Starting phenix.real_space_refine on Sat Jul 4 11:16:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yfn_72902/07_2026/9yfn_72902.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yfn_72902/07_2026/9yfn_72902.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9yfn_72902/07_2026/9yfn_72902.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yfn_72902/07_2026/9yfn_72902.map" model { file = "/net/cci-nas-00/data/ceres_data/9yfn_72902/07_2026/9yfn_72902.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yfn_72902/07_2026/9yfn_72902.cif" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.028 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: 6 Type Number sf(0) Gaussians P 76 5.49 5 S 44 5.16 5 C 6251 2.51 5 N 1804 2.21 5 O 2068 1.98 5 H 9640 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19883 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 5363 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 14, 'TRANS': 320} Chain breaks: 1 Chain: "B" Number of atoms: 1475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 1475 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 6, 'TRANS': 84} Chain: "D" Number of atoms: 5242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5242 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 13, 'TRANS': 314} Chain breaks: 1 Chain: "E" Number of atoms: 1460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 1460 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 6, 'TRANS': 83} Chain: "F" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1030 Classifications: {'peptide': 61} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 55} Chain: "G" Number of atoms: 2080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 2080 Classifications: {'peptide': 128} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 121} Chain: "H" Number of atoms: 782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 782 Classifications: {'peptide': 47} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 42} Chain: "J" Number of atoms: 2451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 2451 Classifications: {'RNA': 76} Modifications used: {'3*END': 1, 'rna2p_pur': 9, 'rna2p_pyr': 4, 'rna3p_pur': 31, 'rna3p_pyr': 32} Link IDs: {'rna2p': 13, 'rna3p': 62} Chain breaks: 4 Time building chain proxies: 3.26, per 1000 atoms: 0.16 Number of scatterers: 19883 At special positions: 0 Unit cell: (88.596, 112.608, 145.728, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 44 16.00 P 76 15.00 O 2068 8.00 N 1804 7.00 C 6251 6.00 H 9640 1.00 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: 1.61 Conformation dependent library (CDL) restraints added in 487.6 milliseconds 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2010 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 12 sheets defined 30.1% alpha, 21.2% beta 28 base pairs and 40 stacking pairs defined. Time for finding SS restraints: 3.06 Creating SS restraints... Processing helix chain 'A' and resid 55 through 59 Processing helix chain 'A' and resid 79 through 83 removed outlier: 4.023A pdb=" N ARG A 83 " --> pdb=" O PRO A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 91 Processing helix chain 'A' and resid 103 through 116 Processing helix chain 'A' and resid 140 through 149 removed outlier: 3.501A pdb=" N ARG A 143 " --> pdb=" O ARG A 140 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LYS A 146 " --> pdb=" O ARG A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 177 removed outlier: 3.726A pdb=" N VAL A 171 " --> pdb=" O ASN A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 239 Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 281 through 288 Processing helix chain 'A' and resid 292 through 296 removed outlier: 4.038A pdb=" N VAL A 296 " --> pdb=" O GLY A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 314 Processing helix chain 'A' and resid 353 through 360 Processing helix chain 'B' and resid 148 through 153 removed outlier: 4.093A pdb=" N PHE B 152 " --> pdb=" O PRO B 148 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU B 153 " --> pdb=" O LEU B 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 148 through 153' Processing helix chain 'D' and resid 84 through 90 removed outlier: 3.598A pdb=" N VAL D 89 " --> pdb=" O ILE D 85 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LYS D 90 " --> pdb=" O ALA D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 116 removed outlier: 3.596A pdb=" N ILE D 111 " --> pdb=" O VAL D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 149 removed outlier: 4.658A pdb=" N LYS D 146 " --> pdb=" O ARG D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 178 removed outlier: 3.866A pdb=" N VAL D 171 " --> pdb=" O ASN D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 239 Processing helix chain 'D' and resid 264 through 279 Processing helix chain 'D' and resid 281 through 288 Processing helix chain 'D' and resid 292 through 295 Processing helix chain 'D' and resid 307 through 313 Processing helix chain 'D' and resid 353 through 359 Processing helix chain 'E' and resid 129 through 133 Processing helix chain 'E' and resid 148 through 153 removed outlier: 4.102A pdb=" N PHE E 152 " --> pdb=" O PRO E 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 52 removed outlier: 3.853A pdb=" N ILE F 48 " --> pdb=" O HIS F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 59 Processing helix chain 'G' and resid 26 through 33 removed outlier: 3.717A pdb=" N CYS G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 57 Processing helix