Starting phenix.real_space_refine on Wed Jan 15 14:53:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yn4_39414/01_2025/8yn4_39414.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yn4_39414/01_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_39414/01_2025/8yn4_39414.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yn4_39414/01_2025/8yn4_39414.map" model { file = "/net/cci-nas-00/data/ceres_data/8yn4_39414/01_2025/8yn4_39414.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yn4_39414/01_2025/8yn4_39414.cif" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.011 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-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: {'GLU:plan': 8, 'ARG:plan': 5, 'ASP:plan': 8} 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: {'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 1} 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: 5.26, per 1000 atoms: 0.61 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: 2.45 Conformation dependent library (CDL) restraints added in 996.7 milliseconds 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: 1.20 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: 2.71 Time building geometry restraints manager: 2.65 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: 0.350 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: 0.020 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 22.590 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 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:13.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.740 ------------------------------------------------------------------------------- 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 8836 Z= 0.103 Angle : 0.396 7.541 12010 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (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 TRP 0.007 0.001 TRP B 339 HIS 0.002 0.001 HIS B 91 PHE 0.009 0.001 PHE A 228 TYR 0.011 0.001 TYR E 190 ARG 0.002 0.000 ARG E 38 *********************** 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 : 0.972 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: 1.2681 time to fit residues: 303.0909 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 : 1.039 ------------------------------------------------------------------------------- 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 92 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 0.0040 chunk 44 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 52 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 overall best weight: 1.7798 ------------------------------------------------------------------------------- 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 E 171 ASN R 46 ASN R 79 GLN R 212 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.159078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.107852 restraints weight = 9782.260| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.99 r_work: 0.3090 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8836 Z= 0.290 Angle : 0.577 8.637 12010 Z= 0.308 Chirality : 0.044 0.151 1391 Planarity : 0.004 0.039 1520 Dihedral : 4.576 30.614 1295 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.73 % Allowed : 12.18 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.25), residues: 1109 helix: 2.38 (0.26), residues: 385 sheet: 0.76 (0.30), residues: 272 loop : 0.41 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP R 275 HIS 0.005 0.001 HIS B 91 PHE 0.018 0.002 PHE B 199 TYR 0.020 0.002 TYR R 256 ARG 0.009 0.001 ARG B 219 *********************** 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 193 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 159 time to evaluate : 0.874 Fit side-chains REVERT: A 14 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.7716 (tt0) REVERT: A 94 ARG cc_start: 0.6875 (ptt-90) cc_final: 0.6615 (ttp-170) REVERT: A 122 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.7989 (mp) REVERT: A 126 LYS cc_start: 0.8458 (mtpp) cc_final: 0.8246 (mtpm) REVERT: A 152 LYS cc_start: 0.8087 (tttt) cc_final: 0.7882 (mtmt) REVERT: A 351 MET cc_start: 0.8459 (mtp) cc_final: 0.8179 (mtm) REVERT: