Starting phenix.real_space_refine on Wed Sep 17 17:00:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9g4e_51036/09_2025/9g4e_51036.cif Found real_map, /net/cci-nas-00/data/ceres_data/9g4e_51036/09_2025/9g4e_51036.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9g4e_51036/09_2025/9g4e_51036.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9g4e_51036/09_2025/9g4e_51036.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9g4e_51036/09_2025/9g4e_51036.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9g4e_51036/09_2025/9g4e_51036.map" } resolution = 3.44 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= 0.000 sd= 0.012 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 38 5.16 5 C 6330 2.51 5 N 1579 2.21 5 O 1713 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 80 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: 9660 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1658 Classifications: {'peptide': 220} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 206} Chain: "D" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1636 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 200} Chain: "A" Number of atoms: 3183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3183 Classifications: {'peptide': 391} Link IDs: {'PTRANS': 14, 'TRANS': 376} Chain: "B" Number of atoms: 3183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3183 Classifications: {'peptide': 391} Link IDs: {'PTRANS': 14, 'TRANS': 376} Time building chain proxies: 2.57, per 1000 atoms: 0.27 Number of scatterers: 9660 At special positions: 0 Unit cell: (71.38, 105.78, 177.16, 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 38 16.00 O 1713 8.00 N 1579 7.00 C 6330 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS C 16 " - pdb=" SG CYS C 90 " distance=2.04 Simple disulfide: pdb=" SG CYS C 130 " - pdb=" SG CYS D 213 " distance=2.03 Simple disulfide: pdb=" SG CYS C 142 " - pdb=" SG CYS C 197 " distance=2.04 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 87 " distance=2.04 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 193 " 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=0, symmetry=0 Time building additional restraints: 0.96 Conformation dependent library (CDL) restraints added in 319.6 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2270 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 12 sheets defined 57.4% alpha, 15.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'C' and resid 22 through 24 No H-bonds generated for 'chain 'C' and resid 22 through 24' Processing helix chain 'C' and resid 56 through 59 Processing helix chain 'C' and resid 158 through 160 No H-bonds generated for 'chain 'C' and resid 158 through 160' Processing helix chain 'D' and resid 120 through 127 Processing helix chain 'D' and resid 182 through 186 Processing helix chain 'A' and resid 10 through 28 Processing helix chain 'A' and resid 31 through 33 No H-bonds generated for 'chain 'A' and resid 31 through 33' Processing helix chain 'A' and resid 34 through 39 Processing helix chain 'A' and resid 48 through 53 removed outlier: 4.024A pdb=" N PHE A 52 " --> pdb=" O ALA A 49 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N TRP A 53 " --> pdb=" O ALA A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 79 removed outlier: 3.990A pdb=" N PHE A 60 " --> pdb=" O ASP A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 125 removed outlier: 4.375A pdb=" N THR A 91 " --> pdb=" O SER A 87 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ALA A 113 " --> pdb=" O ASN A 109 " (cutoff:3.500A) Proline residue: A 114 - end of helix Processing helix chain 'A' and resid 130 through 176 removed outlier: 4.092A pdb=" N PHE A 134 " --> pdb=" O THR A 130 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ILE A 147 " --> pdb=" O GLY A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 182 removed outlier: 3.779A pdb=" N GLN A 180 " --> pdb=" O ASN A 177 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ARG A 182 " --> pdb=" O GLN A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 227 removed outlier: 3.558A pdb=" N ARG A 190 " --> pdb=" O GLY A 186 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N THR A 195 " --> pdb=" O VAL A 191 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N MET A 196 " --> pdb=" O GLN A 192 " (cutoff:3.500A) Proline residue: A 221 - end of helix Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 241 through 261 Processing helix chain 'A' and resid 264 through 288 removed outlier: 3.772A pdb=" N LEU A 268 " --> pdb=" O LYS A 264 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ASP A 288 " --> pdb=" O VAL A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 337 removed outlier: 3.933A pdb=" N ARG A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU A 312 " --> pdb=" O ASN A 308 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N MET A 317 " --> pdb=" O TYR A 313 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N TYR A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N PHE A 319 " --> pdb=" O HIS A 315 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ASN A 331 " --> pdb=" O LEU A 327 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N VAL A 332 " --> pdb=" O GLN A 328 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLY A 334 " --> pdb=" O ASP A 330 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N LEU A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU A 337 " --> pdb=" O PHE A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 