chain 'G' and resid 66 through 77 Processing helix chain 'G' and resid 90 through 94 removed outlier: 3.818A pdb=" N ILE G 93 " --> pdb=" O PRO G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 105 Processing helix chain 'G' and resid 113 through 121 removed outlier: 3.713A pdb=" N ILE G 117 " --> pdb=" O SER G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 135 through 137 No H-bonds generated for 'chain 'G' and resid 135 through 137' Processing helix chain 'G' and resid 138 through 151 Processing helix chain 'H' and resid 41 through 47 Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 66 removed outlier: 6.651A pdb=" N PHE A 302 " --> pdb=" O LEU A 323 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N TYR A 325 " --> pdb=" O ARG A 300 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ARG A 300 " --> pdb=" O TYR A 325 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LYS A 299 " --> pdb=" O VAL A 336 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N VAL A 338 " --> pdb=" O LYS A 299 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N ILE A 301 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N ILE A 349 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N LEU A 368 " --> pdb=" O ILE A 349 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 120 through 122 removed outlier: 3.935A pdb=" N GLY A 92 " --> pdb=" O ILE A 138 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 131 through 132 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 131 through 132 current: chain 'A' and resid 197 through 210 removed outlier: 5.792A pdb=" N SER A 204 " --> pdb=" O SER A 221 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N SER A 221 " --> pdb=" O SER A 204 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N LEU A 206 " --> pdb=" O TRP A 219 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N TRP A 219 " --> pdb=" O LEU A 206 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 215 through 222 current: chain 'A' and resid 256 through 257 Processing sheet with id=AA4, first strand: chain 'B' and resid 68 through 76 removed outlier: 6.776A pdb=" N ILE B 82 " --> pdb=" O GLY B 74 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N TYR B 118 " --> pdb=" O VAL B 85 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU B 110 " --> pdb=" O SER B 121 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ILE B 97 " --> pdb=" O ILE B 105 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N ILE B 141 " --> pdb=" O PRO B 69 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 90 through 91 Processing sheet with id=AA6, first strand: chain 'D' and resid 65 through 66 removed outlier: 6.338A pdb=" N LYS D 299 " --> pdb=" O VAL D 336 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N VAL D 338 " --> pdb=" O LYS D 299 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N ILE D 301 " --> pdb=" O VAL D 338 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA D 346 " --> pdb=" O ILE D 337 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N VAL D 345 " --> pdb=" O VAL D 371 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N VAL D 371 " --> pdb=" O VAL D 345 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU D 347 " --> pdb=" O LYS D 369 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 91 through 98 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 91 through 98 current: chain 'D' and resid 131 through 139 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 131 through 139 current: chain 'D' and resid 197 through 210 removed outlier: 6.342A pdb=" N VAL D 217 " --> pdb=" O LEU D 207 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N PHE D 209 " --> pdb=" O ILE D 215 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE D 215 " --> pdb=" O PHE D 209 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 215 through 222 current: chain 'D' and resid 256 through 257 Processing sheet with id=AA8, first strand: chain 'E' and resid 68 through 77 removed outlier: 7.178A pdb=" N ILE E 82 " --> pdb=" O GLY E 74 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N THR E 76 " --> pdb=" O ASP E 80 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ASP E 80 " --> pdb=" O THR E 76 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N PHE E 119 " --> pdb=" O ILE E 111 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ILE E 111 " --> pdb=" O PHE E 119 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N SER E 121 " --> pdb=" O ASP E 109 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE E 97 " --> pdb=" O ILE E 105 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N PHE E 139 " --> pdb=" O LEU E 70 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 90 through 91 removed outlier: 3.770A pdb=" N VAL E 90 " --> pdb=" O LEU E 147 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 13 through 16 Processing sheet with id=AB2, first strand: chain 'G' and resid 63 through 65 Processing sheet with id=AB3, first strand: chain 'H' and resid 13 through 16 269 hydrogen bonds defined for protein. 705 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 76 hydrogen bonds 148 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 40 stacking parallelities Total time for adding SS restraints: 4.25 Time building geometry restraints manager: 2.