Starting phenix.real_space_refine on Tue Apr 29 17:18:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xjn_38402/04_2025/8xjn_38402.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xjn_38402/04_2025/8xjn_38402.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xjn_38402/04_2025/8xjn_38402.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xjn_38402/04_2025/8xjn_38402.map" model { file = "/net/cci-nas-00/data/ceres_data/8xjn_38402/04_2025/8xjn_38402.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xjn_38402/04_2025/8xjn_38402.cif" } resolution = 3.06 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 58 5.16 5 Cl 1 4.86 5 C 5672 2.51 5 N 1546 2.21 5 O 1671 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 8948 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1825 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 217} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 2622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2622 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 5, 'TRANS': 336} Chain: "C" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "E" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1779 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "R" Number of atoms: 2257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2257 Classifications: {'peptide': 310} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 295} Unresolved non-hydrogen bonds: 125 Unresolved non-hydrogen angles: 157 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 94 Chain: "R" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'A1D5A': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.52, per 1000 atoms: 0.62 Number of scatterers: 8948 At special positions: 0 Unit cell: (114.49, 125.19, 109.14, 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) Cl 1 17.00 S 58 16.00 O 1671 8.00 N 1546 7.00 C 5672 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.03 Simple disulfide: pdb=" SG CYS R 11 " - pdb=" SG CYS R 102 " distance=2.03 Simple disulfide: pdb=" SG CYS R 105 " - pdb=" SG CYS R 183 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.44 Conformation dependent library (CDL) restraints added in 1.0 seconds 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2156 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 16 sheets defined 37.9% alpha, 25.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.613A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG A 32 " --> pdb=" O GLN A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 95 through 99 removed outlier: 3.713A pdb=" N GLN A 98 " --> pdb=" O LYS A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 130 Processing helix chain 'A' and resid 131 through 135 removed outlier: 3.864A pdb=" N ARG A 135 " --> pdb=" O ARG A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 156 Processing helix chain 'A' and resid 159 through 164 removed outlier: 4.242A pdb=" N TYR A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 168 Processing helix chain 'A' and resid 183 through 202 removed outlier: 3.527A pdb=" N ILE A 200 " --> pdb=" O GLU A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 244 Processing helix chain 'B' and resid 3 through 25 removed outlier: 3.509A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 7 through 24 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 55 through 59 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.529A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 29 through 56 removed outlier: 3.988A pdb=" N PHE R 34 " --> pdb=" O PHE R 30 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N CYS R 35 " --> pdb=" O ALA R 31 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY R 51 " --> pdb=" O SER R 47 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA R 52 " --> pdb=" O VAL R 48 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY R 56 " --> pdb=" O ALA R 52 " (cutoff:3.500A) Processing helix chain 'R' and resid 62 through 91 removed outlier: 3.536A pdb=" N THR R 81 " --> pdb=" O GLY R 77 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY R 82 " --> pdb=" O LEU R 78 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA R 90 " --> pdb=" O VAL R 86 " (cutoff:3.500A) Processing helix chain 'R' and resid 102 through 136 Proline residue: R 119 - end of helix removed outlier: 3.568A pdb=" N SER R 128 " --> pdb=" O ALA R 124 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 140 Processing helix chain 'R' and resid 146 through 165 removed outlier: 4.367A pdb=" N THR R 152 " --> pdb=" O ARG R 148 " (cutoff:3.500A) Processing helix chain 'R' and resid 166 through 170 Processing helix chain 'R' and resid 190 through 227 Processing helix chain 'R' and resid 228 through 235 removed outlier: 3.771A pdb=" N GLN R 233 " --> pdb=" O GLN R 229 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ARG R 235 " --> pdb=" O ALA R 231 " (cutoff:3.500A) Processing helix chain 'R' and resid 238 through 270 removed outlier: 3.604A pdb=" N GLN R 246 " --> pdb=" O GLU R 242 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER R 255 " --> pdb=" O MET R 251 " (cutoff:3.500A) Proline residue: R 260 - end of helix Processing helix chain 'R' and resid 283 through 299 removed outlier: 3.710A pdb=" N TRP R 299 " --> pdb=" O ARG R 295 " (cutoff:3.500A) Processing helix chain 'R' and resid 299 through 308 Proline residue: R 305 - end of helix Processing helix chain 'R' and resid 312 through 320 removed outlier: 4.590A pdb=" N ARG R 318 " --> pdb=" O ALA R 314 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU R 319 " --> pdb=" O VAL R 315 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN R 320 " --> pdb=" O LEU R 316 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 70 through 76 removed outlier: 6.380A pdb=" N LEU A 34 " --> pdb=" O HIS A 82 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N PHE A 84 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU A 36 " --> pdb=" O PHE A 84 " (cutoff:3.500A) removed outlier: 9.381A pdb=" N ALA A 105 " --> pdb=" O THR A 33 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ARG A 35 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N ILE A 107 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LEU A 37 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N VAL A 109 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LEU A 39 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 8.821A pdb=" N ASP A 111 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 70 through 76 removed outlier: 6.380A pdb=" N LEU A 34 " --> pdb=" O HIS A 82 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N PHE A 84 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU A 36 " --> pdb=" O PHE A 84 " (cutoff:3.500A) removed outlier: 9.381A pdb=" N ALA A 105 " --> pdb=" O THR A 33 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ARG A 35 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N ILE A 107 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LEU A 37 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N VAL A 109 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LEU A 39 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 8.821A pdb=" N ASP A 111 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N PHE A 142 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N PHE A 108 " --> pdb=" O PHE A 142 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ASN A 144 " --> pdb=" O PHE A 108 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N VAL A 110 " --> pdb=" O ASN A 144 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 45 through 51 removed outlier: 5.652A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.608A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 5.981A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.254A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.809A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.583A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.748A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.867A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 11 through 12 removed outlier: 4.357A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 140 through 141 Processing sheet with id=AB5, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.572A pdb=" N LEU E 174 " --> pdb=" O TYR E 190 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N TYR E 190 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 146 through 148 removed outlier: 4.153A pdb=" N THR E 238 " --> pdb=" O GLN E 231 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'R' and resid 174 through 176 469 hydrogen bonds defined for protein. 1299 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.67 Time building geometry restraints manager: 2.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2936 1.34 - 1.46: 2155 1.46 - 1.58: 3953 1.58 - 1.69: 3 1.69 - 1.81: 86 Bond restraints: 9133 Sorted by residual: bond pdb=" C10 A1D5A R 601 " pdb=" C11 A1D5A R 601 " ideal model delta sigma weight residual 1.543 1.311 0.232 2.00e-02 2.50e+03 1.34e+02 bond pdb=" C14 A1D5A R 601 " pdb=" C15 A1D5A R 601 " ideal model delta sigma weight residual 1.523 1.338 0.185 2.00e-02 2.50e+03 8.53e+01 bond pdb=" C10 A1D5A R 601 " pdb=" C15 A1D5A R 601 " ideal model delta sigma weight residual 1.535 1.694 -0.159 2.00e-02 2.50e+03 6.31e+01 bond pdb=" C21 A1D5A R 601 " pdb=" O20 A1D5A R 601 " ideal model delta sigma weight residual 1.342 1.422 -0.080 2.00e-02 2.50e+03 1.60e+01 bond pdb=" C11 A1D5A R 601 " pdb=" C13 A1D5A R 601 " ideal model delta sigma weight residual 1.538 1.616 -0.078 2.00e-02 2.50e+03 1.52e+01 ... (remaining 9128 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.59: 12340 2.59 - 5.18: 47 5.18 - 7.77: 4 7.77 - 10.36: 1 10.36 - 12.96: 1 Bond angle restraints: 12393 Sorted by residual: angle pdb=" C06 A1D5A R 601 " pdb=" C07 A1D5A R 601 " pdb=" C08 A1D5A R 601 " ideal model delta sigma weight residual 127.33 114.37 12.96 3.00e+00 1.11e-01 1.86e+01 angle pdb=" C07 A1D5A R 601 " pdb=" C08 A1D5A R 601 " pdb=" C09 A1D5A R 601 " ideal model delta sigma weight residual 127.18 118.41 8.77 3.00e+00 1.11e-01 8.54e+00 angle pdb=" N GLU R 242 " pdb=" CA GLU R 242 " pdb=" C GLU R 242 " ideal model delta sigma weight residual 111.82 109.18 2.64 1.16e+00 7.43e-01 5.18e+00 angle pdb=" O01 A1D5A R 601 " pdb=" C02 A1D5A R 601 " pdb=" O03 A1D5A R 601 " ideal model delta sigma weight residual 126.47 120.06 6.41 3.00e+00 1.11e-01 4.56e+00 angle pdb=" C ARG E 191 " pdb=" N MET E 192 " pdb=" CA MET E 192 " ideal model delta sigma weight residual 121.54 125.30 -3.76 1.91e+00 2.74e-01 3.87e+00 ... (remaining 12388 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.04: 5179 17.04 - 34.08: 198 34.08 - 51.11: 39 51.11 - 68.15: 6 68.15 - 85.19: 8 Dihedral angle restraints: 5430 sinusoidal: 2082 harmonic: 3348 Sorted by residual: dihedral pdb=" CA GLN B 75 " pdb=" C GLN B 75 " pdb=" N ASP B 76 " pdb=" CA ASP B 76 " ideal model delta harmonic sigma weight residual 180.00 159.21 20.79 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA ILE R 309 " pdb=" C ILE