345 Processing helix chain 'A' and resid 351 through 365 Processing helix chain 'A' and resid 367 through 389 removed outlier: 3.643A pdb=" N ASN A 371 " --> pdb=" O GLN A 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 28 removed outlier: 3.877A pdb=" N LEU B 14 " --> pdb=" O GLY B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 33 No H-bonds generated for 'chain 'B' and resid 31 through 33' Processing helix chain 'B' and resid 34 through 39 removed outlier: 3.583A pdb=" N ILE B 38 " --> pdb=" O TRP B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 53 removed outlier: 3.618A pdb=" N TRP B 53 " --> pdb=" O ALA B 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 50 through 53' Processing helix chain 'B' and resid 54 through 79 removed outlier: 4.292A pdb=" N PHE B 60 " --> pdb=" O ASP B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 125 removed outlier: 4.344A pdb=" N THR B 91 " --> pdb=" O SER B 87 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ALA B 113 " --> pdb=" O ASN B 109 " (cutoff:3.500A) Proline residue: B 114 - end of helix Processing helix chain 'B' and resid 130 through 176 removed outlier: 4.415A pdb=" N PHE B 134 " --> pdb=" O THR B 130 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ILE B 147 " --> pdb=" O GLY B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 182 removed outlier: 3.856A pdb=" N GLN B 180 " --> pdb=" O ASN B 177 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG B 182 " --> pdb=" O GLN B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 227 removed outlier: 4.815A pdb=" N THR B 195 " --> pdb=" O VAL B 191 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N MET B 196 " --> pdb=" O GLN B 192 " (cutoff:3.500A) Proline residue: B 221 - end of helix Processing helix chain 'B' and resid 228 through 230 No H-bonds generated for 'chain 'B' and resid 228 through 230' Processing helix chain 'B' and resid 241 through 262 Processing helix chain 'B' and resid 264 through 289 removed outlier: 3.961A pdb=" N LEU B 268 " --> pdb=" O LYS B 264 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ASP B 288 " --> pdb=" O VAL B 284 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASP B 289 " --> pdb=" O TYR B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 337 removed outlier: 3.826A pdb=" N ARG B 311 " --> pdb=" O LYS B 307 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LEU B 312 " --> pdb=" O ASN B 308 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N MET B 317 " --> pdb=" O TYR B 313 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N TYR B 318 " --> pdb=" O PHE B 314 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N PHE B 319 " --> pdb=" O HIS B 315 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASN B 331 " --> pdb=" O LEU B 327 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N VAL B 332 " --> pdb=" O GLN B 328 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLY B 334 " --> pdb=" O ASP B 330 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N LEU B 335 " --> pdb=" O ASN B 331 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU B 337 " --> pdb=" O PHE B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 344 Processing helix chain 'B' and resid 351 through 366 removed outlier: 3.655A pdb=" N ILE B 355 " --> pdb=" O LEU B 351 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE B 366 " --> pdb=" O VAL B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 389 removed outlier: 3.730A pdb=" N GLU B 378 " --> pdb=" O THR B 374 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid -3 through 0 removed outlier: 3.862A pdb=" N THR C 72 " --> pdb=" O ASP C 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 4 through 6 removed outlier: 6.438A pdb=" N GLU C 4 " --> pdb=" O THR C 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 52 through 54 removed outlier: 6.790A pdb=" N TRP C 30 " --> pdb=" O ILE C 42 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N ARG C 44 " --> pdb=" O MET C 28 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N MET C 28 " --> pdb=" O ARG C 44 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TRP C 93 " --> pdb=" O TYR C 27 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR C 29 " --> pdb=" O ALA C 91 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 122 through 126 removed outlier: 3.944A pdb=" N GLY C 141 " --> pdb=" O LEU C 126 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N TYR C 177 " --> pdb=" O GLY C 146 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 122 through 126 removed outlier: 3.944A pdb=" N GLY C 141 " --> pdb=" O LEU C 126 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N TYR C 177 " --> pdb=" O GLY C 146 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 153 through 156 Processing sheet with id=AA7, first strand: chain 'D' and resid 5 through 7 removed outlier: 3.822A pdb=" N TYR D 70 " --> pdb=" O CYS D 23 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 52 through 53 removed outlier: 6.591A pdb=" N TRP D 34 " --> pdb=" O TRP D 46 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N TYR D 48 " --> pdb=" O MET D 32 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N MET D 32 " --> pdb=" O TYR D 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 113 through 117 Processing sheet with id=AB1, first strand: chain 'D' and resid 152 through 153 Processing sheet with id=AB2, first strand: chain 'A' and resid 232 through 233 removed outlier: 3.550A pdb=" N GLY A 237 " --> pdb=" O LEU A 233 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 232 through 233 removed outlier: 3.566A pdb=" N GLY B 237 " --> pdb=" O LEU B 233 " (cutoff:3.500A) 621 hydrogen bonds defined for protein. 