Starting phenix.real_space_refine on Wed Apr 30 20:39:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g15_29662/04_2025/8g15_29662.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g15_29662/04_2025/8g15_29662.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g15_29662/04_2025/8g15_29662.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g15_29662/04_2025/8g15_29662.map" model { file = "/net/cci-nas-00/data/ceres_data/8g15_29662/04_2025/8g15_29662.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g15_29662/04_2025/8g15_29662.cif" } resolution = 2.07 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 48 5.16 5 C 6352 2.51 5 N 1744 2.21 5 O 1912 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 10056 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2514 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 12, 'TRANS': 321} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2514 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 12, 'TRANS': 321} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 2514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2514 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 12, 'TRANS': 321} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 2514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2514 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 12, 'TRANS': 321} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.36, per 1000 atoms: 0.63 Number of scatterers: 10056 At special positions: 0 Unit cell: (99.365, 102.705, 89.345, 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 48 16.00 O 1912 8.00 N 1744 7.00 C 6352 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.61 Conformation dependent library (CDL) restraints added in 1.3 seconds 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2408 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 8 sheets defined 38.0% alpha, 22.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.44 Creating SS restraints... Processing helix chain 'A' and resid 12 through 26 Processing helix chain 'A' and resid 39 through 49 Processing helix chain 'A' and resid 81 through 85 removed outlier: 3.565A pdb=" N ILE A 85 " --> pdb=" O PRO A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 91 Processing helix chain 'A' and resid 104 through 109 Processing helix chain 'A' and resid 110 through 115 removed outlier: 3.832A pdb=" N GLN A 113 " --> pdb=" O ALA A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 140 removed outlier: 3.520A pdb=" N TYR A 140 " --> pdb=" O HIS A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 169 Proline residue: A 159 - end of helix Processing helix chain 'A' and resid 196 through 200 Processing helix chain 'A' and resid 216 through 221 Processing helix chain 'A' and resid 222 through 225 Processing helix chain 'A' and resid 254 through 268 Processing helix chain 'A' and resid 282 through 287 removed outlier: 3.517A pdb=" N ASN A 287 " --> pdb=" O SER A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 334 removed outlier: 3.519A pdb=" N VAL A 325 " --> pdb=" O SER A 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 26 Processing helix chain 'B' and resid 39 through 49 Processing helix chain 'B' and resid 81 through 85 removed outlier: 3.566A pdb=" N ILE B 85 " --> pdb=" O PRO B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 91 Processing helix chain 'B' and resid 104 through 109 Processing helix chain 'B' and resid 110 through 115 removed outlier: 3.833A pdb=" N GLN B 113 " --> pdb=" O ALA B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 140 removed outlier: 3.520A pdb=" N TYR B 140 " --> pdb=" O HIS B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 169 Proline residue: B 159 - end of helix Processing helix chain 'B' and resid 196 through 200 Processing helix chain 'B' and resid 216 through 221 Processing helix chain 'B' and resid 222 through 225 Processing helix chain 'B' and resid 254 through 268 Processing helix chain 'B' and resid 282 through 287 removed outlier: 3.517A pdb=" N ASN B 287 " --> pdb=" O SER B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 334 removed outlier: 3.518A pdb=" N VAL B 325 " --> pdb=" O SER B 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 26 Processing helix chain 'C' and resid 39 through 49 Processing helix chain 'C' and resid 81 through 85 removed outlier: 3.564A pdb=" N ILE C 85 " --> pdb=" O PRO C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 91 Processing helix chain 'C' and resid 104 through 109 Processing helix chain 'C' and resid 110 through 115 removed outlier: 3.831A pdb=" N GLN C 113 " --> pdb=" O ALA C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 140 removed outlier: 3.520A pdb=" N TYR C 140 " --> pdb=" O HIS C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 169 Proline residue: C 159 - end