R 309 " pdb=" N LEU R 310 " pdb=" CA LEU R 310 " ideal model delta harmonic sigma weight residual -180.00 -160.62 -19.38 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA ARG E 191 " pdb=" C ARG E 191 " pdb=" N MET E 192 " pdb=" CA MET E 192 " ideal model delta harmonic sigma weight residual 180.00 160.98 19.02 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 5427 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1043 0.037 - 0.073: 256 0.073 - 0.110: 88 0.110 - 0.146: 22 0.146 - 0.183: 3 Chirality restraints: 1412 Sorted by residual: chirality pdb=" C10 A1D5A R 601 " pdb=" C09 A1D5A R 601 " pdb=" C11 A1D5A R 601 " pdb=" C15 A1D5A R 601 " both_signs ideal model delta sigma weight residual False -2.56 -2.74 0.18 2.00e-01 2.50e+01 8.37e-01 chirality pdb=" C15 A1D5A R 601 " pdb=" C10 A1D5A R 601 " pdb=" C14 A1D5A R 601 " pdb=" C16 A1D5A R 601 " both_signs ideal model delta sigma weight residual False 2.59 2.76 -0.17 2.00e-01 2.50e+01 7.06e-01 chirality pdb=" C11 A1D5A R 601 " pdb=" C10 A1D5A R 601 " pdb=" C13 A1D5A R 601 " pdb=" O12 A1D5A R 601 " both_signs ideal model delta sigma weight residual False 2.65 2.49 0.16 2.00e-01 2.50e+01 6.36e-01 ... (remaining 1409 not shown) Planarity restraints: 1582 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.025 5.00e-02 4.00e+02 3.79e-02 2.30e+00 pdb=" N PRO B 236 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG R 235 " -0.016 5.00e-02 4.00e+02 2.47e-02 9.77e-01 pdb=" N PRO R 236 " 0.043 5.00e-02 4.00e+02 pdb=" CA PRO R 236 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO R 236 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 54 " -0.016 5.00e-02 4.00e+02 2.38e-02 9.08e-01 pdb=" N PRO C 55 " 0.041 5.00e-02 4.00e+02 pdb=" CA PRO C 55 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO C 55 " -0.013 5.00e-02 4.00e+02 ... (remaining 1579 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 815 2.75 - 3.28: 8705 3.28 - 3.82: 14877 3.82 - 4.36: 18327 4.36 - 4.90: 31948 Nonbonded interactions: 74672 Sorted by model distance: nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR E 175 " model vdw 2.207 3.040 nonbonded pdb=" O VAL R 307 " pdb=" NH1 ARG R 312 " model vdw 2.236 3.120 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.252 3.040 nonbonded pdb=" ND2 ASN B 230 " pdb=" OD1 ASP B 246 " model vdw 2.255 3.120 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.281 3.040 ... (remaining 74667 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.700 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 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 0.232 9137 Z= 0.213 Angle : 0.428 12.955 12401 Z= 0.211 Chirality : 0.039 0.183 1412 Planarity : 0.003 0.038 1582 Dihedral : 10.298 85.190 3262 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.85 % Allowed : 3.70 % Favored : 95.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.24), residues: 1148 helix: 0.71 (0.26), residues: 407 sheet: 0.82 (0.30), residues: 281 loop : 0.60 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 95 HIS 0.004 0.001 HIS A 209 PHE 0.010 0.001 PHE A 108 TYR 0.010 0.001 TYR E 190 ARG 0.004 0.000 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.25273 ( 452) hydrogen bonds : angle 7.53664 ( 1299) SS BOND : bond 0.00162 ( 4) SS BOND : angle 0.49543 ( 8) covalent geometry : bond 0.00427 ( 9133) covalent geometry : angle 0.42771 (12393) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 265 time to evaluate : 0.919 Fit side-chains revert: symmetry clash REVERT: A 22 GLN cc_start: 0.8763 (tp40) cc_final: 0.8530 (tp-100) REVERT: A 75 GLN cc_start: 0.8040 (tt0) cc_final: 0.7835 (tt0) REVERT: A 123 ASN cc_start: 0.8669 (m-40) cc_final: 0.8442 (m110) REVERT: A 126 LYS cc_start: 0.8723 (ttmt) cc_final: 0.8072 (tttm) REVERT: A 129 TRP cc_start: 0.8375 (t-100) cc_final: 0.8065 (t-100) REVERT: A 185 ARG cc_start: 0.8572 (mtm180) cc_final: 0.8251 (mmm160) REVERT: A 222 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7426 (mp0) REVERT: B 20 ASP cc_start: 0.8588 (m-30) cc_final: 0.8168 (m-30) REVERT: B 59 TYR cc_start: 0.7835 (m-80) cc_final: 0.7372 (m-80) REVERT: B 137 ARG cc_start: 0.7826 (mmt-90) cc_final: 0.7611 (mmt180) REVERT: B 212 ASP cc_start: 0.8578 (t0) cc_final: 0.8298 (t0) REVERT: B 217 MET cc_start: 0.7883 (ppp) cc_final: 0.6749 (ppp) REVERT: B 335 PHE cc_start: 0.8754 (m-10) cc_final: 0.8541 (m-10) REVERT: C 38 MET cc_start: 0.8647 (ttp) cc_final: 0.8419 (ttm) REVERT: E 109 ASP cc_start: 0.8842 (p0) cc_final: 0.8617 (p0) REVERT: E 213 THR cc_start: 0.7800 (m) cc_final: 0.7559 (p) REVERT: R 79 LEU cc_start: 0.9006 (tp) cc_final: 0.8788 (tt) REVERT: R 237 ARG cc_start: 0.7150 (OUTLIER) cc_final: 0.5198 (ppt170) outliers start: 8 outliers final: 2 residues processed: 268 average time/residue: 0.2808 time to fit residues: 96.5081 Evaluate side-chains 191 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 188 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain R residue 237 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 58 optimal weight: 8.9990 chunk 46 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.159789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.114109 restraints weight = 10473.117| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.24 r_work: 0.3015 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9137 Z= 0.138 Angle : 0.527 6.413 12401 Z= 0.280 Chirality : 0.041 0.149 1412 Planarity : 0.004 0.042 1582 Dihedral : 6.623 74.972 1302 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.27 % Allowed : 10.25 