1803 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: 1.15 Time building geometry restraints manager: 1.29 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: 2938 1.34 - 1.46: 2522 1.46 - 1.58: 4422 1.58 - 1.70: 0 1.70 - 1.82: 64 Bond restraints: 9946 Sorted by residual: bond pdb=" CB TRP D 90 " pdb=" CG TRP D 90 " ideal model delta sigma weight residual 1.498 1.419 0.079 3.10e-02 1.04e+03 6.56e+00 bond pdb=" CB TRP D 46 " pdb=" CG TRP D 46 " ideal model delta sigma weight residual 1.498 1.433 0.065 3.10e-02 1.04e+03 4.44e+00 bond pdb=" CA ALA B 50 " pdb=" C ALA B 50 " ideal model delta sigma weight residual 1.523 1.500 0.024 1.56e-02 4.11e+03 2.30e+00 bond pdb=" CA ALA A 50 " pdb=" C ALA A 50 " ideal model delta sigma weight residual 1.523 1.497 0.026 1.80e-02 3.09e+03 2.10e+00 bond pdb=" CB THR A 168 " pdb=" CG2 THR A 168 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.97e+00 ... (remaining 9941 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 13096 1.80 - 3.60: 391 3.60 - 5.40: 59 5.40 - 7.20: 15 7.20 - 9.00: 4 Bond angle restraints: 13565 Sorted by residual: angle pdb=" N PHE B 5 " pdb=" CA PHE B 5 " pdb=" C PHE B 5 " ideal model delta sigma weight residual 110.52 104.26 6.26 1.48e+00 4.57e-01 1.79e+01 angle pdb=" C SER D 62 " pdb=" N GLY D 63 " pdb=" CA GLY D 63 " ideal model delta sigma weight residual 122.18 119.59 2.59 6.90e-01 2.10e+00 1.40e+01 angle pdb=" C ALA A 169 " pdb=" N MET A 170 " pdb=" CA MET A 170 " ideal model delta sigma weight residual 121.14 115.20 5.94 1.75e+00 3.27e-01 1.15e+01 angle pdb=" N PRO B 7 " pdb=" CA PRO B 7 " pdb=" C PRO B 7 " ideal model delta sigma weight residual 112.47 119.04 -6.57 2.06e+00 2.36e-01 1.02e+01 angle pdb=" C ALA B 169 " pdb=" N MET B 170 " pdb=" CA MET B 170 " ideal model delta sigma weight residual 121.14 115.79 5.35 1.75e+00 3.27e-01 9.34e+00 ... (remaining 13560 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.19: 5145 17.19 - 34.38: 472 34.38 - 51.56: 88 51.56 - 68.75: 12 68.75 - 85.94: 10 Dihedral angle restraints: 5727 sinusoidal: 2184 harmonic: 3543 Sorted by residual: dihedral pdb=" CA ASN D 93 " pdb=" C ASN D 93 " pdb=" N PRO D 94 " pdb=" CA PRO D 94 " ideal model delta harmonic sigma weight residual 180.00 124.76 55.24 0 5.00e+00 4.00e-02 1.22e+02 dihedral pdb=" CB CYS C 130 " pdb=" SG CYS C 130 " pdb=" SG CYS D 213 " pdb=" CB CYS D 213 " ideal model delta sinusoidal sigma weight residual -86.00 -143.35 57.35 1 1.00e+01 1.00e-02 4.42e+01 dihedral pdb=" CA ASP C 36 " pdb=" C ASP C 36 " pdb=" N GLN C 37 " pdb=" CA GLN C 37 " ideal model delta harmonic sigma weight residual -180.00 -154.08 -25.92 0 5.00e+00 4.00e-02 2.69e+01 ... (remaining 5724 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 970 0.038 - 0.076: 413 0.076 - 0.114: 97 0.114 - 0.152: 27 0.152 - 0.190: 8 Chirality restraints: 1515 Sorted by residual: chirality pdb=" CA PRO B 7 " pdb=" N PRO B 7 " pdb=" C PRO B 7 " pdb=" CB PRO B 7 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 9.07e-01 chirality pdb=" CA PHE B 5 " pdb=" N PHE B 5 " pdb=" C PHE B 5 " pdb=" CB PHE B 5 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.70e-01 chirality pdb=" CA MET B 170 " pdb=" N MET B 170 " pdb=" C MET B 170 " pdb=" CB MET B 170 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.49e-01 ... (remaining 1512 not shown) Planarity restraints: 1682 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 295 " -0.064 5.00e-02 4.00e+02 9.53e-02 1.45e+01 pdb=" N PRO B 296 " 0.165 5.00e-02 4.00e+02 pdb=" CA PRO B 296 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO B 296 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 5 " 0.029 2.00e-02 2.50e+03 2.22e-02 8.62e+00 pdb=" CG PHE A 5 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 PHE A 5 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE A 5 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 5 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE A 5 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE A 5 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN D 93 " 0.048 5.00e-02 4.00e+02 7.23e-02 8.37e+00 pdb=" N PRO D 94 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO D 94 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO D 94 " 0.039 5.00e-02 4.00e+02 ... (remaining 1679 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 63 2.63 - 3.20: 8653 3.20 - 3.77: 13668 3.77 - 4.33: 17712 4.33 - 4.90: 30576 Nonbonded interactions: 70672 Sorted by model distance: nonbonded pdb=" O SER A 4 " pdb=" NE2 HIS A 81 " model vdw 2.066 3.120 nonbonded pdb=" O SER B 4 " pdb=" NE2 HIS B 81 " model vdw 2.139 3.120 nonbonded pdb=" OE2 GLU B 276 " pdb=" OH TYR B 309 " model vdw 2.162 3.040 nonbonded pdb=" OG1 THR D 192 " pdb=" OG SER D 207 " model vdw 2.241 3.040 nonbonded pdb=" OD2 ASP A 330 " pdb=" NH1 ARG A 363 " model vdw 2.267 3.120 ... (remaining 70667 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 6.710 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 9.410 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 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 : 0.007 0.079 9951 Z= 0.281 Angle : 0.762 8.996 13575 Z= 0.434 Chirality : 0.045 0.190 1515 Planarity : 0.006 0.095 1682 Dihedral : 13.671 85.937 3442 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.43 % Cis-general : 0.00 % Twisted Proline : 1.89 % 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: -0.27 (0.24), residues: 1207 helix: 0.89 (0.20), residues: 658 sheet: -0.12 (0.36), residues: 221 loop : -2.39 (0.30), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 210 TYR 0.030 0.002 TYR A 279 PHE 0.050 0.002 PHE A 5 TRP 0.045 0.002 TRP B 53 HIS 0.009 0.001 HIS B 315 Details of bonding type rmsd covalent geometry : bond 0.00657 ( 9946) covalent geometry : angle 0.76137 (13565) SS BOND : bond 0.00845 ( 5) SS BOND : angle 1.26368 ( 10) hydrogen bonds : bond 0.14586 ( 607) hydrogen bonds : angle 5.47773 ( 1803) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 212 ILE cc_start: 0.8589 (mm) cc_final: 0.8319 (mm) REVERT: B 125 SER cc_start: 0.7599 (m) cc_final: 0.7341 (p) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.1079 time to fit residues: 17.9907 Evaluate side-chains 92 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.6980 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.4980 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.5980 chunk 117 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 76 GLN ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 120 GLN A 273 GLN A 308 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.095062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.072728 restraints weight = 26276.986| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.94 r_work: 0.3104 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9951 Z= 0.152 Angle : 0.577 8.676 13575 Z= 0.307 Chirality : 0.041 0.247 1515 Planarity : 0.005 0.069 1682 Dihedral : 5.003 66.301 1327 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.97 % Allowed : 6.96 % Favored : 92.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.43 % Cis-general : 0.00 % Twisted Proline : 1.89 % 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: 0.55 (0.25), residues: 1207 helix: 1.59 (0.20), residues: 664 sheet: 0.20 (0.36), residues: 220 loop : -2.14 (0.31), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 95 TYR 0.015 0.001 TYR A 316 PHE 0.020 0.001 PHE A 314 TRP 0.027 0.001 TRP D 90 HIS 0.004 0.001 HIS B 315 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 9946) covalent geometry : angle 0.57686 (13565) SS BOND : bond 0.00739 ( 5) SS BOND : angle 0.99969 ( 10) hydrogen bonds : bond 0.07618 ( 607) hydrogen bonds : angle 4.26690 ( 1803) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 115 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 76 GLN cc_start: 0.8728 (tm130) cc_final: 0.8414 (tm-30) REVERT: C 83 GLU cc_start: 0.8296 (tm-30) cc_final: 0.8092 (tm-30) REVERT: D 147 TRP cc_start: 0.8196 (m100) cc_final: 0.7919 (m100) REVERT: D 154 ARG cc_start: 0.9118 (mmm160) cc_final: 0.8661 (tpt-90) REVERT: D 174 MET cc_start: 0.8785 (ttt) cc_final: 0.8051 (tpp) REVERT: D 186 GLU cc_start: 0.9474 (mm-30) cc_final: 0.9249 (mm-30) REVERT: D 191 TYR cc_start: 0.8703 (m-80) cc_final: 0.8413 (m-80) REVERT: A 308 ASN cc_start: 0.8422 (OUTLIER) cc_final: 0.8200 (t0) REVERT: B 289 ASP cc_start: 0.8455 (t70) cc_final: 0.8145 (m-30) outliers start: 10 outliers final: 5 residues processed: 122 average time/residue: 0.0952 time to fit residues: 16.5696 Evaluate side-chains 97 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 91 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 211 ASN Chi-restraints excluded: chain A residue 53 TRP Chi-restraints excluded: chain A residue 308 ASN Chi-restraints excluded: chain B residue 112 TYR Chi-restraints excluded: chain B residue 258 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 70 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 43 optimal weight: 0.0870 chunk 64 optimal weight: 0.9990 chunk 120 optimal weight: 0.4980 chunk 0 optimal weight: 1.9990 chunk 19 optimal weight: 0.0370 chunk 46 optimal weight: 0.6980 chunk 61 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 76 optimal weight: 0.6980 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 123 GLN ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 308 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.098979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.075837 restraints weight = 26281.566| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.93 r_work: 0.3157 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9951 Z= 0.133 Angle : 0.538 7.487 13575 Z= 0.282 Chirality : 0.039 0.211 1515 Planarity : 0.005 0.073 1682 Dihedral : 4.669 62.619 1327 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.55 % Allowed : 9.96 % Favored : 88.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.43 % Cis-general : 0.00 % Twisted Proline : 1.89 % 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: 0.94 (0.25), residues: 1207 helix: 1.87 (0.20), residues: 666 sheet: 0.47 (0.37), residues: 220 loop : -2.01 (0.32), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 95 TYR 0.009 0.001 TYR A 316 PHE 0.011 0.001 PHE A 209 TRP 0.030 0.001 TRP D 90 HIS 0.004 0.001 HIS A 127 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 9946) covalent geometry : angle 0.53764 (13565) SS BOND : bond 0.00523 ( 5) SS BOND : angle 1.02840 ( 10) hydrogen bonds : bond 0.06608 ( 607) hydrogen bonds : angle 3.99194 ( 1803) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 76 GLN cc_start: 0.8700 (tm130) cc_final: 0.8246 (tm-30) REVERT: C 83 GLU cc_start: 0.8459 (tm-30) cc_final: 0.8168 (tm-30) REVERT: C 213 GLU cc_start: 0.8145 (mp0) cc_final: 0.7901 (mp0) REVERT: D 174 MET cc_start: 0.8683 (ttt) cc_final: 