Starting phenix.real_space_refine on Thu Feb 13 18:02:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k27_61992/02_2025/9k27_61992_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k27_61992/02_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_61992/02_2025/9k27_61992.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k27_61992/02_2025/9k27_61992.map" model { file = "/net/cci-nas-00/data/ceres_data/9k27_61992/02_2025/9k27_61992_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k27_61992/02_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-5592/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: 4.90, per 1000 atoms: 0.53 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: 2.40 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.84 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: 2.55 Time building geometry restraints manager: 2.75 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: 8.730 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: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 20.510 Find NCS groups from input model: 0.120 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:17.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.780 ------------------------------------------------------------------------------- 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 0.038 9411 Z= 0.273 Angle : 0.684 10.826 12770 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 *********************** 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 : 1.045 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: 1.4564 time to fit residues: 302.0762 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 : 1.014 ------------------------------------------------------------------------------- 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 = 0.3420 r_free = 0.3420 target = 0.094877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.067745 restraints weight = 18558.106| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 3.72 r_work: 0.2789 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 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 9411 Z= 0.199 Angle : 0.640 10.447 12770 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 *********************** 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 : 1.035 Fit side-chains revert: symmetry clash REVERT: A 60 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.8283 (tppp) REVERT: A 79 CYS cc_start: 0.9409 (m) cc_final: 0.9084 (m) REVERT: A 251 LYS cc_start: 0.8441 (tptp) cc_final: 0.8134 (tptp) REVERT: B 15 LYS cc_start: 0.9442 (tppp) cc_final: 0.9110 (tmmt) REVERT: B 217 MET cc_start: 0.8897 (OUTLIER) cc_final: 0.8283 (pmm) REVERT: C 20 LYS cc_start: 0.8854 (pttm) cc_final: 0.8589 (pttm) REVERT: C 47 GLU cc_start: 0.8317 (tm-30) cc_final: 0.8045 (tm-30) REVERT: D 82 LYS cc_start: 0.8295 (tppt) cc_final: 0.7751 (tptp) REVERT: D 261 LYS cc_start: 0.8028 (ttmm) cc_final: 0.7560 (ttmm) REVERT: E 20 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7638 (mt-10) REVERT: E 289 TYR cc_start: 0.8718 (t80) cc_final: 0.8510 (t80) outliers start: 18 outliers final: 6 residues processed: 172 average time/residue: 1.2316 time to fit residues: 226.0396 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 : 1.042 ------------------------------------------------------------------------------- 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: 0.0570 chunk 55 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 71 optimal weight: 0.5980 chunk 94 optimal weight: 1.9990 overall best weight: 1.2902 ------------------------------------------------------------------------------- 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 = 0.3393 r_free = 0.3393 target = 0.093006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.066521 restraints weight = 18885.105| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 3.67 r_work: 0.2765 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9411 Z= 0.255 Angle : 0.637 10.174 12770 Z= 0.324 Chirality : 0.043 0.175 1452 Planarity : 0.004 0.050 