Starting phenix.real_space_refine on Thu Feb 5 21:00:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yfn_72902/02_2026/9yfn_72902.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yfn_72902/02_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_72902/02_2026/9yfn_72902.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yfn_72902/02_2026/9yfn_72902.map" model { file = "/net/cci-nas-00/data/ceres_data/9yfn_72902/02_2026/9yfn_72902.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yfn_72902/02_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-2.0-5952/lib/python3.9/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: 3.84, per 1000 atoms: 0.19 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: 1.88 Conformation dependent library (CDL) restraints added in 488.9 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: 3.61 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: 4.88 Time building geometry restraints manager: 2.57 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: 2.240 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: 0.120 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 23.380 Find NCS groups from input model: 0.190 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6234 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= 0.230 Angle : 0.803 10.833 14690 Z= 0.453 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 covalent geometry : bond 0.00425 (10614) covalent geometry : angle 0.80286 (14690) hydrogen bonds : bond 0.14751 ( 345) hydrogen bonds : angle 7.51356 ( 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 : 0.502 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: 0.3063 time to fit residues: 75.8770 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 : 0.614 ------------------------------------------------------------------------------- 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: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4430 r_free = 0.4430 target = 0.178289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.148468 restraints weight = 37207.882| |-----------------------------------------------------------------------------| r_work (start): 0.4063 rms_B_bonded: 2.33 r_work: 0.3937 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6354 moved from start: 0.1326 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= 0.217 Angle : 0.610 5.495 14690 Z= 0.317 Chirality : 0.042 0.169 1695 Planarity : 0.005 0.068 1584 Dihedral : 18.705 178.453 2373 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.59 % Allowed : 23.25 % Favored : 75.16 % 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: -1.06 (0.25), residues: 1062 helix: 0.09 (0.30), residues: 279 sheet: -1.69 (0.34), residues: 192 loop : -0.66 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 13 TYR 0.030 0.002 TYR A 155 PHE 0.031 0.002 PHE D 218 TRP 0.010 0.002 TRP B 75 HIS 0.014 0.002 HIS G 96 Details of bonding type rmsd covalent geometry : bond 0.00486 (10614) covalent geometry : angle 0.61011 (14690) hydrogen bonds : bond 0.04473 ( 345) hydrogen bonds : angle 5.71135 ( 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 215 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 200 time to evaluate : 0.486 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 291 LEU cc_start: 0.7828 (pp) cc_final: 0.7530 (pp) REVERT: A 292 GLU cc_start: 0.7702 (mp0) cc_final: 0.7091 (mp0) REVERT: A 367 LYS cc_start: 0.7912 (ttpt) cc_final: 0.7658 (ttpp) REVERT: B 152 PHE cc_start: 0.6399 (m-80) cc_final: 0.5854 (m-80) REVERT: B 153 LEU cc_start: 0.6872 (tp) cc_final: 0.6632 (tp) REVERT: D 343 GLU cc_start: 0.7117 (mt-10) cc_final: 0.6856 (mt-10) REVERT: F 45 ARG cc_start: 0.7734 (mtm-85) cc_final: 0.7022 (ttp-170) REVERT: F 57 THR cc_start: 0.6514 (m) cc_final: 0.4610 (t) REVERT: G 51 LYS cc_start: 0.8051 (mmtt) cc_final: 0.7755 (mmtt) REVERT: G 143 ASP cc_start: 0.7949 (m-30) cc_final: 0.7725 (m-30) REVERT: H 2 TYR cc_start: 0.7385 (m-80) cc_final: 0.7163 (m-80) outliers start: 15 outliers final: 8 residues processed: 209 average time/residue: 0.3033 time to fit residues: 82.9524 Evaluate side-chains 203 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 195 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 204 SER 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 D residue 163 SER Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain F residue 13 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 101 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 103 optimal weight: 0.3980 chunk 45 optimal weight: 3.