Starting phenix.real_space_refine on Wed Sep 17 14:54:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k27_61992/09_2025/9k27_61992_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k27_61992/09_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_61992/09_2025/9k27_61992.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k27_61992/09_2025/9k27_61992.map" model { file = "/net/cci-nas-00/data/ceres_data/9k27_61992/09_2025/9k27_61992_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k27_61992/09_2025/9k27_61992_neut_trim.cif" } resolution = 2.68 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.34, per 1000 atoms: 0.25 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: 0.95 Conformation dependent library (CDL) restraints added in 358.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.25 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: 1.46 Time building geometry restraints manager: 1.24 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: 2.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.320 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:6.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.060 ------------------------------------------------------------------------------- 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 : 9.14 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.007 0.000 ARG B 19 TYR 0.016 0.001 TYR A 311 PHE 0.035 0.001 PHE E 49 TRP 0.040 0.002 TRP A 215 HIS 0.006 0.001 HIS A 206 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 9411) covalent geometry : angle 0.68399 (12770) SS BOND : bond 0.00353 ( 2) SS BOND : angle 0.81685 ( 4) hydrogen bonds : bond 0.14830 ( 419) hydrogen bonds : angle 5.24653 ( 1167) 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 : 0.350 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: 0.8898 (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: 0.6810 time to fit residues: 140.8241 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 : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.3399 r_free = 0.3399 target = 0.093573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.066498 restraints weight = 18712.201| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 3.72 r_work: 0.2769 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9414 Z= 0.160 Angle : 0.650 10.337 12774 Z= 0.333 Chirality : 0.044 0.168 1452 Planarity : 0.005 0.058 1618 Dihedral : 4.481 20.713 1282 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 1.79 % Allowed : 11.24 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.25), residues: 1151 helix: 1.70 (0.28), residues: 401 sheet: -0.71 (0.32), residues: 259 loop : -1.60 (0.26), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 204 TYR 0.019 0.001 TYR D 207 PHE 0.027 0.001 PHE E 49 TRP 0.015 0.001 TRP B 211 HIS 0.006 0.001 HIS A 339 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 9411) covalent geometry : angle 0.64976 (12770) SS BOND : bond 0.00552 ( 2) SS BOND : angle 0.64413 ( 4) hydrogen bonds : bond 0.04408 ( 419) hydrogen bonds : angle 4.27346 ( 1167) Misc. bond : bond 0.00087 ( 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 180 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 162 time to evaluate : 0.389 Fit side-chains revert: symmetry clash REVERT: A 60 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.8260 (tppp) REVERT: A 79 CYS cc_start: 0.9407 (m) cc_final: 0.9083 (m) REVERT: A 219 GLU cc_start: 0.8940 (tp30) cc_final: 0.8232 (tm-30) REVERT: A 223 GLN cc_start: 0.8221 (mp10) cc_final: 0.7929 (mp10) REVERT: A 251 LYS cc_start: 0.8447 (tptp) cc_final: 0.8143 (tptp) REVERT: B 15 LYS cc_start: 0.9432 (tppp) cc_final: 0.9108 (tmmt) REVERT: B 217 MET cc_start: 0.8894 (OUTLIER) cc_final: 0.8262 (pmm) REVERT: C 20 LYS cc_start: 0.8821 (pttm) cc_final: 0.8548 (pttm) REVERT: D 82 LYS cc_start: 0.8317 (tppt) cc_final: 0.7763 (tptp) REVERT: D 251 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8266 (mt-10) REVERT: E 20 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7683 (mt-10) outliers start: 18 outliers final: 6 residues processed: 170 average time/residue: 0.6073 time to fit residues: 110.0306 Evaluate side-chains 151 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 143 time to evaluate : 0.394 ------------------------------------------------------------------------------- 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 286 VAL Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain B residue 217 MET 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 79 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 78 optimal weight: 0.0970 chunk 52 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 54 optimal weight: 0.0870 chunk 84 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 overall best weight: 0.5956 ------------------------------------------------------------------------------- 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 = 0.3426 r_free = 0.3426 target = 0.095278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.068323 restraints weight = 18670.101| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 3.74 r_work: 0.2805 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9414 Z= 0.121 Angle : 0.614 10.432 12774 Z= 0.312 Chirality : 0.042 0.180 1452 Planarity : 0.004 0.050 1618 Dihedral : 4.201 19.009 1282 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 1.49 % Allowed : 14.63 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.26), residues: 1151 helix: 1.74 (0.28), residues: 402 sheet: -0.44 (0.32), residues: 264 loop : -1.46 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 204 TYR 0.015 0.001 TYR D 207 PHE 0.024 0.001 PHE E 49 TRP 0.015 0.001 TRP B 211 HIS 0.004 0.001 HIS A 339 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 9411) covalent geometry : angle 0.61449 (12770) SS BOND : bond 0.00467 ( 2) SS BOND : angle 0.57653 ( 4) hydrogen bonds : bond 0.03784 ( 419) hydrogen bonds : angle 3.99117 ( 1167) Misc. bond : bond 0.00031 ( 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 171 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 156 time to evaluate : 0.342 Fit side-chains revert: symmetry clash REVERT: A 79 CYS cc_start: 0.9431 (m) cc_final: 0.9078 (m) REVERT: A 219 GLU cc_start: 0.8947 (tp30) cc_final: 0.8272 (tp30) REVERT: A 223 GLN cc_start: 0.8210 (mp10) cc_final: 0.7920 (mp10) REVERT: A 251 LYS cc_start: 0.8459 (tptp) cc_final: 0.8162 (tptp) REVERT: B 15 LYS cc_start: 0.9449 (tppp) cc_final: 0.9134 (tmmt) REVERT: B 301 LYS cc_start: 0.8816 (mtpp) cc_final: 0.8453 (mtpp) REVERT: C 20 LYS cc_start: 0.8754 (pttm) cc_final: 0.8504 (pttm) REVERT: D 82 LYS cc_start: 0.8255 (tppt) cc_final: 0.7725 (tptp) REVERT: D 157 MET cc_start: 0.9026 (OUTLIER) cc_final: 0.8328 (mtp) REVERT: D 251 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8273 (mt-10) REVERT: E 20 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7691 (mt-10) outliers start: 15 outliers final: 5 residues processed: 163 average time/residue: 0.6101 time to fit residues: 105.8752 Evaluate side-chains 150 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 144 time to evaluate : 0.359 ------------------------------------------------------------------------------- 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 329 CYS Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain D residue 157 MET 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 98 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 = 0.3390 r_free = 0.3390 target = 0.092831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.066251 restraints weight = 18896.470| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 3.69 r_work: 0.2759 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9414 Z= 0.167 Angle : 0.647 11.965 12774 Z= 0.326 Chirality : 0.043 0.144 1452 Planarity : 0.004 0.047 1618 Dihedral : 4.216 18.125 1282 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 