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 9621 1.02 - 1.22: 32 1.22 - 1.42: 4583 1.42 - 1.62: 5949 1.62 - 1.83: 69 Bond restraints: 20254 Sorted by residual: bond pdb=" N VAL G 82 " pdb=" CA VAL G 82 " ideal model delta sigma weight residual 1.459 1.504 -0.046 1.20e-02 6.94e+03 1.45e+01 bond pdb=" N ILE B 105 " pdb=" CA ILE B 105 " ideal model delta sigma weight residual 1.456 1.491 -0.035 9.50e-03 1.11e+04 1.32e+01 bond pdb=" CA SER D 355 " pdb=" CB SER D 355 " ideal model delta sigma weight residual 1.528 1.472 0.057 1.56e-02 4.11e+03 1.32e+01 bond pdb=" C VAL G 82 " pdb=" O VAL G 82 " ideal model delta sigma weight residual 1.237 1.202 0.035 1.11e-02 8.12e+03 1.02e+01 bond pdb=" CA PHE G 83 " pdb=" C PHE G 83 " ideal model delta sigma weight residual 1.521 1.486 0.035 1.17e-02 7.31e+03 8.95e+00 ... (remaining 20249 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 36031 2.17 - 4.33: 578 4.33 - 6.50: 56 6.50 - 8.67: 11 8.67 - 10.83: 4 Bond angle restraints: 36680 Sorted by residual: angle pdb=" N ASP E 126 " pdb=" CA ASP E 126 " pdb=" C ASP E 126 " ideal model delta sigma weight residual 112.54 101.71 10.83 1.22e+00 6.72e-01 7.88e+01 angle pdb=" CA GLY G 80 " pdb=" C GLY G 80 " pdb=" O GLY G 80 " ideal model delta sigma weight residual 120.79 115.50 5.29 8.60e-01 1.35e+00 3.78e+01 angle pdb=" CA PHE B 128 " pdb=" CB PHE B 128 " pdb=" CG PHE B 128 " ideal model delta sigma weight residual 113.80 108.34 5.46 1.00e+00 1.00e+00 2.99e+01 angle pdb=" CA ILE G 81 " pdb=" C ILE G 81 " pdb=" N VAL G 82 " ideal model delta sigma weight residual 116.31 122.49 -6.18 1.14e+00 7.69e-01 2.94e+01 angle pdb=" N ASP G 143 " pdb=" CA ASP G 143 " pdb=" C ASP G 143 " ideal model delta sigma weight residual 113.41 107.15 6.26 1.22e+00 6.72e-01 2.64e+01 ... (remaining 36675 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.38: 9078 35.38 - 70.77: 441 70.77 - 106.15: 45 106.15 - 141.54: 1 141.54 - 176.92: 2 Dihedral angle restraints: 9567 sinusoidal: 5905 harmonic: 3662 Sorted by residual: dihedral pdb=" O4' C J 31 " pdb=" C1' C J 31 " pdb=" N1 C J 31 " pdb=" C2 C J 31 " ideal model delta sinusoidal sigma weight residual 232.00 61.55 170.45 1 1.70e+01 3.46e-03 6.60e+01 dihedral pdb=" CD ARG A 194 " pdb=" NE ARG A 194 " pdb=" CZ ARG A 194 " pdb=" NH1 ARG A 194 " ideal model delta sinusoidal sigma weight residual 0.00 60.16 -60.16 1 1.00e+01 1.00e-02 4.82e+01 dihedral pdb=" O4' C J 70 " pdb=" C1' C J 70 " pdb=" N1 C J 70 " pdb=" C2 C J 70 " ideal model delta sinusoidal sigma weight residual -128.00 -53.73 -74.27 1 1.70e+01 3.46e-03 2.42e+01 ... (remaining 9564 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 1648 0.118 - 0.236: 41 0.236 - 0.354: 1 0.354 - 0.472: 3 0.472 - 0.590: 2 Chirality restraints: 1695 Sorted by residual: chirality pdb=" P A J 30 " pdb=" OP1 A J 30 " pdb=" OP2 A J 30 " pdb=" O5' A J 30 " both_signs ideal model delta sigma weight residual True 2.41 3.00 -0.59 2.00e-01 2.50e+01 8.71e+00 chirality pdb=" P G J 33 " pdb=" OP1 G J 33 " pdb=" OP2 G J 33 " pdb=" O5' G J 33 " both_signs ideal model delta sigma weight residual True 2.41 -2.97 -0.56 2.00e-01 2.50e+01 7.81e+00 chirality pdb=" P A J 65 " pdb=" OP1 A J 65 " pdb=" OP2 A J 65 " pdb=" O5' A J 65 " both_signs ideal model delta sigma weight residual True 2.41 -2.88 -0.47 2.00e-01 2.50e+01 5.55e+00 ... (remaining 1692 not shown) Planarity restraints: 2668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN D 272 " -0.196 2.00e-02 2.50e+03 4.16e-01 2.60e+03 pdb=" CD GLN D 272 " 0.015 2.00e-02 2.50e+03 pdb=" OE1 GLN D 272 " 0.189 2.00e-02 2.50e+03 pdb=" NE2 GLN D 272 " 0.001 2.00e-02 2.50e+03 pdb="HE21 GLN D 272 " -0.700 2.00e-02 2.50e+03 pdb="HE22 GLN D 272 " 0.689 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 194 " -0.792 9.50e-02 1.11e+02 2.65e-01 8.71e+01 pdb=" NE ARG A 194 " 0.067 2.00e-02 2.50e+03 pdb=" CZ ARG A 194 " -0.047 2.00e-02 2.50e+03 pdb=" NH1 ARG A 194 " 0.018 2.00e-02 2.50e+03 pdb=" NH2 ARG A 194 " -0.002 2.00e-02 2.50e+03 pdb="HH11 ARG A 194 " -0.000 2.00e-02 2.50e+03 pdb="HH12 ARG A 194 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG A 194 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 194 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 179 " 0.567 9.50e-02 1.11e+02 1.90e-01 4.57e+01 pdb=" NE ARG A 179 " -0.049 2.00e-02 2.50e+03 pdb=" CZ ARG A 179 " 0.037 2.00e-02 2.50e+03 pdb=" NH1 ARG A 179 " -0.018 2.00e-02 2.50e+03 pdb=" NH2 ARG A 179 " 0.003 2.00e-02 2.50e+03 pdb="HH11 ARG A 179 " -0.000 2.00e-02 2.50e+03 pdb="HH12 ARG A 179 " 0.001 2.00e-02 2.50e+03 pdb="HH21 ARG A 179 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 179 " 0.001 2.00e-02 2.50e+03 ... (remaining 2665 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.28: 4016 2.28 - 2.86: 43770 2.86 - 3.44: 50257 3.44 - 4.02: 72284 4.02 - 4.60: 107574 Nonbonded interactions: 277901 Sorted by model distance: nonbonded pdb=" HG1 THR F 16 " pdb=" H ALA F 18 " model vdw 1.705 2.100 nonbonded pdb=" OD2 ASP F 39 " pdb="HH22 ARG F 45 " model vdw 1.739 2.450 nonbonded pdb=" HG1 THR D 131 " pdb=" H GLY D 132 " model vdw 1.740 2.100 nonbonded pdb=" H SER G 34 " pdb=" O GLY G 86 " model vdw 1.765 2.450 nonbonded pdb=" O ARG D 83 " pdb="HH22 ARG D 285 " model vdw 1.788 2.450 ... (remaining 277896 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' and (resid 55 through 188 or (resid 196 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD1 or name CD2 or name HA or name H \ B2 or name HB3 or name HG or name HD11 or name HD12 or name HD13 or name HD21 or \ name HD22 or name HD23)) or resid 197 through 389)) selection = chain 'D' } ncs_group { reference = (chain 'B' and ((resid 65 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name OE1 or name OE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3)) or