B 13 GLN cc_start: 0.8599 (tm-30) cc_final: 0.8256 (tm-30) REVERT: B 17 GLN cc_start: 0.8727 (tt0) cc_final: 0.8287 (tt0) REVERT: B 44 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.7841 (mt0) REVERT: B 214 ARG cc_start: 0.8256 (mmt180) cc_final: 0.7906 (mmt180) REVERT: C 17 GLU cc_start: 0.8896 (tp30) cc_final: 0.8263 (tm-30) REVERT: C 46 LYS cc_start: 0.8732 (mppt) cc_final: 0.8531 (mppt) REVERT: R 31 ILE cc_start: 0.8540 (OUTLIER) cc_final: 0.8241 (mp) REVERT: R 78 TYR cc_start: 0.8227 (t80) cc_final: 0.8016 (t80) outliers start: 34 outliers final: 16 residues processed: 179 average time/residue: 1.3244 time to fit residues: 251.1635 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 : 0.919 ------------------------------------------------------------------------------- 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 223 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 139 VAL Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain R residue 31 ILE Chi-restraints excluded: chain R residue 140 VAL 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 31 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 61 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 108 optimal weight: 7.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.158734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.107078 restraints weight = 10012.790| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.03 r_work: 0.3092 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8836 Z= 0.267 Angle : 0.538 6.505 12010 Z= 0.290 Chirality : 0.043 0.173 1391 Planarity : 0.004 0.039 1520 Dihedral : 4.446 29.606 1293 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 4.50 % Allowed : 14.05 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.25), residues: 1109 helix: 2.33 (0.26), residues: 392 sheet: 0.52 (0.30), residues: 272 loop : 0.44 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 275 HIS 0.004 0.001 HIS B 225 PHE 0.016 0.002 PHE B 199 TYR 0.014 0.001 TYR E 227 ARG 0.006 0.001 ARG B 219 *********************** 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 184 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 143 time to evaluate : 0.962 Fit side-chains REVERT: A 14 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.7629 (tt0) REVERT: A 94 ARG cc_start: 0.6836 (ptt-90) cc_final: 0.6606 (ttp-170) REVERT: A 122 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.8021 (mp) REVERT: A 152 LYS cc_start: 0.8076 (tttt) cc_final: 0.7711 (mtpt) REVERT: A 351 MET cc_start: 0.8431 (mtp) cc_final: 0.8156 (mtm) REVERT: B 17 GLN cc_start: 0.8544 (tt0) cc_final: 0.8315 (tt0) REVERT: B 44 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.7895 (mt0) REVERT: B 214 ARG cc_start: 0.8236 (mmt180) cc_final: 0.7867 (mmt180) REVERT: B 215 GLU cc_start: 0.8471 (mm-30) cc_final: 0.8086 (mm-30) REVERT: B 217 MET cc_start: 0.8471 (OUTLIER) cc_final: 0.7096 (pmt) REVERT: C 17 GLU cc_start: 0.8924 (tp30) cc_final: 0.8308 (tm-30) REVERT: R 31 ILE cc_start: 0.8515 (OUTLIER) cc_final: 0.8216 (mp) REVERT: R 51 ASN cc_start: 0.7342 (p0) cc_final: 0.6974 (p0) REVERT: R 233 THR cc_start: 0.8360 (m) cc_final: 0.7980 (p) outliers start: 41 outliers final: 18 residues processed: 164 average time/residue: 1.3490 time to fit residues: 234.3977 Evaluate side-chains 153 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 1.041 ------------------------------------------------------------------------------- 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 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 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 93 ILE Chi-restraints excluded: chain R residue 140 VAL Chi-restraints excluded: chain R residue 141 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 29 optimal weight: 3.9990 chunk 98 optimal weight: 20.0000 chunk 72 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 14 optimal weight: 10.0000 chunk 62 optimal weight: 8.9990 chunk 66 optimal weight: 0.9990 chunk 75 optimal weight: 8.9990 chunk 18 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 92 optimal weight: 7.