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 59 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.174723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.144716 restraints weight = 37958.254| |-----------------------------------------------------------------------------| r_work (start): 0.4019 rms_B_bonded: 2.38 r_work: 0.3892 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6415 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 10614 Z= 0.223 Angle : 0.613 5.895 14690 Z= 0.319 Chirality : 0.042 0.174 1695 Planarity : 0.005 0.073 1584 Dihedral : 18.660 178.403 2368 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.34 % Allowed : 22.40 % Favored : 75.27 % 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: -1.14 (0.24), residues: 1062 helix: 0.02 (0.30), residues: 270 sheet: -1.74 (0.36), residues: 170 loop : -0.76 (0.24), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 13 TYR 0.026 0.002 TYR A 155 PHE 0.032 0.002 PHE D 218 TRP 0.012 0.002 TRP D 219 HIS 0.012 0.002 HIS A 298 Details of bonding type rmsd covalent geometry : bond 0.00497 (10614) covalent geometry : angle 0.61328 (14690) hydrogen bonds : bond 0.04593 ( 345) hydrogen bonds : angle 5.62593 ( 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 218 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 196 time to evaluate : 0.511 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: 0.7767 (mp0) cc_final: 0.7186 (mp0) REVERT: A 367 LYS cc_start: 0.7922 (ttpt) cc_final: 0.7682 (ttpp) REVERT: B 152 PHE cc_start: 0.6518 (m-80) cc_final: 0.5930 (m-80) REVERT: D 286 ARG cc_start: 0.7464 (mmt90) cc_final: 0.7221 (mmt90) REVERT: D 343 GLU cc_start: 0.7176 (mt-10) cc_final: 0.6868 (mt-10) REVERT: F 45 ARG cc_start: 0.7860 (mtm-85) cc_final: 0.7435 (mtm-85) REVERT: F 57 THR cc_start: 0.6524 (m) cc_final: 0.4604 (t) REVERT: G 51 LYS cc_start: 0.8099 (mmtt) cc_final: 0.7806 (mmtt) REVERT: H 2 TYR cc_start: 0.7487 (m-80) cc_final: 0.7272 (m-80) outliers start: 22 outliers final: 10 residues processed: 210 average time/residue: 0.3020 time to fit residues: 82.8140 Evaluate side-chains 202 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 192 time to evaluate : 0.478 ------------------------------------------------------------------------------- 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 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 223 GLU Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain F residue 13 ARG Chi-restraints excluded: chain G residue 67 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 52 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 49 optimal weight: 0.0970 chunk 102 optimal weight: 1.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.174578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.145006 restraints weight = 37649.221| |-----------------------------------------------------------------------------| r_work (start): 0.4030 rms_B_bonded: 2.37 r_work: 0.3899 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6416 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10614 Z= 0.187 Angle : 0.571 5.795 14690 Z= 0.295 Chirality : 0.041 0.173 1695 Planarity : 0.004 0.062 1584 Dihedral : 18.646 177.078 2368 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.34 % Allowed : 23.14 % Favored : 74.52 % 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: -1.09 (0.24), residues: 1062 helix: 0.12 (0.31), residues: 270 sheet: -1.74 (0.36), residues: 170 loop : -0.75 (0.24), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 13 TYR 0.022 0.002 TYR A 155 PHE 0.030 0.002 PHE D 218 TRP 0.014 0.002 TRP D 219 HIS 0.009 0.002 HIS A 298 Details of bonding type rmsd covalent geometry : bond 0.00420 (10614) covalent geometry : angle 