2.59 % Allowed : 16.42 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.26), residues: 1151 helix: 1.79 (0.28), residues: 402 sheet: -0.38 (0.32), residues: 259 loop : -1.46 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 89 TYR 0.014 0.001 TYR D 207 PHE 0.034 0.001 PHE E 49 TRP 0.010 0.001 TRP B 211 HIS 0.004 0.001 HIS A 339 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 9411) covalent geometry : angle 0.64744 (12770) SS BOND : bond 0.00524 ( 2) SS BOND : angle 0.54709 ( 4) hydrogen bonds : bond 0.04251 ( 419) hydrogen bonds : angle 4.00254 ( 1167) Misc. bond : bond 0.00056 ( 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 175 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 149 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 CYS cc_start: 0.9438 (m) cc_final: 0.9051 (m) REVERT: A 219 GLU cc_start: 0.8955 (tp30) cc_final: 0.8512 (tp30) REVERT: A 251 LYS cc_start: 0.8483 (tptp) cc_final: 0.8195 (tptp) REVERT: B 15 LYS cc_start: 0.9442 (tppp) cc_final: 0.9106 (tmmt) REVERT: B 301 LYS cc_start: 0.8798 (mtpp) cc_final: 0.8448 (mtpp) REVERT: C 20 LYS cc_start: 0.8782 (pttm) cc_final: 0.8487 (ptpp) REVERT: C 22 GLU cc_start: 0.7979 (tt0) cc_final: 0.7733 (tt0) REVERT: D 82 LYS cc_start: 0.8397 (tppt) cc_final: 0.7813 (tptp) REVERT: D 110 MET cc_start: 0.7828 (mmm) cc_final: 0.7449 (mmm) REVERT: D 157 MET cc_start: 0.8993 (OUTLIER) cc_final: 0.8353 (mtp) REVERT: D 247 MET cc_start: 0.9079 (ttp) cc_final: 0.8765 (ttp) REVERT: D 248 GLN cc_start: 0.8863 (pp30) cc_final: 0.8498 (pp30) REVERT: D 251 GLU cc_start: 0.8544 (mt-10) cc_final: 0.8235 (mt-10) REVERT: E 20 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7683 (mt-10) outliers start: 26 outliers final: 12 residues processed: 164 average time/residue: 0.6179 time to fit residues: 107.9550 Evaluate side-chains 154 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 141 time to evaluate : 0.365 ------------------------------------------------------------------------------- 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 264 SER Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 286 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 F residue 19 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 105 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 chunk 87 optimal weight: 7.9990 chunk 103 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 56 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 = 0.3381 r_free = 0.3381 target = 0.092370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.065740 restraints weight = 18778.730| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 3.70 r_work: 0.2748 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9414 Z= 0.171 Angle : 0.652 10.810 12774 Z= 0.329 Chirality : 0.043 0.149 1452 Planarity : 0.004 0.044 1618 Dihedral : 4.217 17.613 1282 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 2.79 % Allowed : 18.31 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.26), residues: 1151 helix: 1.83 (0.28), residues: 402 sheet: -0.35 (0.32), residues: 259 loop : -1.43 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 24 TYR 0.013 0.001 TYR D 207 PHE 0.028 0.001 PHE E 49 TRP 0.011 0.001 TRP B 211 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00404 ( 9411) covalent geometry : angle 0.65251 (12770) SS BOND : bond 0.00522 ( 2) SS BOND : angle 0.54782 ( 4) hydrogen bonds : bond 0.04248 ( 419) hydrogen bonds : angle 3.99591 ( 1167) Misc. bond : bond 0.00054 ( 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 178 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 150 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 CYS cc_start: 0.9447 (m) cc_final: 0.9051 (m) REVERT: A 219 GLU cc_start: 0.8924 (tp30) cc_final: 0.8314 (tp30) REVERT: A 223 GLN cc_start: 0.8260 (mp10) cc_final: 0.7707 (mp10) REVERT: A 251 LYS cc_start: 0.8497 (tptp) cc_final: 0.8218 (tptp) REVERT: B 15 LYS cc_start: 0.9443 (tppp) cc_final: 0.9123 (tmmt) REVERT: B 259 GLN cc_start: 0.8605 (mm-40) cc_final: 0.8047 (mm110) REVERT: B 301 LYS cc_start: 0.8780 (mtpp) cc_final: 0.8440 (mtpp) REVERT: C 20 LYS cc_start: 0.8862 (pttm) cc_final: 0.8542 (pttm) REVERT: C 22 GLU cc_start: 0.7947 (tt0) cc_final: 0.7705 (tt0) REVERT: D 82 LYS cc_start: 0.8425 (tppt) cc_final: 0.7807 (tptp) REVERT: D 93 LYS cc_start: 0.8943 (mtmm) cc_final: 0.8371 (pmmt) REVERT: D 110 MET cc_start: 0.7823 (mmm) cc_final: 0.7506 (mmm) REVERT: D 157 MET cc_start: 0.8976 (OUTLIER) cc_final: 0.8329 (mtp) REVERT: D 240 ASP cc_start: 0.8253 (m-30) cc_final: 0.7945 (m-30) REVERT: D 248 GLN cc_start: 0.8884 (pp30) cc_final: 0.8605 (pp30) REVERT: E 20 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7645 (mt-10) outliers start: 28 outliers final: 14 residues processed: 168 average time/residue: 0.6340 time to fit residues: 113.0245 Evaluate side-chains 157 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 142 time to evaluate : 0.420 ------------------------------------------------------------------------------- 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 264 SER Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 286 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 64 optimal weight: 10.0000 chunk 17 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 25 optimal weight: 0.0980 chunk 35 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- 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 = 0.3370 r_free = 0.3370 target = 0.091528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.064983 restraints weight = 18914.547| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 3.70 r_work: 0.2730 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 9414 Z= 0.192 Angle : 0.676 11.020 12774 Z= 0.342 Chirality : 0.044 0.166 1452 Planarity : 0.004 0.044 1618 Dihedral : 4.258 17.455 1282 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 3.38 % Allowed : 18.91 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.26), residues: 1151 helix: 1.84 (0.27), residues: 402 sheet: -0.35 (0.32), residues: 264 loop : -1.41 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 24 TYR 0.013 0.001 TYR D 207 PHE 0.029 0.001 PHE E 49 TRP 0.010 0.001 TRP B 211 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00455 ( 9411) covalent geometry : angle 0.67648 (12770) SS BOND : bond 0.00533 ( 2) SS BOND : angle 0.53318 ( 4) hydrogen bonds : bond 0.04469 ( 419) hydrogen bonds : angle 4.06859 ( 1167) Misc. bond : bond 0.00068 ( 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 183 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 149 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 CYS cc_start: 0.9449 (m) cc_final: 0.9056 (m) REVERT: A 219 GLU cc_start: 0.8880 (tp30) cc_final: 0.8352 (tp30) REVERT: A 251 LYS cc_start: 0.8475 (tptp) cc_final: 0.8196 (tptp) REVERT: B 15 LYS cc_start: 0.9412 (tppp) cc_final: 0.9069 (tmmt) REVERT: B 217 MET cc_start: 0.8890 (OUTLIER) cc_final: 0.8271 (pmm) REVERT: B 259 GLN cc_start: 0.8658 (mm-40) cc_final: 0.8119 (mm110) REVERT: B 301 LYS cc_start: 0.8770 (mtpp) cc_final: 0.8438 (mtpp) REVERT: C 20 LYS cc_start: 0.8895 (pttm) cc_final: 0.8583 (pttm) REVERT: C 22 GLU cc_start: 0.7933 (tt0) cc_final: 0.7675 (tt0) REVERT: C 46 LYS cc_start: 0.9315 (mmmm) cc_final: 0.9032 (mmmm) REVERT: D 23 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.6419 (pt0) REVERT: D 82 LYS cc_start: 0.8470 (tppt) cc_final: 0.7858 (tptp) REVERT: D 93 LYS cc_start: 0.8943 (mtmm) cc_final: 0.8355 (pmmt) REVERT: D 110 MET cc_start: 0.7822 (mmm) cc_final: 0.7460 (mmm) REVERT: D 113 CYS cc_start: 0.8392 (OUTLIER) cc_final: 0.7605 (p) REVERT: D 157 MET cc_start: 0.8956 (OUTLIER) cc_final: 0.8293 (mtp) REVERT: D 240 ASP cc_start: 0.8312 (m-30) cc_final: 0.7907 (m-30) REVERT: D 248 GLN cc_start: 0.8923 (pp30) cc_final: 0.8339 (pp30) REVERT: E 20 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7665 (mt-10) REVERT: E 