1618 Dihedral : 4.323 19.371 1282 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 1.49 % Allowed : 14.83 % 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: -0.27 (0.25), residues: 1151 helix: 1.71 (0.28), residues: 401 sheet: -0.67 (0.32), residues: 258 loop : -1.51 (0.27), residues: 492 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 0.029 0.001 PHE E 49 TYR 0.015 0.001 TYR D 207 ARG 0.007 0.000 ARG E 204 *********************** 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 171 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 156 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 CYS cc_start: 0.9428 (m) cc_final: 0.9068 (m) REVERT: A 219 GLU cc_start: 0.9040 (tp30) cc_final: 0.8553 (tm-30) REVERT: A 251 LYS cc_start: 0.8483 (tptp) cc_final: 0.8186 (tptp) REVERT: B 15 LYS cc_start: 0.9450 (tppp) cc_final: 0.9123 (tmmt) REVERT: B 30 LEU cc_start: 0.6444 (tt) cc_final: 0.6215 (tt) REVERT: C 20 LYS cc_start: 0.8781 (pttm) cc_final: 0.8525 (pttm) REVERT: C 47 GLU cc_start: 0.8377 (tm-30) cc_final: 0.8112 (tm-30) REVERT: D 82 LYS cc_start: 0.8370 (tppt) cc_final: 0.7790 (tptp) REVERT: D 218 ASP cc_start: 0.8698 (p0) cc_final: 0.8440 (p0) REVERT: D 247 MET cc_start: 0.9079 (ttp) cc_final: 0.8811 (ttp) REVERT: E 20 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7699 (mt-10) REVERT: E 289 TYR cc_start: 0.8751 (t80) cc_final: 0.8537 (t80) REVERT: E 351 ASN cc_start: 0.8998 (m110) cc_final: 0.8756 (m-40) outliers start: 15 outliers final: 9 residues processed: 165 average time/residue: 1.3394 time to fit residues: 235.0385 Evaluate side-chains 163 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 154 time to evaluate : 1.103 ------------------------------------------------------------------------------- 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 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: 0.0000 chunk 55 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 75 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 74 optimal weight: 0.2980 chunk 5 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 overall best weight: 1.0188 ------------------------------------------------------------------------------- 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 = 0.3399 r_free = 0.3399 target = 0.093623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.066704 restraints weight = 18583.583| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 3.72 r_work: 0.2768 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9411 Z= 0.222 Angle : 0.632 11.853 12770 Z= 0.320 Chirality : 0.043 0.147 1452 Planarity : 0.004 0.046 1618 Dihedral : 4.245 18.364 1282 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 2.19 % Allowed : 17.01 % Favored : 80.80 % 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: -0.11 (0.26), residues: 1151 helix: 1.76 (0.28), residues: 401 sheet: -0.37 (0.32), residues: 259 loop : -1.48 (0.27), residues: 491 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 204 *********************** 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 177 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 155 time to evaluate : 1.071 Fit side-chains revert: symmetry clash REVERT: A 79 CYS cc_start: 0.9449 (m) cc_final: 0.9074 (m) REVERT: A 212 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7084 (pp20) REVERT: A 213 GLU cc_start: 0.8527 (mt-10) cc_final: 0.8284 (mt-10) REVERT: A 219 GLU cc_start: 0.9026 (tp30) cc_final: 0.8446 (tp30) REVERT: A 223 GLN cc_start: 0.8088 (mp10) cc_final: 0.7671 (mp10) REVERT: A 251 LYS cc_start: 0.8473 (tptp) cc_final: 0.8192 (tptp) REVERT: B 15 LYS cc_start: 0.9451 (tppp) cc_final: 0.9119 (tmmt) REVERT: C 20 LYS cc_start: 0.8795 (pttm) cc_final: 0.8544 (pttm) REVERT: C 32 LYS cc_start: 0.8855 (mtpp) cc_final: 0.8636 (tppp) REVERT: C 46 LYS cc_start: 0.9338 (mmmm) cc_final: 0.9044 (mmmm) REVERT: C 47 GLU cc_start: 0.8483 (tm-30) cc_final: 0.8255 (tm-30) REVERT: D 82 LYS cc_start: 0.8357 (tppt) cc_final: 0.7790 (tptp) REVERT: D 93 LYS cc_start: 0.8979 (mtmm) cc_final: 0.8434 (pmmt) REVERT: D 