of helix Processing helix chain 'C' and resid 196 through 200 Processing helix chain 'C' and resid 216 through 221 Processing helix chain 'C' and resid 222 through 225 Processing helix chain 'C' and resid 254 through 268 Processing helix chain 'C' and resid 282 through 287 removed outlier: 3.516A pdb=" N ASN C 287 " --> pdb=" O SER C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 334 removed outlier: 3.516A pdb=" N VAL C 325 " --> pdb=" O SER C 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 26 Processing helix chain 'D' and resid 39 through 49 Processing helix chain 'D' and resid 81 through 85 removed outlier: 3.565A pdb=" N ILE D 85 " --> pdb=" O PRO D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 91 Processing helix chain 'D' and resid 104 through 109 Processing helix chain 'D' and resid 110 through 115 removed outlier: 3.900A pdb=" N GLN D 113 " --> pdb=" O ALA D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 140 removed outlier: 3.521A pdb=" N TYR D 140 " --> pdb=" O HIS D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 169 Proline residue: D 159 - end of helix Processing helix chain 'D' and resid 196 through 200 Processing helix chain 'D' and resid 216 through 221 Processing helix chain 'D' and resid 222 through 225 Processing helix chain 'D' and resid 254 through 268 Processing helix chain 'D' and resid 282 through 287 removed outlier: 3.518A pdb=" N ASN D 287 " --> pdb=" O SER D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 334 removed outlier: 3.518A pdb=" N VAL D 325 " --> pdb=" O SER D 321 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 63 removed outlier: 5.941A pdb=" N VAL A 31 " --> pdb=" O PRO A 73 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N VAL A 8 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ILE A 33 " --> pdb=" O VAL A 8 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N VAL A 95 " --> pdb=" O ILE A 120 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 208 through 210 removed outlier: 3.571A pdb=" N THR A 229 " --> pdb=" O GLY A 173 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU A 172 " --> pdb=" O ARG A 248 " (cutoff:3.500A) removed outlier: 12.260A pdb=" N PHE A 307 " --> pdb=" O GLY A 300 " (cutoff:3.500A) removed outlier: 11.116A pdb=" N GLY A 300 " --> pdb=" O PHE A 307 " (cutoff:3.500A) removed outlier: 10.834A pdb=" N LYS A 309 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 8.855A pdb=" N GLY A 298 " --> pdb=" O LYS A 309 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ILE A 311 " --> pdb=" O ASP A 296 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 60 through 63 removed outlier: 5.938A pdb=" N VAL B 31 " --> pdb=" O PRO B 73 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N VAL B 6 " --> pdb=" O ILE B 30 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA B 32 " --> pdb=" O VAL B 6 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N VAL B 95 " --> pdb=" O ILE B 120 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 208 through 210 removed outlier: 3.531A pdb=" N THR B 229 " --> pdb=" O GLY B 173 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU B 172 " --> pdb=" O ARG B 248 " (cutoff:3.500A) removed outlier: 12.258A pdb=" N PHE B 307 " --> pdb=" O GLY B 300 " (cutoff:3.500A) removed outlier: 11.116A pdb=" N GLY B 300 " --> pdb=" O PHE B 307 " (cutoff:3.500A) removed outlier: 10.832A pdb=" N LYS B 309 " --> pdb=" O GLY B 298 " (cutoff:3.500A) removed outlier: 8.850A pdb=" N GLY B 298 " --> pdb=" O LYS B 309 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ILE B 311 " --> pdb=" O ASP B 296 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 60 through 63 removed outlier: 5.939A pdb=" N VAL C 31 " --> pdb=" O PRO C 73 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N VAL C 6 " --> pdb=" O ILE C 30 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA C 32 " --> pdb=" O VAL C 6 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL C 95 " --> pdb=" O ILE C 120 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 208 through 210 removed outlier: 3.585A pdb=" N THR C 229 " --> pdb=" O GLY C 173 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU C 172 " --> pdb=" O ARG C 248 " (cutoff:3.500A) removed outlier: 12.256A pdb=" N PHE C 307 " --> pdb=" O GLY C 300 " (cutoff:3.500A) removed outlier: 11.113A pdb=" N GLY C 300 " --> pdb=" O PHE C 307 " (cutoff:3.500A) removed outlier: 10.832A pdb=" N LYS C 309 " --> pdb=" O GLY C 298 " (cutoff:3.500A) removed outlier: 8.853A pdb=" N GLY C 298 " --> pdb=" O LYS C 309 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ILE C 311 " --> pdb=" O ASP C 296 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 60 through 63 removed outlier: 5.941A pdb=" N VAL D 31 " --> pdb=" O PRO D 73 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N VAL D 8 " --> pdb=" O