293 GLN cc_start: 0.7665 (tm-30) cc_final: 0.7461 (tm130) outliers start: 34 outliers final: 17 residues processed: 172 average time/residue: 0.6257 time to fit residues: 114.4117 Evaluate side-chains 163 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 206 HIS Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 303 LEU 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 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain D residue 23 GLU 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 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 15 optimal weight: 4.9990 chunk 104 optimal weight: 0.5980 chunk 69 optimal weight: 6.9990 chunk 95 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 chunk 112 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 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 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 = 0.3402 r_free = 0.3402 target = 0.093724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.067235 restraints weight = 18681.950| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 3.70 r_work: 0.2776 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2138 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= 0.133 Angle : 0.662 11.232 12774 Z= 0.333 Chirality : 0.042 0.160 1452 Planarity : 0.004 0.065 1618 Dihedral : 4.110 17.151 1282 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 2.69 % Allowed : 20.30 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.26), residues: 1151 helix: 1.88 (0.27), residues: 401 sheet: -0.31 (0.32), residues: 270 loop : -1.37 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG E 204 TYR 0.014 0.001 TYR D 207 PHE 0.031 0.001 PHE E 49 TRP 0.015 0.001 TRP B 211 HIS 0.002 0.001 HIS A 321 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 9411) covalent geometry : angle 0.66235 (12770) SS BOND : bond 0.00483 ( 2) SS BOND : angle 0.56141 ( 4) hydrogen bonds : bond 0.03819 ( 419) hydrogen bonds : angle 3.93324 ( 1167) Misc. bond : bond 0.00032 ( 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 182 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 155 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 CYS cc_start: 0.9459 (m) cc_final: 0.9043 (m) REVERT: A 219 GLU cc_start: 0.8888 (tp30) cc_final: 0.8343 (tp30) REVERT: A 251 LYS cc_start: 0.8490 (tptp) cc_final: 0.8216 (tptp) REVERT: B 15 LYS cc_start: 0.9418 (tppp) cc_final: 0.9092 (tmmt) REVERT: B 259 GLN cc_start: 0.8667 (mm-40) cc_final: 0.8067 (mm110) REVERT: B 301 LYS cc_start: 0.8728 (mtpp) cc_final: 0.8393 (mtpp) REVERT: C 20 LYS cc_start: 0.8914 (pttm) cc_final: 0.8599 (pttm) REVERT: C 22 GLU cc_start: 0.7891 (tt0) cc_final: 0.7677 (tt0) REVERT: C 46 LYS cc_start: 0.9296 (mmmm) cc_final: 0.9016 (mmmm) REVERT: D 23 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.6382 (pt0) REVERT: D 82 LYS cc_start: 0.8352 (tppt) cc_final: 0.7774 (tptp) REVERT: D 90 ASP cc_start: 0.7055 (OUTLIER) cc_final: 0.6816 (t0) REVERT: D 110 MET cc_start: 0.7796 (mmm) cc_final: 0.7403 (mmm) REVERT: D 113 CYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7560 (p) REVERT: D 157 MET cc_start: 0.8934 (OUTLIER) cc_final: 0.7712 (mtp) REVERT: D 240 ASP cc_start: 0.8293 (m-30) cc_final: 0.7960 (m-30) REVERT: D 248 GLN cc_start: 0.8885 (pp30) cc_final: 0.8538 (pp30) REVERT: E 20 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7656 (mt-10) REVERT: E 293 GLN cc_start: 0.7609 (tm-30) cc_final: 0.7381 (tm130) REVERT: F 16 ASN cc_start: 0.8453 (t0) cc_final: 0.7987 (m-40) outliers start: 27 outliers final: 12 residues processed: 173 average time/residue: 0.6217 time to fit residues: 114.5649 Evaluate side-chains 156 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 140 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 206 HIS Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 329 CYS 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 23 GLU 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 38 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 52 optimal weight: 0.0970 chunk 13 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 chunk 102 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 64 optimal weight: 3.