Starting phenix.real_space_refine on Thu Jul 2 09:41:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k4s_36890/07_2026/8k4s_36890_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k4s_36890/07_2026/8k4s_36890.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8k4s_36890/07_2026/8k4s_36890_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k4s_36890/07_2026/8k4s_36890_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8k4s_36890/07_2026/8k4s_36890.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k4s_36890/07_2026/8k4s_36890.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.138 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 55 5.16 5 C 5249 2.51 5 N 1394 2.21 5 O 1497 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8196 Number of models: 1 Model: "" Number of chains: 6 Chain: "E" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1956 Classifications: {'peptide': 255} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 8, 'TRANS': 246} Chain breaks: 1 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 4, 'PHE:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 57 Chain: "A" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1673 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 6, 'TRANS': 215} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 8, 'PHE:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 5, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 94 Chain: "B" Number of atoms: 2481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2481 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 6, 'GLN:plan1': 3, 'ARG:plan': 7, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 88 Chain: "C" Number of atoms: 329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 329 Classifications: {'peptide': 47} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 4, 'TRANS': 42} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "D" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1725 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 10, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'JW0': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.35, per 1000 atoms: 0.16 Number of scatterers: 8196 At special positions: 0 Unit cell: (119.6, 96.72, 117.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 55 16.00 P 1 15.00 O 1497 8.00 N 1394 7.00 C 5249 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 251 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 217 " 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: 0.45 Conformation dependent library (CDL) restraints added in 321.0 milliseconds 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2046 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 14 sheets defined 34.1% alpha, 22.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'E' and resid 27 through 55 removed outlier: 3.775A pdb=" N TYR E 54 " --> pdb=" O TRP E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 83 Processing helix chain 'E' and resid 84 through 87 removed outlier: 3.799A pdb=" N LEU E 87 " --> pdb=" O PRO E 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 84 through 87' Processing helix chain 'E' and resid 93 through 126 removed outlier: 3.883A pdb=" N ILE E 97 " --> pdb=" O LEU E 93 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N PHE E 104 " --> pdb=" O SER E 100 " (cutoff:3.500A) Proline residue: E 105 - end of helix Processing helix chain 'E' and resid 126 through 133 Processing helix chain 'E' and resid 137 through 152 Processing helix chain 'E' and resid 178 through 204 Processing helix chain 'E' and resid 213 through 227 Processing helix chain 'E' and resid 229 through 242 Processing helix chain 'E' and resid 252 through 279 Proline residue: E 269 - end of helix removed outlier: 4.727A pdb=" N VAL E 275 " --> pdb=" O ILE E 271 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N GLY E 276 " --> pdb=" O TYR E 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.920A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 99 Processing helix chain 'A' and resid 117 through 130 Processing helix chain 'A' and resid 146 through 156 removed outlier: 3.625A pdb=" N GLY A 156 " --> pdb=" O LYS A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 164 removed outlier: 3.931A pdb=" N TYR A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 168 removed outlier: 3.982A pdb=" N ALA A 168 " --> pdb=" O PRO A 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 165 through 168' Processing helix chain 'A' and resid 183 through 204 removed outlier: 4.441A pdb=" N ILE A 200 " --> pdb=" O GLU A 196 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N SER A 204 " --> pdb=" O ILE A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 243 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'C' and resid 17 through 22 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 55 through 59 Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 53 through 56 removed outlier: 4.109A pdb=" N GLY D 56 " --> pdb=" O SER D 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 53 through 56' Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 76 removed outlier: 4.864A pdb=" N VAL A 86 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N GLY A 40 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA A 105 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE A 106 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N PHE A 142 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N PHE A 108 " --> pdb=" O PHE A 142 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N VAL A 139 " --> pdb=" O TYR A 212 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N HIS A 214 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU A 141 " --> pdb=" O HIS A 214 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.603A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.524A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.694A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.981A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.550A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.302A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.522A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 3 through 7 removed outlier: 3.588A pdb=" N ARG D 18 " --> pdb=" O MET D 83 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 11 through 12 Processing sheet with id=AB2, first strand: chain 'D' and resid 58 through 60 removed outlier: 4.730A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 128 through 129 Processing sheet with id=AB4, first strand: chain 'D' and resid 134 through 136 removed outlier: 3.571A pdb=" N GLU D 234 " --> pdb=" O VAL D 135 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 182 through 183 removed outlier: 6.677A pdb=" N TRP D 164 " --> pdb=" O LEU D 176 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N TYR D 178 " --> pdb=" O LEU D 162 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LEU D 162 " --> pdb=" O TYR D 178 " (cutoff:3.500A) 403 hydrogen bonds defined for protein. 1152 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: 0.95 Time building geometry restraints manager: 0.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2073 1.33 - 1.45: 1658 1.45 - 1.57: 4563 1.57 - 1.70: 3 1.70 - 1.82: 75 Bond restraints: 8372 Sorted by residual: bond pdb=" C10 JW0 E 601 " pdb=" C14 JW0 E 601 " ideal model delta sigma weight residual 1.538 1.459 0.079 2.00e-02 2.50e+03 1.57e+01 bond pdb=" C12 JW0 E 601 " pdb=" C17 JW0 E 601 " ideal model delta sigma weight residual 1.545 1.471 0.074 2.00e-02 2.50e+03 1.36e+01 bond pdb=" C5 JW0 E 601 " pdb=" C6 JW0 E 601 " ideal model delta sigma weight residual 1.538 1.471 0.067 2.00e-02 2.50e+03 1.13e+01 bond pdb=" C15 JW0 E 601 " pdb=" C16 JW0 E 601 " ideal model delta sigma weight residual 1.549 1.613 -0.064 2.00e-02 2.50e+03 1.02e+01 bond pdb=" C13 JW0 E 601 " pdb=" O1 JW0 E 601 " ideal model delta sigma weight residual 1.416 1.353 0.063 2.00e-02 2.50e+03 9.80e+00 ... (remaining 8367 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 11173 1.83 - 3.67: 176 3.67 - 5.50: 51 5.50 - 7.33: 15 7.33 - 9.16: 4 Bond angle restraints: 11419 Sorted by residual: angle pdb=" N TYR D 223 " pdb=" CA TYR D 223 " pdb=" C TYR D 223 " ideal model delta sigma weight residual 109.81 117.06 -7.25 2.21e+00 2.05e-01 1.08e+01 angle pdb=" N VAL E 248 " pdb=" CA VAL E 248 " pdb=" C VAL E 248 " ideal model delta sigma weight residual 113.53 110.49 3.04 9.80e-01 1.04e+00 9.64e+00 angle pdb=" C12 JW0 E 601 " pdb=" C17 JW0 E 601 " pdb=" C18 JW0 E 601 " ideal model delta sigma weight residual 118.30 109.14 9.16 3.00e+00 1.11e-01 9.33e+00 angle pdb=" CA LEU E 51 " pdb=" CB LEU E 51 " pdb=" CG LEU E 51 " ideal model delta sigma weight residual 116.30 125.45 -9.15 3.50e+00 8.16e-02 6.83e+00 angle pdb=" C ARG D 179 " pdb=" N MET D 180 " pdb=" CA MET D 180 " ideal model delta sigma weight residual 121.54 126.40 -4.86 1.91e+00 2.74e-01 6.48e+00 ... (remaining 11414 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 4236 17.68 - 35.36: 525 35.36 - 53.03: 160 53.03 - 70.71: 26 70.71 - 88.39: 6 Dihedral angle restraints: 4953 sinusoidal: 1784 harmonic: 3169 Sorted by residual: dihedral pdb=" CB CYS E 23 " pdb=" SG CYS E 23 " pdb=" SG CYS E 251 " pdb=" CB CYS E 251 " ideal model delta sinusoidal sigma weight residual 93.00 23.78 69.22 1 1.00e+01 1.00e-02 6.19e+01 dihedral pdb=" CB CYS D 147 " pdb=" SG CYS D 147 " pdb=" SG CYS D 217 " pdb=" CB CYS D 217 " ideal model delta sinusoidal sigma weight residual 93.00 146.62 -53.62 1 1.00e+01 1.00e-02 3.91e+01 dihedral pdb=" CA LEU A 143 " pdb=" C LEU A 143 " pdb=" N ASN A 144 " pdb=" CA ASN A 144 " ideal model delta harmonic sigma weight residual 180.00 -157.89 -22.11 0 5.00e+00 4.00e-02 1.96e+01 ... (remaining 4950 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 1302 0.101 - 0.203: 41 0.203 - 0.304: 6 0.304 - 0.406: 0 0.406 - 0.507: 2 Chirality restraints: 1351 Sorted by residual: chirality pdb=" C17 JW0 E 601 " pdb=" C12 JW0 E 601 " pdb=" C16 JW0 E 601 " pdb=" C18 JW0 E 601 " both_signs ideal model delta sigma weight residual False 2.36 2.87 -0.51 2.00e-01 2.50e+01 6.42e+00 chirality pdb=" C11 JW0 E 601 " pdb=" C12 JW0 E 601 " pdb=" C15 JW0 E 601 " pdb=" C9 JW0 E 601 " both_signs ideal model delta sigma weight residual False -2.37 -2.82 0.45 2.00e-01 2.50e+01 5.01e+00 chirality pdb=" C12 JW0 E 601 " pdb=" C11 JW0 E 601 " pdb=" C13 JW0 E 601 " pdb=" C17 JW0 E 601 " both_signs ideal model delta sigma weight residual False 2.87 2.59 0.28 2.00e-01 2.50e+01 1.94e+00 ... (remaining 1348 not shown) Planarity restraints: 1430 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 48 " 0.039 5.00e-02 4.00e+02 5.93e-02 5.64e+00 pdb=" N PRO C 49 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO C 49 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 49 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 163 " 0.011 2.00e-02 2.50e+03 2.20e-02 4.86e+00 pdb=" CG ASP B 163 " -0.038 2.00e-02 2.50e+03 pdb=" OD1 ASP B 163 " 0.014 2.00e-02 2.50e+03 pdb=" OD2 ASP B 163 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 196 " -0.009 2.00e-02 2.50e+03 1.76e-02 3.09e+00 pdb=" C THR B 196 " 0.030 2.00e-02 2.50e+03 pdb=" O THR B 196 " -0.012 2.00e-02 2.50e+03 pdb=" N ARG B 197 " -0.010 2.00e-02 2.50e+03 ... (remaining 1427 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 196 2.68 - 3.23: 7673 3.23 - 3.79: 13211 3.79 - 4.34: 17723 4.34 - 4.90: 30102 Nonbonded interactions: 68905 Sorted by model distance: nonbonded pdb=" OH TYR E 106 " pdb=" O GLY E 229 " model vdw 2.122 3.040 nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.198 3.040 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR D 163 " model vdw 2.208 3.040 nonbonded pdb=" O SER A 44 " pdb=" ND2 ASN A 144 " model vdw 2.221 3.120 nonbonded pdb=" OE1 GLN A 98 " pdb=" NH1 ARG B 314 " model vdw 2.224 3.120 ... (remaining 68900 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: 1.050 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: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.710 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:5.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 8375 Z= 0.168 Angle : 0.661 9.165 11425 Z= 0.326 Chirality : 0.050 0.507 1351 Planarity : 0.004 0.059 1430 Dihedral : 17.108 88.389 2898 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 4.46 % Allowed : 31.69 % Favored : 63.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.26), residues: 1075 helix: 1.99 (0.29), residues: 337 sheet: 0.18 (0.29), residues: 267 loop : -0.83 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 219 TYR 0.022 0.001 TYR E 240 PHE 0.024 0.001 PHE E 78 TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.17 ( 8372) covalent geometry : angle 0.66035 / 0.33 (11419) SS BOND : bond 0.00408 / 0.26 ( 3) SS BOND : angle 1.20801 / 0.72 ( 6) hydrogen bonds : bond 0.12711 / 8.85 ( 403) hydrogen bonds : angle 5.12094 / 3.76 ( 1152) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 115 time to evaluate : 0.327 Fit side-chains revert: symmetry clash REVERT: E 155 MET cc_start: 0.3704 (mmt) cc_final: 0.2592 (pmm) outliers start: 37 outliers final: 30 residues processed: 146 average time/residue: 0.4245 time to fit residues: 67.0556 Evaluate side-chains 142 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 112 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain D residue 201 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 8.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 0.4980 chunk 38 optimal weight: 7.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 101 ASN B 259 GLN D 130 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.188350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.145702 restraints weight = 8990.195| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 1.96 r_work: 0.3507 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.0841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8375 Z= 0.148 Angle : 0.598 8.014 11425 Z= 0.306 Chirality : 0.044 0.229 1351 Planarity : 0.004 0.054 1430 Dihedral : 7.329 58.064 1293 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 6.02 % Allowed : 26.99 % Favored : 66.