resid 66 through 153)) selection = (chain 'E' and resid 65 through 153) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.780 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: 0.130 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 20.830 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6359 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 10614 Z= 0.248 Angle : 0.803 10.833 14690 Z= 0.498 Chirality : 0.053 0.590 1695 Planarity : 0.015 0.356 1584 Dihedral : 19.494 176.923 4527 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.53 % Allowed : 24.84 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.25), residues: 1062 helix: 0.10 (0.32), residues: 273 sheet: -1.33 (0.36), residues: 176 loop : -0.60 (0.25), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.070 0.003 ARG F 34 TYR 0.025 0.002 TYR A 155 PHE 0.029 0.002 PHE B 128 TRP 0.026 0.003 TRP D 273 HIS 0.007 0.001 HIS A 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.25 (10614) covalent geometry : angle 0.80289 / 0.50 (14690) hydrogen bonds : bond 0.14751 / 9.34 ( 345) hydrogen bonds : angle 7.51356 / 5.30 ( 853) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 187 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 108 ILE cc_start: 0.6785 (OUTLIER) cc_final: 0.6265 (mm) REVERT: B 152 PHE cc_start: 0.6215 (m-80) cc_final: 0.5645 (m-80) REVERT: D 169 LYS cc_start: 0.6661 (mttt) cc_final: 0.6457 (mttt) REVERT: D 199 ARG cc_start: 0.7687 (mpt180) cc_final: 0.7270 (mmt90) REVERT: D 352 MET cc_start: 0.6279 (mtp) cc_final: 0.5998 (mtp) REVERT: F 45 ARG cc_start: 0.7693 (mtm-85) cc_final: 0.7348 (ttp-110) REVERT: G 51 LYS cc_start: 0.8013 (mmtt) cc_final: 0.7704 (mmtt) REVERT: H 2 TYR cc_start: 0.7288 (m-80) cc_final: 0.6992 (m-80) outliers start: 5 outliers final: 3 residues processed: 189 average time/residue: 0.2763 time to fit residues: 69.5538 Evaluate side-chains 188 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 184 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain D residue 231 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 10.0000 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 7.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 266 HIS F 59 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.177743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.147697 restraints weight = 37678.034| |-----------------------------------------------------------------------------| r_work (start): 0.4071 rms_B_bonded: 2.36 r_work: 0.3947 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6438 moved from start: 0.0904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 10614 Z= 0.216 Angle : 0.589 5.375 14690 Z= 0.321 Chirality : 0.041 0.174 1695 Planarity : 0.005 0.062 1584 Dihedral : 18.768 174.472 2373 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.70 % Allowed : 23.67 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.25), residues: 1062 helix: 0.06 (0.31), residues: 276 sheet: -1.48 (0.35), residues: 189 loop : -0.68 (0.24), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 194 TYR 0.027 0.002 TYR A 155 PHE 0.026 0.003 PHE D 218 TRP 0.013 0.002 TRP D 273 HIS 0.008 0.002 HIS A 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.22 (10614) covalent geometry : angle 0.58874 / 0.32 (14690) hydrogen bonds : bond 0.05116 / 3.40 ( 345) hydrogen bonds : angle 5.96667 / 4.25 ( 853) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 195 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 GLU cc_start: 0.7541 (mt-10) cc_final: 0.7304 (mt-10) REVERT: A 367 LYS cc_start: 0.7915 (ttpt) cc_final: 0.7611 (ttpp) REVERT: B 152 PHE cc_start: 0.6314 (m-80) cc_final: 0.5772 (m-80) REVERT: B 153 LEU cc_start: 0.6658 (tp) cc_final: 0.6404 (tp) REVERT: F 45 ARG cc_start: 0.7730 (mtm-85) cc_final: 0.7011 (ttm-80) REVERT: F 57 THR cc_start: 0.6531 (m) cc_final: 0.4589 (t) REVERT: G 51 LYS cc_start: 0.8044 (mmtt) cc_final: 0.7748 (mmtt) REVERT: G 114 ARG cc_start: 0.5989 (ttp-110) cc_final: 0.5457 (ptm-80) REVERT: G 144 GLU cc_start: 0.6557 (OUTLIER) cc_final: 0.6346 (tm-30) REVERT: H 2 TYR cc_start: 0.7398 (m-80) cc_final: 0.7119 (m-80) outliers start: 16 outliers final: 10 residues processed: 202 average time/residue: 0.2762 time to fit residues: 74.3816 Evaluate side-chains 199 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 188 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 151 ARG Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 223 GLU Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain F residue 13 ARG Chi-restraints excluded: chain G residue 144 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 101 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 35 optimal weight: 0.0270 chunk 63 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 109 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 overall best weight: 1.4042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 256 GLN F 59 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.176004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.146101 restraints weight = 38071.517| |-----------------------------------------------------------------------------| r_work (start): 0.4088 rms_B_bonded: 2.36 r_work: 0.3963 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6474 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 10614 Z= 0.211 Angle : 0.568 5.616 14690 Z= 0.305 Chirality : 0.041 0.161 1695 Planarity : 0.005 0.067 1584 Dihedral : 18.704 178.475 2370 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.80 % Allowed : 22.82 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.24), residues: 1062 helix: -0.04 (0.30), residues: 276 sheet: -1.83 (0.33), residues: 193 loop : -0.72 (0.24), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 13 TYR 0.026 0.002 TYR A 155 PHE 0.027 0.002 PHE D 218 TRP 0.010 0.002 TRP D 219 HIS 0.011 0.002 HIS F 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.21 (10614) covalent geometry : angle 0.56838 / 0.31 (14690) hydrogen bonds : bond 0.04939 / 3.25 ( 345) hydrogen bonds : angle 5.77068 / 4.10 ( 853) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 189 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 GLU cc_start: 0.7541 (mt-10) cc_final: 0.7316 (mt-10) REVERT: A 367 LYS cc_start: 0.7979 (ttpt) cc_final: 0.7720 (ttpp) REVERT: B 152 PHE cc_start: 0.6380 (m-80) cc_final: 0.5827 (m-80) REVERT: B 153 LEU cc_start: 0.6790 (tp) cc_final: 0.6556 (tp) REVERT: D 343 GLU cc_start: 0.7130 (mt-10) cc_final: 0.6866 (mt-10) REVERT: F 45 ARG cc_start: 0.7782 (mtm-85) cc_final: 0.7403 (mtm-85) REVERT: F 57 THR cc_start: 0.6467 (m) cc_final: 0.4564 (t) REVERT: G 51 LYS cc_start: 0.8066 (mmtt) cc_final: 0.7770 (mmtt) REVERT: H 2 TYR cc_start: 0.7439 (m-80) cc_final: 0.7206 (m-80) outliers start: 17 outliers final: 11 residues processed: 197 average time/residue: 0.2820 time to fit residues: 73.6099 Evaluate side-chains 198 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 187 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 151 ARG Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain F residue 13 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 52 optimal weight: 0.6980 chunk 32 optimal weight: 0.1980 chunk 83 optimal weight: 3.9990 chunk 71 optimal weight: 0.2980 chunk 107 optimal weight: 7.9990 chunk 78 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 59 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.177064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.147479 restraints weight = 37840.666| |-----------------------------------------------------------------------------| r_work (start): 0.4064 rms_B_bonded: 2.35 r_work: 0.3939 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6457 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10614 Z= 0.132 Angle : 0.513 5.365 14690 Z= 0.273 Chirality : 0.040 0.153 1695 Planarity : 0.004 0.044 1584 Dihedral : 18.643 179.315 2368 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.59 % Allowed : 22.61 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.24), residues: 1062 helix: 0.19 (0.30), residues: 279 sheet: -1.83 (0.34), residues: 180 loop : -0.66 (0.24), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 13 TYR 0.018 0.001 TYR A 155 PHE 0.020 0.002 PHE D 218 TRP 0.010 0.001 TRP D 219 HIS 0.013 0.001 HIS F 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (10614) covalent geometry : angle 0.51310 / 0.27 (14690) hydrogen bonds : bond 0.04298 / 2.86 ( 345) hydrogen bonds : angle 5.47774 / 3.87 ( 853) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 189 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 GLU cc_start: 0.7506 (mt-10) cc_final: 0.7266 (mt-10) REVERT: A 291 LEU cc_start: 0.7903 (pp) cc_final: 0.7645 (pp) REVERT: A 292 GLU cc_start: 0.7736 (mp0) cc_final: 0.7150 (mp0) REVERT: A 367 LYS cc_start: 0.7932 (ttpt) cc_final: 0.7674 (ttpp) REVERT: B 152 PHE cc_start: 0.6336 (m-80) cc_final: 0.5758 (m-80) REVERT: B 153 LEU cc_start: 0.6836 (tp) cc_final: 0.6599 (tp) REVERT: D 113 ARG cc_start: 0.7417 (mtt180) cc_final: 0.7217 (mtt90) REVERT: D 343 GLU cc_start: 0.7108 (mt-10) cc_final: 0.6829 (mt-10) REVERT: F 45 ARG cc_start: 0.7758 (mtm-85) cc_final: 0.7394 (mtm-85) REVERT: F 57 THR cc_start: 0.6493 (m) cc_final: 0.4575 (t) REVERT: G 114 ARG cc_start: 0.5958 (ttp-110) cc_final: 0.5425 (ptm-80) REVERT: H 2 TYR cc_start: 0.7457 (m-80) cc_final: 0.7223 (m-80) outliers start: 15 outliers final: 11 residues processed: 200 average time/residue: 0.2692 time to fit residues: 71.9858 Evaluate side-chains 198 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 187 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 246 ILE Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 151 ARG Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 223 GLU Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain F residue 13 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 53 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 46 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 85 optimal weight: 0.0980 chunk 106 optimal weight: 8.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 59 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.178635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.149241 restraints weight = 37564.290| |-----------------------------------------------------------------------------| r_work (start): 0.4058 rms_B_bonded: 2.36 r_work: 0.3932 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6469 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10614 Z= 0.138 Angle : 0.510 6.434 14690 Z= 0.271 Chirality : 0.040 0.149 1695 Planarity : 0.004 0.048 1584 Dihedral : 18.589 179.930 2368 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.91 % Allowed : 22.08 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.25), residues: 1062 helix: 0.36 (0.31), residues: 279 sheet: -1.86 (0.34), residues: 180 loop : -0.60 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 13 TYR 0.018 0.001 TYR A 155 PHE 0.021 0.002 PHE D 218 TRP 0.010 0.001 TRP D 219 HIS 0.013 0.001 