VAL D 31 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ILE D 33 " --> pdb=" O VAL D 8 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N VAL D 95 " --> pdb=" O ILE D 120 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 208 through 210 removed outlier: 3.586A pdb=" N THR D 229 " --> pdb=" O GLY D 173 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU D 172 " --> pdb=" O ARG D 248 " (cutoff:3.500A) removed outlier: 12.257A pdb=" N PHE D 307 " --> pdb=" O GLY D 300 " (cutoff:3.500A) removed outlier: 11.116A pdb=" N GLY D 300 " --> pdb=" O PHE D 307 " (cutoff:3.500A) removed outlier: 10.831A pdb=" N LYS D 309 " --> pdb=" O GLY D 298 " (cutoff:3.500A) removed outlier: 8.853A pdb=" N GLY D 298 " --> pdb=" O LYS D 309 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N ILE D 311 " --> pdb=" O ASP D 296 " (cutoff:3.500A) 468 hydrogen bonds defined for protein. 1260 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.90 Time building geometry restraints manager: 3.00 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: 3109 1.34 - 1.45: 1446 1.45 - 1.57: 5617 1.57 - 1.69: 0 1.69 - 1.81: 84 Bond restraints: 10256 Sorted by residual: bond pdb=" C SER D 312 " pdb=" N TRP D 313 " ideal model delta sigma weight residual 1.329 1.482 -0.152 1.38e-02 5.25e+03 1.22e+02 bond pdb=" C SER B 312 " pdb=" N TRP B 313 " ideal model delta sigma weight residual 1.329 1.477 -0.148 1.38e-02 5.25e+03 1.15e+02 bond pdb=" C SER C 312 " pdb=" N TRP C 313 " ideal model delta sigma weight residual 1.329 1.475 -0.146 1.38e-02 5.25e+03 1.12e+02 bond pdb=" N PRO D 208 " pdb=" CD PRO D 208 " ideal model delta sigma weight residual 1.473 1.542 -0.069 1.40e-02 5.10e+03 2.42e+01 bond pdb=" N VAL D 188 " pdb=" CA VAL D 188 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.23e-02 6.61e+03 9.60e+00 ... (remaining 10251 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.66: 13875 5.66 - 11.32: 10 11.32 - 16.98: 5 16.98 - 22.64: 3 22.64 - 28.30: 3 Bond angle restraints: 13896 Sorted by residual: angle pdb=" O SER B 312 " pdb=" C SER B 312 " pdb=" N TRP B 313 " ideal model delta sigma weight residual 123.24 94.94 28.30 1.23e+00 6.61e-01 5.30e+02 angle pdb=" O SER D 312 " pdb=" C SER D 312 " pdb=" N TRP D 313 " ideal model delta sigma weight residual 123.24 94.94 28.30 1.23e+00 6.61e-01 5.29e+02 angle pdb=" O SER C 312 " pdb=" C SER C 312 " pdb=" N TRP C 313 " ideal model delta sigma weight residual 123.24 95.09 28.15 1.23e+00 6.61e-01 5.24e+02 angle pdb=" CA SER D 312 " pdb=" C SER D 312 " pdb=" N TRP D 313 " ideal model delta sigma weight residual 115.58 134.88 -19.30 1.48e+00 4.57e-01 1.70e+02 angle pdb=" CA SER B 312 " pdb=" C SER B 312 " pdb=" N TRP B 313 " ideal model delta sigma weight residual 115.58 134.81 -19.23 1.48e+00 4.57e-01 1.69e+02 ... (remaining 13891 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.21: 5348 17.21 - 34.42: 514 34.42 - 51.63: 147 51.63 - 68.84: 53 68.84 - 86.05: 13 Dihedral angle restraints: 6075 sinusoidal: 2299 harmonic: 3776 Sorted by residual: dihedral pdb=" CA ASN B 239 " pdb=" C ASN B 239 " pdb=" N VAL B 240 " pdb=" CA VAL B 240 " ideal model delta harmonic sigma weight residual -180.00 -161.46 -18.54 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA ASN D 239 " pdb=" C ASN D 239 " pdb=" N VAL D 240 " pdb=" CA VAL D 240 " ideal model delta harmonic sigma weight residual -180.00 -161.48 -18.52 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA ASN C 239 " pdb=" C ASN C 239 " pdb=" N VAL C 240 " pdb=" CA VAL C 240 " ideal model delta harmonic sigma weight residual -180.00 -161.67 -18.33 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 6072 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 968 0.040 - 0.080: 381 0.080 - 0.120: 172 0.120 - 0.160: 46 0.160 - 0.200: 9 Chirality restraints: 1576 Sorted by residual: chirality pdb=" CA ILE C 207 " pdb=" N ILE C 207 " pdb=" C ILE C 207 " pdb=" CB ILE C 207 " both_signs ideal model delta sigma weight residual False 2.43 2.23 0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CA ILE D 207 " pdb=" N ILE D 207 " pdb=" C ILE D 207 " pdb=" CB ILE D 207 " both_signs ideal model delta sigma weight residual False 2.43 2.23 0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CA ILE A 207 " pdb=" N ILE A 207 " pdb=" C ILE A 207 " pdb=" CB ILE A 207 " both_signs ideal model delta sigma weight residual False 2.43 2.23 0.20 2.00e-01 2.50e+01 9.97e-01 ... (remaining 1573 not shown) Planarity restraints: 1804 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER C 312 " -0.069 2.00e-02 2.50e+03 1.08e-01 1.16e+02 pdb=" C SER C 312 " 0.187 2.00e-02 2.50e+03 pdb=" O SER C 312 " -0.058 2.00e-02 2.50e+03 pdb=" N TRP C 313 " -0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 312 " 0.068 2.00e-02 2.50e+03 1.06e-01 1.12e+02 pdb=" C SER B 312 " -0.183 2.00e-02 