0.57069 (14690) hydrogen bonds : bond 0.04087 ( 345) hydrogen bonds : angle 5.39589 ( 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 222 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 200 time to evaluate : 0.564 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 292 GLU cc_start: 0.7836 (mp0) cc_final: 0.7303 (mp0) REVERT: A 367 LYS cc_start: 0.7934 (ttpt) cc_final: 0.7670 (ttpp) REVERT: B 152 PHE cc_start: 0.6557 (m-80) cc_final: 0.5996 (m-80) REVERT: D 343 GLU cc_start: 0.7157 (mt-10) cc_final: 0.6850 (mt-10) REVERT: F 45 ARG cc_start: 0.7805 (mtm-85) cc_final: 0.7370 (mtm-85) REVERT: F 57 THR cc_start: 0.6484 (m) cc_final: 0.5996 (p) REVERT: G 51 LYS cc_start: 0.8115 (mmtt) cc_final: 0.7818 (mmtt) REVERT: G 114 ARG cc_start: 0.6056 (ttp-110) cc_final: 0.5490 (ptm-80) REVERT: H 2 TYR cc_start: 0.7608 (m-80) cc_final: 0.7408 (m-80) outliers start: 22 outliers final: 16 residues processed: 213 average time/residue: 0.3067 time to fit residues: 85.2085 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 : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 283 TYR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain B residue 84 LYS 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 144 LEU Chi-restraints excluded: chain D residue 223 GLU Chi-restraints excluded: chain D residue 335 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 53 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 69 optimal weight: 0.6980 chunk 40 optimal weight: 5.9990 chunk 46 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 85 optimal weight: 0.0170 chunk 106 optimal weight: 4.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.176286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.146540 restraints weight = 37442.751| |-----------------------------------------------------------------------------| r_work (start): 0.4046 rms_B_bonded: 2.38 r_work: 0.3916 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6379 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10614 Z= 0.114 Angle : 0.517 5.700 14690 Z= 0.264 Chirality : 0.039 0.148 1695 Planarity : 0.004 0.039 1584 Dihedral : 18.558 176.628 2368 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.91 % Allowed : 23.14 % Favored : 74.95 % 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: -0.77 (0.25), residues: 1062 helix: 0.48 (0.32), residues: 270 sheet: -1.59 (0.37), residues: 169 loop : -0.58 (0.24), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 13 TYR 0.014 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 F 31 Details of bonding type rmsd covalent geometry : bond 0.00258 (10614) covalent geometry : angle 0.51728 (14690) hydrogen bonds : bond 0.03667 ( 345) hydrogen bonds : angle 5.06913 ( 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 215 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 197 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: symmetry clash REVERT: A 357 MET cc_start: 0.7570 (OUTLIER) cc_final: 0.6948 (mmt) REVERT: A 367 LYS cc_start: 0.7922 (ttpt) cc_final: 0.7674 (ttpp) REVERT: B 152 PHE cc_start: 0.6556 (m-80) cc_final: 0.5989 (m-80) REVERT: D 106 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7147 (tm-30) REVERT: D 245 MET cc_start: 0.7119 (ttp) cc_final: 0.6875 (ttp) REVERT: D 343 GLU cc_start: 0.7149 (mt-10) cc_final: 0.6850 (mt-10) REVERT: F 57 THR cc_start: 0.6542 (m) cc_final: 0.6072 (p) REVERT: G 114 ARG cc_start: 0.5887 (ttp-110) cc_final: 0.5361 (ptm-80) REVERT: H 2 TYR cc_start: 0.7587 (m-80) cc_final: 0.7308 (m-80) outliers start: 18 outliers final: 14 residues processed: 207 average time/residue: 0.3020 time to fit residues: 82.1717 Evaluate side-chains 210 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 194 time to evaluate : 0.500 ------------------------------------------------------------------------------- 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 354 THR Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain B residue 84 LYS 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 144 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 258 GLU 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 127 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 110 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 42 optimal weight: 9.