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.25), residues: 1148 helix: 1.88 (0.26), residues: 412 sheet: 0.79 (0.31), residues: 273 loop : 0.64 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 211 HIS 0.007 0.001 HIS A 209 PHE 0.009 0.001 PHE B 199 TYR 0.013 0.001 TYR E 190 ARG 0.007 0.001 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.04257 ( 452) hydrogen bonds : angle 4.71272 ( 1299) SS BOND : bond 0.00209 ( 4) SS BOND : angle 0.81677 ( 8) covalent geometry : bond 0.00304 ( 9133) covalent geometry : angle 0.52640 (12393) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 208 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 GLN cc_start: 0.8341 (tp40) cc_final: 0.8133 (tp-100) REVERT: A 75 GLN cc_start: 0.8197 (tt0) cc_final: 0.7965 (tt0) REVERT: A 126 LYS cc_start: 0.8326 (ttmt) cc_final: 0.7746 (tttm) REVERT: A 161 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7398 (mm-30) REVERT: A 195 LYS cc_start: 0.8792 (tptp) cc_final: 0.8535 (tptp) REVERT: B 59 TYR cc_start: 0.8397 (m-80) cc_final: 0.7645 (m-80) REVERT: B 137 ARG cc_start: 0.7683 (mmt-90) cc_final: 0.7276 (mmt180) REVERT: B 214 ARG cc_start: 0.7684 (mmp80) cc_final: 0.7380 (mmt-90) REVERT: B 266 HIS cc_start: 0.8590 (t70) cc_final: 0.8100 (t70) REVERT: E 144 THR cc_start: 0.7885 (m) cc_final: 0.7561 (p) REVERT: E 160 ARG cc_start: 0.8372 (ttp80) cc_final: 0.8095 (ttp80) REVERT: E 213 THR cc_start: 0.8062 (m) cc_final: 0.7805 (p) REVERT: E 215 THR cc_start: 0.8002 (m) cc_final: 0.7390 (p) REVERT: R 163 LEU cc_start: 0.8155 (tp) cc_final: 0.7813 (tp) outliers start: 12 outliers final: 5 residues processed: 217 average time/residue: 0.2493 time to fit residues: 70.7143 Evaluate side-chains 191 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 186 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 237 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 96 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 105 optimal weight: 0.9990 chunk 81 optimal weight: 7.9990 chunk 75 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.159011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.119758 restraints weight = 10675.868| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.47 r_work: 0.3014 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9137 Z= 0.136 Angle : 0.495 6.121 12401 Z= 0.262 Chirality : 0.041 0.144 1412 Planarity : 0.004 0.042 1582 Dihedral : 6.151 76.152 1298 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.33 % Allowed : 11.95 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.25), residues: 1148 helix: 2.33 (0.26), residues: 408 sheet: 0.51 (0.30), residues: 275 loop : 0.65 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 169 HIS 0.006 0.001 HIS A 209 PHE 0.009 0.001 PHE A 74 TYR 0.011 0.001 TYR R 226 ARG 0.006 0.001 ARG E 218 Details of bonding type rmsd hydrogen bonds : bond 0.03789 ( 452) hydrogen bonds : angle 4.37810 ( 1299) SS BOND : bond 0.00137 ( 4) SS BOND : angle 0.59044 ( 8) covalent geometry : bond 0.00311 ( 9133) covalent geometry : angle 0.49473 (12393) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 194 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 GLN cc_start: 0.8182 (mm-40) cc_final: 0.7975 (mm110) REVERT: A 29 VAL cc_start: 0.8566 (OUTLIER) cc_final: 0.8337 (p) REVERT: A 126 LYS cc_start: 0.8358 (ttmt) cc_final: 0.7823 (tttm) REVERT: A 161 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7533 (mm-30) REVERT: B 137 ARG cc_start: 0.7698 (mmt-90) cc_final: 0.7258 (mmt180) REVERT: B 189 SER cc_start: 0.9321 (p) cc_final: 0.8872 (t) REVERT: B 266 HIS cc_start: 0.8558 (t70) cc_final: 0.8104 (t70) REVERT: C 20 LYS cc_start: 0.9102 (ttmm) cc_final: 0.8706 (mtmm) REVERT: E 160 ARG cc_start: 0.8396 (ttp80) cc_final: 0.8173 (ttp80) REVERT: R 30 PHE cc_start: 0.7518 (OUTLIER) cc_final: 0.7129 (t80) REVERT: R 106 ARG cc_start: 0.7967 (mpp80) cc_final: 0.7624 (mpp80) REVERT: R 108 MET cc_start: 0.6875 (tpt) cc_final: 0.6522 (tpt) REVERT: R 163 LEU cc_start: 0.8118 (tp) cc_final: 0.7738 (tp) REVERT: R 203 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7697 (tp) REVERT: R 271 ARG cc_start: 0.7535 (ttp80) cc_final: 0.7225 (ttp-170) outliers start: 22 outliers final: 13 residues processed: 207 average time/residue: 0.2518 time to fit residues: 68.9252 Evaluate side-chains 197 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 181 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain R residue 30 PHE Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 198 LEU Chi-restraints excluded: chain R residue 203 LEU Chi-restraints excluded: chain R residue 237 ARG Chi-restraints excluded: chain R residue 259 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 49 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 43 optimal weight: 0.2980 chunk 14 optimal weight: 0.0970 chunk 24 optimal weight: 8.9990 chunk 3 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 100 optimal weight: 7.