0.8185 (tpp) REVERT: A 308 ASN cc_start: 0.8372 (OUTLIER) cc_final: 0.8103 (t0) REVERT: A 384 LYS cc_start: 0.9222 (ttpp) cc_final: 0.8914 (tppt) REVERT: B 281 LYS cc_start: 0.8624 (ttpp) cc_final: 0.8421 (ttpp) REVERT: B 289 ASP cc_start: 0.8294 (t70) cc_final: 0.8033 (m-30) outliers start: 16 outliers final: 10 residues processed: 116 average time/residue: 0.0911 time to fit residues: 15.2268 Evaluate side-chains 104 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 211 ASN Chi-restraints excluded: chain A residue 53 TRP Chi-restraints excluded: chain A residue 67 CYS Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 308 ASN Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain B residue 112 TYR Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 384 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 54 optimal weight: 3.9990 chunk 90 optimal weight: 0.0970 chunk 101 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 51 ASN ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 308 ASN A 367 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.094972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.071438 restraints weight = 26865.095| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 2.92 r_work: 0.3017 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9951 Z= 0.218 Angle : 0.604 8.524 13575 Z= 0.321 Chirality : 0.041 0.188 1515 Planarity : 0.005 0.075 1682 Dihedral : 4.826 59.718 1327 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.32 % Allowed : 11.70 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.43 % Cis-general : 0.00 % Twisted Proline : 1.89 % 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: 0.92 (0.25), residues: 1207 helix: 1.82 (0.20), residues: 664 sheet: 0.46 (0.36), residues: 220 loop : -1.91 (0.33), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 99 TYR 0.018 0.002 TYR A 279 PHE 0.030 0.002 PHE A 5 TRP 0.029 0.001 TRP D 90 HIS 0.003 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00503 ( 9946) covalent geometry : angle 0.60329 (13565) SS BOND : bond 0.00846 ( 5) SS BOND : angle 1.23720 ( 10) hydrogen bonds : bond 0.08542 ( 607) hydrogen bonds : angle 4.33467 ( 1803) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 92 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 83 GLU cc_start: 0.8540 (tm-30) cc_final: 0.8176 (tm-30) REVERT: D 174 MET cc_start: 0.8866 (ttt) cc_final: 0.8082 (tpp) REVERT: A 253 MET cc_start: 0.8206 (tmm) cc_final: 0.7988 (tmm) REVERT: A 367 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.8120 (tm-30) REVERT: A 384 LYS cc_start: 0.9260 (ttpp) cc_final: 0.8965 (tppt) REVERT: B 289 ASP cc_start: 0.8382 (t70) cc_final: 0.8093 (m-30) outliers start: 24 outliers final: 16 residues processed: 112 average time/residue: 0.0886 time to fit residues: 14.5051 Evaluate side-chains 105 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 88 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 211 ASN Chi-restraints excluded: chain A residue 53 TRP Chi-restraints excluded: chain A residue 67 CYS Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 367 GLN Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 34 TRP Chi-restraints excluded: chain B residue 53 TRP Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 294 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 50 optimal weight: 2.9990 chunk 82 optimal weight: 0.0980 chunk 120 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 110 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 63 optimal weight: 4.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 123 GLN D 165 GLN ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 308 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.095898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.072571 restraints weight = 26789.209| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.91 r_work: 0.3040 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9951 Z= 0.180 Angle : 0.572 8.966 13575 Z= 0.304 Chirality : 0.040 0.168 1515 Planarity : 0.005 0.071 1682 Dihedral : 4.779 58.667 1327 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.93 % Allowed : 14.51 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.43 % Cis-general : 0.00 % Twisted Proline : 1.89 % 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: 1.02 (0.25), residues: 1207 helix: 1.90 (0.20), residues: 664 sheet: 0.47 (0.36), residues: 220 loop : -1.83 (0.33), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 197 TYR 0.014 0.001 TYR D 31 PHE 0.021 0.001 PHE A 5 TRP 0.026 0.001 TRP D 90 HIS 0.005 0.001 HIS A 127 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 9946) covalent geometry : angle 0.57107 (13565) SS BOND : bond 0.00647 ( 5) SS BOND : angle 1.30230 ( 10) hydrogen bonds : bond 0.08025 ( 607) hydrogen bonds : angle 4.17957 ( 1803) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 83 GLU cc_start: 0.8519 (tm-30) cc_final: 0.8150 (tm-30) REVERT: D 174 MET cc_start: 0.8748 (ttt) cc_final: 0.7967 (tpp) REVERT: A 384 LYS cc_start: 0.9253 (ttpp) cc_final: 0.8959 (tppt) REVERT: B 236 ILE cc_start: 0.8931 (OUTLIER) cc_final: 0.8593 (pt) REVERT: B 289 ASP cc_start: 0.8386 (t70) cc_final: 0.8136 (m-30) outliers start: 20 outliers final: 15 residues processed: 104 average time/residue: 0.0841 time to fit residues: 13.0754 Evaluate side-chains 104 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 TRP Chi-restraints excluded: chain A residue 67 CYS Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 34 TRP Chi-restraints