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.26), residues: 1075 helix: 1.89 (0.29), residues: 345 sheet: 0.06 (0.30), residues: 273 loop : -0.75 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 219 TYR 0.015 0.001 TYR D 223 PHE 0.019 0.001 PHE E 78 TRP 0.011 0.001 TRP A 96 HIS 0.003 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 ( 8372) covalent geometry : angle 0.59793 / 0.31 (11419) SS BOND : bond 0.00348 / 0.22 ( 3) SS BOND : angle 0.92298 / 0.49 ( 6) hydrogen bonds : bond 0.03673 / 2.53 ( 403) hydrogen bonds : angle 4.46930 / 3.27 ( 1152) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 122 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 34 THR cc_start: 0.5799 (t) cc_final: 0.5500 (m) REVERT: E 93 LEU cc_start: 0.6654 (pt) cc_final: 0.6270 (mm) REVERT: B 44 GLN cc_start: 0.7236 (OUTLIER) cc_final: 0.6661 (mm-40) REVERT: D 18 ARG cc_start: 0.7840 (tpp-160) cc_final: 0.7502 (tpp-160) REVERT: D 179 ARG cc_start: 0.8267 (tpp80) cc_final: 0.8059 (mpp-170) outliers start: 50 outliers final: 20 residues processed: 160 average time/residue: 0.4301 time to fit residues: 74.4269 Evaluate side-chains 135 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 240 TYR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 160 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 75 optimal weight: 3.9990 chunk 104 optimal weight: 7.9990 chunk 79 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 22 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 83 optimal weight: 0.3980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.187906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.145183 restraints weight = 8969.506| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 1.97 r_work: 0.3465 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3336 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8375 Z= 0.142 Angle : 0.583 7.478 11425 Z= 0.298 Chirality : 0.044 0.220 1351 Planarity : 0.004 0.050 1430 Dihedral : 6.688 58.765 1267 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 6.75 % Allowed : 26.99 % Favored : 66.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.26), residues: 1075 helix: 1.92 (0.29), residues: 345 sheet: 0.11 (0.30), residues: 279 loop : -0.75 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 134 TYR 0.018 0.001 TYR E 106 PHE 0.023 0.001 PHE E 232 TRP 0.013 0.001 TRP A 96 HIS 0.003 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 8372) covalent geometry : angle 0.58198 / 0.30 (11419) SS BOND : bond 0.00333 / 0.21 ( 3) SS BOND : angle 1.29624 / 0.67 ( 6) hydrogen bonds : bond 0.03473 / 2.40 ( 403) hydrogen bonds : angle 4.37251 / 3.18 ( 1152) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 116 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 34 THR cc_start: 0.5777 (t) cc_final: 0.5465 (m) REVERT: E 93 LEU cc_start: 0.6681 (pt) cc_final: 0.6324 (mp) REVERT: A 9 ASP cc_start: 0.8340 (OUTLIER) cc_final: 0.8110 (m-30) REVERT: A 46 LYS cc_start: 0.7928 (OUTLIER) cc_final: 0.7213 (mtpt) REVERT: B 45 MET cc_start: 0.8489 (mtt) cc_final: 0.8220 (mtt) REVERT: B 93 ILE cc_start: 0.7028 (OUTLIER) cc_final: 0.6528 (pp) REVERT: D 18 ARG cc_start: 0.7810 (tpp-160) cc_final: 0.7529 (ttt180) REVERT: D 67 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.7650 (ptm-80) REVERT: D 90 ASP cc_start: 0.7651 (t0) cc_final: 0.7415 (t0) REVERT: D 179 ARG cc_start: 0.8234 (tpp80) cc_final: 0.7994 (mpp-170) outliers start: 56 outliers final: 26 residues processed: 162 average time/residue: 0.4143 time to fit residues: 72.8760 Evaluate side-chains 137 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 107 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 240 TYR Chi-restraints excluded: chain A residue 9 ASP Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 218 MET Chi-restraints excluded: chain D residue 226 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 92 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 103 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 104 optimal weight: 7.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 43 ASN B 32 GLN B 155 ASN B 259 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.183978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.141831 restraints weight = 9124.791| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 1.89 r_work: 0.3430 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 8375 Z= 0.225 Angle : 0.642 8.824 11425 Z= 0.330 Chirality : 0.046 0.263 1351 Planarity : 0.005 0.051 1430 Dihedral : 6.641 58.564 1263 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 7.59 % Allowed : 27.71 % Favored : 64.