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.158269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.118468 restraints weight = 10898.376| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.44 r_work: 0.3137 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9137 Z= 0.097 Angle : 0.455 6.469 12401 Z= 0.241 Chirality : 0.040 0.144 1412 Planarity : 0.003 0.043 1582 Dihedral : 5.719 73.657 1298 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.90 % Allowed : 13.64 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.25), residues: 1148 helix: 2.67 (0.26), residues: 409 sheet: 0.44 (0.30), residues: 272 loop : 0.64 (0.30), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.004 0.001 HIS A 209 PHE 0.009 0.001 PHE B 151 TYR 0.012 0.001 TYR E 190 ARG 0.006 0.000 ARG E 218 Details of bonding type rmsd hydrogen bonds : bond 0.03219 ( 452) hydrogen bonds : angle 4.09910 ( 1299) SS BOND : bond 0.00142 ( 4) SS BOND : angle 0.48671 ( 8) covalent geometry : bond 0.00210 ( 9133) covalent geometry : angle 0.45517 (12393) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 192 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 GLN cc_start: 0.8334 (mm-40) cc_final: 0.8055 (mm110) REVERT: A 29 VAL cc_start: 0.8671 (OUTLIER) cc_final: 0.8459 (p) REVERT: A 126 LYS cc_start: 0.8443 (ttmt) cc_final: 0.7913 (tttm) REVERT: A 161 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7508 (mm-30) REVERT: A 233 ASP cc_start: 0.8871 (t0) cc_final: 0.8521 (t0) REVERT: B 57 LYS cc_start: 0.8515 (mtmm) cc_final: 0.8007 (mtmm) REVERT: B 59 TYR cc_start: 0.8277 (m-80) cc_final: 0.7901 (m-80) REVERT: B 75 GLN cc_start: 0.8874 (mt0) cc_final: 0.8395 (mt0) REVERT: B 266 HIS cc_start: 0.8631 (t70) cc_final: 0.8214 (t70) REVERT: B 303 ASP cc_start: 0.7973 (m-30) cc_final: 0.7754 (m-30) REVERT: C 20 LYS cc_start: 0.9108 (ttmm) cc_final: 0.8691 (mtmm) REVERT: E 160 ARG cc_start: 0.8495 (ttp80) cc_final: 0.8293 (ttp80) REVERT: E 215 THR cc_start: 0.8351 (OUTLIER) cc_final: 0.7692 (p) REVERT: R 30 PHE cc_start: 0.7484 (OUTLIER) cc_final: 0.7027 (t80) REVERT: R 106 ARG cc_start: 0.8031 (mpp80) cc_final: 0.7705 (mpp80) REVERT: R 108 MET cc_start: 0.6943 (tpt) cc_final: 0.6636 (tpt) REVERT: R 163 LEU cc_start: 0.8126 (tp) cc_final: 0.7668 (tp) REVERT: R 203 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7661 (tp) REVERT: R 271 ARG cc_start: 0.7636 (ttp80) cc_final: 0.7264 (ttp-170) outliers start: 18 outliers final: 8 residues processed: 202 average time/residue: 0.2627 time to fit residues: 70.6346 Evaluate side-chains 188 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 176 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain R residue 30 PHE Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 198 LEU Chi-restraints excluded: chain R residue 203 LEU Chi-restraints excluded: chain R residue 237 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 37 optimal weight: 0.2980 chunk 55 optimal weight: 0.6980 chunk 95 optimal weight: 6.9990 chunk 100 optimal weight: 8.9990 chunk 82 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 111 optimal weight: 8.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.158187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.118054 restraints weight = 10875.666| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.47 r_work: 0.3128 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9137 Z= 0.122 Angle : 0.467 6.863 12401 Z= 0.245 Chirality : 0.040 0.143 1412 Planarity : 0.003 0.044 1582 Dihedral : 5.680 74.325 1298 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.54 % Allowed : 14.90 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.25), residues: 1148 helix: 2.73 (0.26), residues: 409 sheet: 0.33 (0.30), residues: 278 loop : 0.69 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.005 0.001 HIS A 209 PHE 0.009 0.001 PHE B 151 TYR 0.011 0.001 TYR R 226 ARG 0.007 0.000 ARG E 218 Details of bonding type rmsd hydrogen bonds : bond 0.03283 ( 452) hydrogen bonds : angle 4.06289 ( 1299) SS BOND : bond 0.00116 ( 4) SS BOND : angle 0.54171 ( 8) covalent geometry : bond 0.00278 ( 9133) covalent geometry : angle 0.46660 (12393) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 188 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 126 LYS cc_start: 0.8432 (ttmt) cc_final: 0.7903 (tttm) REVERT: A 161 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7449 (mm-30) REVERT: B 57 LYS cc_start: 0.8557 (mtmm) cc_final: 0.7961 (mtmm) REVERT: B 59 TYR cc_start: 0.8385 (m-80) cc_final: 0.7974 (m-80) REVERT: C 17 GLU cc_start: 0.9166 (tp30) cc_final: 0.8778 (tp30) REVERT: C 20 LYS cc_start: 0.9112 (ttmm) cc_final: 0.8681 (mtmm) REVERT: E 160 ARG cc_start: 0.8375 (ttp80) cc_final: 0.8171 (ttp80) REVERT: E 215 THR cc_start: 0.8343 (OUTLIER) cc_final: 0.7694 (p) REVERT: R 30 PHE cc_start: 0.7538 (OUTLIER) cc_final: 0.7018 (t80) REVERT: R 106 ARG cc_start: 0.7970 (mpp80) cc_final: 0.7702 (mpp80) REVERT: R 108 MET cc_start: 0.6936 (tpt) cc_final: 0.6613 (tpt) REVERT: R 163 LEU cc_start: 0.8100 (tp) cc_final: 0.7646 (tp) REVERT: R 203 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7643 (tp) REVERT: R 271 ARG cc_start: 0.7651 (ttp80) cc_final: 0.7406 (ttp80) outliers start: 24 outliers final: 15 residues processed: 199 average time/residue: 0.2323 time to fit residues: 62.2610 Evaluate side-chains 195 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 177 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain R residue 30 PHE Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 166 LEU Chi-restraints excluded: chain R residue 198 LEU Chi-restraints excluded: chain R residue 203 LEU Chi-restraints excluded: chain R residue 237 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 19 optimal weight: 0.4980 chunk 21 optimal weight: 0.8980 chunk 70 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 93 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 110 optimal weight: 8.9990 chunk 74 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.158287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.118003 restraints weight = 10878.383| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.47 