110 MET cc_start: 0.7823 (mmm) cc_final: 0.7450 (mmm) REVERT: D 157 MET cc_start: 0.9048 (OUTLIER) cc_final: 0.7837 (mtp) REVERT: D 218 ASP cc_start: 0.8655 (p0) cc_final: 0.8403 (p0) REVERT: D 247 MET cc_start: 0.9108 (ttp) cc_final: 0.8787 (ttp) REVERT: D 248 GLN cc_start: 0.8830 (pp30) cc_final: 0.8406 (pp30) REVERT: D 261 LYS cc_start: 0.8058 (ttmm) cc_final: 0.7834 (ttmm) REVERT: E 20 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7656 (mt-10) REVERT: E 289 TYR cc_start: 0.8731 (t80) cc_final: 0.8520 (t80) REVERT: E 351 ASN cc_start: 0.8967 (m110) cc_final: 0.8755 (m-40) outliers start: 22 outliers final: 12 residues processed: 169 average time/residue: 1.3178 time to fit residues: 237.2568 Evaluate side-chains 157 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 143 time to evaluate : 1.053 ------------------------------------------------------------------------------- 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 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 138 GLU 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 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: 0.9990 chunk 20 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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 = 0.3366 r_free = 0.3366 target = 0.091480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.064965 restraints weight = 18630.994| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 3.65 r_work: 0.2730 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 9411 Z= 0.313 Angle : 0.665 10.770 12770 Z= 0.336 Chirality : 0.044 0.152 1452 Planarity : 0.004 0.045 1618 Dihedral : 4.317 17.880 1282 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 3.18 % Allowed : 18.01 % Favored : 78.81 % 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: -0.11 (0.26), residues: 1151 helix: 1.75 (0.27), residues: 402 sheet: -0.40 (0.32), residues: 259 loop : -1.46 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 211 HIS 0.004 0.001 HIS A 339 PHE 0.026 0.001 PHE E 49 TYR 0.013 0.001 TYR D 207 ARG 0.009 0.000 ARG E 204 *********************** 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 184 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 152 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 CYS cc_start: 0.9453 (m) cc_final: 0.9070 (m) REVERT: A 219 GLU cc_start: 0.9001 (tp30) cc_final: 0.8444 (tm-30) REVERT: A 223 GLN cc_start: 0.8074 (mp10) cc_final: 0.7770 (mp10) REVERT: A 251 LYS cc_start: 0.8476 (tptp) cc_final: 0.8197 (tptp) REVERT: B 15 LYS cc_start: 0.9450 (tppp) cc_final: 0.9131 (tmmt) REVERT: B 217 MET cc_start: 0.8864 (OUTLIER) cc_final: 0.8220 (pmm) REVERT: C 20 LYS cc_start: 0.8840 (pttm) cc_final: 0.8549 (pttm) REVERT: C 46 LYS cc_start: 0.9354 (mmmm) cc_final: 0.9066 (mmmm) REVERT: C 47 GLU cc_start: 0.8562 (tm-30) cc_final: 0.8312 (tm-30) REVERT: C 62 PHE cc_start: 0.7079 (OUTLIER) cc_final: 0.6860 (m-10) REVERT: D 82 LYS cc_start: 0.8473 (tppt) cc_final: 0.7837 (tptp) REVERT: D 93 LYS cc_start: 0.8958 (mtmm) cc_final: 0.8366 (pmmt) REVERT: D 110 MET cc_start: 0.7826 (mmm) cc_final: 0.7525 (mmm) REVERT: D 157 MET cc_start: 0.8872 (OUTLIER) cc_final: 0.8074 (mtp) REVERT: D 218 ASP cc_start: 0.8710 (p0) cc_final: 0.8485 (p0) REVERT: D 240 ASP cc_start: 0.8364 (m-30) cc_final: 0.8009 (m-30) REVERT: D 248 GLN cc_start: 0.8832 (pp30) cc_final: 0.8255 (pp30) REVERT: E 20 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7682 (mt-10) REVERT: E 53 MET cc_start: 0.8923 (mtt) cc_final: 0.8683 (mtt) REVERT: E 289 TYR cc_start: 0.8688 (t80) cc_final: 0.8459 (t80) REVERT: E 351 ASN cc_start: 0.9020 (m110) cc_final: 0.8809 (m-40) outliers start: 32 outliers final: 13 residues processed: 171 average time/residue: 1.3563 time to fit residues: 246.4932 Evaluate side-chains 158 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 142 time to evaluate : 1.127 ------------------------------------------------------------------------------- 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 135 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 62 