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.26), residues: 1075 helix: 1.63 (0.28), residues: 345 sheet: -0.05 (0.30), residues: 278 loop : -0.91 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 134 TYR 0.025 0.002 TYR E 106 PHE 0.021 0.002 PHE E 232 TRP 0.015 0.002 TRP D 47 HIS 0.004 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00536 / 0.22 ( 8372) covalent geometry : angle 0.64136 / 0.33 (11419) SS BOND : bond 0.00262 / 0.14 ( 3) SS BOND : angle 1.35278 / 0.68 ( 6) hydrogen bonds : bond 0.03908 / 2.70 ( 403) hydrogen bonds : angle 4.67245 / 3.38 ( 1152) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 116 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 34 THR cc_start: 0.6231 (t) cc_final: 0.5974 (m) REVERT: E 58 ARG cc_start: 0.6840 (mmt90) cc_final: 0.6536 (mmt90) REVERT: E 93 LEU cc_start: 0.6785 (OUTLIER) cc_final: 0.6445 (mp) REVERT: E 95 ARG cc_start: 0.5528 (ttp-110) cc_final: 0.5209 (ttp-110) REVERT: E 106 TYR cc_start: 0.8628 (t80) cc_final: 0.8402 (t80) REVERT: E 133 ARG cc_start: 0.8494 (mpp80) cc_final: 0.8231 (mpt-90) REVERT: A 46 LYS cc_start: 0.7971 (OUTLIER) cc_final: 0.7236 (mtpt) REVERT: A 144 ASN cc_start: 0.8033 (t0) cc_final: 0.7818 (t0) REVERT: B 45 MET cc_start: 0.8627 (mtt) cc_final: 0.8324 (mtt) REVERT: B 93 ILE cc_start: 0.6975 (OUTLIER) cc_final: 0.6665 (pp) REVERT: C 48 ASP cc_start: 0.8556 (p0) cc_final: 0.8292 (p0) REVERT: D 20 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7169 (pp) REVERT: D 90 ASP cc_start: 0.7906 (t0) cc_final: 0.7564 (t0) REVERT: D 190 ARG cc_start: 0.8059 (mtm-85) cc_final: 0.7614 (mtm-85) outliers start: 63 outliers final: 33 residues processed: 166 average time/residue: 0.4580 time to fit residues: 82.0453 Evaluate side-chains 150 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 113 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 30 PHE Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 240 TYR Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 214 VAL Chi-restraints excluded: chain D residue 226 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 11 optimal weight: 0.2980 chunk 75 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 29 optimal weight: 0.0980 chunk 105 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 101 ASN B 32 GLN B 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.188064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.145618 restraints weight = 9059.520| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 1.95 r_work: 0.3514 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8375 Z= 0.125 Angle : 0.570 7.731 11425 Z= 0.294 Chirality : 0.043 0.239 1351 Planarity : 0.004 0.047 1430 Dihedral : 6.044 56.296 1261 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 5.66 % Allowed : 28.92 % Favored : 65.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.26), residues: 1075 helix: 1.83 (0.29), residues: 345 sheet: -0.01 (0.30), residues: 273 loop : -0.88 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 134 TYR 0.017 0.001 TYR E 106 PHE 0.017 0.001 PHE E 232 TRP 0.016 0.001 TRP A 96 HIS 0.003 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 ( 8372) covalent geometry : angle 0.56987 / 0.29 (11419) SS BOND : bond 0.00256 / 0.15 ( 3) SS BOND : angle 0.94124 / 0.47 ( 6) hydrogen bonds : bond 0.03322 / 2.30 ( 403) hydrogen bonds : angle 4.35417 / 3.16 ( 1152) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 123 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 34 THR cc_start: 0.6303 (t) cc_final: 0.6009 (m) REVERT: E 67 ASN cc_start: 0.6783 (p0) cc_final: 0.6477 (p0) REVERT: E 93 LEU cc_start: 0.6562 (OUTLIER) cc_final: 0.6266 (mp) REVERT: E 95 ARG cc_start: 0.5516 (ttp-110) cc_final: 0.5273 (ttp-110) REVERT: E 133 ARG cc_start: 0.8491 (mpp80) cc_final: 0.8275 (mpt-90) REVERT: B 45 MET cc_start: 0.8525 (mtt) cc_final: 0.8259 (mtt) REVERT: B 93 ILE cc_start: 0.6995 (OUTLIER) cc_final: 0.6559 (pp) REVERT: D 18 ARG cc_start: 0.7799 (tpp-160) cc_final: 0.7399 (ttt180) REVERT: D 20 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7893 (pp) REVERT: D 67 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.7603 (ptm-80) REVERT: D 190 ARG cc_start: 0.8128 (mtm-85) cc_final: 0.7760 (mtm-85) REVERT: D 222 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7663 (mt-10) outliers start: 47 outliers final: 22 residues processed: 161 average time/residue: 0.4806 time to fit residues: 83.3004 Evaluate side-chains 146 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 119 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 30 PHE Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 240 TYR Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 222 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 24 optimal weight: 0.7980 chunk 49 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 6 optimal weight: 20.0000 chunk 17 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 101 ASN A 144 ASN B 32 GLN B 259 GLN D 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.186590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.144136 restraints weight = 9031.682| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 1.95 r_work: 0.3454 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8375 Z= 0.153 Angle : 0.591 7.932 11425 Z= 0.304 Chirality : 0.044 0.248 1351 Planarity : 0.004 0.054 1430 Dihedral : 6.060 55.984 1261 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 5.30 % Allowed : 30.00 % Favored : 64.