Starting phenix.real_space_refine on Wed Sep 17 11:53:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yn4_39414/09_2025/8yn4_39414.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yn4_39414/09_2025/8yn4_39414.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yn4_39414/09_2025/8yn4_39414.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yn4_39414/09_2025/8yn4_39414.map" model { file = "/net/cci-nas-00/data/ceres_data/8yn4_39414/09_2025/8yn4_39414.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yn4_39414/09_2025/8yn4_39414.cif" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 57 5.16 5 C 5509 2.51 5 N 1491 2.21 5 O 1604 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8661 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1754 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 6, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 8, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 81 Chain: "B" Number of atoms: 2622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2622 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 5, 'TRANS': 336} Chain: "C" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "E" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1779 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "R" Number of atoms: 2034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2034 Classifications: {'peptide': 268} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 7, 'TRANS': 260} Chain breaks: 2 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 37 Chain: "R" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {'CLR': 1, 'HSM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.23, per 1000 atoms: 0.26 Number of scatterers: 8661 At special positions: 0 Unit cell: (109.14, 115.56, 110.21, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 57 16.00 O 1604 8.00 N 1491 7.00 C 5509 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.03 Simple disulfide: pdb=" SG CYS R 91 " - pdb=" SG CYS R 174 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.61 Conformation dependent library (CDL) restraints added in 510.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2106 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 14 sheets defined 38.6% alpha, 24.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 6 through 29 removed outlier: 3.991A pdb=" N LYS A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 95 through 101 removed outlier: 3.548A pdb=" N GLN A 98 " --> pdb=" O LYS A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 130 Processing helix chain 'A' and resid 145 through 156 Processing helix chain 'A' and resid 159 through 164 removed outlier: 4.024A pdb=" N TYR A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 168 Processing helix chain 'A' and resid 183 through 204 removed outlier: 3.525A pdb=" N ILE A 200 " --> pdb=" O GLU A 196 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N SER A 204 " --> pdb=" O ILE A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 356 Processing helix chain 'B' and resid 3 through 25 removed outlier: 3.516A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 7 through 24 removed outlier: 3.513A pdb=" N MET C 21 " --> pdb=" O GLU C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 55 through 59 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.538A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 16 through 46 removed outlier: 3.509A pdb=" N VAL R 39 " --> pdb=" O GLY R 35 " (cutoff:3.500A) Processing helix chain 'R' and resid 51 through 53 No H-bonds generated for 'chain 'R' and resid 51 through 53' Processing helix chain 'R' and resid 54 through 71 Processing helix chain 'R' and resid 71 through 82 Processing helix chain 'R' and resid 87 through 122 removed outlier: 3.510A pdb=" N ASN R 92 " --> pdb=" O LYS R 88 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE R 93 " --> pdb=" O VAL R 89 " (cutoff:3.500A) Processing helix chain 'R' and resid 125 through 130 Processing helix chain 'R' and resid 131 through 156 removed outlier: 3.653A pdb=" N LEU R 152 " --> pdb=" O THR R 148 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N SER R 153 " --> pdb=" O LEU R 149 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE R 154 " --> pdb=" O SER R 150 " (cutoff:3.500A) Processing helix chain 'R' and resid 179 through 191 Processing helix chain 'R' and resid 191 through 216 Processing helix chain 'R' and resid 230 through 261 removed outlier: 3.550A pdb=" N PHE R 243 " --> pdb=" O VAL R 239 " (cutoff:3.500A) Proline residue: R 249 - end of helix Processing helix chain 'R' and resid 266 through 288 removed outlier: 3.676A pdb=" N GLY R 277 " --> pdb=" O VAL R 273 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR R 278 " --> pdb=" O LEU R 274 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N SER R 281 " --> pdb=" O GLY R 277 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ALA R 282 " --> pdb=" O TYR R 278 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU R 283 " --> pdb=" O ALA R 279 " (cutoff:3.500A) Proline residue: R 285 - end of helix Processing helix chain 'R' and resid 292 through 301 removed outlier: 3.737A pdb=" N GLN R 300 " --> pdb=" O ARG R 296 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 70 through 75 removed outlier: 6.154A pdb=" N LEU A 34 " --> pdb=" O HIS A 82 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N PHE A 84 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LEU A 36 " --> pdb=" O PHE A 84 " (cutoff:3.500A) removed outlier: 9.821A pdb=" N ALA A 105 " --> pdb=" O THR A 33 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ARG A 35 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ILE A 107 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU A 37 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N VAL A 109 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU A 39 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 8.635A pdb=" N ASP A 111 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 70 through 75 removed outlier: 6.154A pdb=" N LEU A 34 " --> pdb=" O HIS A 82 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N PHE A 84 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LEU A 36 " --> pdb=" O PHE A 84 " (cutoff:3.500A) removed outlier: 9.821A pdb=" N ALA A 105 " --> pdb=" O THR A 33 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ARG A 35 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ILE A 107 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU A 37 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N VAL A 109 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU A 39 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 8.635A pdb=" N ASP A 111 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N PHE A 142 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N PHE A 108 " --> pdb=" O PHE A 142 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ASN A 144 " --> pdb=" O PHE A 108 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL A 110 " --> pdb=" O ASN A 144 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.599A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.559A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.181A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.331A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 4.466A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 4.530A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.727A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.805A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 11 through 12 removed outlier: 4.442A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 140 through 141 Processing sheet with id=AB5, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.152A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) 465 hydrogen bonds defined for protein. 1311 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.45 Time building geometry restraints manager: 0.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2825 1.35 - 1.46: 2153 1.46 - 1.58: 3777 1.58 - 1.70: 0 1.70 - 1.82: 81 Bond restraints: 8836 Sorted by residual: bond pdb=" CG HSM R 701 " pdb=" ND1 HSM R 701 " ideal model delta sigma weight residual 1.383 1.340 0.043 2.00e-02 2.50e+03 4.61e+00 bond pdb=" C5 CLR R 702 " pdb=" C6 CLR R 702 " ideal model delta sigma weight residual 1.332 1.300 0.032 2.00e-02 2.50e+03 2.55e+00 bond pdb=" C10 CLR R 702 " pdb=" C9 CLR R 702 " ideal model delta sigma weight residual 1.551 1.521 0.030 2.00e-02 2.50e+03 2.30e+00 bond pdb=" CG HSM R 701 " pdb=" CD2 HSM R 701 " ideal model delta sigma weight residual 1.373 1.347 0.026 2.00e-02 2.50e+03 1.74e+00 bond pdb=" C13 CLR R 702 " pdb=" C17 CLR R 702 " ideal model delta sigma weight residual 1.550 1.529 0.021 2.00e-02 2.50e+03 1.10e+00 ... (remaining 8831 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 11901 1.51 - 3.02: 85 3.02 - 4.52: 15 4.52 - 6.03: 8 6.03 - 7.54: 1 Bond angle restraints: 12010 Sorted by residual: angle pdb=" C13 CLR R 702 " pdb=" C17 CLR R 702 " pdb=" C20 CLR R 702 " ideal model delta sigma weight residual 119.60 112.06 7.54 3.00e+00 1.11e-01 6.32e+00 angle pdb=" C ARG E 191 " pdb=" N MET E 192 " pdb=" CA MET E 192 " ideal model delta sigma weight residual 121.54 125.35 -3.81 1.91e+00 2.74e-01 3.97e+00 angle pdb=" C23 CLR R 702 " pdb=" C24 CLR R 702 " pdb=" C25 CLR R 702 " ideal model delta sigma weight residual 115.14 109.81 5.33 3.00e+00 1.11e-01 3.16e+00 angle pdb=" C20 CLR R 702 " pdb=" C22 CLR R 702 " pdb=" C23 CLR R 702 " ideal model delta sigma weight residual 115.57 110.39 5.18 3.00e+00 1.11e-01 2.99e+00 angle pdb=" CA HSM R 701 " pdb=" CB HSM R 701 " pdb=" CG HSM R 701 " ideal model delta sigma weight residual 114.47 109.47 5.00 3.00e+00 1.11e-01 2.78e+00 ... (remaining 12005 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.68: 5065 15.68 - 31.35: 161 31.35 - 47.03: 37 47.03 - 62.71: 5 62.71 - 78.38: 1 Dihedral angle restraints: 5269 sinusoidal: 2003 harmonic: 3266 Sorted by residual: dihedral pdb=" CA GLN B 75 " pdb=" C GLN B 75 " pdb=" N ASP B 76 " pdb=" CA ASP B 76 " ideal model delta harmonic sigma weight residual 180.00 159.27 20.73 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA ARG E 191 " pdb=" C ARG E 191 " pdb=" N MET E 192 " pdb=" CA MET E 192 " ideal model delta harmonic sigma weight residual 180.00 161.01 18.99 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA PHE E 32 " pdb=" C PHE E 32 " pdb=" N GLY E 33 " pdb=" CA GLY E 33 " ideal model delta harmonic sigma weight residual 180.00 162.13 17.87 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 5266 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1322 0.093 - 0.186: 66 0.186 - 0.279: 1 0.279 - 0.372: 1 0.372 - 0.465: 1 Chirality restraints: 1391 Sorted by residual: chirality pdb=" C14 CLR R 702 " pdb=" C13 CLR R 702 " pdb=" C15 CLR R 702 " pdb=" C8 CLR R 702 " both_signs ideal model delta sigma weight residual False -2.32 -2.78 0.47 2.00e-01 2.50e+01 5.42e+00 chirality pdb=" C10 CLR R 702 " pdb=" C1 CLR R 702 " pdb=" C5 CLR R 702 " pdb=" C9 CLR R 702 " both_signs ideal model delta sigma weight residual False -2.85 -2.50 -0.35 2.00e-01 2.50e+01 3.12e+00 chirality pdb=" C17 CLR R 702 " pdb=" C13 CLR R 702 " pdb=" C16 CLR R 702 " pdb=" C20 CLR R 702 " both_signs ideal model delta sigma weight residual False 2.55 2.82 -0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 1388 not shown) Planarity restraints: 1520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.028 5.00e-02 4.00e+02 4.31e-02 2.98e+00 pdb=" N PRO B 236 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN R 284 " 0.018 5.00e-02 4.00e+02 2.65e-02 1.13e+00 pdb=" N PRO R 285 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO R 285 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO R 285 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU R 193 " 0.017 5.00e-02 4.00e+02 2.51e-02 1.01e+00 pdb=" N PRO R 194 " -0.043 5.00e-02 4.00e+02 pdb=" CA PRO R 194 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO R 194 " 0.014 5.00e-02 4.00e+02 ... (remaining 1517 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2213 2.80 - 3.33: 8012 3.33 - 3.85: 14441 3.85 - 4.38: 17491 4.38 - 4.90: 30345 Nonbonded interactions: 72502 Sorted by model distance: nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.276 3.040 nonbonded pdb=" O LYS C 20 " pdb=" ND2 ASN C 24 " model vdw 2.293 3.120 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR E 175 " model vdw 2.298 3.040 nonbonded pdb=" O SER E 30 " pdb=" OG SER E 53 " model vdw 2.305 3.040 nonbonded pdb=" O GLY R 44 " pdb=" NH2 ARG R 50 " model vdw 2.311 3.120 ... (remaining 72497 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.650 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 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 : 0.002 0.043 8839 Z= 0.077 Angle : 0.396 7.541 12016 Z= 0.198 Chirality : 0.043 0.465 1391 Planarity : 0.003 0.043 1520 Dihedral : 8.469 78.384 3154 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 0.33 % Allowed : 2.74 % Favored : 96.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.49 (0.25), residues: 1109 helix: 1.73 (0.26), residues: 386 sheet: 0.83 (0.29), residues: 288 loop : 0.57 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 38 TYR 0.011 0.001 TYR E 190 PHE 0.009 0.001 PHE A 228 TRP 0.007 0.001 TRP B 339 HIS 0.002 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00154 ( 8836) covalent geometry : angle 0.39569 (12010) SS BOND : bond 0.00118 ( 3) SS BOND : angle 0.58756 ( 6) hydrogen bonds : bond 0.23830 ( 454) hydrogen bonds : angle 7.24494 ( 1311) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 224 time to evaluate : 0.303 Fit side-chains revert: symmetry clash REVERT: A 94 ARG cc_start: 0.6786 (ptt-90) cc_final: 0.6585 (ttp-170) REVERT: A 132 ARG cc_start: 0.7969 (ttp-110) cc_final: 0.7594 (ttt-90) REVERT: C 17 GLU cc_start: 0.8546 (tp30) cc_final: 0.8194 (tm-30) REVERT: R 233 THR cc_start: 0.8575 (m) cc_final: 0.8230 (p) outliers start: 3 outliers final: 1 residues processed: 225 average time/residue: 0.6068 time to fit residues: 144.5953 Evaluate side-chains 143 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 142 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 228 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.0000 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 6.9990 chunk 106 optimal weight: 8.