PHE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 92 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 106 optimal weight: 8.9990 chunk 104 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 57 optimal weight: 0.7980 chunk 110 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 = 0.3355 r_free = 0.3355 target = 0.090728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.063838 restraints weight = 18673.352| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 3.70 r_work: 0.2713 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 9411 Z= 0.344 Angle : 0.687 10.950 12770 Z= 0.349 Chirality : 0.044 0.160 1452 Planarity : 0.004 0.045 1618 Dihedral : 4.376 18.760 1282 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 3.48 % Allowed : 19.10 % Favored : 77.41 % 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: 1.74 (0.27), residues: 401 sheet: -0.36 (0.32), residues: 258 loop : -1.49 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 211 HIS 0.004 0.001 HIS A 339 PHE 0.025 0.001 PHE E 49 TYR 0.013 0.001 TYR D 207 ARG 0.010 0.000 ARG E 24 *********************** 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 182 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 147 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 CYS cc_start: 0.9459 (m) cc_final: 0.9088 (m) REVERT: A 219 GLU cc_start: 0.8928 (tp30) cc_final: 0.8414 (tm-30) REVERT: A 223 GLN cc_start: 0.8091 (mp10) cc_final: 0.7803 (mp10) REVERT: A 251 LYS cc_start: 0.8470 (tptp) cc_final: 0.8188 (tptp) REVERT: B 15 LYS cc_start: 0.9428 (tppp) cc_final: 0.9101 (tmmt) REVERT: B 217 MET cc_start: 0.8859 (OUTLIER) cc_final: 0.8213 (pmm) REVERT: C 20 LYS cc_start: 0.8862 (pttm) cc_final: 0.8531 (pttm) REVERT: C 46 LYS cc_start: 0.9360 (mmmm) cc_final: 0.9102 (mmmm) REVERT: C 47 GLU cc_start: 0.8607 (tm-30) cc_final: 0.8330 (tm-30) REVERT: C 62 PHE cc_start: 0.7073 (OUTLIER) cc_final: 0.6762 (m-10) REVERT: D 82 LYS cc_start: 0.8502 (tppt) cc_final: 0.7869 (tptp) REVERT: D 110 MET cc_start: 0.7837 (mmm) cc_final: 0.7456 (mmm) REVERT: D 157 MET cc_start: 0.8795 (OUTLIER) cc_final: 0.7966 (mtp) REVERT: D 218 ASP cc_start: 0.8717 (p0) cc_final: 0.8492 (p0) REVERT: D 240 ASP cc_start: 0.8421 (m-30) cc_final: 0.8011 (m-30) REVERT: D 248 GLN cc_start: 0.8851 (pp30) cc_final: 0.8441 (pp30) REVERT: E 20 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7655 (mt-10) REVERT: E 289 TYR cc_start: 0.8668 (t80) cc_final: 0.8457 (t80) REVERT: E 351 ASN cc_start: 0.9083 (m110) cc_final: 0.8869 (m-40) outliers start: 35 outliers final: 14 residues processed: 172 average time/residue: 1.3070 time to fit residues: 239.2365 Evaluate side-chains 158 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 141 time to evaluate : 1.154 ------------------------------------------------------------------------------- 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 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 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: 0.0980 chunk 102 optimal weight: 5.9990 chunk 1 optimal weight: 0.4980 chunk 74 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 27 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 overall best weight: 0.6384 ------------------------------------------------------------------------------- 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 = 0.3406 r_free = 0.3406 target = 0.094042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.067523 restraints weight = 18610.882| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 3.68 r_work: 0.2786 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9411 Z= 0.197 Angle : 0.665 10.822 12770 Z= 0.334 Chirality : 0.042 0.160 1452 Planarity : 0.004 0.060 1618 Dihedral : 4.121 17.753 1282 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.89 % Allowed : 20.20 % Favored : 76.92 % 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: 1.85 (0.27), residues: 400 sheet: -0.26 (0.32), residues: 268 loop : -1.38 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 211 HIS 0.003 0.001 HIS A 339 PHE 0.033 0.001 PHE E 49 TYR 