excluded: chain B residue 53 TRP Chi-restraints excluded: chain B residue 112 TYR Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 294 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 63 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 18 optimal weight: 6.9990 chunk 72 optimal weight: 0.4980 chunk 24 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 367 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.093429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.070579 restraints weight = 26355.376| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.96 r_work: 0.3048 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9951 Z= 0.167 Angle : 0.556 9.217 13575 Z= 0.294 Chirality : 0.040 0.168 1515 Planarity : 0.005 0.073 1682 Dihedral : 4.670 57.043 1327 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.22 % Allowed : 14.89 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.43 % Cis-general : 0.00 % Twisted Proline : 1.89 % 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: 1.14 (0.25), residues: 1207 helix: 2.01 (0.20), residues: 664 sheet: 0.46 (0.36), residues: 223 loop : -1.79 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 197 TYR 0.013 0.001 TYR D 31 PHE 0.019 0.001 PHE A 5 TRP 0.023 0.001 TRP D 90 HIS 0.004 0.001 HIS A 127 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 9946) covalent geometry : angle 0.55535 (13565) SS BOND : bond 0.00612 ( 5) SS BOND : angle 1.21476 ( 10) hydrogen bonds : bond 0.07660 ( 607) hydrogen bonds : angle 4.08536 ( 1803) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 92 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 83 GLU cc_start: 0.8585 (tm-30) cc_final: 0.8196 (tm-30) REVERT: D 147 TRP cc_start: 0.8348 (m100) cc_final: 0.8100 (m100) REVERT: D 174 MET cc_start: 0.8777 (ttt) cc_final: 0.7965 (tpp) REVERT: A 112 TYR cc_start: 0.8964 (OUTLIER) cc_final: 0.8306 (t80) REVERT: A 308 ASN cc_start: 0.8585 (OUTLIER) cc_final: 0.8278 (t0) REVERT: A 384 LYS cc_start: 0.9246 (ttpp) cc_final: 0.8955 (tppt) REVERT: B 236 ILE cc_start: 0.8878 (OUTLIER) cc_final: 0.8584 (pt) REVERT: B 289 ASP cc_start: 0.8375 (t70) cc_final: 0.8130 (m-30) outliers start: 23 outliers final: 15 residues processed: 110 average time/residue: 0.0874 time to fit residues: 14.0133 Evaluate side-chains 108 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain D residue 211 ASN Chi-restraints excluded: chain A residue 53 TRP Chi-restraints excluded: chain A residue 67 CYS Chi-restraints excluded: chain A residue 112 TYR Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 308 ASN Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 34 TRP Chi-restraints excluded: chain B residue 53 TRP Chi-restraints excluded: chain B residue 112 TYR Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 294 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 23 optimal weight: 0.8980 chunk 42 optimal weight: 0.4980 chunk 73 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 chunk 11 optimal weight: 0.6980 chunk 118 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 123 GLN ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.094146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.071450 restraints weight = 26162.516| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.95 r_work: 0.3068 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9951 Z= 0.153 Angle : 0.547 9.280 13575 Z= 0.288 Chirality : 0.040 0.163 1515 Planarity : 0.005 0.071 1682 Dihedral : 4.573 54.660 1327 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.22 % Allowed : 15.67 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.43 % Cis-general : 0.00 % Twisted Proline : 1.89 % 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: 1.26 (0.25), residues: 1207 helix: 2.09 (0.20), residues: 664 sheet: 0.53 (0.36), residues: 221 loop : -1.70 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 99 TYR 0.011 0.001 TYR D 31 PHE 0.017 0.001 PHE A 314 TRP 0.023 0.001 TRP D 90 HIS 0.004 0.001 HIS A 127 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 9946) covalent geometry : angle 0.54643 (13565) SS BOND : bond 0.00564 ( 5) SS BOND : angle 1.15050 ( 10) hydrogen bonds : bond 0.07285 ( 607) hydrogen bonds : angle 3.98619 ( 1803) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 95 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 83 GLU cc_start: 0.8617 (tm-30) cc_final: 0.8225 (tm-30) REVERT: C 173 GLN cc_start: 0.8212 (pp30) cc_final: 0.8002 (pp30) REVERT: D 147 TRP cc_start: 0.8368 (m100) cc_final: 0.8079 (m100) REVERT: D 154 ARG cc_start: 0.9207 (mmm160) cc_final: 0.8520 (tpt-90) REVERT: D 174 MET cc_start: 0.8768 (ttt) cc_final: 0.7981 (tpp) REVERT: A 112 TYR cc_start: 0.8912 (OUTLIER) cc_final: 0.8306 (t80) REVERT: A 308 ASN cc_start: 0.8567 (OUTLIER) cc_final: 0.8289 (t0) REVERT: A 384 LYS cc_start: 0.9232 (ttpp) cc_final: 0.8914 (tppt) REVERT: B 236 ILE cc_start: 0.8892 (OUTLIER) cc_final: 0.8604 (pt) REVERT: B 289 ASP cc_start: 0.8335 (t70) cc_final: 0.8085 (m-30) outliers start: 23 outliers final: 16 residues processed: 112 average time/residue: 0.0993 time to fit residues: 15.7460 Evaluate side-chains 112 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain D residue 211 ASN Chi-restraints excluded: chain A residue 53 TRP Chi-restraints excluded: chain A residue 67 CYS Chi-restraints excluded: chain A residue 112 TYR Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 308 ASN Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 34 TRP Chi-restraints excluded: chain B residue 53 TRP Chi-restraints excluded: chain B residue 112 TYR Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 384 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 11 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 101 optimal weight: 0.7980 chunk 40 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 42 optimal weight: 9.