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A 123 ASN A 130 ASN B 91 HIS B 259 GLN R 46 ASN R 79 GLN R 212 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.161510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.111216 restraints weight = 9847.034| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.99 r_work: 0.3134 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8839 Z= 0.139 Angle : 0.541 8.685 12016 Z= 0.290 Chirality : 0.043 0.150 1391 Planarity : 0.004 0.038 1520 Dihedral : 4.392 29.645 1295 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 3.29 % Allowed : 12.18 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.86 (0.25), residues: 1109 helix: 2.49 (0.26), residues: 385 sheet: 0.84 (0.30), residues: 273 loop : 0.47 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 219 TYR 0.019 0.001 TYR R 256 PHE 0.013 0.001 PHE B 199 TRP 0.020 0.002 TRP R 275 HIS 0.004 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 8836) covalent geometry : angle 0.54095 (12010) SS BOND : bond 0.00179 ( 3) SS BOND : angle 0.81398 ( 6) hydrogen bonds : bond 0.04898 ( 454) hydrogen bonds : angle 5.00647 ( 1311) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 172 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.7704 (tt0) REVERT: A 94 ARG cc_start: 0.6899 (ptt-90) cc_final: 0.6643 (ttp-170) REVERT: A 122 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.8040 (mp) REVERT: A 351 MET cc_start: 0.8438 (mtp) cc_final: 0.8154 (mtm) REVERT: B 13 GLN cc_start: 0.8603 (tm-30) cc_final: 0.8318 (tm-30) REVERT: B 17 GLN cc_start: 0.8691 (tt0) cc_final: 0.8250 (tt0) REVERT: B 44 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.7749 (mt0) REVERT: B 214 ARG cc_start: 0.8146 (mmt180) cc_final: 0.7800 (mmt180) REVERT: C 17 GLU cc_start: 0.8874 (tp30) cc_final: 0.8238 (tm-30) REVERT: R 31 ILE cc_start: 0.8536 (OUTLIER) cc_final: 0.8243 (mp) REVERT: R 281 SER cc_start: 0.8169 (m) cc_final: 0.7830 (p) outliers start: 30 outliers final: 12 residues processed: 189 average time/residue: 0.6002 time to fit residues: 120.1263 Evaluate side-chains 153 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain R residue 31 ILE Chi-restraints excluded: chain R residue 141 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 4 optimal weight: 0.7980 chunk 71 optimal weight: 0.4980 chunk 55 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 69 optimal weight: 7.9990 chunk 43 optimal weight: 7.9990 chunk 27 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN B 155 ASN E 171 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.161859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.115562 restraints weight = 9771.032| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.14 r_work: 0.3150 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8839 Z= 0.124 Angle : 0.500 5.755 12016 Z= 0.268 Chirality : 0.042 0.177 1391 Planarity : 0.003 0.037 1520 Dihedral : 4.223 29.410 1293 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.73 % Allowed : 15.26 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.80 (0.25), residues: 1109 helix: 2.53 (0.26), residues: 386 sheet: 0.60 (0.30), residues: 274 loop : 0.50 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 48 TYR 0.014 0.001 TYR E 190 PHE 0.012 0.001 PHE B 199 TRP 0.015 0.001 TRP B 169 HIS 0.003 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 8836) covalent geometry : angle 0.49967 (12010) SS BOND : bond 0.00179 ( 3) SS BOND : angle 0.72803 ( 6) hydrogen bonds : bond 0.04278 ( 454) hydrogen bonds : angle 4.65683 ( 1311) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 157 time to evaluate : 0.342 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.7692 (tt0) REVERT: A 21 LYS cc_start: 0.8352 (ttpp) cc_final: 0.7986 (ttmt) REVERT: A 94 ARG cc_start: 0.6766 (ptt-90) cc_final: 0.6517 (ttp-170) REVERT: A 122 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7947 (mp) REVERT: A 351 MET cc_start: 0.8402 (mtp) cc_final: 0.8140 (mtm) REVERT: B 44 GLN cc_start: 0.8467 (OUTLIER) cc_final: 0.7777 (mt0) REVERT: B 214 ARG cc_start: 0.8128 (mmt180) cc_final: 0.7830 (mmt180) REVERT: B 215 GLU cc_start: 0.8500 (mm-30) cc_final: 0.8114 (mm-30) REVERT: B 217 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.6982 (pmt) REVERT: C 17 GLU cc_start: 0.8847 (tp30) cc_final: 0.8241 (tm-30) REVERT: E 82 GLN cc_start: 0.8748 (tp40) cc_final: 0.8523 (tp-100) REVERT: R 31 ILE cc_start: 0.8508 (OUTLIER) cc_final: 0.8214 (mp) REVERT: R 51 ASN cc_start: 0.7232 (p0) cc_final: 0.6883 (p0) outliers start: 34 outliers final: 15 residues processed: 170 average time/residue: 0.6501 time to fit residues: 116.8738 Evaluate side-chains 158 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 138 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain R residue 31 ILE Chi-restraints excluded: chain R residue 93 ILE Chi-restraints excluded: chain R residue 141 LEU Chi-restraints excluded: chain R residue 149 LEU Chi-restraints excluded: chain R residue 196 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 32 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 90 optimal weight: 6.9990 chunk 59 optimal weight: 0.0870 chunk 1 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 69 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.1762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 268 ASN C 18 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.160755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.113424 restraints weight = 9987.295| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.09 r_work: 0.3134 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8839 