0.015 0.001 TYR D 207 ARG 0.014 0.000 ARG E 204 *********************** 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 184 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 155 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 CYS cc_start: 0.9458 (m) cc_final: 0.9044 (m) REVERT: A 219 GLU cc_start: 0.8948 (tp30) cc_final: 0.8402 (tm-30) REVERT: A 223 GLN cc_start: 0.8132 (mp10) cc_final: 0.7772 (mp10) REVERT: A 251 LYS cc_start: 0.8485 (tptp) cc_final: 0.8212 (tptp) REVERT: B 15 LYS cc_start: 0.9436 (tppp) cc_final: 0.9127 (tmmt) REVERT: B 259 GLN cc_start: 0.8561 (mm-40) cc_final: 0.8000 (mm110) REVERT: C 20 LYS cc_start: 0.8866 (pttm) cc_final: 0.8536 (pttm) REVERT: C 46 LYS cc_start: 0.9349 (mmmm) cc_final: 0.9078 (mmmm) REVERT: C 47 GLU cc_start: 0.8655 (tm-30) cc_final: 0.8355 (tm-30) REVERT: D 82 LYS cc_start: 0.8337 (tppt) cc_final: 0.7749 (tptp) REVERT: D 90 ASP cc_start: 0.7172 (OUTLIER) cc_final: 0.6869 (t0) REVERT: D 110 MET cc_start: 0.7783 (mmm) cc_final: 0.7378 (mmm) REVERT: D 157 MET cc_start: 0.8799 (OUTLIER) cc_final: 0.7912 (mtp) REVERT: D 240 ASP cc_start: 0.8345 (m-30) cc_final: 0.8034 (m-30) REVERT: E 20 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7664 (mt-10) REVERT: E 289 TYR cc_start: 0.8687 (t80) cc_final: 0.8449 (t80) REVERT: F 16 ASN cc_start: 0.8430 (t0) cc_final: 0.7942 (m-40) outliers start: 29 outliers final: 11 residues processed: 174 average time/residue: 1.3331 time to fit residues: 247.2113 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 : 1.041 ------------------------------------------------------------------------------- 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 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 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 157 MET Chi-restraints excluded: chain D residue 261 LYS 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: 4.9990 chunk 15 optimal weight: 0.0000 chunk 113 optimal weight: 0.0770 chunk 56 optimal weight: 0.1980 chunk 63 optimal weight: 3.9990 chunk 111 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 7 optimal weight: 6.9990 overall best weight: 0.4542 ------------------------------------------------------------------------------- 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 = 0.3446 r_free = 0.3446 target = 0.095732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.068812 restraints weight = 18370.555| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 3.71 r_work: 0.2819 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9411 Z= 0.191 Angle : 0.682 11.537 12770 Z= 0.340 Chirality : 0.042 0.171 1452 Planarity : 0.004 0.066 1618 Dihedral : 4.019 17.508 1282 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.29 % Allowed : 22.49 % Favored : 75.22 % 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: 0.11 (0.26), residues: 1151 helix: 1.83 (0.27), residues: 400 sheet: -0.13 (0.32), residues: 279 loop : -1.34 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.003 0.001 HIS A 339 PHE 0.043 0.001 PHE E 49 TYR 0.014 0.001 TYR D 207 ARG 0.016 0.000 ARG E 204 *********************** 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 176 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 153 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 CYS cc_start: 0.9458 (m) cc_final: 0.8997 (m) REVERT: A 219 GLU cc_start: 0.8956 (tp30) cc_final: 0.8376 (tm-30) REVERT: A 223 GLN cc_start: 0.8178 (mp10) cc_final: 0.7766 (mp10) REVERT: A 251 LYS cc_start: 0.8450 (tptp) cc_final: 0.8133 (tptp) REVERT: B 15 LYS cc_start: 0.9424 (tppp) cc_final: 0.9105 (tmmt) REVERT: B 138 GLU cc_start: 0.9128 (OUTLIER) cc_final: 0.8853 (tp30) REVERT: B 259 GLN cc_start: 0.8589 (mm-40) cc_final: 0.8031 (mm110) REVERT: B 301 LYS cc_start: 0.8760 (mtpp) cc_final: 0.8349 (mtpp) REVERT: C 20 LYS cc_start: 0.8889 (pttm) cc_final: 0.8626 (pttm) REVERT: C 46 LYS cc_start: 0.9333 (mmmm) cc_final: 0.9061 (mmmm) REVERT: C 47 GLU cc_start: 0.8630 (tm-30) cc_final: 0.8323 (tm-30) REVERT: D 82 LYS cc_start: 0.8320 (tppt) cc_final: 0.7726 (tptp) REVERT: D 90 