Starting phenix.real_space_refine on Wed Sep 17 13:07:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xjn_38402/09_2025/8xjn_38402.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xjn_38402/09_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_38402/09_2025/8xjn_38402.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xjn_38402/09_2025/8xjn_38402.map" model { file = "/net/cci-nas-00/data/ceres_data/8xjn_38402/09_2025/8xjn_38402.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xjn_38402/09_2025/8xjn_38402.cif" } resolution = 3.06 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ARG:plan': 1, 'GLU: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: {'PHE:plan': 2, 'ARG:plan': 7, 'ASN:plan1': 1, 'GLU:plan': 4, 'GLN:plan1': 5, 'HIS:plan': 1, 'ASP:plan': 1} 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: 2.25, per 1000 atoms: 0.25 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: 0.81 Conformation dependent library (CDL) restraints added in 239.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.37 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: 1.59 Time building geometry restraints manager: 1.04 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: 0.720 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.710 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.070 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 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 ARG 0.004 0.000 ARG B 314 TYR 0.010 0.001 TYR E 190 PHE 0.010 0.001 PHE A 108 TRP 0.009 0.001 TRP R 95 HIS 0.004 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00427 ( 9133) covalent geometry : angle 0.42771 (12393) SS BOND : bond 0.00162 ( 4) SS BOND : angle 0.49543 ( 8) hydrogen bonds : bond 0.25273 ( 452) hydrogen bonds : angle 7.53664 ( 1299) *********************** 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 : 0.351 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: 0.8066 (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: 0.8175 (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: 0.1397 time to fit residues: 47.9774 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 : 0.375 ------------------------------------------------------------------------------- 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 108 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 0.6980 chunk 53 optimal weight: 0.0980 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 6.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.3858 r_free = 0.3858 target = 0.158715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.113090 restraints weight = 10572.588| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.23 r_work: 0.2995 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9137 Z= 0.161 Angle : 0.541 6.507 12401 Z= 0.288 Chirality : 0.042 0.149 1412 Planarity : 0.004 0.042 1582 Dihedral : 6.650 77.046 1302 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.48 % Allowed : 10.36 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.55 (0.25), residues: 1148 helix: 1.81 (0.26), residues: 412 sheet: 0.80 (0.30), residues: 283 loop : 0.62 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 134 TYR 0.011 0.001 TYR E 190 PHE 0.010 0.001 PHE A 167 TRP 0.018 0.001 TRP B 211 HIS 0.007 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 9133) covalent geometry : angle 0.54090 (12393) SS BOND : bond 0.00203 ( 4) SS BOND : angle 0.85100 ( 8) hydrogen bonds : bond 0.04592 ( 452) hydrogen bonds : angle 4.80206 ( 1299) *********************** 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 216 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 202 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 GLN cc_start: 0.8366 (tp40) cc_final: 0.8162 (tp-100) REVERT: A 75 GLN cc_start: 0.8195 (tt0) cc_final: 0.7964 (tt0) REVERT: A 126 LYS cc_start: 0.8348 (ttmt) cc_final: 0.7769 (tttm) REVERT: A 161 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7372 (mm-30) REVERT: A 195 LYS cc_start: 0.8872 (tptp) cc_final: 0.8603 (tptp) REVERT: B 59 TYR cc_start: 0.8444 (m-80) cc_final: 0.7704 (m-80) REVERT: B 137 ARG cc_start: 0.7715 (mmt-90) cc_final: 0.7317 (mmt180) REVERT: B 243 THR cc_start: 0.8620 (p) cc_final: 0.8396 (p) REVERT: B 266 HIS cc_start: 0.8571 (t70) cc_final: 0.8068 (t70) REVERT: B 304 ARG cc_start: 0.8466 (ttm-80) cc_final: 0.8252 (ttm170) REVERT: C 38 MET cc_start: 0.8433 (ttp) cc_final: 0.8188 (ttm) REVERT: E 144 THR cc_start: 0.7866 (m) cc_final: 0.7542 (p) REVERT: E 213 THR cc_start: 0.8090 (m) cc_final: 0.7850 (p) REVERT: E 215 THR cc_start: 0.8018 (m) cc_final: 0.7398 (p) REVERT: E 218 ARG cc_start: 0.7308 (ttp-110) cc_final: 0.7076 (ptt90) REVERT: R 106 ARG cc_start: 0.7472 (mpp80) cc_final: 0.7009 (mpt-90) REVERT: R 163 LEU cc_start: 0.8209 (tp) cc_final: 0.7908 (tp) outliers start: 14 outliers final: 8 residues processed: 211 average time/residue: 0.1206 time to fit residues: 33.3243 Evaluate side-chains 189 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 181 time to evaluate : 0.378 ------------------------------------------------------------------------------- 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 216 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 228 ASP 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 47 optimal weight: 0.5980 chunk 35 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 112 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 22 optimal weight: 0.2980 chunk 33 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3878 r_free = 0.3878 target = 0.160179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.121368 restraints weight = 10587.682| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.47 r_work: 0.3057 