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.093556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.069941 restraints weight = 26858.760| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 2.91 r_work: 0.2978 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 9951 Z= 0.249 Angle : 0.644 9.707 13575 Z= 0.340 Chirality : 0.042 0.176 1515 Planarity : 0.005 0.074 1682 Dihedral : 4.849 52.404 1327 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.61 % Allowed : 15.67 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.43 % Cis-general : 0.00 % Twisted Proline : 1.89 % 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: 0.99 (0.25), residues: 1207 helix: 1.81 (0.20), residues: 666 sheet: 0.39 (0.36), residues: 223 loop : -1.67 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 99 TYR 0.018 0.002 TYR D 31 PHE 0.028 0.002 PHE A 5 TRP 0.019 0.002 TRP D 90 HIS 0.005 0.001 HIS A 127 Details of bonding type rmsd covalent geometry : bond 0.00585 ( 9946) covalent geometry : angle 0.63988 (13565) SS BOND : bond 0.00798 ( 5) SS BOND : angle 2.63096 ( 10) hydrogen bonds : bond 0.09096 ( 607) hydrogen bonds : angle 4.39992 ( 1803) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 90 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 83 GLU cc_start: 0.8721 (tm-30) cc_final: 0.8325 (tm-30) REVERT: C 173 GLN cc_start: 0.8337 (pp30) cc_final: 0.7949 (pp30) REVERT: D 17 GLU cc_start: 0.8268 (mp0) cc_final: 0.7908 (mp0) REVERT: D 147 TRP cc_start: 0.8365 (m100) cc_final: 0.8095 (m100) REVERT: D 154 ARG cc_start: 0.9203 (mmm160) cc_final: 0.8888 (mmm160) REVERT: D 174 MET cc_start: 0.8925 (ttt) cc_final: 0.8070 (tpp) REVERT: A 308 ASN cc_start: 0.8606 (OUTLIER) cc_final: 0.8297 (t0) REVERT: A 384 LYS cc_start: 0.9273 (ttpp) cc_final: 0.8984 (tppt) REVERT: B 5 PHE cc_start: 0.8047 (OUTLIER) cc_final: 0.7604 (m-80) REVERT: B 236 ILE cc_start: 0.8907 (OUTLIER) cc_final: 0.8653 (pt) REVERT: B 264 LYS cc_start: 0.8154 (OUTLIER) cc_final: 0.7792 (ttpt) REVERT: B 289 ASP cc_start: 0.8396 (t70) cc_final: 0.8171 (m-30) outliers start: 27 outliers final: 18 residues processed: 110 average time/residue: 0.0966 time to fit residues: 15.0642 Evaluate side-chains 111 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 89 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain D residue 211 ASN Chi-restraints excluded: chain A residue 53 TRP Chi-restraints excluded: chain A residue 67 CYS Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 308 ASN Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 5 PHE Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 34 TRP Chi-restraints excluded: chain B residue 53 TRP Chi-restraints excluded: chain B residue 112 TYR Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 264 LYS Chi-restraints excluded: chain B residue 294 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 16 optimal weight: 8.9990 chunk 105 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 65 optimal weight: 0.4980 chunk 12 optimal weight: 6.9990 chunk 86 optimal weight: 0.2980 chunk 92 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.095769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.072723 restraints weight = 26707.904| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.88 r_work: 0.3056 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9951 Z= 0.151 Angle : 0.567 13.798 13575 Z= 0.295 Chirality : 0.040 0.159 1515 Planarity : 0.005 0.070 1682 Dihedral : 4.613 52.176 1327 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.42 % Allowed : 16.44 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.43 % Cis-general : 0.00 % Twisted Proline : 1.89 % 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: 1.29 (0.25), residues: 1207 helix: 2.07 (0.20), residues: 666 sheet: 0.57 (0.37), residues: 221 loop : -1.60 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 99 TYR 0.011 0.001 TYR D 31 PHE 0.016 0.001 PHE A 5 TRP 0.019 0.001 TRP D 90 HIS 0.005 0.001 HIS A 127 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 9946) covalent geometry : angle 0.56496 (13565) SS BOND : bond 0.00550 ( 5) SS BOND : angle 1.92389 ( 10) hydrogen bonds : bond 0.07383 ( 607) hydrogen bonds : angle 4.02260 ( 1803) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 94 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 83 GLU cc_start: 0.8698 (tm-30) cc_final: 0.8303 (tm-30) REVERT: C 190 TRP cc_start: 0.9153 (t60) cc_final: 0.8837 (t60) REVERT: D 90 TRP cc_start: 0.7068 (t-100) cc_final: 0.6487 (t-100) REVERT: D 147 TRP cc_start: 0.8369 (m100) cc_final: 0.8159 (m100) REVERT: D 154 ARG cc_start: 0.9215 (mmm160) cc_final: 0.8546 (tpt-90) REVERT: D 174 MET cc_start: 0.8815 (ttt) cc_final: 0.8079 (tpp) REVERT: A 112 TYR cc_start: 0.8943 (OUTLIER) cc_final: 0.8225 (t80) REVERT: A 308 ASN cc_start: 0.8594 (OUTLIER) cc_final: 0.8289 (t0) REVERT: A 367 GLN cc_start: 0.8639 (OUTLIER) cc_final: 0.8153 (tm-30) REVERT: A 384 LYS cc_start: 0.9237 (ttpp) cc_final: 0.8960 (tppt) REVERT: B 236 ILE cc_start: 0.8897 (OUTLIER) cc_final: 0.8599 (pt) REVERT: B 264 LYS cc_start: 0.8031 (OUTLIER) cc_final: 0.7676 (ttpt) REVERT: B 289 ASP cc_start: 0.8283 (t70) cc_final: 