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 231 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.159130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.112351 restraints weight = 9919.505| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.13 r_work: 0.3108 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8836 Z= 0.222 Angle : 0.518 7.142 12010 Z= 0.277 Chirality : 0.043 0.201 1391 Planarity : 0.003 0.043 1520 Dihedral : 4.257 28.848 1293 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 4.17 % Allowed : 16.14 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.25), residues: 1109 helix: 2.49 (0.26), residues: 393 sheet: 0.31 (0.30), residues: 276 loop : 0.42 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 169 HIS 0.003 0.001 HIS B 225 PHE 0.014 0.001 PHE B 199 TYR 0.011 0.001 TYR E 190 ARG 0.008 0.000 ARG B 19 *********************** 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 184 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 146 time to evaluate : 0.871 Fit side-chains REVERT: A 14 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.7598 (tt0) REVERT: A 21 LYS cc_start: 0.8408 (ttpp) cc_final: 0.8069 (ttmt) REVERT: A 94 ARG cc_start: 0.6807 (ptt-90) cc_final: 0.6601 (ttp-170) REVERT: A 152 LYS cc_start: 0.8048 (tttt) cc_final: 0.7713 (mtmt) REVERT: A 351 MET cc_start: 0.8454 (mtp) cc_final: 0.8202 (mtm) REVERT: B 44 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.7866 (mt0) REVERT: B 214 ARG cc_start: 0.8276 (mmt180) cc_final: 0.7839 (mmt180) REVERT: B 215 GLU cc_start: 0.8410 (mm-30) cc_final: 0.8046 (mm-30) REVERT: B 217 MET cc_start: 0.8399 (OUTLIER) cc_final: 0.7015 (pmt) REVERT: B 237 ASN cc_start: 0.8736 (p0) cc_final: 0.8352 (p0) REVERT: B 280 LYS cc_start: 0.8573 (tttt) cc_final: 0.8354 (tttm) REVERT: C 17 GLU cc_start: 0.8902 (tp30) cc_final: 0.8258 (tm-30) REVERT: C 42 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7274 (tp30) REVERT: C 46 LYS cc_start: 0.8862 (mppt) cc_final: 0.8620 (mppt) REVERT: R 31 ILE cc_start: 0.8489 (OUTLIER) cc_final: 0.8187 (mp) REVERT: R 51 ASN cc_start: 0.7363 (p0) cc_final: 0.6987 (p0) REVERT: R 233 THR cc_start: 0.8280 (m) cc_final: 0.7897 (p) outliers start: 38 outliers final: 18 residues processed: 162 average time/residue: 1.3304 time to fit residues: 228.7120 Evaluate side-chains 154 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 0.946 ------------------------------------------------------------------------------- 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 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 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 93 ILE Chi-restraints excluded: chain R residue 141 LEU 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 59 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 74 optimal weight: 0.3980 chunk 5 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 84 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 E 231 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.161278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.111278 restraints weight = 9841.617| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.98 r_work: 0.3146 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8836 Z= 0.152 Angle : 0.498 9.293 12010 Z= 0.260 Chirality : 0.041 0.159 1391 Planarity : 0.003 0.044 1520 Dihedral : 4.046 29.469 1293 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 3.51 % Allowed : 17.56 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.25), residues: 1109 helix: 2.58 (0.26), residues: 394 sheet: 0.24 (0.30), residues: 277 loop : 0.46 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.003 0.001 HIS B 225 PHE 0.011 0.001 PHE A 228 TYR 0.013 0.001 TYR E 190 ARG 0.006 0.000 ARG B 19 *********************** 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 175 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 143 time to evaluate : 0.941 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.7660 (tt0) REVERT: A 21 LYS cc_start: 0.8357 (ttpp) cc_final: 0.8014 (ttmt) REVERT: A 94 ARG cc_start: 0.6721 (ptt-90) cc_final: 0.6448 (ttp-170) REVERT: A 152 LYS cc_start: 0.8013 (tttt) cc_final: 0.7775 (mtmt) REVERT: A 351 MET cc_start: 0.8405 (mtp) cc_final: 0.8167 (mtm) REVERT: B 44 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.7845 (mt0) REVERT: B 214 ARG cc_start: 0.8264 (mmt180) cc_final: 0.7909 (mmt180) REVERT: B 217 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.7049 (pmt) REVERT: C 17 GLU cc_start: 0.8911 (tp30) cc_final: 0.8253 (tm-30) REVERT: C 42 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7268 (tp30) REVERT: C 46 LYS cc_start: 0.8874 (mppt) cc_final: 0.8673 (mppt) REVERT: R 51 ASN cc_start: 0.7339 (p0) cc_final: 0.6979 (p0) REVERT: R 233 THR cc_start: 0.8234 (m) cc_final: 0.7863 (p) outliers start: 32 outliers final: 15 residues processed: 159 average time/residue: 1.4423 time to fit residues: 242.2057 Evaluate side-chains 149 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 0.925 ------------------------------------------------------------------------------- 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 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 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 E residue 195 LEU 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 38 optimal weight: 6.9990 chunk 46 optimal weight: 0.9980 chunk 92 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 chunk 80 optimal weight: 6.9990 chunk 42 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 108 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN A 223 ASN B 175 GLN E 231 GLN ** R 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.158324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.111322 restraints weight = 9804.744| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.17 r_work: 0.3090 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8836 Z= 0.284 Angle : 0.543 8.840 12010 Z= 0.285 Chirality : 0.043 0.140 1391 Planarity : 0.003 0.043 1520 Dihedral : 4.197 28.692 1293 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 4.50 % Allowed : 17.01 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.25), residues: 1109 helix: 2.49 (0.26), residues: 395 sheet: 0.19 (0.30), residues: 276 loop : 0.39 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 169 HIS 0.004 0.001 HIS E 167 PHE 0.016 0.002 PHE B 199 TYR 0.013 0.001 TYR E 227 ARG 0.006 0.000 ARG B 19 *********************** 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 185 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 144 time to evaluate : 0.966 Fit side-chains REVERT: A 14 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.7627 (tt0) REVERT: A 18 MET cc_start: 0.8330 (OUTLIER) cc_final: 0.8079 (ttt) REVERT: A 132 ARG cc_start: 0.8463 (ttp80) cc_final: 0.8106 (ttp80) REVERT: A 152 LYS cc_start: 0.8108 (tttt) cc_final: 0.7709 (mtpt) REVERT: A 351 MET cc_start: 0.8452 (mtp) cc_final: 0.8208 (mtm) REVERT: B 44 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.7942 (mt0) REVERT: B 214 ARG cc_start: 0.8269 (mmt180) cc_final: 0.7896 (mmt180) REVERT: B 215 GLU cc_start: 0.8347 (mm-30) cc_final: 0.7962 (mm-30) REVERT: B 217 MET cc_start: 0.8486 (OUTLIER) cc_final: 0.7067 (pmt) REVERT: C 17 GLU cc_start: 0.8908 (tp30) cc_final: 0.8230 (tm-30) REVERT: C 42 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7339 (tp30) REVERT: C 46 LYS cc_start: 0.8896 (mppt) cc_final: 0.8664 (mppt) REVERT: R 51 ASN cc_start: 0.7416 (p0) cc_final: 0.7011 (p0) REVERT: R 233 THR cc_start: 0.8119 (m) cc_final: 0.7770 (p) outliers start: 41 outliers final: 21 residues processed: 160 average time/residue: 1.4582 time to fit residues: 247.2558 Evaluate side-chains 160 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 0.898 ------------------------------------------------------------------------------- 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 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 65 THR 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 R residue 41 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 94 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 93 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 ** 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 = 0.3900 r_free = 0.3900 target = 0.160322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.114075 restraints weight = 