Z= 0.143 Angle : 0.511 5.520 12016 Z= 0.272 Chirality : 0.042 0.207 1391 Planarity : 0.003 0.041 1520 Dihedral : 4.175 29.957 1293 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 4.50 % Allowed : 15.81 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.71 (0.25), residues: 1109 helix: 2.56 (0.26), residues: 389 sheet: 0.41 (0.30), residues: 270 loop : 0.43 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 19 TYR 0.011 0.001 TYR E 227 PHE 0.013 0.001 PHE B 199 TRP 0.015 0.002 TRP B 169 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 8836) covalent geometry : angle 0.51095 (12010) SS BOND : bond 0.00202 ( 3) SS BOND : angle 0.80459 ( 6) hydrogen bonds : bond 0.04096 ( 454) hydrogen bonds : angle 4.57894 ( 1311) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 145 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.7682 (tt0) REVERT: A 94 ARG cc_start: 0.6845 (ptt-90) cc_final: 0.6552 (ttp-170) REVERT: A 351 MET cc_start: 0.8436 (mtp) cc_final: 0.8183 (mtm) REVERT: B 44 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.7823 (mt0) REVERT: B 214 ARG cc_start: 0.8181 (mmt180) cc_final: 0.7801 (mmt180) REVERT: B 215 GLU cc_start: 0.8406 (mm-30) cc_final: 0.8038 (mm-30) REVERT: B 217 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.6961 (pmt) REVERT: C 17 GLU cc_start: 0.8898 (tp30) cc_final: 0.8249 (tm-30) REVERT: C 42 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7329 (tp30) REVERT: R 31 ILE cc_start: 0.8498 (OUTLIER) cc_final: 0.8192 (mp) REVERT: R 51 ASN cc_start: 0.7385 (p0) cc_final: 0.7039 (p0) outliers start: 41 outliers final: 17 residues processed: 162 average time/residue: 0.6518 time to fit residues: 111.7188 Evaluate side-chains 156 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 134 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain R residue 31 ILE Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 75 SER Chi-restraints excluded: chain R residue 93 ILE Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 240 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 73 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 76 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 88 optimal weight: 6.9990 chunk 42 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 47 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 107 optimal weight: 9.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 175 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.158673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.106969 restraints weight = 9948.457| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.04 r_work: 0.3080 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 8839 Z= 0.195 Angle : 0.559 8.212 12016 Z= 0.293 Chirality : 0.044 0.163 1391 Planarity : 0.004 0.039 1520 Dihedral : 4.303 29.437 1293 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 4.83 % Allowed : 16.47 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.62 (0.25), residues: 1109 helix: 2.44 (0.26), residues: 395 sheet: 0.26 (0.29), residues: 283 loop : 0.48 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 19 TYR 0.014 0.002 TYR A 115 PHE 0.016 0.002 PHE B 199 TRP 0.016 0.002 TRP B 169 HIS 0.005 0.001 HIS E 167 Details of bonding type rmsd covalent geometry : bond 0.00455 ( 8836) covalent geometry : angle 0.55832 (12010) SS BOND : bond 0.00144 ( 3) SS BOND : angle 0.92207 ( 6) hydrogen bonds : bond 0.04268 ( 454) hydrogen bonds : angle 4.69082 ( 1311) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 136 time to evaluate : 0.227 Fit side-chains REVERT: A 14 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.7642 (tt0) REVERT: A 18 MET cc_start: 0.8313 (OUTLIER) cc_final: 0.8056 (ttt) REVERT: A 351 MET cc_start: 0.8480 (mtp) cc_final: 0.8238 (mtm) REVERT: B 44 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.7901 (mt0) REVERT: B 214 ARG cc_start: 0.8293 (mmt180) cc_final: 0.7896 (mmt180) REVERT: B 215 GLU cc_start: 0.8451 (mm-30) cc_final: 0.8083 (mm-30) REVERT: B 217 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.7095 (pmt) REVERT: C 17 GLU cc_start: 0.8924 (tp30) cc_final: 0.8271 (tm-30) REVERT: C 18 GLN cc_start: 0.8866 (tp40) cc_final: 0.8612 (tp-100) REVERT: C 42 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7348 (tp30) REVERT: C 46 LYS cc_start: 0.8887 (mppt) cc_final: 0.8675 (mppt) outliers start: 44 outliers final: 21 residues processed: 156 average time/residue: 0.6994 time to fit residues: 115.0367 Evaluate side-chains 159 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 133 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 75 SER Chi-restraints excluded: chain R residue 93 ILE Chi-restraints excluded: chain R residue 140 VAL Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 240 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 56 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 16 optimal weight: 8.9990 chunk 31 optimal weight: 0.6980 chunk 6 optimal weight: 5.9990 chunk 97 optimal