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 266 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.173148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.143819 restraints weight = 38020.619| |-----------------------------------------------------------------------------| r_work (start): 0.4010 rms_B_bonded: 2.35 r_work: 0.3879 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6454 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 10614 Z= 0.243 Angle : 0.623 6.344 14690 Z= 0.324 Chirality : 0.042 0.193 1695 Planarity : 0.005 0.081 1584 Dihedral : 18.680 175.282 2368 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 2.87 % Allowed : 23.25 % Favored : 73.89 % 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: -1.29 (0.24), residues: 1062 helix: -0.18 (0.30), residues: 274 sheet: -1.68 (0.38), residues: 169 loop : -0.87 (0.24), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 13 TYR 0.021 0.002 TYR A 378 PHE 0.038 0.002 PHE D 218 TRP 0.014 0.002 TRP D 219 HIS 0.010 0.002 HIS H 31 Details of bonding type rmsd covalent geometry : bond 0.00544 (10614) covalent geometry : angle 0.62306 (14690) hydrogen bonds : bond 0.04370 ( 345) hydrogen bonds : angle 5.39830 ( 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 224 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 197 time to evaluate : 0.514 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 129 LYS cc_start: 0.8211 (tptt) cc_final: 0.7955 (tppt) REVERT: A 330 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7554 (mp0) REVERT: A 367 LYS cc_start: 0.7961 (ttpt) cc_final: 0.7704 (ttpp) REVERT: B 152 PHE cc_start: 0.6632 (m-80) cc_final: 0.6030 (m-80) REVERT: D 106 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7181 (tm-30) REVERT: D 133 CYS cc_start: 0.3977 (m) cc_final: 0.3610 (m) REVERT: D 262 MET cc_start: 0.6943 (ttm) cc_final: 0.6680 (ttt) REVERT: D 343 GLU cc_start: 0.7112 (mt-10) cc_final: 0.6807 (mt-10) REVERT: F 57 THR cc_start: 0.6532 (m) cc_final: 0.6068 (p) REVERT: G 114 ARG cc_start: 0.6077 (ttp-110) cc_final: 0.5369 (ptm160) REVERT: H 2 TYR cc_start: 0.7663 (m-80) cc_final: 0.7450 (m-80) outliers start: 27 outliers final: 21 residues processed: 213 average time/residue: 0.3003 time to fit residues: 83.7900 Evaluate side-chains 214 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 192 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 223 GLU 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 B residue 84 LYS 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 144 LEU Chi-restraints excluded: chain D residue 223 GLU Chi-restraints excluded: chain D residue 258 GLU 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 Chi-restraints excluded: chain G residue 127 CYS Chi-restraints excluded: chain H residue 13 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 101 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 71 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 77 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.174948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.145481 restraints weight = 38406.158| |-----------------------------------------------------------------------------| r_work (start): 0.4028 rms_B_bonded: 2.39 r_work: 0.3901 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6407 moved from start: 0.3113 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= 0.133 Angle : 0.543 5.915 14690 Z= 0.277 Chirality : 0.040 0.165 1695 Planarity : 0.004 0.047 1584 Dihedral : 18.601 174.765 2368 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.44 % Allowed : 23.25 % Favored : 74.31 % 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: -1.07 (0.25), residues: 1062 helix: 0.09 (0.30), residues: 279 sheet: -1.69 (0.38), residues: 167 loop : -0.74 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 13 TYR 0.015 0.001 TYR A 155 PHE 0.022 0.001 PHE D 218 TRP 0.013 0.001 TRP D 219 HIS 0.008 0.001 HIS F 31 Details of bonding type rmsd covalent geometry : bond 0.00302 (10614) covalent