HIS F 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (10614) covalent geometry : angle 0.51009 / 0.27 (14690) hydrogen bonds : bond 0.04220 / 2.82 ( 345) hydrogen bonds : angle 5.35006 / 3.77 ( 853) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 188 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 367 LYS cc_start: 0.7944 (ttpt) cc_final: 0.7683 (ttpp) REVERT: B 152 PHE cc_start: 0.6410 (m-80) cc_final: 0.5839 (m-80) REVERT: B 153 LEU cc_start: 0.6892 (tp) cc_final: 0.6661 (tp) REVERT: D 106 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7233 (tm-30) REVERT: D 113 ARG cc_start: 0.7443 (mtt180) cc_final: 0.7224 (mtt90) REVERT: D 343 GLU cc_start: 0.7115 (mt-10) cc_final: 0.6827 (mt-10) REVERT: F 45 ARG cc_start: 0.7773 (mtm-85) cc_final: 0.7396 (mtm-85) REVERT: F 57 THR cc_start: 0.6463 (m) cc_final: 0.4558 (t) REVERT: G 114 ARG cc_start: 0.5992 (ttp-110) cc_final: 0.5508 (ptm-80) REVERT: H 2 TYR cc_start: 0.7499 (m-80) cc_final: 0.7273 (m-80) outliers start: 18 outliers final: 11 residues processed: 200 average time/residue: 0.2563 time to fit residues: 68.3747 Evaluate side-chains 198 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 186 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 151 ARG Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain F residue 13 ARG Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 67 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 110 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 69 optimal weight: 0.0370 chunk 50 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 93 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.1062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.176071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.146226 restraints weight = 37774.634| |-----------------------------------------------------------------------------| r_work (start): 0.4040 rms_B_bonded: 2.38 r_work: 0.3913 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6497 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10614 Z= 0.174 Angle : 0.534 6.528 14690 Z= 0.284 Chirality : 0.041 0.153 1695 Planarity : 0.004 0.058 1584 Dihedral : 18.580 179.194 2368 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.80 % Allowed : 21.97 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.25), residues: 1062 helix: 0.28 (0.31), residues: 273 sheet: -1.86 (0.36), residues: 169 loop : -0.64 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 13 TYR 0.023 0.002 TYR A 155 PHE 0.026 0.002 PHE D 218 TRP 0.010 0.002 TRP D 219 HIS 0.013 0.002 HIS F 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 (10614) covalent geometry : angle 0.53412 / 0.28 (14690) hydrogen bonds : bond 0.04248 / 2.84 ( 345) hydrogen bonds : angle 5.32113 / 3.76 ( 853) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 190 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 367 LYS cc_start: 0.7945 (ttpt) cc_final: 0.7641 (ttpp) REVERT: A 370 ARG cc_start: 0.6491 (tpt170) cc_final: 0.6256 (tpt170) REVERT: B 152 PHE cc_start: 0.6470 (m-80) cc_final: 0.5892 (m-80) REVERT: D 106 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7253 (tm-30) REVERT: D 113 ARG cc_start: 0.7462 (mtt180) cc_final: 0.7246 (mtt90) REVERT: D 199 ARG cc_start: 0.7354 (mmt90) cc_final: 0.6962 (mmt90) REVERT: D 286 ARG cc_start: 0.7499 (mmt90) cc_final: 0.7283 (mmt90) REVERT: D 343 GLU cc_start: 0.7134 (mt-10) cc_final: 0.6837 (mt-10) REVERT: F 57 THR cc_start: 0.6547 (m) cc_final: 0.4603 (t) REVERT: G 114 ARG cc_start: 0.6020 (ttp-110) cc_final: 0.5525 (ptm-80) REVERT: H 2 TYR cc_start: 0.7502 (m-80) cc_final: 0.7297 (m-80) outliers start: 17 outliers final: 14 residues processed: 199 average time/residue: 0.2807 time to fit residues: 74.2845 Evaluate side-chains 205 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 190 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 151 ARG Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 223 GLU Chi-restraints excluded: chain D residue 238 MET Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain F residue 13 ARG Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 67 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 101 optimal weight: 0.2980 chunk 25 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 46 optimal weight: 0.0270 chunk 14 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 48 optimal weight: 0.0670 chunk 13 optimal weight: 0.5980 chunk 77 optimal weight: 0.0570 overall best weight: 0.2094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 59 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.179713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.150244 restraints weight = 37857.063| |-----------------------------------------------------------------------------| r_work (start): 0.4092 rms_B_bonded: 2.38 r_work: 0.3967 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6448 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10614 Z= 0.086 Angle : 0.483 6.010 14690 Z= 0.254 Chirality : 0.039 0.140 1695 Planarity : 0.003 0.033 1584 Dihedral : 18.569 178.851 2368 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.38 % Allowed : 22.29 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.25), residues: 1062 helix: 0.66 (0.32), residues: 273 sheet: -1.84 (0.36), residues: 169 loop : -0.47 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 179 TYR 0.012 0.001 TYR A 88 PHE 0.014 0.001 PHE D 218 TRP 0.011 0.001 TRP D 219 HIS 0.005 0.001 HIS F 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00198 / 0.09 (10614) covalent geometry : angle 0.48323 / 0.25 (14690) hydrogen bonds : bond 0.03874 / 2.58 ( 345) hydrogen bonds : angle 5.08726 / 3.56 ( 853) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 188 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 GLU cc_start: 0.7785 (mp0) cc_final: 0.7211 (mp0) REVERT: A 357 MET cc_start: 0.7673 (OUTLIER) cc_final: 0.7087 (mmt) REVERT: A 367 LYS cc_start: 0.7916 (ttpt) cc_final: 0.7658 (ttpp) REVERT: B 152 PHE cc_start: 0.6390 (m-80) cc_final: 0.5839 (m-80) REVERT: D 343 GLU cc_start: 0.7110 (mt-10) cc_final: 0.6819 (mt-10) REVERT: F 57 THR cc_start: 0.6444 (m) cc_final: 0.4572 (t) REVERT: G 114 ARG cc_start: 0.5889 (ttp-110) cc_final: 0.5417 (ptm-80) REVERT: H 2 TYR cc_start: 0.7456 (m-80) cc_final: 0.7216 (m-80) outliers start: 13 outliers final: 12 residues processed: 196 average time/residue: 0.2480 time to fit residues: 65.2653 Evaluate side-chains 200 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 187 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 151 ARG Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 223 GLU Chi-restraints excluded: chain D residue 238 MET Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain F residue 13 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 111 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 107 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 0 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.175192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.145395 restraints weight = 37837.853| |-----------------------------------------------------------------------------| r_work (start): 0.4033 rms_B_bonded: 2.39 r_work: 0.3905 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6520 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 10614 Z= 0.216 Angle : 0.556 5.509 14690 Z= 0.298 Chirality : 0.041 0.158 1695 Planarity : 0.004 0.069 1584 Dihedral : 18.551 178.485 2368 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.52 % Favored : 95.39 % Rotamer: Outliers : 2.02 % Allowed : 22.29 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.25), residues: 1062 helix: 0.25 (0.31), residues: 270 sheet: -1.85 (0.37), residues: 170 loop : -0.66 (0.24), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 13 TYR 0.029 0.002 TYR A 155 PHE 0.030 0.002 PHE B 119 TRP 0.010 0.002 TRP D 219 HIS 0.010 0.002 HIS A 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.22 (10614) covalent geometry : angle 0.55596 / 0.30 (14690) hydrogen bonds : bond 0.04334 / 2.91 ( 345) hydrogen bonds : angle 5.33001 / 3.77 ( 853) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 196 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 MET cc_start: 0.7589 (OUTLIER) cc_final: 0.7039 (mmt) REVERT: A 367 LYS cc_start: 0.7952 (ttpt) cc_final: 0.7642 (ttpp) REVERT: A 370 ARG cc_start: 0.6547 (tpt170) cc_final: 0.6322 (tpt170) REVERT: B 152 PHE cc_start: 0.6482 (m-80) cc_final: 0.5938 (m-80) REVERT: D 106 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7218 (tm-30) REVERT: D 343 GLU cc_start: 0.7130 (mt-10) cc_final: 0.6832 (mt-10) REVERT: F 57 THR cc_start: 0.6578 (m) cc_final: 0.4630 (t) REVERT: G 114 ARG cc_start: 0.6015 (ttp-110) cc_final: 0.5536 (ptm-80) REVERT: H 2 TYR cc_start: 0.7535 (m-80) cc_final: 0.7334 (m-80) outliers start: 19 outliers final: 16 residues processed: 206 average time/residue: 0.2805 time to fit residues: 77.2517 Evaluate side-chains 210 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 192 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 151 ARG Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 223 GLU Chi-restraints excluded: chain D residue 238 MET Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain F residue 13 ARG Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 67 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 24 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 18 optimal weight: 0.4980 chunk 83 optimal weight: 1.9990 chunk 111 optimal weight: 10.0000 chunk 28 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 40 optimal weight: 10.0000 chunk 26 optimal weight: 0.5980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 59 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.177825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.148025 restraints weight = 37498.057| |-----------------------------------------------------------------------------| r_work (start): 0.4042 rms_B_bonded: 2.36 r_work: 0.3914 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6508 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10614 Z= 0.153 Angle : 0.527 5.425 14690 Z= 0.280 Chirality : 0.040 0.152 1695 Planarity : 0.004 0.051 1584 Dihedral : 18.570 178.002 2368 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.52 % Favored : 95.39 % Rotamer: Outliers : 1.91 % Allowed : 22.29 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.25), residues: 1062 helix: 0.30 (0.31), residues: 270 sheet: -1.93 (0.35), residues: 178 loop : -0.68 (0.24), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 13 TYR 0.021 0.001 TYR A 155 PHE 0.024 0.002 PHE D 218 TRP 0.011 0.002 TRP D 219 HIS 0.006 0.001 HIS A 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (10614) covalent geometry : angle 0.52685 / 0.28 (14690) hydrogen bonds : bond 0.04129 / 2.77 ( 345) hydrogen bonds : angle 5.21811 / 3.68 ( 853) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 196 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 MET cc_start: 0.7657 (OUTLIER) cc_final: 0.7025 (mmt) REVERT: A 367 LYS cc_start: 