weight: 9.9990 chunk 54 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 ASN B 175 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.159769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.112939 restraints weight = 9938.962| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.07 r_work: 0.3122 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8839 Z= 0.148 Angle : 0.523 7.341 12016 Z= 0.276 Chirality : 0.042 0.160 1391 Planarity : 0.003 0.042 1520 Dihedral : 4.166 28.754 1293 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 3.95 % Allowed : 18.77 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.59 (0.25), residues: 1109 helix: 2.49 (0.26), residues: 396 sheet: 0.23 (0.30), residues: 273 loop : 0.38 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 19 TYR 0.012 0.001 TYR A 115 PHE 0.013 0.001 PHE B 199 TRP 0.016 0.001 TRP B 169 HIS 0.003 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 8836) covalent geometry : angle 0.52281 (12010) SS BOND : bond 0.00221 ( 3) SS BOND : angle 0.82795 ( 6) hydrogen bonds : bond 0.04013 ( 454) hydrogen bonds : angle 4.59017 ( 1311) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 144 time to evaluate : 0.336 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.7637 (tt0) REVERT: A 21 LYS cc_start: 0.8414 (ttpp) cc_final: 0.8074 (ttmt) REVERT: A 351 MET cc_start: 0.8444 (mtp) cc_final: 0.8208 (mtm) REVERT: B 44 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.7888 (mt0) REVERT: B 214 ARG cc_start: 0.8262 (mmt180) cc_final: 0.7904 (mmt180) REVERT: B 215 GLU cc_start: 0.8362 (mm-30) cc_final: 0.8022 (mm-30) REVERT: B 217 MET cc_start: 0.8484 (OUTLIER) cc_final: 0.7015 (pmt) REVERT: C 17 GLU cc_start: 0.8930 (tp30) cc_final: 0.8252 (tm-30) REVERT: C 18 GLN cc_start: 0.8917 (tp40) cc_final: 0.8534 (tp-100) REVERT: C 22 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7832 (mt-10) REVERT: C 42 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7365 (tp30) REVERT: R 233 THR cc_start: 0.8246 (m) cc_final: 0.7861 (p) outliers start: 36 outliers final: 19 residues processed: 157 average time/residue: 0.6787 time to fit residues: 112.7917 Evaluate side-chains 160 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 136 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 75 SER Chi-restraints excluded: chain R residue 93 ILE Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 240 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 70 optimal weight: 5.9990 chunk 72 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 chunk 106 optimal weight: 7.9990 chunk 67 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 50 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN E 231 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.160593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.113317 restraints weight = 10030.458| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.17 r_work: 0.3125 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8839 Z= 0.132 Angle : 0.522 8.991 12016 Z= 0.274 Chirality : 0.042 0.134 1391 Planarity : 0.003 0.043 1520 Dihedral : 4.110 29.799 1293 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.95 % Allowed : 18.33 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.60 (0.26), residues: 1109 helix: 2.54 (0.26), residues: 397 sheet: 0.15 (0.30), residues: 275 loop : 0.41 (0.31), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 19 TYR 0.011 0.001 TYR E 190 PHE 0.019 0.001 PHE E 68 TRP 0.016 0.001 TRP B 169 HIS 0.003 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 8836) covalent geometry : angle 0.52177 (12010) SS BOND : bond 0.00208 ( 3) SS BOND : angle 0.80130 ( 6) hydrogen bonds : bond 0.03856 ( 454) hydrogen bonds : angle 4.53517 ( 1311) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 142 time to evaluate : 0.348 Fit side-chains REVERT: A 14 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.7615 (tt0) REVERT: A 21 LYS cc_start: 0.8411 (ttpp) cc_final: 0.8054 (ttmt) REVERT: A 132 ARG cc_start: 0.8396 (ttp80) cc_final: 0.8049 (ttp80) REVERT: A 351 MET cc_start: 0.8449 (mtp) cc_final: 0.8220 (mtm) REVERT: B 44 GLN cc_start: 0.8517 (OUTLIER) cc_final: 0.7867 (mt0) REVERT: B 214 ARG cc_start: 0.8297 (mmt180) cc_final: 0.7875 (mpt180) REVERT: B 215 GLU cc_start: 0.8357 (mm-30) cc_final: 0.8036 (mm-30) REVERT: B 217 MET cc_start: 0.8514 (OUTLIER) cc_final: 0.7050 (pmt) REVERT: C 17 GLU cc_start: 0.8946 (tp30) cc_final: 0.8230 (tm-30) REVERT: C 18 GLN cc_start: 0.8902 (tp40) cc_final: 0.8607 (tp-100) REVERT: C 42 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7329 (tp30) REVERT: E 46 GLU cc_start: 0.8376 (tt0) cc_final: 0.7847 (pt0) REVERT: R 31 ILE cc_start: 0.8371 (OUTLIER) cc_final: 0.8033 (mp) REVERT: R 51 ASN cc_start: 0.7383 (p0) cc_final: 0.6971 (p0) REVERT: R 233 THR cc_start: 0.8228 (m) cc_final: 0.7837 (p) outliers start: 36 outliers final: 24 residues processed: 157 average time/residue: 0.6746 time to fit residues: 111.8553 Evaluate side-chains 165 