2.50e+03 pdb=" O SER B 312 " 0.057 2.00e-02 2.50e+03 pdb=" N TRP B 313 " 0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER D 312 " -0.068 2.00e-02 2.50e+03 1.06e-01 1.11e+02 pdb=" C SER D 312 " 0.183 2.00e-02 2.50e+03 pdb=" O SER D 312 " -0.056 2.00e-02 2.50e+03 pdb=" N TRP D 313 " -0.058 2.00e-02 2.50e+03 ... (remaining 1801 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1932 2.77 - 3.31: 8802 3.31 - 3.84: 16550 3.84 - 4.37: 20098 4.37 - 4.90: 35079 Nonbonded interactions: 82461 Sorted by model distance: nonbonded pdb=" O ASN B 239 " pdb=" OD1 ASN B 316 " model vdw 2.243 3.040 nonbonded pdb=" O ASN D 239 " pdb=" OD1 ASN D 316 " model vdw 2.243 3.040 nonbonded pdb=" O ASN C 239 " pdb=" OD1 ASN C 316 " model vdw 2.251 3.040 nonbonded pdb=" O ASN A 239 " pdb=" OD1 ASN A 316 " model vdw 2.255 3.040 nonbonded pdb=" NH2 ARG C 118 " pdb=" OD1 ASN C 142 " model vdw 2.257 3.120 ... (remaining 82456 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 32.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 26.220 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 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:11.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 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 : 0.005 0.152 10256 Z= 0.331 Angle : 0.963 28.304 13896 Z= 0.638 Chirality : 0.054 0.200 1576 Planarity : 0.009 0.120 1804 Dihedral : 16.072 86.054 3667 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 1.59 % Allowed : 16.21 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.22), residues: 1328 helix: -2.29 (0.18), residues: 388 sheet: 0.29 (0.40), residues: 220 loop : -0.71 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 87 HIS 0.003 0.001 HIS B 53 PHE 0.009 0.001 PHE B 233 TYR 0.010 0.002 TYR D 42 ARG 0.021 0.001 ARG D 80 Details of bonding type rmsd hydrogen bonds : bond 0.25045 ( 468) hydrogen bonds : angle 8.47828 ( 1260) covalent geometry : bond 0.00542 (10256) covalent geometry : angle 0.96295 (13896) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 1.095 Fit side-chains outliers start: 17 outliers final: 15 residues processed: 104 average time/residue: 1.5492 time to fit residues: 171.6161 Evaluate side-chains 97 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 243 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 0.9980 chunk 100 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 67 optimal weight: 6.9990 chunk 53 optimal weight: 20.0000 chunk 103 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 119 optimal weight: 6.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN B 149 ASN C 149 ASN D 149 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.092228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.080771 restraints weight = 16957.169| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.91 r_work: 0.3164 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10256 Z= 0.170 Angle : 0.589 6.925 13896 Z= 0.326 Chirality : 0.048 0.155 1576 Planarity : 0.006 0.054 1804 Dihedral : 6.106 46.822 1431 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.00 % Allowed : 14.71 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.23), residues: 1328 helix: -0.06 (0.24), residues: 392 sheet: 0.49 (0.40), residues: 212 loop : -0.59 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 87 HIS 0.002 0.001 HIS B 53 PHE 0.010 0.001 PHE A 286 TYR 0.014 0.001 TYR C 314 ARG 0.008 0.001 ARG B 80 Details of bonding type rmsd hydrogen bonds : bond 0.05242 ( 468) hydrogen bonds : angle 6.16934 ( 1260) covalent geometry : bond 0.00399 (10256) covalent geometry : angle 0.58877 (13896) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 78 time to evaluate : 1.256 Fit side-chains outliers start: 32 outliers final: 23 residues processed: 101 average time/residue: 1.4996 time to fit residues: 161.6343 Evaluate side-chains 94 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 71 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 HIS Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain B residue 57 HIS Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain C residue 57 HIS Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain D residue 57 HIS Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 318 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 111 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 77 optimal weight: 9.9990 chunk 53 optimal weight: 20.0000 chunk 3 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 70 optimal weight: 6.9990 chunk 88 optimal weight: 0.6980 chunk 86 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- 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 = 0.3448 r_free = 0.3448 target = 0.089565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.077898 restraints weight = 17207.037| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.95 