0.7931 (ttpt) cc_final: 0.7631 (ttpp) REVERT: A 370 ARG cc_start: 0.6541 (tpt170) cc_final: 0.6316 (tpt170) REVERT: B 152 PHE cc_start: 0.6477 (m-80) cc_final: 0.5940 (m-80) REVERT: D 106 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7178 (tm-30) REVERT: D 199 ARG cc_start: 0.7994 (mpt180) cc_final: 0.7612 (mmt90) REVERT: D 343 GLU cc_start: 0.7141 (mt-10) cc_final: 0.6829 (mt-10) REVERT: F 57 THR cc_start: 0.6591 (m) cc_final: 0.6085 (p) REVERT: G 114 ARG cc_start: 0.5980 (ttp-110) cc_final: 0.5504 (ptm-80) REVERT: H 2 TYR cc_start: 0.7493 (m-80) cc_final: 0.7270 (m-80) outliers start: 18 outliers final: 13 residues processed: 207 average time/residue: 0.2659 time to fit residues: 73.9660 Evaluate side-chains 209 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 194 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 283 TYR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 151 ARG Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 223 GLU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 238 MET Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain F residue 13 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 98 optimal weight: 3.9990 chunk 106 optimal weight: 8.9990 chunk 77 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 92 optimal weight: 0.1980 chunk 10 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 48 optimal weight: 0.0170 chunk 93 optimal weight: 0.5980 overall best weight: 0.9622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.175725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.145903 restraints weight = 37724.698| |-----------------------------------------------------------------------------| r_work (start): 0.4043 rms_B_bonded: 2.38 r_work: 0.3915 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6510 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10614 Z= 0.157 Angle : 0.529 5.913 14690 Z= 0.282 Chirality : 0.040 0.155 1695 Planarity : 0.004 0.053 1584 Dihedral : 18.568 177.689 2368 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.90 % Favored : 95.01 % Rotamer: Outliers : 1.91 % Allowed : 22.40 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.25), residues: 1062 helix: 0.31 (0.31), residues: 270 sheet: -1.92 (0.35), residues: 178 loop : -0.71 (0.24), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 13 TYR 0.023 0.002 TYR A 155 PHE 0.025 0.002 PHE D 218 TRP 0.011 0.002 TRP D 219 HIS 0.007 0.001 HIS A 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 (10614) covalent geometry : angle 0.52949 / 0.28 (14690) hydrogen bonds : bond 0.04090 / 2.74 ( 345) hydrogen bonds : angle 5.22357 / 3.69 ( 853) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 193 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 MET cc_start: 0.7630 (OUTLIER) cc_final: 0.6997 (mmt) REVERT: A 367 LYS cc_start: 0.7945 (ttpt) cc_final: 0.7634 (ttpp) REVERT: A 370 ARG cc_start: 0.6559 (tpt170) cc_final: 0.6326 (tpt170) REVERT: B 152 PHE cc_start: 0.6486 (m-80) cc_final: 0.5955 (m-80) REVERT: D 106 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7102 (tm-30) REVERT: D 199 ARG cc_start: 0.7967 (mpt180) cc_final: 0.7581 (mmt90) REVERT: D 343 GLU cc_start: 0.7152 (mt-10) cc_final: 0.6865 (mt-10) REVERT: F 57 THR cc_start: 0.6557 (m) cc_final: 0.6056 (p) REVERT: G 114 ARG cc_start: 0.5971 (ttp-110) cc_final: 0.5495 (ptm-80) REVERT: H 2 TYR cc_start: 0.7500 (m-80) cc_final: 0.7274 (m-80) outliers start: 18 outliers final: 16 residues processed: 203 average time/residue: 0.2736 time to fit residues: 74.3005 Evaluate side-chains 211 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 193 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 283 TYR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 151 ARG Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 223 GLU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 238 MET Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain F residue 13 ARG Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 67 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 43 optimal weight: 0.0470 chunk 30 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 39 optimal weight: 0.2980 chunk 88 optimal weight: 1.9990 overall best weight: 0.6480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.178236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.148619 restraints weight = 37703.309| |-----------------------------------------------------------------------------| r_work (start): 0.4093 rms_B_bonded: 2.36 r_work: 0.3964 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6488 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10614 Z= 0.116 Angle : 0.506 5.755 14690 Z= 0.268 Chirality : 0.040 0.149 1695 Planarity : 0.004 0.038 1584 Dihedral : 18.560 177.288 2368 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.05 % Favored : 95.86 % Rotamer: Outliers : 1.91 % Allowed : 22.61 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.25), residues: 1062 helix: 0.46 (0.31), residues: 270 sheet: -1.83 (0.36), residues: 178 loop : -0.68 (0.24), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 13 TYR 0.016 0.001 TYR A 155 PHE 0.019 0.001 PHE D 218 TRP 0.012 0.001 TRP D 219 HIS 0.005 0.001 HIS A 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (10614) covalent geometry : angle 0.50613 / 0.27 (14690) hydrogen bonds : bond 0.03882 / 2.60 ( 345) hydrogen bonds : angle 5.10997 / 3.60 ( 853) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6393.89 seconds wall clock time: 109 minutes 1.50 seconds (6541.50 seconds total)