) cc_final: 0.8128 (tptp) REVERT: B 15 LYS cc_start: 0.9417 (tppp) cc_final: 0.9078 (tmmt) REVERT: B 57 LYS cc_start: 0.8162 (mtpp) cc_final: 0.7703 (mtpp) REVERT: B 138 GLU cc_start: 0.9151 (OUTLIER) cc_final: 0.8781 (tp30) REVERT: B 217 MET cc_start: 0.8829 (OUTLIER) cc_final: 0.8231 (pmm) REVERT: C 20 LYS cc_start: 0.8888 (pttm) cc_final: 0.8627 (pttm) REVERT: C 22 GLU cc_start: 0.7755 (tt0) cc_final: 0.7546 (tt0) REVERT: C 46 LYS cc_start: 0.9338 (mmmm) cc_final: 0.9064 (mmmm) REVERT: C 47 GLU cc_start: 0.8647 (tm-30) cc_final: 0.8346 (tm-30) REVERT: D 60 LYS cc_start: 0.7848 (mmtm) cc_final: 0.7559 (mmpt) REVERT: D 82 LYS cc_start: 0.8307 (tppt) cc_final: 0.7713 (tptp) REVERT: D 90 ASP cc_start: 0.7118 (OUTLIER) cc_final: 0.6813 (t0) REVERT: D 110 MET cc_start: 0.7762 (mmm) cc_final: 0.7333 (mmm) REVERT: D 113 CYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7630 (p) REVERT: D 157 MET cc_start: 0.8775 (OUTLIER) cc_final: 0.7880 (mtp) REVERT: D 240 ASP cc_start: 0.8045 (m-30) cc_final: 0.7738 (m-30) REVERT: D 248 GLN cc_start: 0.8804 (pp30) cc_final: 0.8413 (pp30) REVERT: E 20 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7646 (mt-10) REVERT: E 53 MET cc_start: 0.8765 (mtt) cc_final: 0.8357 (mtt) REVERT: E 289 TYR cc_start: 0.8664 (t80) cc_final: 0.8446 (t80) REVERT: F 16 ASN cc_start: 0.8378 (t0) cc_final: 0.7941 (m-40) outliers start: 15 outliers final: 9 residues processed: 149 average time/residue: 1.2071 time to fit residues: 192.3422 Evaluate side-chains 155 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 141 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 206 HIS Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 62 PHE Chi-restraints excluded: chain D residue 90 ASP Chi-restraints excluded: chain D residue 113 CYS Chi-restraints excluded: chain D residue 157 MET Chi-restraints excluded: chain F residue 19 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 32 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 chunk 87 optimal weight: 6.9990 chunk 46 optimal weight: 0.1980 chunk 39 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 108 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 96 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN E 22 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.095859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.070025 restraints weight = 18156.705| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 3.65 r_work: 0.2826 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9414 Z= 0.136 Angle : 0.712 12.502 12774 Z= 0.353 Chirality : 0.043 0.221 1452 Planarity : 0.004 0.056 1618 Dihedral : 3.935 16.159 1282 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 1.69 % Allowed : 23.58 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 0.20 (0.26), residues: 1151 helix: 1.83 (0.27), residues: 402 sheet: 0.01 (0.33), residues: 275 loop : -1.30 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.002 0.000 HIS A 321 PHE 0.037 0.001 PHE E 49 TYR 0.012 0.001 TYR D 207 ARG 0.014 0.000 ARG E 204 Details of bonding type rmsd hydrogen bonds : bond 0.03633 ( 419) hydrogen bonds : angle 3.84483 ( 1167) SS BOND : bond 0.00409 ( 2) SS BOND : angle 0.54987 ( 4) covalent geometry : bond 0.00322 ( 9411) covalent geometry : angle 0.71177 (12770) Misc. bond : bond 0.00029 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7691.09 seconds wall clock time: 135 minutes 15.72 seconds (8115.72 seconds total)