9981.369| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.16 r_work: 0.3135 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8836 Z= 0.175 Angle : 0.509 9.186 12010 Z= 0.268 Chirality : 0.041 0.135 1391 Planarity : 0.003 0.044 1520 Dihedral : 4.055 28.147 1293 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.51 % Allowed : 18.88 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.26), residues: 1109 helix: 2.62 (0.26), residues: 395 sheet: 0.14 (0.30), residues: 277 loop : 0.44 (0.31), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.003 0.001 HIS B 225 PHE 0.022 0.001 PHE E 68 TYR 0.015 0.001 TYR E 227 ARG 0.008 0.000 ARG B 19 *********************** 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 174 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 142 time to evaluate : 1.011 Fit side-chains REVERT: A 14 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.7708 (tt0) REVERT: A 21 LYS cc_start: 0.8466 (ttpp) cc_final: 0.8147 (ttmt) REVERT: A 71 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7483 (tp30) REVERT: A 132 ARG cc_start: 0.8434 (ttp80) cc_final: 0.8160 (ttp80) REVERT: A 152 LYS cc_start: 0.8125 (tttt) cc_final: 0.7728 (mtpt) REVERT: A 351 MET cc_start: 0.8438 (mtp) cc_final: 0.8223 (mtm) REVERT: B 44 GLN cc_start: 0.8529 (OUTLIER) cc_final: 0.7923 (mt0) REVERT: B 214 ARG cc_start: 0.8317 (mmt180) cc_final: 0.8057 (mpt180) REVERT: B 215 GLU cc_start: 0.8394 (mm-30) cc_final: 0.8030 (mm-30) REVERT: B 217 MET cc_start: 0.8439 (OUTLIER) cc_final: 0.7092 (pmt) REVERT: C 17 GLU cc_start: 0.8895 (tp30) cc_final: 0.8269 (tm-30) REVERT: C 42 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7300 (tp30) REVERT: C 46 LYS cc_start: 0.8869 (mppt) cc_final: 0.8634 (mppt) REVERT: E 46 GLU cc_start: 0.8356 (tt0) cc_final: 0.7944 (pt0) REVERT: R 31 ILE cc_start: 0.8349 (OUTLIER) cc_final: 0.7980 (mp) REVERT: R 51 ASN cc_start: 0.7457 (p0) cc_final: 0.7044 (p0) REVERT: R 233 THR cc_start: 0.8111 (m) cc_final: 0.7782 (p) outliers start: 32 outliers final: 18 residues processed: 156 average time/residue: 1.3326 time to fit residues: 220.6583 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 : 0.909 ------------------------------------------------------------------------------- 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 65 THR 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 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 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 196 LEU Chi-restraints excluded: chain R residue 240 MET Chi-restraints excluded: chain R residue 252 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 73 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 22 optimal weight: 9.9990 chunk 40 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 105 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 ** 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 = 0.3890 r_free = 0.3890 target = 0.159653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.108658 restraints weight = 10005.711| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.04 r_work: 0.3113 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8836 Z= 0.224 Angle : 0.538 9.328 12010 Z= 0.280 Chirality : 0.042 0.136 1391 Planarity : 0.003 0.045 1520 Dihedral : 4.110 28.180 1293 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.73 % Allowed : 18.99 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.26), residues: 1109 helix: 2.55 (0.26), residues: 396 sheet: 0.22 (0.30), residues: 274 loop : 0.43 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.004 0.001 HIS B 225 PHE 0.014 0.001 PHE B 199 TYR 0.012 0.001 TYR E 227 ARG 0.009 0.000 ARG B 19 *********************** 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: 34 poor density : 143 time to evaluate : 0.975 Fit side-chains REVERT: A 14 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.7656 (tt0) REVERT: A 21 LYS cc_start: 0.8445 (ttpp) cc_final: 0.8095 (ttmt) REVERT: A 132 ARG cc_start: 0.8466 (ttp80) cc_final: 0.8175 (ttp80) REVERT: A 152 LYS cc_start: 0.8106 (tttt) cc_final: 0.7697 (mtpt) REVERT: A 351 MET cc_start: 0.8446 (mtp) cc_final: 0.8222 (mtm) REVERT: B 44 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.7918 (mt0) REVERT: B 214 ARG cc_start: 0.8246 (mmt180) cc_final: 0.7754 (mmt180) REVERT: B 215 GLU cc_start: 0.8399 (mm-30) cc_final: 0.8019 (mm-30) REVERT: B 217 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.7062 (pmt) REVERT: C 17 GLU cc_start: 0.8891 (tp30) cc_final: 0.8265 (tm-30) REVERT: C 42 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7282 (tp30) REVERT: C 46 LYS cc_start: 0.8876 (mppt) cc_final: 0.8611 (mppt) REVERT: E 46 GLU cc_start: 0.8330 (tt0) cc_final: 0.7871 (pt0) REVERT: R 51 ASN cc_start: 0.7436 (p0) cc_final: 0.7021 (p0) REVERT: R 233 THR cc_start: 0.8129 (m) cc_final: 0.7777 (p) outliers start: 34 outliers final: 22 residues processed: 155 average time/residue: 1.2986 time to fit residues: 213.5353 Evaluate side-chains 164 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 0.876 ------------------------------------------------------------------------------- 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 65 THR 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 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 196 LEU Chi-restraints excluded: chain R residue 240 MET Chi-restraints excluded: chain R residue 252 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 100 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 65 optimal weight: 0.0970 chunk 106 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 37 optimal weight: 0.4980 chunk 85 optimal weight: 10.0000 chunk 77 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 ** 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 = 0.3876 r_free = 0.3876 target = 0.159792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.113808 restraints weight = 9991.636| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.16 r_work: 0.3104 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8836 Z= 0.155 Angle : 0.518 9.398 12010 Z= 0.268 Chirality : 0.041 0.133 1391 Planarity : 0.003 0.045 1520 Dihedral : 3.957 27.874 1293 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.07 % Allowed : 19.43 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.26), residues: 1109 helix: 2.62 (0.26), residues: 396 sheet: 0.25 (0.30), residues: 278 loop : 0.41 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.004 0.001 HIS B 225 PHE 0.017 0.001 PHE E 68 TYR 0.010 0.001 TYR E 190 ARG 0.004 0.000 ARG E 18 *********************** 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 176 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 148 time to evaluate : 1.046 Fit side-chains REVERT: A 14 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.7624 (tt0) REVERT: A 21 LYS cc_start: 0.8415 (ttpp) cc_final: 0.8058 (ttmt) REVERT: A 152 LYS cc_start: 0.8027 (tttt) cc_final: 0.7621 (mtpt) REVERT: A 351 MET cc_start: 0.8339 (mtp) cc_final: 0.8107 (mtm) REVERT: B 214 ARG cc_start: 0.8112 (mmt180) cc_final: 0.7864 (mpt180) REVERT: B 217 MET cc_start: 0.8516 (OUTLIER) cc_final: 0.8312 (ppp) REVERT: C 17 GLU cc_start: 0.8900 (tp30) cc_final: 0.8220 (tm-30) REVERT: C 42 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7253 (tp30) REVERT: C 46 LYS cc_start: 0.8879 (mppt) cc_final: 0.8585 (mppt) REVERT: E 46 GLU cc_start: 0.8261 (tt0) cc_final: 0.7773 (pt0) REVERT: E 218 ARG cc_start: 0.7510 (mmm160) cc_final: 0.7163 (mmm160) REVERT: R 51 ASN cc_start: 0.7492 (p0) cc_final: 0.7129 (p0) REVERT: R 137 ILE cc_start: 0.7923 (mp) cc_final: 0.7701 (mp) outliers start: 28 outliers final: 14 residues processed: 157 average time/residue: 1.3001 time to fit residues: 216.9324 Evaluate side-chains 154 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 137 time to evaluate : 0.885 ------------------------------------------------------------------------------- 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 101 MET Chi-restraints excluded: chain B residue 135 VAL 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 R residue 93 ILE Chi-restraints excluded: chain R residue 121 MET Chi-restraints excluded: chain R residue 196 LEU Chi-restraints excluded: chain R residue 240 MET Chi-restraints excluded: chain R residue 252 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 103 optimal weight: 0.0970 chunk 25 