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- 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 = 0.3412 r_free = 0.3412 target = 0.094539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.067629 restraints weight = 18541.879| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 3.75 r_work: 0.2783 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9414 Z= 0.134 Angle : 0.686 11.817 12774 Z= 0.343 Chirality : 0.042 0.174 1452 Planarity : 0.004 0.046 1618 Dihedral : 4.029 16.942 1282 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 2.19 % Allowed : 21.99 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.26), residues: 1151 helix: 1.93 (0.27), residues: 400 sheet: -0.27 (0.32), residues: 270 loop : -1.35 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 204 TYR 0.013 0.001 TYR D 207 PHE 0.030 0.001 PHE E 49 TRP 0.014 0.001 TRP B 211 HIS 0.002 0.000 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 9411) covalent geometry : angle 0.68565 (12770) SS BOND : bond 0.00444 ( 2) SS BOND : angle 0.54578 ( 4) hydrogen bonds : bond 0.03744 ( 419) hydrogen bonds : angle 3.89981 ( 1167) Misc. bond : bond 0.00029 ( 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 169 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 147 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 CYS cc_start: 0.9447 (m) cc_final: 0.9011 (m) REVERT: A 219 GLU cc_start: 0.8912 (tp30) cc_final: 0.8391 (tp30) REVERT: A 251 LYS cc_start: 0.8465 (tptp) cc_final: 0.8148 (tptp) REVERT: B 15 LYS cc_start: 0.9410 (tppp) cc_final: 0.9082 (tmmt) REVERT: B 217 MET cc_start: 0.8888 (OUTLIER) cc_final: 0.8286 (pmm) REVERT: B 259 GLN cc_start: 0.8686 (mm-40) cc_final: 0.8073 (mm110) REVERT: B 301 LYS cc_start: 0.8765 (mtpp) cc_final: 0.8467 (mtpp) REVERT: C 20 LYS cc_start: 0.8910 (pttm) cc_final: 0.8597 (pttm) REVERT: C 22 GLU cc_start: 0.7934 (tt0) cc_final: 0.7697 (tt0) REVERT: C 46 LYS cc_start: 0.9299 (mmmm) cc_final: 0.9027 (mmmm) REVERT: D 23 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.6319 (pt0) REVERT: D 82 LYS cc_start: 0.8306 (tppt) cc_final: 0.7711 (tptp) REVERT: D 90 ASP cc_start: 0.7058 (OUTLIER) cc_final: 0.6817 (t0) REVERT: D 110 MET cc_start: 0.7785 (mmm) cc_final: 0.7371 (mmm) REVERT: D 113 CYS cc_start: 0.8221 (OUTLIER) cc_final: 0.7512 (p) REVERT: D 157 MET cc_start: 0.8725 (OUTLIER) cc_final: 0.7845 (mtp) REVERT: D 240 ASP cc_start: 0.8209 (m-30) cc_final: 0.7869 (m-30) REVERT: D 248 GLN cc_start: 0.8874 (pp30) cc_final: 0.8504 (pp30) REVERT: E 20 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7621 (mt-10) REVERT: E 293 GLN cc_start: 0.7596 (tm-30) cc_final: 0.7315 (tm130) REVERT: F 16 ASN cc_start: 0.8424 (t0) cc_final: 0.8027 (m-40) outliers start: 22 outliers final: 10 residues processed: 161 average time/residue: 0.6052 time to fit residues: 103.8106 Evaluate side-chains 154 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 139 time to evaluate : 0.371 ------------------------------------------------------------------------------- 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 329 CYS Chi-restraints excluded: chain B residue 14 LEU 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 262 MET Chi-restraints excluded: chain C residue 62 PHE Chi-restraints excluded: chain D residue 23 GLU 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 17 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 72 optimal weight: 0.2980 chunk 86 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 98 optimal weight: 0.5980 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.3424 r_free = 0.3424 target = 0.094202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.067482 restraints weight = 18184.781| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 