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.26), residues: 1075 helix: 1.79 (0.29), residues: 346 sheet: -0.02 (0.30), residues: 279 loop : -0.88 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 134 TYR 0.016 0.002 TYR E 106 PHE 0.017 0.001 PHE E 232 TRP 0.014 0.001 TRP A 96 HIS 0.003 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 ( 8372) covalent geometry : angle 0.59058 / 0.30 (11419) SS BOND : bond 0.00221 / 0.13 ( 3) SS BOND : angle 0.97832 / 0.48 ( 6) hydrogen bonds : bond 0.03450 / 2.39 ( 403) hydrogen bonds : angle 4.38120 / 3.18 ( 1152) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 113 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 34 THR cc_start: 0.6312 (t) cc_final: 0.6045 (m) REVERT: E 67 ASN cc_start: 0.6766 (p0) cc_final: 0.6539 (p0) REVERT: E 93 LEU cc_start: 0.6654 (OUTLIER) cc_final: 0.6345 (mp) REVERT: E 95 ARG cc_start: 0.5605 (ttp-110) cc_final: 0.5398 (ttp-110) REVERT: A 20 ASP cc_start: 0.8677 (OUTLIER) cc_final: 0.8155 (m-30) REVERT: B 45 MET cc_start: 0.8561 (mtt) cc_final: 0.8299 (mtt) REVERT: B 93 ILE cc_start: 0.6939 (OUTLIER) cc_final: 0.6504 (pp) REVERT: D 20 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.6929 (pp) REVERT: D 190 ARG cc_start: 0.8150 (mtm-85) cc_final: 0.7692 (mtm-85) outliers start: 44 outliers final: 31 residues processed: 146 average time/residue: 0.4772 time to fit residues: 75.0210 Evaluate side-chains 147 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 112 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 30 PHE Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 240 TYR Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 39 GLN Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 218 MET Chi-restraints excluded: chain D residue 226 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 86 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 37 optimal weight: 0.3980 chunk 13 optimal weight: 0.0270 chunk 24 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 overall best weight: 0.8844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.186494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.144201 restraints weight = 9129.859| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 1.94 r_work: 0.3455 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8375 Z= 0.153 Angle : 0.594 8.643 11425 Z= 0.305 Chirality : 0.044 0.231 1351 Planarity : 0.004 0.058 1430 Dihedral : 6.018 55.405 1261 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 5.78 % Allowed : 29.52 % Favored : 64.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.26), residues: 1075 helix: 1.78 (0.28), residues: 346 sheet: -0.03 (0.30), residues: 279 loop : -0.90 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 134 TYR 0.014 0.001 TYR E 106 PHE 0.017 0.001 PHE E 232 TRP 0.014 0.001 TRP A 96 HIS 0.003 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 ( 8372) covalent geometry : angle 0.59349 / 0.31 (11419) SS BOND : bond 0.00234 / 0.14 ( 3) SS BOND : angle 0.95672 / 0.47 ( 6) hydrogen bonds : bond 0.03447 / 2.38 ( 403) hydrogen bonds : angle 4.38033 / 3.17 ( 1152) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 119 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 34 THR cc_start: 0.6344 (t) cc_final: 0.6074 (m) REVERT: E 58 ARG cc_start: 0.6702 (mmt90) cc_final: 0.6445 (mmt90) REVERT: E 67 ASN cc_start: 0.6659 (p0) cc_final: 0.6410 (p0) REVERT: E 93 LEU cc_start: 0.6466 (OUTLIER) cc_final: 0.6198 (mp) REVERT: E 95 ARG cc_start: 0.5903 (ttp-110) cc_final: 0.5670 (ttp-110) REVERT: E 155 MET cc_start: 0.2934 (mpm) cc_final: 0.2298 (pmm) REVERT: A 20 ASP cc_start: 0.8676 (OUTLIER) cc_final: 0.8153 (m-30) REVERT: B 45 MET cc_start: 0.8584 (mtt) cc_final: 0.8348 (mtt) REVERT: B 93 ILE cc_start: 0.6942 (OUTLIER) cc_final: 0.6502 (pp) REVERT: D 18 ARG cc_start: 0.7901 (tpp-160) cc_final: 0.7504 (ttt180) REVERT: D 20 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.6803 (pp) REVERT: D 67 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.7686 (ptm-80) REVERT: D 87 ARG cc_start: 0.7330 (OUTLIER) cc_final: 0.7005 (ptp-170) REVERT: D 190 ARG cc_start: 0.8126 (mtm-85) cc_final: 0.7667 (mtm-85) outliers start: 48 outliers final: 30 residues processed: 152 average time/residue: 0.4646 time to fit residues: 76.2113 Evaluate side-chains 148 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 112 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 30 PHE Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 133 ARG Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 240 TYR Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 39 GLN Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 87 ARG Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 218 MET Chi-restraints excluded: chain D residue 226 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 98 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 37 optimal weight: 7.9990 chunk 36 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 68 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 52 optimal weight: 3.