r_work: 0.3123 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9137 Z= 0.124 Angle : 0.466 7.052 12401 Z= 0.244 Chirality : 0.040 0.142 1412 Planarity : 0.003 0.043 1582 Dihedral : 6.004 79.825 1298 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.22 % Allowed : 15.12 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.26), residues: 1148 helix: 2.71 (0.26), residues: 413 sheet: 0.31 (0.29), residues: 281 loop : 0.66 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.004 0.001 HIS A 209 PHE 0.009 0.001 PHE B 151 TYR 0.010 0.001 TYR R 226 ARG 0.006 0.000 ARG E 218 Details of bonding type rmsd hydrogen bonds : bond 0.03176 ( 452) hydrogen bonds : angle 4.01751 ( 1299) SS BOND : bond 0.00196 ( 4) SS BOND : angle 0.51839 ( 8) covalent geometry : bond 0.00284 ( 9133) covalent geometry : angle 0.46634 (12393) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 188 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 126 LYS cc_start: 0.8441 (ttmt) cc_final: 0.7909 (tttm) REVERT: A 161 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7447 (mm-30) REVERT: B 57 LYS cc_start: 0.8544 (mtmm) cc_final: 0.8136 (mtmm) REVERT: B 59 TYR cc_start: 0.8338 (m-80) cc_final: 0.8087 (m-80) REVERT: B 215 GLU cc_start: 0.8565 (mp0) cc_final: 0.8235 (mp0) REVERT: B 266 HIS cc_start: 0.8602 (t70) cc_final: 0.8234 (t70) REVERT: C 17 GLU cc_start: 0.9091 (tp30) cc_final: 0.8678 (tp30) REVERT: C 20 LYS cc_start: 0.9128 (ttmm) cc_final: 0.8709 (mtmm) REVERT: E 160 ARG cc_start: 0.8370 (ttp80) cc_final: 0.8156 (ttp80) REVERT: E 201 ASP cc_start: 0.7708 (p0) cc_final: 0.7425 (t0) REVERT: E 215 THR cc_start: 0.8353 (OUTLIER) cc_final: 0.7705 (p) REVERT: R 30 PHE cc_start: 0.7478 (OUTLIER) cc_final: 0.6982 (t80) REVERT: R 108 MET cc_start: 0.6949 (tpt) cc_final: 0.6748 (tpp) REVERT: R 163 LEU cc_start: 0.8147 (tp) cc_final: 0.7690 (tp) REVERT: R 203 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7638 (tp) REVERT: R 271 ARG cc_start: 0.7610 (ttp80) cc_final: 0.7356 (ttp80) outliers start: 21 outliers final: 16 residues processed: 198 average time/residue: 0.2393 time to fit residues: 63.5313 Evaluate side-chains 198 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 179 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain R residue 30 PHE Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 166 LEU Chi-restraints excluded: chain R residue 198 LEU Chi-restraints excluded: chain R residue 203 LEU Chi-restraints excluded: chain R residue 237 ARG Chi-restraints excluded: chain R residue 255 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 67 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 98 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 88 optimal weight: 8.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.157058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.110253 restraints weight = 10896.709| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.37 r_work: 0.3116 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 9137 Z= 0.119 Angle : 0.473 10.279 12401 Z= 0.245 Chirality : 0.040 0.145 1412 Planarity : 0.003 0.043 1582 Dihedral : 5.998 80.673 1298 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.75 % Allowed : 15.75 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.26), residues: 1148 helix: 2.73 (0.26), residues: 412 sheet: 0.24 (0.29), residues: 283 loop : 0.68 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.004 0.001 HIS A 209 PHE 0.011 0.001 PHE R 184 TYR 0.010 0.001 TYR R 226 ARG 0.009 0.000 ARG E 218 Details of bonding type rmsd hydrogen bonds : bond 0.03124 ( 452) hydrogen bonds : angle 3.98772 ( 1299) SS BOND : bond 0.00196 ( 4) SS BOND : angle 0.50742 ( 8) covalent geometry : bond 0.00272 ( 9133) covalent geometry : angle 0.47289 (12393) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 181 time to evaluate : 0.935 Fit side-chains revert: symmetry clash REVERT: A 126 LYS cc_start: 0.8467 (ttmt) cc_final: 0.7952 (tttm) REVERT: A 161 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7432 (mm-30) REVERT: B 57 LYS cc_start: 0.8568 (mtmm) cc_final: 0.8211 (mtmm) REVERT: B 59 TYR cc_start: 0.8346 (m-80) cc_final: 0.8104 (m-80) REVERT: B 214 ARG cc_start: 0.7709 (mmp80) cc_final: 0.7449 (mmt-90) REVERT: B 215 GLU cc_start: 0.8591 (mp0) cc_final: 0.8246 (mp0) REVERT: B 266 HIS cc_start: 0.8506 (t70) cc_final: 0.8128 (t70) REVERT: C 17 GLU cc_start: 0.9079 (tp30) cc_final: 0.8873 (tp30) REVERT: C 20 LYS cc_start: 0.9132 (ttmm) cc_final: 0.8691 (mtmm) REVERT: E 160 ARG cc_start: 0.8398 (ttp80) cc_final: 0.8187 (ttp80) REVERT: E 201 ASP cc_start: 0.7706 (OUTLIER) cc_final: 0.7437 (t0) REVERT: R 30 PHE cc_start: 0.7451 (OUTLIER) cc_final: 0.6918 (t80) REVERT: R 106 ARG cc_start: 0.8147 (mpp80) cc_final: 0.7698 (mpp80) REVERT: R 108 MET cc_start: 0.6955 (tpt) cc_final: 0.6628 (tpt) REVERT: R 163 LEU cc_start: 0.8130 (tp) cc_final: 0.7660 (tp) REVERT: R 203 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7581 (tp) outliers start: 26 outliers final: 18 residues processed: 192 average time/residue: 0.2503 time to fit residues: 64.1963 Evaluate side-chains 197 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 176 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain R residue 30 PHE Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 166 LEU Chi-restraints excluded: chain R residue 198 LEU Chi-restraints excluded: chain R residue 203 LEU Chi-restraints excluded: chain R residue 237 ARG Chi-restraints excluded: chain R residue 255 