ASP cc_start: 0.7132 (OUTLIER) cc_final: 0.6822 (t0) REVERT: D 110 MET cc_start: 0.7813 (mmm) cc_final: 0.7404 (mmm) REVERT: D 157 MET cc_start: 0.8789 (OUTLIER) cc_final: 0.7963 (mtp) REVERT: D 240 ASP cc_start: 0.8273 (m-30) cc_final: 0.7945 (m-30) REVERT: D 248 GLN cc_start: 0.8779 (pp30) cc_final: 0.8334 (pp30) REVERT: D 250 LEU cc_start: 0.9040 (mt) cc_final: 0.8838 (mt) REVERT: E 20 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7668 (mt-10) REVERT: E 289 TYR cc_start: 0.8684 (t80) cc_final: 0.8435 (t80) REVERT: F 16 ASN cc_start: 0.8424 (t0) cc_final: 0.7881 (m-40) outliers start: 23 outliers final: 9 residues processed: 167 average time/residue: 1.2822 time to fit residues: 228.1065 Evaluate side-chains 154 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 142 time to evaluate : 1.039 ------------------------------------------------------------------------------- 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 138 GLU Chi-restraints excluded: chain B residue 160 SER 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 D residue 261 LYS 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: 0.4980 chunk 39 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 84 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 111 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- 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 281 HIS ** 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 = 0.3371 r_free = 0.3371 target = 0.091718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.065169 restraints weight = 18641.936| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 3.69 r_work: 0.2732 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9411 Z= 0.338 Angle : 0.733 12.106 12770 Z= 0.368 Chirality : 0.044 0.178 1452 Planarity : 0.005 0.080 1618 Dihedral : 4.216 17.386 1282 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 2.19 % Allowed : 22.59 % Favored : 75.22 % 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: 0.07 (0.26), residues: 1151 helix: 1.84 (0.27), residues: 400 sheet: -0.15 (0.33), residues: 263 loop : -1.39 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 215 HIS 0.004 0.001 HIS A 339 PHE 0.045 0.001 PHE E 49 TYR 0.012 0.001 TYR D 207 ARG 0.018 0.000 ARG E 204 *********************** 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 167 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 145 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 CYS cc_start: 0.9429 (m) cc_final: 0.8978 (m) REVERT: A 219 GLU cc_start: 0.8898 (tp30) cc_final: 0.8441 (tm-30) REVERT: A 223 GLN cc_start: 0.8124 (mp10) cc_final: 0.7812 (mp10) REVERT: A 251 LYS cc_start: 0.8424 (tptp) cc_final: 0.8150 (tptp) REVERT: B 15 LYS cc_start: 0.9413 (tppp) cc_final: 0.9106 (tmmt) REVERT: B 301 LYS cc_start: 0.8712 (mtpp) cc_final: 0.8410 (mtpp) REVERT: C 20 LYS cc_start: 0.8828 (pttm) cc_final: 0.8557 (pttm) REVERT: C 46 LYS cc_start: 0.9346 (mmmm) cc_final: 0.9093 (mmmm) REVERT: C 47 GLU cc_start: 0.8643 (tm-30) cc_final: 0.8326 (tm-30) REVERT: D 82 LYS cc_start: 0.8459 (tppt) cc_final: 0.7949 (tptp) REVERT: D 90 ASP cc_start: 0.7072 (OUTLIER) cc_final: 0.6765 (t0) REVERT: D 110 MET cc_start: 0.7779 (mmm) cc_final: 0.7352 (mmm) REVERT: D 113 CYS cc_start: 0.8359 (OUTLIER) cc_final: 0.7551 (p) REVERT: D 157 MET cc_start: 0.8788 (OUTLIER) cc_final: 0.7970 (mtp) REVERT: D 218 ASP cc_start: 0.8691 (p0) cc_final: 0.8415 (p0) REVERT: D 240 ASP cc_start: 0.8240 (m-30) cc_final: 0.7890 (m-30) REVERT: D 248 GLN cc_start: 0.8858 (pp30) cc_final: 0.8400 (pp30) REVERT: E 20 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7638 (mt-10) REVERT: E 289 TYR cc_start: 0.8643 (t80) cc_final: 0.8435 (t80) REVERT: F 16 ASN cc_start: 0.8439 (t0) cc_final: 0.8062 (m-40) outliers start: 22 outliers final: 11 residues processed: 158 average time/residue: 1.3751 time to fit residues: 232.4715 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 : 1.091 ------------------------------------------------------------------------------- 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 