optimal weight: 0.0070 chunk 55 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- 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** B 268 ASN E 231 GLN ** R 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.160950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.110331 restraints weight = 10071.553| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.10 r_work: 0.3116 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8836 Z= 0.149 Angle : 0.528 9.602 12010 Z= 0.271 Chirality : 0.042 0.162 1391 Planarity : 0.003 0.044 1520 Dihedral : 3.881 28.049 1293 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.63 % Allowed : 20.75 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.26), residues: 1109 helix: 2.65 (0.26), residues: 396 sheet: 0.21 (0.30), residues: 285 loop : 0.44 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.005 0.001 HIS B 225 PHE 0.017 0.001 PHE E 68 TYR 0.013 0.001 TYR E 190 ARG 0.009 0.000 ARG B 19 ********************** 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 169 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 145 time to evaluate : 1.019 Fit side-chains REVERT: A 14 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.7642 (tt0) REVERT: A 21 LYS cc_start: 0.8433 (ttpp) cc_final: 0.8076 (ttmt) REVERT: A 132 ARG cc_start: 0.8295 (ttp80) cc_final: 0.7781 (ttp80) REVERT: A 152 LYS cc_start: 0.8029 (tttt) cc_final: 0.7770 (mtmt) REVERT: A 351 MET cc_start: 0.8356 (mtp) cc_final: 0.8137 (mtm) REVERT: B 214 ARG cc_start: 0.8095 (mmt180) cc_final: 0.7731 (mmt180) REVERT: C 17 GLU cc_start: 0.8910 (tp30) cc_final: 0.8210 (tm-30) REVERT: C 20 LYS cc_start: 0.9137 (mttp) cc_final: 0.8891 (mttp) REVERT: C 42 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7253 (tp30) REVERT: C 46 LYS cc_start: 0.8928 (mppt) cc_final: 0.8644 (mppt) REVERT: E 46 GLU cc_start: 0.8254 (tt0) cc_final: 0.7636 (pt0) REVERT: E 59 TYR cc_start: 0.8007 (m-10) cc_final: 0.7755 (m-10) REVERT: E 218 ARG cc_start: 0.7480 (mmm160) cc_final: 0.7141 (mmm160) REVERT: R 51 ASN cc_start: 0.7486 (p0) cc_final: 0.7148 (p0) REVERT: R 78 TYR cc_start: 0.8155 (t80) cc_final: 0.7883 (t80) REVERT: R 137 ILE cc_start: 0.7961 (mp) cc_final: 0.7705 (mp) REVERT: R 280 ASN cc_start: 0.8294 (t0) cc_final: 0.8090 (t0) outliers start: 24 outliers final: 12 residues processed: 156 average time/residue: 1.2805 time to fit residues: 213.4823 Evaluate side-chains 154 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 140 time to evaluate : 0.948 ------------------------------------------------------------------------------- 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 101 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 181 THR 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 E residue 192 MET Chi-restraints excluded: chain R residue 93 ILE Chi-restraints excluded: chain R residue 140 VAL Chi-restraints excluded: chain R residue 240 MET Chi-restraints excluded: chain R residue 252 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 23 optimal weight: 8.9990 chunk 75 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 91 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 175 GLN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN E 231 GLN ** R 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.158706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.107320 restraints weight = 10014.614| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.05 r_work: 0.3093 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8836 Z= 0.307 Angle : 0.600 10.452 12010 Z= 0.308 Chirality : 0.045 0.170 1391 Planarity : 0.004 0.043 1520 Dihedral : 4.174 28.023 1293 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.18 % Allowed : 19.32 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.26), residues: 1109 helix: 2.44 (0.26), residues: 397 sheet: 0.07 (0.30), residues: 286 loop : 0.48 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 169 HIS 0.008 0.002 HIS B 225 PHE 0.016 0.002 PHE B 199 TYR 0.014 0.002 TYR E 227 ARG 0.004 0.000 ARG E 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7625.58 seconds wall clock time: 135 minutes 0.79 seconds (8100.79 seconds total)