r_work: 0.3107 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8969 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 10256 Z= 0.271 Angle : 0.676 9.616 13896 Z= 0.372 Chirality : 0.053 0.152 1576 Planarity : 0.006 0.055 1804 Dihedral : 6.820 57.077 1423 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.00 % Allowed : 15.46 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.24), residues: 1328 helix: 0.62 (0.25), residues: 372 sheet: 0.45 (0.39), residues: 204 loop : -0.57 (0.24), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP D 87 HIS 0.003 0.001 HIS D 53 PHE 0.015 0.002 PHE D 318 TYR 0.015 0.002 TYR C 314 ARG 0.006 0.001 ARG D 80 Details of bonding type rmsd hydrogen bonds : bond 0.06108 ( 468) hydrogen bonds : angle 6.25649 ( 1260) covalent geometry : bond 0.00661 (10256) covalent geometry : angle 0.67600 (13896) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 73 time to evaluate : 1.129 Fit side-chains outliers start: 32 outliers final: 23 residues processed: 96 average time/residue: 1.6726 time to fit residues: 170.2005 Evaluate side-chains 95 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 72 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 HIS Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain B residue 57 HIS Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain C residue 57 HIS Chi-restraints excluded: chain C residue 142 ASN Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain D residue 57 HIS Chi-restraints excluded: chain D residue 142 ASN Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 318 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 3.9990 chunk 50 optimal weight: 8.9990 chunk 61 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 149 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.092553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.081107 restraints weight = 16935.040| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.93 r_work: 0.3168 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8922 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10256 Z= 0.129 Angle : 0.540 7.608 13896 Z= 0.295 Chirality : 0.047 0.139 1576 Planarity : 0.005 0.053 1804 Dihedral : 6.499 59.685 1423 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.19 % Allowed : 15.84 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.24), residues: 1328 helix: 0.99 (0.26), residues: 380 sheet: 0.31 (0.37), residues: 228 loop : -0.46 (0.25), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 313 HIS 0.002 0.001 HIS A 179 PHE 0.007 0.001 PHE B 286 TYR 0.010 0.001 TYR D 314 ARG 0.008 0.001 ARG B 80 Details of bonding type rmsd hydrogen bonds : bond 0.04148 ( 468) hydrogen bonds : angle 5.85702 ( 1260) covalent geometry : bond 0.00298 (10256) covalent geometry : angle 0.54023 (13896) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 79 time to evaluate : 1.180 Fit side-chains outliers start: 34 outliers final: 23 residues processed: 107 average time/residue: 1.2867 time to fit residues: 147.7422 Evaluate side-chains 94 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 71 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 HIS Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain B residue 57 HIS Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain C residue 57 HIS Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 142 ASN Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 57 HIS Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 142 ASN Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 243 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 1 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 chunk 96 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 62 optimal weight: 9.9990 chunk 9 optimal weight: 2.9990 chunk 17 optimal weight: 8.9990 chunk 53 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 149 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.090033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.078503 restraints weight = 17005.796| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.91 r_work: 0.3118 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8954 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 10256 Z= 0.221 Angle : 0.632 9.338 13896 Z= 0.347 Chirality : 0.051 0.146 1576 Planarity : 0.006 0.064 1804 Dihedral : 6.205 50.672 1423 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.72 % Allowed : 15.56 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.24), residues: 1328 helix: 0.95 (0.26), residues: 376 sheet: 0.41 (0.38), residues: 204 loop : -0.54 (0.25), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP D 87 HIS 0.003 0.001 HIS D 53 PHE 0.011 0.002 PHE C 286 TYR 0.015 0.002 TYR D 314 ARG 0.009 0.001 ARG B 80 Details of bonding type rmsd hydrogen bonds : bond 0.05404 ( 468) hydrogen