0.8076 (m-30) outliers start: 25 outliers final: 18 residues processed: 113 average time/residue: 0.0943 time to fit residues: 15.1481 Evaluate side-chains 116 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain D residue 211 ASN Chi-restraints excluded: chain A residue 53 TRP Chi-restraints excluded: chain A residue 67 CYS Chi-restraints excluded: chain A residue 112 TYR Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 308 ASN Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 367 GLN Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 34 TRP Chi-restraints excluded: chain B residue 53 TRP Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 112 TYR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 264 LYS Chi-restraints excluded: chain B residue 294 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 9 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 20 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 38 optimal weight: 0.0770 chunk 28 optimal weight: 5.9990 chunk 46 optimal weight: 7.9990 overall best weight: 0.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 123 GLN ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.096215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.073085 restraints weight = 26501.135| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.88 r_work: 0.3065 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9951 Z= 0.151 Angle : 0.565 12.571 13575 Z= 0.293 Chirality : 0.040 0.162 1515 Planarity : 0.005 0.073 1682 Dihedral : 4.543 51.107 1327 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.22 % Allowed : 16.54 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.43 % Cis-general : 0.00 % Twisted Proline : 1.89 % 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: 1.34 (0.25), residues: 1207 helix: 2.12 (0.20), residues: 664 sheet: 0.60 (0.36), residues: 221 loop : -1.59 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 99 TYR 0.012 0.001 TYR D 31 PHE 0.019 0.001 PHE A 17 TRP 0.021 0.001 TRP D 90 HIS 0.005 0.001 HIS A 127 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 9946) covalent geometry : angle 0.56288 (13565) SS BOND : bond 0.00572 ( 5) SS BOND : angle 1.79285 ( 10) hydrogen bonds : bond 0.07212 ( 607) hydrogen bonds : angle 3.98804 ( 1803) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 83 GLU cc_start: 0.8696 (tm-30) cc_final: 0.8294 (tm-30) REVERT: D 90 TRP cc_start: 0.7082 (t-100) cc_final: 0.6500 (t-100) REVERT: D 147 TRP cc_start: 0.8343 (m100) cc_final: 0.7915 (m100) REVERT: D 154 ARG cc_start: 0.9227 (mmm160) cc_final: 0.8890 (mmm160) REVERT: D 174 MET cc_start: 0.8800 (ttt) cc_final: 0.8072 (tpp) REVERT: A 112 TYR cc_start: 0.8936 (OUTLIER) cc_final: 0.8291 (t80) REVERT: A 308 ASN cc_start: 0.8587 (OUTLIER) cc_final: 0.8292 (t0) REVERT: A 367 GLN cc_start: 0.8626 (OUTLIER) cc_final: 0.8137 (tm-30) REVERT: A 384 LYS cc_start: 0.9232 (ttpp) cc_final: 0.8923 (tppt) REVERT: B 5 PHE cc_start: 0.7979 (OUTLIER) cc_final: 0.7382 (m-80) REVERT: B 236 ILE cc_start: 0.8902 (OUTLIER) cc_final: 0.8607 (pt) REVERT: B 289 ASP cc_start: 0.8223 (t70) cc_final: 0.8011 (m-30) outliers start: 23 outliers final: 17 residues processed: 112 average time/residue: 0.0954 time to fit residues: 15.2762 Evaluate side-chains 115 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 93 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain D residue 211 ASN Chi-restraints excluded: chain A residue 53 TRP Chi-restraints excluded: chain A residue 67 CYS Chi-restraints excluded: chain A residue 112 TYR Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 308 ASN Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 367 GLN Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 5 PHE Chi-restraints excluded: chain B residue 34 TRP Chi-restraints excluded: chain B residue 53 TRP Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 112 TYR Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 294 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 10 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 43 optimal weight: 0.0370 chunk 32 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 93 optimal weight: 0.4980 chunk 69 optimal weight: 0.6980 overall best weight: 1.2462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.093049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.070230 restraints weight = 26159.223| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 2.94 r_work: 0.3045 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9951 Z= 0.169 Angle : 0.575 12.172 13575 Z= 0.300 Chirality : 0.040 0.163 1515 Planarity : 0.005 0.072 1682 Dihedral : 4.579 51.551 1327 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.32 % Allowed : 16.54 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.43 % Cis-general : 0.00 % Twisted Proline : 1.89 % 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: 1.31 (0.25), residues: 1207 helix: 2.08 (0.20), residues: 664 sheet: 0.62 (0.36), residues: 221 loop : -1.61 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 99 TYR 0.014 0.001 TYR D 31 PHE 0.019 0.001 PHE A 5 TRP 0.020 0.001 TRP D 90 HIS 0.005 0.001 HIS A 127 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 9946) covalent geometry : angle 0.57392 (13565) SS BOND : bond 0.00609 ( 5) SS BOND : angle 1.64196 ( 10) hydrogen bonds : bond 0.07494 ( 607) hydrogen bonds : angle 4.02845 ( 1803) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2089.58 seconds wall clock time: 36 minutes 31.56 seconds (2191.56 seconds total)