289 VAL Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 160 SER 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 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: 0.8980 chunk 31 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 chunk 86 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.093655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.067122 restraints weight = 18783.180| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 3.71 r_work: 0.2770 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9411 Z= 0.236 Angle : 0.726 12.499 12770 Z= 0.362 Chirality : 0.043 0.186 1452 Planarity : 0.004 0.082 1618 Dihedral : 4.150 16.936 1282 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 1.49 % Allowed : 23.58 % Favored : 74.93 % 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: 0.10 (0.26), residues: 1151 helix: 1.85 (0.27), residues: 399 sheet: -0.10 (0.33), residues: 263 loop : -1.37 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.003 0.001 HIS A 339 PHE 0.045 0.001 PHE E 49 TYR 0.013 0.001 TYR D 207 ARG 0.019 0.000 ARG E 204 ********************** 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 160 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 145 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 CYS cc_start: 0.9443 (m) cc_final: 0.8992 (m) REVERT: A 219 GLU cc_start: 0.8900 (tp30) cc_final: 0.8438 (tm-30) REVERT: A 223 GLN cc_start: 0.8116 (mp10) cc_final: 0.7818 (mp10) REVERT: A 251 LYS cc_start: 0.8478 (tptp) cc_final: 0.8204 (tptp) REVERT: B 15 LYS cc_start: 0.9408 (tppp) cc_final: 0.9092 (tmmt) REVERT: B 301 LYS cc_start: 0.8742 (mtpp) cc_final: 0.8453 (mtpp) REVERT: C 20 LYS cc_start: 0.8878 (pttm) cc_final: 0.8613 (pttm) REVERT: C 46 LYS cc_start: 0.9347 (mmmm) cc_final: 0.9097 (mmmm) REVERT: C 47 GLU cc_start: 0.8652 (tm-30) cc_final: 0.8344 (tm-30) REVERT: D 82 LYS cc_start: 0.8365 (tppt) cc_final: 0.7886 (tptp) REVERT: D 90 ASP cc_start: 0.7089 (OUTLIER) cc_final: 0.6781 (t0) REVERT: D 110 MET cc_start: 0.7790 (mmm) cc_final: 0.7348 (mmm) REVERT: D 113 CYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7572 (p) REVERT: D 157 MET cc_start: 0.8805 (OUTLIER) cc_final: 0.7913 (mtp) REVERT: D 240 ASP cc_start: 0.8249 (m-30) cc_final: 0.7922 (m-30) REVERT: D 248 GLN cc_start: 0.8842 (pp30) cc_final: 0.8425 (pp30) REVERT: E 20 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7635 (mt-10) REVERT: E 289 TYR cc_start: 0.8653 (t80) cc_final: 0.8434 (t80) REVERT: F 16 ASN cc_start: 0.8392 (t0) cc_final: 0.7993 (m-40) outliers start: 15 outliers final: 9 residues processed: 156 average time/residue: 1.3166 time to fit residues: 219.1348 Evaluate side-chains 150 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 138 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 135 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 254 ASP 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: 0.9980 chunk 95 optimal weight: 0.6980 chunk 87 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 102 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 96 optimal weight: 4.9990 chunk 33 optimal weight: 10.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.094396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.068544 restraints weight = 18243.581| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 3.63 r_work: 0.2795 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9411 Z= 0.220 Angle : 0.717 12.527 12770 Z= 0.358 Chirality : 0.043 0.181 1452 Planarity : 0.004 0.059 1618 Dihedral : 4.077 16.851 1282 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 1.59 % Allowed : 23.38 % 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: 0.14 (0.26), residues: 1151 helix: 1.87 (0.27), residues: 399 sheet: -0.04 (0.33), residues: 263 loop : -1.35 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.003 0.001 HIS A 339 PHE 0.044 0.001 PHE E 49 TYR 0.015 0.001 TYR B 59 ARG 0.013 0.000 ARG E 204 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6762.00 seconds wall clock time: 120 minutes 12.24 seconds (7212.24 seconds total)