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 136 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain R residue 31 ILE Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 75 SER Chi-restraints excluded: chain R residue 93 ILE Chi-restraints excluded: chain R residue 121 MET Chi-restraints excluded: chain R residue 140 VAL Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 240 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 102 optimal weight: 0.7980 chunk 88 optimal weight: 6.9990 chunk 105 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 74 optimal weight: 0.0470 chunk 61 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 28 optimal weight: 0.7980 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN C 18 GLN E 231 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.161108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.111661 restraints weight = 9951.786| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.99 r_work: 0.3151 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8839 Z= 0.113 Angle : 0.509 8.632 12016 Z= 0.267 Chirality : 0.042 0.139 1391 Planarity : 0.003 0.043 1520 Dihedral : 3.995 28.192 1293 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.29 % Allowed : 19.43 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.68 (0.26), residues: 1109 helix: 2.59 (0.26), residues: 397 sheet: 0.18 (0.30), residues: 279 loop : 0.48 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 219 TYR 0.011 0.001 TYR E 190 PHE 0.010 0.001 PHE B 199 TRP 0.015 0.001 TRP B 169 HIS 0.003 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 8836) covalent geometry : angle 0.50884 (12010) SS BOND : bond 0.00224 ( 3) SS BOND : angle 0.83359 ( 6) hydrogen bonds : bond 0.03681 ( 454) hydrogen bonds : angle 4.45671 ( 1311) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 147 time to evaluate : 0.357 Fit side-chains REVERT: A 14 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.7688 (tt0) REVERT: A 21 LYS cc_start: 0.8416 (ttpp) cc_final: 0.8065 (ttmt) REVERT: A 132 ARG cc_start: 0.8427 (ttp80) cc_final: 0.8100 (ttp80) REVERT: A 351 MET cc_start: 0.8400 (mtp) cc_final: 0.8190 (mtm) REVERT: B 44 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.7879 (mt0) REVERT: B 214 ARG cc_start: 0.8226 (mmt180) cc_final: 0.7763 (mmt180) REVERT: B 215 GLU cc_start: 0.8415 (mm-30) cc_final: 0.8087 (mm-30) REVERT: B 217 MET cc_start: 0.8458 (OUTLIER) cc_final: 0.7042 (pmt) REVERT: C 42 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7335 (tp30) REVERT: E 46 GLU cc_start: 0.8327 (tt0) cc_final: 0.7811 (pt0) REVERT: R 31 ILE cc_start: 0.8356 (OUTLIER) cc_final: 0.7990 (mp) REVERT: R 51 ASN cc_start: 0.7457 (p0) cc_final: 0.7079 (p0) REVERT: R 233 THR cc_start: 0.8185 (m) cc_final: 0.7808 (p) outliers start: 30 outliers final: 17 residues processed: 161 average time/residue: 0.6323 time to fit residues: 107.7686 Evaluate side-chains 159 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 137 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain R residue 31 ILE Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 93 ILE Chi-restraints excluded: chain R residue 121 MET Chi-restraints excluded: chain R residue 140 VAL Chi-restraints excluded: chain R residue 240 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 91 optimal weight: 10.0000 chunk 43 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 108 optimal weight: 9.9990 chunk 82 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 96 optimal weight: 8.9990 chunk 31 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 231 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.158197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.106531 restraints weight = 9881.531| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.05 r_work: 0.3084 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8839 Z= 0.197 Angle : 0.591 9.848 12016 Z= 0.305 Chirality : 0.044 0.137 1391 Planarity : 0.004 0.042 1520 Dihedral : 4.236 28.997 1293 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 3.40 % Allowed : 19.98 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.55 (0.25), residues: 1109 helix: 2.44 (0.26), residues: 397 sheet: 0.17 (0.29), residues: 283 loop : 0.42 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 19 TYR 0.011 0.002 TYR R 126 PHE 0.016 0.002 PHE E 68 TRP 0.016 0.002 TRP B 169 HIS 0.010 0.002 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00464 ( 8836) covalent geometry : angle 0.59024 (12010) SS BOND : bond 0.00191 ( 3) SS BOND : angle 1.26361 ( 6) hydrogen bonds : bond 0.04159 ( 454) hydrogen bonds : angle 4.67482 ( 1311) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 139 time to evaluate : 0.284 Fit side-chains REVERT: A 14 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.7649 (tt0) REVERT: A 18 MET cc_start: 0.8369 (ttp) cc_final: 0.8113 (ttt) REVERT: A 132 ARG cc_start: 0.8428 (ttp80) cc_final: 0.8084 (ttp80) REVERT: A 351 MET cc_start: 0.8428 (mtp) cc_final: 0.8177 (mtm) REVERT: B 44 