3.68 r_work: 0.2793 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9414 Z= 0.151 Angle : 0.704 12.250 12774 Z= 0.353 Chirality : 0.043 0.175 1452 Planarity : 0.004 0.050 1618 Dihedral : 4.059 16.639 1282 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 2.19 % Allowed : 21.89 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.26), residues: 1151 helix: 1.86 (0.27), residues: 402 sheet: -0.19 (0.32), residues: 275 loop : -1.30 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 24 TYR 0.013 0.001 TYR A 311 PHE 0.040 0.001 PHE E 49 TRP 0.012 0.001 TRP B 211 HIS 0.002 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 9411) covalent geometry : angle 0.70454 (12770) SS BOND : bond 0.00456 ( 2) SS BOND : angle 0.53634 ( 4) hydrogen bonds : bond 0.03952 ( 419) hydrogen bonds : angle 3.92356 ( 1167) Misc. bond : bond 0.00042 ( 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 167 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 145 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 CYS cc_start: 0.9457 (m) cc_final: 0.9022 (m) REVERT: A 219 GLU cc_start: 0.8876 (tp30) cc_final: 0.8388 (tp30) REVERT: A 251 LYS cc_start: 0.8500 (tptp) cc_final: 0.8225 (tptp) REVERT: B 15 LYS cc_start: 0.9408 (tppp) cc_final: 0.9083 (tmmt) REVERT: B 217 MET cc_start: 0.8859 (OUTLIER) cc_final: 0.8242 (pmm) REVERT: B 301 LYS cc_start: 0.8826 (mtpp) cc_final: 0.8429 (mtpp) REVERT: C 20 LYS cc_start: 0.8935 (pttm) cc_final: 0.8667 (pttm) REVERT: C 22 GLU cc_start: 0.7939 (tt0) cc_final: 0.7683 (tt0) REVERT: C 46 LYS cc_start: 0.9300 (mmmm) cc_final: 0.9043 (mmmm) REVERT: D 23 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.6300 (pt0) REVERT: D 82 LYS cc_start: 0.8403 (tppt) cc_final: 0.7789 (tptp) REVERT: D 90 ASP cc_start: 0.7129 (OUTLIER) cc_final: 0.6883 (t0) REVERT: D 110 MET cc_start: 0.7838 (mmm) cc_final: 0.7427 (mmm) REVERT: D 113 CYS cc_start: 0.8324 (OUTLIER) cc_final: 0.7604 (p) REVERT: D 157 MET cc_start: 0.8792 (OUTLIER) cc_final: 0.8036 (mtp) REVERT: D 240 ASP cc_start: 0.8213 (m-30) cc_final: 0.7884 (m-30) REVERT: D 248 GLN cc_start: 0.8885 (pp30) cc_final: 0.8439 (pp30) REVERT: E 20 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7670 (mt-10) REVERT: E 53 MET cc_start: 0.8891 (mtt) cc_final: 0.8607 (mtt) REVERT: E 293 GLN cc_start: 0.7635 (tm-30) cc_final: 0.7339 (tm130) REVERT: F 16 ASN cc_start: 0.8471 (t0) cc_final: 0.8103 (m-40) outliers start: 22 outliers final: 10 residues processed: 160 average time/residue: 0.6212 time to fit residues: 105.7035 Evaluate side-chains 154 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 139 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 206 HIS Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain B residue 14 LEU 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 23 GLU 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 24 optimal weight: 1.9990 chunk 88 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 36 optimal weight: 0.9980 chunk 104 optimal weight: 0.4980 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 E 22 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.092170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.066379 restraints weight = 18734.887| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 3.64 r_work: 0.2746 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 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 0.047 9414 Z= 0.190 Angle : 0.739 12.576 12774 Z= 0.371 Chirality : 0.044 0.190 1452 Planarity : 0.004 0.048 1618 Dihedral : 4.176 16.387 1282 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 1.99 % Allowed : 22.29 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.26), residues: 1151 helix: 1.84 (0.27), residues: 402 sheet: -0.16 (0.33), residues: 262 loop : -1.35 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 24 TYR 0.012 0.001 TYR D 207 PHE 0.037 0.001 PHE E 49 TRP 0.009 0.001 TRP B 211 