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 19 optimal weight: 0.0670 chunk 111 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 93 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 23 optimal weight: 9.9990 chunk 97 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 overall best weight: 0.8720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.157630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.117533 restraints weight = 11059.290| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.52 r_work: 0.3132 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9137 Z= 0.113 Angle : 0.473 9.664 12401 Z= 0.246 Chirality : 0.040 0.143 1412 Planarity : 0.003 0.044 1582 Dihedral : 6.040 82.341 1298 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.43 % Allowed : 16.28 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.26), residues: 1148 helix: 2.79 (0.26), residues: 412 sheet: 0.23 (0.29), residues: 283 loop : 0.71 (0.31), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.004 0.001 HIS A 209 PHE 0.022 0.001 PHE R 184 TYR 0.011 0.001 TYR E 190 ARG 0.009 0.000 ARG E 218 Details of bonding type rmsd hydrogen bonds : bond 0.03062 ( 452) hydrogen bonds : angle 3.95172 ( 1299) SS BOND : bond 0.00193 ( 4) SS BOND : angle 0.50792 ( 8) covalent geometry : bond 0.00257 ( 9133) covalent geometry : angle 0.47304 (12393) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 186 time to evaluate : 0.948 Fit side-chains revert: symmetry clash REVERT: A 126 LYS cc_start: 0.8434 (ttmt) cc_final: 0.7919 (tttm) REVERT: A 161 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7419 (mm-30) REVERT: B 57 LYS cc_start: 0.8551 (mtmm) cc_final: 0.8223 (mtmm) REVERT: B 59 TYR cc_start: 0.8361 (m-80) cc_final: 0.8123 (m-80) REVERT: B 130 GLU cc_start: 0.8878 (mp0) cc_final: 0.8656 (mp0) REVERT: B 214 ARG cc_start: 0.7681 (mmp80) cc_final: 0.7419 (mmt-90) REVERT: B 215 GLU cc_start: 0.8562 (mp0) cc_final: 0.8206 (mp0) REVERT: B 266 HIS cc_start: 0.8500 (t70) cc_final: 0.8092 (t70) REVERT: C 17 GLU cc_start: 0.9070 (tp30) cc_final: 0.8840 (tp30) REVERT: C 20 LYS cc_start: 0.9122 (ttmm) cc_final: 0.8677 (mtmm) REVERT: E 160 ARG cc_start: 0.8396 (ttp80) cc_final: 0.8176 (ttp80) REVERT: E 201 ASP cc_start: 0.7686 (OUTLIER) cc_final: 0.7418 (t0) REVERT: R 30 PHE cc_start: 0.7452 (OUTLIER) cc_final: 0.6919 (t80) REVERT: R 108 MET cc_start: 0.6961 (tpt) cc_final: 0.6741 (tpp) REVERT: R 163 LEU cc_start: 0.8105 (tp) cc_final: 0.7702 (tp) REVERT: R 203 LEU cc_start: 0.7896 (OUTLIER) cc_final: 0.7609 (tp) REVERT: R 312 ARG cc_start: 0.7831 (mmp80) cc_final: 0.6382 (mmp80) outliers start: 23 outliers final: 19 residues processed: 196 average time/residue: 0.2314 time to fit residues: 61.0061 Evaluate side-chains 201 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 179 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain R residue 30 PHE Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 166 LEU Chi-restraints excluded: chain R residue 198 LEU Chi-restraints excluded: chain R residue 203 LEU Chi-restraints excluded: chain R residue 237 ARG Chi-restraints excluded: chain R residue 255 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 43 optimal weight: 0.4980 chunk 24 optimal weight: 6.9990 chunk 96 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 106 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.157690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.117080 restraints weight = 10961.537| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.47 r_work: 0.3154 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9137 Z= 0.113 Angle : 0.473 9.341 12401 Z= 0.246 Chirality : 0.040 0.143 1412 Planarity : 0.003 0.045 1582 Dihedral : 6.020 80.903 1298 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.75 % Allowed : 15.96 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.26), residues: 1148 helix: 2.87 (0.27), residues: 406 sheet: 0.20 (0.29), residues: 284 loop : 0.75 (0.31), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.004 0.001 HIS A 209 PHE 0.021 0.001 PHE R 184 TYR 0.011 0.001 TYR E 190 ARG 0.009 0.000 ARG E 218 Details of bonding type rmsd hydrogen bonds : bond 0.03047 ( 452) hydrogen bonds : angle 3.95019 ( 1299) SS BOND : bond 0.00209 ( 4) SS BOND : angle 0.56107 ( 8) covalent geometry : bond 0.00259 ( 9133) covalent geometry : angle 0.47294 (12393) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 185 time to evaluate : 0.942 Fit side-chains revert: symmetry clash REVERT: A 113 SER cc_start: 0.8547 (p) cc_final: 0.8324 (m) REVERT: A 126 LYS cc_start: 0.8495 (ttmt) cc_final: 0.7987 (tttm) REVERT: A 161 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7413 (mm-30) REVERT: B 57 LYS cc_start: 0.8576 (mtmm) cc_final: 0.8283 (mtmm) REVERT: B 59 TYR cc_start: 0.8366 (m-80) cc_final: 0.8163 (m-80) REVERT: B 130 GLU cc_start: 0.8875 (mp0) cc_final: 0.8669 (mp0) REVERT: B 214 ARG cc_start: 0.7680 (mmp80) cc_final: 0.7459 (mmt-90) REVERT: B 215 GLU cc_start: 0.8569 (mp0) cc_final: 0.8230 (mp0) REVERT: C 17 GLU cc_start: 0.9053 (tp30) cc_final: 0.8813 (tp30) REVERT: C 20 LYS cc_start: 0.9132 (ttmm) cc_final: 0.8689 (mtmm) REVERT: E 201 ASP cc_start: 0.7709 (OUTLIER) cc_final: 0.7465 (t0) REVERT: E 218 ARG cc_start: 0.7057 (ttp-110) cc_final: 0.6685 (tmm-80) REVERT: R 30 PHE cc_start: 0.7435 (OUTLIER) cc_final: 0.6882 (t80) REVERT: R 108 MET cc_start: 0.7020 (tpt) cc_final: 0.6808 (tpp) REVERT: R 163 LEU cc_start: 0.8149 (tp) cc_final: 0.7694 (tp) REVERT: R 203 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7579 (tp) REVERT: R 294 LEU cc_start: 0.8130 (tp) cc_final: 0.7846 (tt) REVERT: R 312 ARG cc_start: 0.7884 (mmp80) cc_final: 0.6569 (mmp80) outliers start: 26 outliers final: 19 residues processed: 196 average time/residue: 0.2324 time to fit residues: 61.2786 Evaluate side-chains 205 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 183 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain R residue 30 PHE Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 166 LEU Chi-restraints excluded: chain R residue 198 LEU Chi-restraints excluded: chain R residue 203 LEU Chi-restraints excluded: chain R residue 237 ARG Chi-restraints excluded: chain R residue 255 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 35 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 70 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 5 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 84 optimal weight: 30.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.157568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.117699 restraints weight = 10901.945| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.50 r_work: 0.3136 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9137 Z= 0.113 Angle : 0.483 9.176 12401 Z= 0.251 Chirality : 0.040 0.143 1412 Planarity : 0.003 0.044 1582 Dihedral : 6.018 80.607 1298 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.33 % Allowed : 17.12 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.26), residues: 1148 helix: 2.85 (0.27), residues: 407 sheet: 0.26 (0.30), residues: 278 loop : 0.66 (0.30), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.004 0.001 HIS A 209 PHE 0.017 0.001 PHE R 184 TYR 0.010 0.001 TYR E 190 ARG 0.012 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.03047 ( 452) hydrogen bonds : angle 3.94235 ( 1299) SS BOND : bond 0.00217 ( 4) SS BOND : angle 0.54175 ( 8) covalent geometry : bond 0.00260 ( 9133) covalent geometry : angle 0.48328 (12393) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2296 Ramachandran restraints generated. 1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 185 time to evaluate : 0.776 Fit side-chains revert: symmetry clash REVERT: A 113 SER cc_start: 0.8537 (p) cc_final: 0.8324 (m) REVERT: A 126 LYS cc_start: 0.8416 (ttmt) cc_final: 0.7909 (tttm) REVERT: A 161 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7423 (mm-30) REVERT: B 57 LYS cc_start: 0.8548 (mtmm) cc_final: 0.8255 (mtmm) REVERT: B 130 GLU cc_start: 0.8893 (mp0) cc_final: 0.8680 (mp0) REVERT: B 214 ARG cc_start: 0.7706 (mmp80) cc_final: 0.7456 (mmt-90) REVERT: B 215 GLU cc_start: 0.8551 (mp0) cc_final: 0.8189 (mp0) REVERT: B 266 HIS cc_start: 0.8481 (t70) cc_final: 0.8174 (t70) REVERT: C 17 GLU cc_start: 0.9052 (tp30) cc_final: 0.8774 (tp30) REVERT: C 20 LYS cc_start: 0.9130 (ttmm) cc_final: 0.8691 (mtmm) REVERT: E 201 ASP cc_start: 0.7666 (OUTLIER) cc_final: 0.7411 (t0) REVERT: E 218 ARG cc_start: 0.7049 (ttp-110) cc_final: 0.6593 (tmm-80) REVERT: E 220 GLU cc_start: 0.8358 (mt-10) cc_final: 0.8026 (mt-10) REVERT: R 30 PHE cc_start: 0.7348 (OUTLIER) cc_final: 0.6907 (t80) REVERT: R 108 MET cc_start: 0.6938 (tpt) cc_final: 0.6716 (tpp) REVERT: R 163 LEU cc_start: 0.8132 (tp) cc_final: 0.7670 (tp) REVERT: R 203 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7537 (tp) REVERT: R 294 LEU cc_start: 0.8056 (tp) cc_final: 0.7790 (tt) REVERT: R 312 ARG cc_start: 0.7916 (mmp80) cc_final: 0.6559 (mmp80) outliers start: 22 outliers final: 17 residues processed: 194 average time/residue: 0.2197 time to fit residues: 57.6029 Evaluate side-chains 202 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 182 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 98 GLN Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain R residue 30 PHE Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 198 LEU Chi-restraints excluded: chain R residue 203 LEU Chi-restraints excluded: chain R residue 237 ARG Chi-restraints excluded: chain R residue 255 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 5 optimal weight: 0.2980 chunk 18 optimal weight: 8.9990 chunk 113 optimal weight: 0.6980 chunk 60 optimal weight: 0.3980 chunk 58 optimal weight: 0.9990 chunk 111 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 52 optimal weight: 6.9990 chunk 104 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 25 optimal weight: 0.0870 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.160243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.116028 restraints weight = 10978.830| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.37 r_work: 0.3170 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9137 Z= 0.092 Angle : 0.466 9.036 12401 Z= 0.242 Chirality : 0.039 0.142 1412 Planarity : 0.003 0.043 1582 Dihedral : 6.019 83.807 1298 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.80 % Allowed : 17.86 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.26), residues: 1148 helix: 2.95 (0.27), residues: 407 sheet: 0.22 (0.29), residues: 283 loop : 0.74 (0.31), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.003 0.001 HIS A 209 PHE 0.016 0.001 PHE R 184 TYR 0.013 0.001 TYR B 59 ARG 0.009 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.02882 ( 452) hydrogen bonds : angle 3.86557 ( 1299) SS BOND : bond 0.00202 ( 4) SS BOND : angle 0.47177 ( 8) covalent geometry : bond 0.00203 ( 9133) covalent geometry : angle 0.46589 (12393) Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 6290.65 seconds wall clock time: 108 minutes 7.55 seconds (6487.55 seconds total)