bonds : angle 6.06088 ( 1260) covalent geometry : bond 0.00535 (10256) covalent geometry : angle 0.63187 (13896) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 72 time to evaluate : 1.105 Fit side-chains outliers start: 29 outliers final: 24 residues processed: 97 average time/residue: 1.4522 time to fit residues: 150.0865 Evaluate side-chains 96 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 72 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 HIS Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain B residue 57 HIS Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain C residue 57 HIS Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 142 ASN Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain D residue 57 HIS Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 142 ASN Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 318 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 100 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 31 optimal weight: 8.9990 chunk 38 optimal weight: 7.9990 chunk 17 optimal weight: 6.9990 chunk 78 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN C 149 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.092425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.080977 restraints weight = 17017.445| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.93 r_work: 0.3167 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8916 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10256 Z= 0.127 Angle : 0.544 7.742 13896 Z= 0.297 Chirality : 0.047 0.139 1576 Planarity : 0.005 0.057 1804 Dihedral : 5.772 48.635 1420 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 1.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.81 % Allowed : 15.09 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.25), residues: 1328 helix: 1.24 (0.27), residues: 376 sheet: 0.44 (0.38), residues: 212 loop : -0.47 (0.25), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 313 HIS 0.002 0.001 HIS D 179 PHE 0.007 0.001 PHE C 286 TYR 0.010 0.001 TYR B 314 ARG 0.010 0.001 ARG B 80 Details of bonding type rmsd hydrogen bonds : bond 0.04034 ( 468) hydrogen bonds : angle 5.77827 ( 1260) covalent geometry : bond 0.00293 (10256) covalent geometry : angle 0.54418 (13896) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 76 time to evaluate : 1.135 Fit side-chains outliers start: 30 outliers final: 24 residues processed: 101 average time/residue: 1.4427 time to fit residues: 155.8122 Evaluate side-chains 99 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 75 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 HIS Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain B residue 57 HIS Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain C residue 57 HIS Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 142 ASN Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain D residue 57 HIS Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 142 ASN Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 318 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 28 optimal weight: 5.9990 chunk 108 optimal weight: 0.4980 chunk 50 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 124 optimal weight: 9.9990 chunk 36 optimal weight: 6.9990 chunk 22 optimal weight: 6.9990 chunk 123 optimal weight: 4.9990 chunk 91 optimal weight: 10.0000 chunk 58 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- 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 = 0.3485 r_free = 0.3485 target = 0.091918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.080352 restraints weight = 17220.913| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.94 r_work: 0.3152 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10256 Z= 0.145 Angle : 0.565 8.059 13896 Z= 0.309 Chirality : 0.048 0.142 1576 Planarity : 0.006 0.063 1804 Dihedral : 5.771 47.562 1420 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 1.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.72 % Allowed : 15.28 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.24), residues: 1328 helix: 1.24 (0.27), residues: 376 sheet: 0.48 (0.38), residues: 204 loop : -0.55 (0.25), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 87 HIS 0.002 0.001 HIS B 53 PHE 0.007 0.001 PHE D 286 TYR 0.010 0.001 TYR D 314 ARG 0.011 0.001 ARG B 80 Details of bonding type rmsd hydrogen bonds : bond 0.04330 ( 468) hydrogen bonds : angle 5.80290 ( 1260) covalent geometry : bond 0.00343 (10256) covalent geometry : angle 0.56458 (13896) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 76 time to evaluate : 1.673 Fit side-chains outliers start: 29 outliers final: 28 residues processed: 101 average time/residue: 1.6137 time to fit residues: 174.0911 Evaluate side-chains 103 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 75 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 