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00454 ( 9411) covalent geometry : angle 0.73913 (12770) SS BOND : bond 0.00505 ( 2) SS BOND : angle 0.55722 ( 4) hydrogen bonds : bond 0.04433 ( 419) hydrogen bonds : angle 4.04300 ( 1167) Misc. bond : bond 0.00067 ( 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 162 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 142 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 CYS cc_start: 0.9430 (m) cc_final: 0.9012 (m) REVERT: A 219 GLU cc_start: 0.8866 (tp30) cc_final: 0.8312 (tp30) REVERT: A 251 LYS cc_start: 0.8475 (tptp) cc_final: 0.8196 (tptp) REVERT: B 15 LYS cc_start: 0.9382 (tppp) cc_final: 0.9032 (tmmt) REVERT: B 217 MET cc_start: 0.8778 (OUTLIER) cc_final: 0.8158 (pmm) REVERT: B 301 LYS cc_start: 0.8763 (mtpp) cc_final: 0.8358 (mtpp) REVERT: C 20 LYS cc_start: 0.8907 (pttm) cc_final: 0.8604 (pttm) REVERT: C 22 GLU cc_start: 0.7923 (tt0) cc_final: 0.7659 (tt0) REVERT: C 46 LYS cc_start: 0.9325 (mmmm) cc_final: 0.9075 (mmmm) REVERT: D 23 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.6365 (pt0) REVERT: D 82 LYS cc_start: 0.8443 (tppt) cc_final: 0.7817 (tptp) REVERT: D 90 ASP cc_start: 0.7097 (OUTLIER) cc_final: 0.6806 (t0) REVERT: D 110 MET cc_start: 0.7798 (mmm) cc_final: 0.7369 (mmm) REVERT: D 113 CYS cc_start: 0.8396 (OUTLIER) cc_final: 0.7561 (p) REVERT: D 157 MET cc_start: 0.8759 (OUTLIER) cc_final: 0.7929 (mtp) REVERT: D 240 ASP cc_start: 0.8175 (m-30) cc_final: 0.7862 (m-30) REVERT: D 248 GLN cc_start: 0.8878 (pp30) cc_final: 0.8209 (pp30) REVERT: E 20 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7640 (mt-10) REVERT: E 53 MET cc_start: 0.8867 (mtt) cc_final: 0.8613 (mtt) REVERT: E 293 GLN cc_start: 0.7615 (tm-30) cc_final: 0.7302 (tm130) REVERT: E 351 ASN cc_start: 0.9001 (m-40) cc_final: 0.8743 (m-40) REVERT: F 16 ASN cc_start: 0.8359 (t0) cc_final: 0.8127 (m-40) outliers start: 20 outliers final: 10 residues processed: 156 average time/residue: 0.6286 time to fit residues: 104.2286 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 : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 206 HIS Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain B residue 14 LEU 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 23 GLU 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 14 optimal weight: 0.0770 chunk 46 optimal weight: 2.9990 chunk 87 optimal weight: 7.9990 chunk 41 optimal weight: 0.7980 chunk 95 optimal weight: 0.8980 chunk 6 optimal weight: 0.0570 chunk 99 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 overall best weight: 0.5056 ------------------------------------------------------------------------------- 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 = 0.3444 r_free = 0.3444 target = 0.095595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.068796 restraints weight = 18045.061| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 3.69 r_work: 0.2815 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2404 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= 0.134 Angle : 0.716 12.530 12774 Z= 0.357 Chirality : 0.043 0.255 1452 Planarity : 0.004 0.047 1618 Dihedral : 4.027 15.858 1282 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 1.79 % Allowed : 22.29 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.26), residues: 1151 helix: 1.84 (0.27), residues: 401 sheet: -0.11 (0.32), residues: 275 loop : -1.32 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 24 TYR 0.014 0.001 TYR A 311 PHE 0.037 0.001 PHE E 49 TRP 0.015 0.001 TRP B 211 HIS 0.002 0.000 HIS A 92 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 9411) covalent geometry : angle 0.71580 (12770) SS BOND : bond 0.00434 ( 2) SS BOND : angle 0.51319 ( 4) hydrogen bonds : bond 0.03693 ( 419) hydrogen bonds : angle 3.92484 ( 1167) Misc. bond : bond 0.00024 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3718.10 seconds wall clock time: 64 minutes 12.44 seconds (3852.44 seconds total)