geometry : angle 0.54323 (14690) hydrogen bonds : bond 0.03749 ( 345) hydrogen bonds : angle 5.08042 ( 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 214 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 191 time to evaluate : 0.518 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 330 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7565 (mp0) REVERT: A 357 MET cc_start: 0.7572 (OUTLIER) cc_final: 0.6651 (mmt) REVERT: A 367 LYS cc_start: 0.7969 (ttpt) cc_final: 0.7705 (ttpp) REVERT: B 152 PHE cc_start: 0.6610 (m-80) cc_final: 0.5984 (m-80) REVERT: D 106 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7112 (tm-30) REVERT: D 133 CYS cc_start: 0.3983 (m) cc_final: 0.3646 (m) REVERT: D 214 ASN cc_start: 0.6910 (t0) cc_final: 0.6645 (t0) REVERT: D 262 MET cc_start: 0.6942 (ttm) cc_final: 0.6709 (ttt) REVERT: D 343 GLU cc_start: 0.7101 (mt-10) cc_final: 0.6846 (mt-10) REVERT: F 57 THR cc_start: 0.6509 (m) cc_final: 0.6060 (p) REVERT: G 92 GLU cc_start: 0.7323 (mp0) cc_final: 0.7095 (mp0) REVERT: G 114 ARG cc_start: 0.5983 (ttp-110) cc_final: 0.5334 (ptm160) outliers start: 23 outliers final: 18 residues processed: 204 average time/residue: 0.2757 time to fit residues: 74.2914 Evaluate side-chains 206 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 186 time to evaluate : 0.351 ------------------------------------------------------------------------------- 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 161 LEU Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain B residue 84 LYS 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 144 LEU 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 67 LEU Chi-restraints excluded: chain G residue 127 CYS Chi-restraints excluded: chain G residue 132 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 111 optimal weight: 8.9990 chunk 91 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 92 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.173837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.144400 restraints weight = 37942.326| |-----------------------------------------------------------------------------| r_work (start): 0.4011 rms_B_bonded: 2.36 r_work: 0.3882 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6444 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10614 Z= 0.189 Angle : 0.579 5.769 14690 Z= 0.299 Chirality : 0.041 0.182 1695 Planarity : 0.004 0.069 1584 Dihedral : 18.645 174.486 2368 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.27 % Favored : 94.63 % Rotamer: Outliers : 3.08 % Allowed : 22.72 % Favored : 74.20 % 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: -1.20 (0.25), residues: 1062 helix: -0.08 (0.30), residues: 278 sheet: -1.53 (0.39), residues: 163 loop : -0.88 (0.24), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 13 TYR 0.018 0.002 TYR A 155 PHE 0.032 0.002 PHE D 218 TRP 0.013 0.002 TRP D 219 HIS 0.009 0.002 HIS H 31 Details of bonding type rmsd covalent geometry : bond 0.00427 (10614) covalent geometry : angle 0.57950 (14690) hydrogen bonds : bond 0.04025 ( 345) hydrogen bonds : angle 5.18865 ( 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 219 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 190 time to evaluate : 0.333 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 330 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7527 (mp0) REVERT: A 357 MET cc_start: 0.7575 (OUTLIER) cc_final: 0.6861 (mmt) REVERT: A 367 LYS cc_start: 0.7951 (ttpt) cc_final: 0.7691 (ttpp) REVERT: B 152 PHE cc_start: 0.6673 (m-80) cc_final: 0.6040 (m-80) REVERT: D 106 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7101 (tm-30) REVERT: D 183 PHE cc_start: 0.6879 (m-10) cc_final: 0.6570 (m-10) REVERT: D 343 GLU cc_start: 0.7081 (mt-10) cc_final: 0.6853 (mt-10) REVERT: F 57 THR cc_start: 0.6558 (m) cc_final: 0.6093 (p) REVERT: G 92 GLU cc_start: 0.7293 (mp0) cc_final: 0.7056 (mp0) REVERT: G 114 ARG cc_start: 0.6043 (ttp-110) cc_final: 0.5377 (ptm160) outliers start: 29 outliers final: 21 residues processed: 209 average time/residue: 0.2755 time to fit residues: 75.6426 Evaluate side-chains 211 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 