HIS Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain B residue 57 HIS Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain C residue 57 HIS Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 142 ASN Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain D residue 57 HIS Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 142 ASN Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 318 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 108 optimal weight: 0.5980 chunk 94 optimal weight: 2.9990 chunk 55 optimal weight: 0.0050 chunk 18 optimal weight: 7.9990 chunk 51 optimal weight: 8.9990 chunk 12 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 126 optimal weight: 7.9990 overall best weight: 1.0998 ------------------------------------------------------------------------------- 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 = 0.3516 r_free = 0.3516 target = 0.093513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.082280 restraints weight = 17211.037| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.93 r_work: 0.3197 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8895 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10256 Z= 0.103 Angle : 0.504 6.973 13896 Z= 0.273 Chirality : 0.046 0.135 1576 Planarity : 0.005 0.063 1804 Dihedral : 5.387 44.148 1420 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 1.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.97 % Allowed : 16.96 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.25), residues: 1328 helix: 1.14 (0.27), residues: 396 sheet: 0.47 (0.39), residues: 212 loop : -0.44 (0.26), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 313 HIS 0.002 0.000 HIS D 179 PHE 0.005 0.001 PHE C 286 TYR 0.008 0.001 TYR A 314 ARG 0.012 0.001 ARG B 80 Details of bonding type rmsd hydrogen bonds : bond 0.03529 ( 468) hydrogen bonds : angle 5.56415 ( 1260) covalent geometry : bond 0.00231 (10256) covalent geometry : angle 0.50404 (13896) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 71 time to evaluate : 1.069 Fit side-chains REVERT: A 113 GLN cc_start: 0.8459 (pm20) cc_final: 0.8254 (pm20) REVERT: A 264 GLN cc_start: 0.8562 (mt0) cc_final: 0.8284 (tm-30) REVERT: B 264 GLN cc_start: 0.8568 (mt0) cc_final: 0.8294 (tm-30) REVERT: C 113 GLN cc_start: 0.8463 (pm20) cc_final: 0.8255 (pm20) REVERT: C 264 GLN cc_start: 0.8550 (mt0) cc_final: 0.8273 (tm-30) REVERT: D 113 GLN cc_start: 0.8463 (pm20) cc_final: 0.8243 (pm20) REVERT: D 264 GLN cc_start: 0.8566 (mt0) cc_final: 0.8291 (tm-30) outliers start: 21 outliers final: 20 residues processed: 87 average time/residue: 1.4108 time to fit residues: 131.3783 Evaluate side-chains 91 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 71 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 HIS Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain B residue 57 HIS Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain C residue 57 HIS Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 142 ASN Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain D residue 57 HIS Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 142 ASN Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 318 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 59 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 56 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 84 optimal weight: 7.9990 chunk 115 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 = 0.3487 r_free = 0.3487 target = 0.091690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.080293 restraints weight = 17133.597| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.93 r_work: 0.3158 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8925 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10256 Z= 0.151 Angle : 0.569 7.706 13896 Z= 0.310 Chirality : 0.048 0.144 1576 Planarity : 0.006 0.077 1804 Dihedral : 5.487 45.032 1416 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 1.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.62 % Allowed : 17.24 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.24), residues: 1328 helix: 1.29 (0.27), residues: 376 sheet: 0.48 (0.39), residues: 204 loop : -0.57 (0.25), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 87 HIS 0.002 0.001 HIS A 53 PHE 0.007 0.001 PHE B 286 TYR 0.011 0.001 TYR D 314 ARG 0.018 0.001 ARG A 80 Details of bonding type rmsd hydrogen bonds : bond 0.04344 ( 468) hydrogen bonds : angle 5.74664 ( 1260) covalent geometry : bond 0.00359 (10256) covalent geometry : angle 0.56856 (13896) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 72 time to evaluate : 1.128 Fit side-chains REVERT: A 264 GLN cc_start: 0.8571 (mt0) cc_final: 0.8275 (tm-30) REVERT: B 264 GLN cc_start: 0.8573 (mt0) cc_final: 0.8291 (tm-30) REVERT: C 264 GLN cc_start: 0.8553 (mt0) cc_final: 