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.7937 (mt0) REVERT: B 214 ARG cc_start: 0.8286 (mmt180) cc_final: 0.7775 (mmt180) REVERT: B 217 MET cc_start: 0.8543 (OUTLIER) cc_final: 0.7134 (pmt) REVERT: R 51 ASN cc_start: 0.7426 (p0) cc_final: 0.7040 (p0) REVERT: R 233 THR cc_start: 0.8231 (m) cc_final: 0.7848 (p) outliers start: 31 outliers final: 18 residues processed: 151 average time/residue: 0.6619 time to fit residues: 105.6433 Evaluate side-chains 157 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 75 SER Chi-restraints excluded: chain R residue 93 ILE Chi-restraints excluded: chain R residue 140 VAL Chi-restraints excluded: chain R residue 240 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 62 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 88 optimal weight: 0.8980 chunk 59 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 chunk 22 optimal weight: 6.9990 chunk 25 optimal weight: 0.3980 chunk 96 optimal weight: 2.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 231 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.158912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.107882 restraints weight = 10045.958| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.04 r_work: 0.3091 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8839 Z= 0.178 Angle : 0.600 10.886 12016 Z= 0.308 Chirality : 0.044 0.144 1391 Planarity : 0.004 0.043 1520 Dihedral : 4.238 27.583 1293 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 3.29 % Allowed : 20.31 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.47 (0.25), residues: 1109 helix: 2.35 (0.26), residues: 395 sheet: 0.11 (0.29), residues: 282 loop : 0.42 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 19 TYR 0.010 0.001 TYR R 126 PHE 0.017 0.002 PHE E 68 TRP 0.015 0.002 TRP B 169 HIS 0.010 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00418 ( 8836) covalent geometry : angle 0.59976 (12010) SS BOND : bond 0.00207 ( 3) SS BOND : angle 1.27245 ( 6) hydrogen bonds : bond 0.04130 ( 454) hydrogen bonds : angle 4.69424 ( 1311) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 141 time to evaluate : 0.397 Fit side-chains REVERT: A 14 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.7654 (tt0) REVERT: A 18 MET cc_start: 0.8368 (ttp) cc_final: 0.8124 (ttt) REVERT: A 21 LYS cc_start: 0.8445 (ttpp) cc_final: 0.8092 (ttmt) REVERT: A 132 ARG cc_start: 0.8414 (ttp80) cc_final: 0.8082 (ttp80) REVERT: A 350 GLN cc_start: 0.8562 (mm110) cc_final: 0.8342 (mp10) REVERT: A 351 MET cc_start: 0.8470 (mtp) cc_final: 0.8209 (mtm) REVERT: B 44 GLN cc_start: 0.8572 (OUTLIER) cc_final: 0.7916 (mt0) REVERT: B 214 ARG cc_start: 0.8239 (mmt180) cc_final: 0.7763 (mmt180) REVERT: B 215 GLU cc_start: 0.8381 (mm-30) cc_final: 0.8048 (mm-30) REVERT: B 217 MET cc_start: 0.8521 (OUTLIER) cc_final: 0.7140 (pmt) REVERT: E 46 GLU cc_start: 0.8384 (tt0) cc_final: 0.7905 (pt0) REVERT: R 51 ASN cc_start: 0.7439 (p0) cc_final: 0.7044 (p0) REVERT: R 233 THR cc_start: 0.8104 (m) cc_final: 0.7744 (p) outliers start: 30 outliers final: 20 residues processed: 154 average time/residue: 0.6568 time to fit residues: 106.9984 Evaluate side-chains 159 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 136 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 75 SER Chi-restraints excluded: chain R residue 93 ILE Chi-restraints excluded: chain R residue 140 VAL Chi-restraints excluded: chain R residue 172 SER Chi-restraints excluded: chain R residue 240 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 21 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 96 optimal weight: 0.9980 chunk 99 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 73 optimal weight: 10.0000 chunk 44 optimal weight: 0.7980 chunk 56 optimal weight: 6.9990 chunk 24 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 231 GLN ** R 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.159512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.109055 restraints weight = 9875.684| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.01 r_work: 0.3118 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8839 Z= 0.153 Angle : 0.580 11.207 12016 Z= 0.298 Chirality : 0.043 0.154 1391 Planarity : 0.003 0.044 1520 Dihedral : 4.169 27.726 1293 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.29 % Allowed : 20.20 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.46 (0.26), residues: 1109 helix: 2.31 (0.26), residues: 399 sheet: 0.06 (0.30), residues: 278 loop : 0.44 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 218 TYR 0.009 0.001 TYR R 126 PHE 0.019 0.001 PHE E 68 TRP 0.016 0.001 TRP B 169 HIS 0.008 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 8836) covalent geometry : angle 0.57942 (12010) SS BOND : bond 0.00228 ( 3) SS BOND : angle 1.24114 ( 6) hydrogen bonds : bond 0.03949 ( 454) hydrogen bonds : angle 4.64975 ( 1311) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3757.76 seconds wall clock time: 64 minutes 46.17 seconds (3886.17 seconds total)