188 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 223 GLU 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 84 LYS Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain D residue 97 ASP Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 223 GLU Chi-restraints excluded: chain D residue 238 MET Chi-restraints excluded: chain D residue 251 VAL 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 67 LEU Chi-restraints excluded: chain G residue 127 CYS Chi-restraints excluded: chain G residue 132 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 24 optimal weight: 0.0770 chunk 6 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 83 optimal weight: 0.6980 chunk 111 optimal weight: 8.9990 chunk 28 optimal weight: 0.5980 chunk 93 optimal weight: 1.9990 chunk 40 optimal weight: 9.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.176742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.147546 restraints weight = 37870.862| |-----------------------------------------------------------------------------| r_work (start): 0.4032 rms_B_bonded: 2.34 r_work: 0.3903 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6411 moved from start: 0.3379 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= 0.126 Angle : 0.544 6.403 14690 Z= 0.276 Chirality : 0.040 0.158 1695 Planarity : 0.004 0.047 1584 Dihedral : 18.594 174.275 2368 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.24 % Favored : 95.57 % Rotamer: Outliers : 2.12 % Allowed : 23.04 % Favored : 74.84 % 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: -0.96 (0.25), residues: 1062 helix: 0.28 (0.31), residues: 273 sheet: -1.35 (0.39), residues: 165 loop : -0.81 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 13 TYR 0.014 0.001 TYR A 155 PHE 0.022 0.001 PHE D 218 TRP 0.013 0.001 TRP D 219 HIS 0.007 0.001 HIS F 31 Details of bonding type rmsd covalent geometry : bond 0.00288 (10614) covalent geometry : angle 0.54357 (14690) hydrogen bonds : bond 0.03667 ( 345) hydrogen bonds : angle 5.00539 ( 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 205 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 185 time to evaluate : 0.325 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: A 330 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7545 (mp0) REVERT: A 357 MET cc_start: 0.7576 (OUTLIER) cc_final: 0.6749 (mmt) REVERT: A 367 LYS cc_start: 0.7957 (ttpt) cc_final: 0.7705 (ttpp) REVERT: B 152 PHE cc_start: 0.6628 (m-80) cc_final: 0.5981 (m-80) REVERT: D 106 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7096 (tm-30) REVERT: D 133 CYS cc_start: 0.3864 (m) cc_final: 0.3535 (m) REVERT: D 183 PHE cc_start: 0.6879 (m-10) cc_final: 0.6641 (m-10) REVERT: D 214 ASN cc_start: 0.6844 (t0) cc_final: 0.6526 (t0) REVERT: D 343 GLU cc_start: 0.7083 (mt-10) cc_final: 0.6854 (mt-10) REVERT: F 57 THR cc_start: 0.6537 (m) cc_final: 0.6094 (p) REVERT: G 51 LYS cc_start: 0.8031 (mmtt) cc_final: 0.7789 (mmtt) REVERT: G 92 GLU cc_start: 0.7245 (mp0) cc_final: 0.7019 (mp0) REVERT: G 114 ARG cc_start: 0.5963 (ttp-110) cc_final: 0.5322 (ptm160) outliers start: 20 outliers final: 16 residues processed: 197 average time/residue: 0.2424 time to fit residues: 63.2213 Evaluate side-chains 202 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 184 time to evaluate : 0.317 ------------------------------------------------------------------------------- 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 161 LEU Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain B residue 84 LYS Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 144 LEU 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 G residue 67 LEU Chi-restraints excluded: chain G residue 127 CYS Chi-restraints excluded: chain G residue 132 VAL 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: 4.9990 chunk 77 optimal weight: 0.0970 chunk 53 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 135 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.172679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.143360 restraints weight = 38353.278| |-----------------------------------------------------------------------------| r_work (start): 0.4001 rms_B_bonded: 2.38 r_work: 0.3869 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6471 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 10614 Z= 0.220 Angle : 0.602 5.969 14690 Z= 0.311 Chirality : 0.042 0.196 1695 Planarity : 0.005 0.074 1584 Dihedral : 18.729 174.754 2368 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.84 % Favored : 93.97 % Rotamer: Outliers : 2.55 % Allowed : 22.82 % 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: -1.26 (0.25), residues: 1062 helix: -0.02 (0.31), residues: 272 sheet: -1.55 (0.39), residues: 163 loop : -0.97 (0.24), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 13 TYR 0.020 0.002 TYR A 88 PHE 0.036 0.002 PHE D 218 TRP 0.012 0.002 TRP D 219 HIS 0.011 0.002 HIS H 31 Details of bonding type rmsd covalent geometry : bond 0.00495 (10614) covalent geometry : angle 0.60186 (14690) hydrogen bonds : bond 0.04113 ( 345) hydrogen bonds : angle 5.26568 ( 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 217 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 193 time to evaluate : 0.533 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: A 330 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7530 (mp0) REVERT: A 367 LYS cc_start: 0.7967 (ttpt) cc_final: 0.7682 (ttpp) REVERT: B 152 PHE cc_start: 0.6739 (m-80) cc_final: 0.6069 (m-80) REVERT: D 106 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7120 (tm-30) REVERT: D 133 CYS cc_start: 0.3874 (m) cc_final: 0.3527 (m) REVERT: D 183 PHE cc_start: 0.6835 (m-10) cc_final: 0.6363 (m-10) REVERT: D 214 ASN cc_start: 0.6813 (t0) cc_final: 0.6511 (t0) REVERT: D 272 GLN cc_start: 0.4807 (tp-100) cc_final: 0.4548 (tp-100) REVERT: D 343 GLU cc_start: 0.7115 (mt-10) cc_final: 0.6871 (mt-10) REVERT: F 57 THR cc_start: 0.6602 (m) cc_final: 0.6353 (m) REVERT: G 51 LYS cc_start: 0.8137 (mmtt) cc_final: 0.7880 (mmtt) REVERT: G 114 ARG cc_start: 0.6078 (ttp-110) cc_final: 0.5389 (ptm160) outliers start: 24 outliers final: 20 residues processed: 206 average time/residue: 0.2939 time to fit residues: 80.1692 Evaluate side-chains 212 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 191 time to evaluate : 0.497 ------------------------------------------------------------------------------- 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 161 LEU Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain B residue 84 LYS Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 144 LEU Chi-restraints excluded: chain D residue 223 GLU Chi-restraints excluded: chain D residue 238 MET Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 13 ARG Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 127 CYS Chi-restraints excluded: chain G residue 132 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 56 optimal weight: 0.0980 chunk 78 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.172760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.143627 restraints weight = 38514.538| |-----------------------------------------------------------------------------| r_work (start): 0.4006 rms_B_bonded: 2.38 r_work: 0.3874 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6455 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10614 Z= 0.183 Angle : 0.577 5.899 14690 Z= 0.295 Chirality : 0.041 0.181 1695 Planarity : 0.004 0.063 1584 Dihedral : 18.734 175.158 2368 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.46 % Favored : 94.35 % Rotamer: Outliers : 2.23 % Allowed : 23.25 % Favored : 74.52 % 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: -1.18 (0.25), residues: 1062 helix: 0.09 (0.31), residues: 271 sheet: -1.51 (0.40), residues: 161 loop : -0.95 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 13 TYR 0.017 0.002 TYR A 155 PHE 0.031 0.002 PHE D 218 TRP 0.013 0.002 TRP D 219 HIS 0.009 0.001 HIS H 31 Details of bonding type rmsd covalent geometry : bond 0.00412 (10614) covalent geometry : angle 0.57706 (14690) hydrogen bonds : bond 0.03910 ( 345) hydrogen bonds : angle 5.19216 ( 853) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6814.64 seconds wall clock time: 116 minutes 1.50 seconds (6961.50 seconds total)