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 101 ASN A 144 ASN B 32 GLN B 259 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.179427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.138499 restraints weight = 9092.713| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 2.08 r_work: 0.3371 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8375 Z= 0.195 Angle : 0.626 8.214 11425 Z= 0.324 Chirality : 0.046 0.272 1351 Planarity : 0.005 0.056 1430 Dihedral : 6.169 54.200 1261 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 5.18 % Allowed : 30.72 % Favored : 64.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.26), residues: 1075 helix: 1.66 (0.28), residues: 346 sheet: -0.05 (0.30), residues: 276 loop : -0.94 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 134 TYR 0.016 0.002 TYR D 223 PHE 0.017 0.002 PHE E 232 TRP 0.013 0.002 TRP D 47 HIS 0.004 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.19 ( 8372) covalent geometry : angle 0.62568 / 0.32 (11419) SS BOND : bond 0.00255 / 0.15 ( 3) SS BOND : angle 1.01485 / 0.49 ( 6) hydrogen bonds : bond 0.03707 / 2.55 ( 403) hydrogen bonds : angle 4.54439 / 3.29 ( 1152) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 118 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 34 THR cc_start: 0.6444 (t) cc_final: 0.6222 (m) REVERT: E 93 LEU cc_start: 0.6475 (OUTLIER) cc_final: 0.6190 (mp) REVERT: E 95 ARG cc_start: 0.5846 (ttp-110) cc_final: 0.5637 (ttp-110) REVERT: A 20 ASP cc_start: 0.8662 (OUTLIER) cc_final: 0.8083 (m-30) REVERT: A 22 ASN cc_start: 0.8123 (t0) cc_final: 0.7708 (m-40) REVERT: B 45 MET cc_start: 0.8626 (mtt) cc_final: 0.8187 (mtt) REVERT: B 93 ILE cc_start: 0.6923 (OUTLIER) cc_final: 0.6581 (pp) REVERT: D 18 ARG cc_start: 0.7944 (tpp-160) cc_final: 0.7662 (ttt180) REVERT: D 20 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.6826 (pp) REVERT: D 67 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.7996 (ptm-80) REVERT: D 87 ARG cc_start: 0.7306 (OUTLIER) cc_final: 0.6965 (ptp-170) REVERT: D 190 ARG cc_start: 0.8093 (mtm-85) cc_final: 0.7582 (mtm-85) outliers start: 43 outliers final: 31 residues processed: 146 average time/residue: 0.4811 time to fit residues: 75.5073 Evaluate side-chains 149 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 112 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 30 PHE Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 133 ARG Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 240 TYR Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 39 GLN Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 87 ARG Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 226 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 65 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 chunk 78 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 91 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 101 ASN B 32 GLN B 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.186254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.143961 restraints weight = 9059.290| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 1.94 r_work: 0.3497 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3366 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8375 Z= 0.147 Angle : 0.600 9.345 11425 Z= 0.310 Chirality : 0.044 0.271 1351 Planarity : 0.004 0.052 1430 Dihedral : 5.969 55.317 1261 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 4.94 % Allowed : 31.45 % Favored : 63.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.26), residues: 1075 helix: 1.73 (0.28), residues: 346 sheet: -0.05 (0.30), residues: 279 loop : -0.94 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 134 TYR 0.014 0.001 TYR D 223 PHE 0.016 0.001 PHE E 232 TRP 0.015 0.001 TRP A 96 HIS 0.003 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 ( 8372) covalent geometry : angle 0.60005 / 0.31 (11419) SS BOND : bond 0.00247 / 0.15 ( 3) SS BOND : angle 0.90455 / 0.44 ( 6) hydrogen bonds : bond 0.03452 / 2.38 ( 403) hydrogen bonds : angle 4.40152 / 3.20 ( 1152) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 114 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 58 ARG cc_start: 0.6688 (mmt90) cc_final: 0.6467 (mmt90) REVERT: E 93 LEU cc_start: 0.6187 (OUTLIER) cc_final: 0.5981 (mp) REVERT: E 95 ARG cc_start: 0.6057 (ttp-110) cc_final: 0.5844 (ttp-110) REVERT: E 155 MET cc_start: 0.3089 (mpm) cc_final: 0.2722 (pmm) REVERT: A 20 ASP cc_start: 0.8654 (OUTLIER) cc_final: 0.8130 (m-30) REVERT: B 45 MET cc_start: 0.8523 (mtt) cc_final: 0.8081 (mtt) REVERT: B 93 ILE cc_start: 0.6937 (OUTLIER) cc_final: 0.6510 (pp) REVERT: D 18 ARG cc_start: 0.7921 (tpp-160) cc_final: 0.7661 (ttt180) REVERT: D 20 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.6806 (pp) REVERT: D 67 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.7702 (ptm-80) REVERT: D 87 ARG cc_start: 0.7288 (OUTLIER) cc_final: 0.6964 (ptp-170) outliers start: 41 outliers final: 29 residues processed: 142 average time/residue: 0.5003 time to fit residues: 76.1962 Evaluate side-chains 144 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 109 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 133 ARG Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 240 TYR Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 39 GLN Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 87 ARG Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 218 MET Chi-restraints excluded: chain D residue 226 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 97 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 0 optimal weight: 30.0000 chunk 38 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 80 optimal weight: 0.0770 overall best weight: 0.7744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 101 ASN B 32 GLN B 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.186586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.144441 restraints weight = 8994.361| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 1.91 r_work: 0.3508 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3373 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8375 Z= 0.145 Angle : 0.599 9.249 11425 Z= 0.309 Chirality : 0.044 0.271 1351 Planarity : 0.004 0.052 1430 Dihedral : 5.903 55.698 1261 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 4.82 % Allowed : 31.93 % Favored : 63.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.26), residues: 1075 helix: 1.80 (0.29), residues: 346 sheet: -0.06 (0.30), residues: 279 loop : -0.93 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 134 TYR 0.013 0.001 TYR D 223 PHE 0.016 0.001 PHE E 232 TRP 0.015 0.001 TRP A 96 HIS 0.003 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 ( 8372) covalent geometry : angle 0.59861 / 0.31 (11419) SS BOND : bond 0.00243 / 0.14 ( 3) SS BOND : angle 0.88584 / 0.43 ( 6) hydrogen bonds : bond 0.03435 / 2.37 ( 403) hydrogen bonds : angle 4.37378 / 3.18 ( 1152) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 114 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 58 ARG cc_start: 0.6853 (mmt90) cc_final: 0.6626 (mmt90) REVERT: E 67 ASN cc_start: 0.6555 (p0) cc_final: 0.6206 (p0) REVERT: E 155 MET cc_start: 0.3122 (mpm) cc_final: 0.2907 (pmm) REVERT: A 20 ASP cc_start: 0.8639 (OUTLIER) cc_final: 0.8115 (m-30) REVERT: B 45 MET cc_start: 0.8509 (mtt) cc_final: 0.8074 (mtt) REVERT: B 93 ILE cc_start: 0.6920 (OUTLIER) cc_final: 0.6487 (pp) REVERT: D 18 ARG cc_start: 0.7905 (tpp-160) cc_final: 0.7635 (ttt180) REVERT: D 20 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.6839 (pp) REVERT: D 67 ARG cc_start: 0.8467 (OUTLIER) cc_final: 0.7687 (ptm-80) REVERT: D 87 ARG cc_start: 0.7291 (OUTLIER) cc_final: 0.6954 (ptp-170) outliers start: 40 outliers final: 30 residues processed: 141 average time/residue: 0.5201 time to fit residues: 78.4410 Evaluate side-chains 142 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 107 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 133 ARG Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 240 TYR Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 295 ASN Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 87 ARG Chi-restraints excluded: chain D residue 126 ILE Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain D residue 218 MET Chi-restraints excluded: chain D residue 226 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 30 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 53 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN B 259 GLN D 174 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.181215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.139588 restraints weight = 9022.077| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 1.95 r_work: 0.3409 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8375 Z= 0.153 Angle : 0.626 8.944 11425 Z= 0.318 Chirality : 0.045 0.274 1351 Planarity : 0.004 0.052 1430 Dihedral : 6.194 55.698 1261 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 4.70 % Allowed : 32.29 % Favored : 63.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.26), residues: 1075 helix: 1.80 (0.28), residues: 346 sheet: -0.07 (0.30), residues: 279 loop : -0.94 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 134 TYR 0.014 0.002 TYR B 59 PHE 0.016 0.001 PHE E 232 TRP 0.014 0.001 TRP A 96 HIS 0.003 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 ( 8372) covalent geometry : angle 0.62564 / 0.32 (11419) SS BOND : bond 0.00246 / 0.14 ( 3) SS BOND : angle 0.90711 / 0.44 ( 6) hydrogen bonds : bond 0.03514 / 2.42 ( 403) hydrogen bonds : angle 4.41770 / 3.22 ( 1152) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3334.13 seconds wall clock time: 57 minutes 49.22 seconds (3469.22 seconds total)