0.8268 (tm-30) REVERT: D 264 GLN cc_start: 0.8576 (mt0) cc_final: 0.8286 (tm-30) outliers start: 28 outliers final: 20 residues processed: 94 average time/residue: 1.4623 time to fit residues: 147.0327 Evaluate side-chains 91 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 71 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 HIS Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain B residue 57 HIS Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain C residue 57 HIS Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 142 ASN Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain D residue 57 HIS Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 142 ASN Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 318 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 14 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 116 optimal weight: 10.0000 chunk 100 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 118 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 123 optimal weight: 8.9990 chunk 65 optimal weight: 2.9990 chunk 114 optimal weight: 0.8980 overall best weight: 1.2582 ------------------------------------------------------------------------------- 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 = 0.3515 r_free = 0.3515 target = 0.093455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.082177 restraints weight = 17124.592| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.92 r_work: 0.3194 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8895 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10256 Z= 0.110 Angle : 0.528 7.294 13896 Z= 0.285 Chirality : 0.046 0.136 1576 Planarity : 0.006 0.080 1804 Dihedral : 5.258 43.138 1416 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 1.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.25 % Allowed : 17.53 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.25), residues: 1328 helix: 1.11 (0.27), residues: 396 sheet: 0.49 (0.39), residues: 212 loop : -0.49 (0.26), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 313 HIS 0.002 0.000 HIS D 179 PHE 0.006 0.001 PHE B 286 TYR 0.008 0.001 TYR D 314 ARG 0.019 0.001 ARG B 80 Details of bonding type rmsd hydrogen bonds : bond 0.03607 ( 468) hydrogen bonds : angle 5.55437 ( 1260) covalent geometry : bond 0.00250 (10256) covalent geometry : angle 0.52754 (13896) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 70 time to evaluate : 1.219 Fit side-chains REVERT: A 264 GLN cc_start: 0.8524 (mt0) cc_final: 0.8236 (tm-30) REVERT: B 264 GLN cc_start: 0.8535 (mt0) cc_final: 0.8249 (tm-30) REVERT: C 264 GLN cc_start: 0.8516 (mt0) cc_final: 0.8224 (tm-30) REVERT: D 264 GLN cc_start: 0.8530 (mt0) cc_final: 0.8241 (tm-30) outliers start: 24 outliers final: 20 residues processed: 89 average time/residue: 1.4641 time to fit residues: 139.5003 Evaluate side-chains 90 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 70 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 HIS Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain B residue 57 HIS Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain C residue 57 HIS Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 142 ASN Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain D residue 57 HIS Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 142 ASN Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 318 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 94 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 chunk 85 optimal weight: 0.0670 chunk 52 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 59 optimal weight: 4.9990 chunk 84 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- 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 = 0.3554 r_free = 0.3554 target = 0.095937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.084508 restraints weight = 17026.947| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.94 r_work: 0.3238 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10256 Z= 0.093 Angle : 0.507 6.888 13896 Z= 0.273 Chirality : 0.045 0.130 1576 Planarity : 0.006 0.081 1804 Dihedral : 4.887 37.336 1416 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.97 % Allowed : 18.09 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.25), residues: 1328 helix: 1.21 (0.27), residues: 396 sheet: 0.55 (0.39), residues: 212 loop : -0.52 (0.26), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 313 HIS 0.001 0.000 HIS D 179 PHE 0.005 0.001 PHE A 233 TYR 0.007 0.001 TYR D 140 ARG 0.019 0.001 ARG A 80 Details of bonding type rmsd hydrogen bonds : bond 0.03072 ( 468) hydrogen bonds : angle 5.36428 ( 1260) covalent geometry : bond 0.00206 (10256) covalent geometry : angle 0.50659 (13896) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8604.87 seconds wall clock time: 150 minutes 30.79 seconds (9030.79 seconds total)