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9137 Z= 0.113 Angle : 0.473 6.301 12401 Z= 0.251 Chirality : 0.040 0.144 1412 Planarity : 0.003 0.042 1582 Dihedral : 6.277 75.040 1300 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.22 % Allowed : 11.73 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.77 (0.25), residues: 1148 helix: 2.34 (0.26), residues: 408 sheet: 0.53 (0.31), residues: 274 loop : 0.66 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 219 TYR 0.012 0.001 TYR E 190 PHE 0.009 0.001 PHE B 151 TRP 0.016 0.001 TRP B 169 HIS 0.005 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 9133) covalent geometry : angle 0.47329 (12393) SS BOND : bond 0.00135 ( 4) SS BOND : angle 0.53754 ( 8) hydrogen bonds : bond 0.03650 ( 452) hydrogen bonds : angle 4.34283 ( 1299) *********************** 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 210 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 189 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 GLN cc_start: 0.8149 (mm-40) cc_final: 0.7932 (mm110) REVERT: A 29 VAL cc_start: 0.8533 (OUTLIER) cc_final: 0.8310 (p) REVERT: A 126 LYS cc_start: 0.8348 (ttmt) cc_final: 0.7812 (tttm) REVERT: A 161 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7485 (mm-30) REVERT: A 195 LYS cc_start: 0.8585 (tptp) cc_final: 0.7855 (tptp) REVERT: A 233 ASP cc_start: 0.8795 (t0) cc_final: 0.8385 (t0) REVERT: B 59 TYR cc_start: 0.8447 (m-80) cc_final: 0.7862 (m-80) REVERT: B 137 ARG cc_start: 0.7678 (mmt-90) cc_final: 0.7253 (mmt180) REVERT: B 189 SER cc_start: 0.9293 (p) cc_final: 0.8851 (t) REVERT: B 266 HIS cc_start: 0.8591 (t70) cc_final: 0.8114 (t70) REVERT: C 17 GLU cc_start: 0.9110 (tp30) cc_final: 0.8846 (tp30) REVERT: C 20 LYS cc_start: 0.9091 (ttmm) cc_final: 0.8732 (mtmm) REVERT: E 144 THR cc_start: 0.7829 (m) cc_final: 0.7481 (p) REVERT: R 30 PHE cc_start: 0.7443 (OUTLIER) cc_final: 0.6992 (t80) REVERT: R 108 MET cc_start: 0.6795 (tpt) cc_final: 0.6494 (tpt) REVERT: R 163 LEU cc_start: 0.8080 (tp) cc_final: 0.7681 (tp) REVERT: R 203 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7698 (tp) outliers start: 21 outliers final: 11 residues processed: 201 average time/residue: 0.1220 time to fit residues: 32.5784 Evaluate side-chains 188 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 174 time to evaluate : 0.410 ------------------------------------------------------------------------------- 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 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 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 76 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 73 optimal weight: 0.3980 chunk 5 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 100 optimal weight: 8.9990 chunk 64 optimal weight: 0.8980 chunk 71 optimal weight: 0.5980 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.3827 r_free = 0.3827 target = 0.154863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.107848 restraints weight = 11053.337| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.37 r_work: 0.3104 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2761 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= 0.138 Angle : 0.483 6.192 12401 Z= 0.255 Chirality : 0.040 0.143 1412 Planarity : 0.004 0.043 1582 Dihedral : 5.831 75.437 1300 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.69 % Allowed : 13.85 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.81 (0.25), residues: 1148 helix: 2.50 (0.26), residues: 409 sheet: 0.43 (0.30), residues: 272 loop : 0.63 (0.30), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 218 TYR 0.011 0.001 TYR R 226 PHE 0.009 0.001 PHE B 151 TRP 0.016 0.001 TRP B 169 HIS 0.005 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 9133) covalent geometry : angle 0.48270 (12393) SS BOND : bond 0.00130 ( 4) SS BOND : angle 0.56207 ( 8) hydrogen bonds : bond 0.03514 ( 452) hydrogen bonds : angle 4.26119 ( 1299) *********************** 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 203 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 187 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 VAL cc_start: 0.8650 (OUTLIER) cc_final: 0.8411 (p) REVERT: A 126 LYS cc_start: 0.8441 (ttmt) cc_final: 0.7900 (tttm) REVERT: A 161 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7502 (mm-30) REVERT: A 195 LYS cc_start: 0.8496 (tptp) cc_final: 0.8099 (tptp) REVERT: B 59 TYR cc_start: 0.8359 (m-80) cc_final: 0.7887 (m-80) REVERT: B 137 ARG cc_start: 0.7777 (mmt-90) cc_final: 0.7353 (mmt180) REVERT: B 333 ASP cc_start: 0.8837 (p0) cc_final: 0.8621 (p0) REVERT: C 17 GLU cc_start: 0.9092 (tp30) cc_final: 0.8882 (tp30) REVERT: C 20 LYS cc_start: 0.9129 (ttmm) cc_final: 0.8725 (mtmm) REVERT: R 30 PHE cc_start: 0.7477 (OUTLIER) cc_final: 0.7025 (t80) REVERT: R 106 ARG cc_start: 0.8089 (mpp80) cc_final: 0.7742 (mpp80) REVERT: R 108 MET cc_start: 0.7050 (tpt) cc_final: 0.6710 (tpt) REVERT: R 163 LEU cc_start: 0.8066 (tp) cc_final: 0.7671 (tp) REVERT: R 203 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7663 (tp) outliers start: 16 outliers final: 12 residues processed: 196 average time/residue: 0.1211 time to fit residues: 31.6314 Evaluate side-chains 195 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 180 time to evaluate : 0.367 ------------------------------------------------------------------------------- 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 184 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 331 SER 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 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 Chi-restraints excluded: chain R residue 259 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 112 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 chunk 68 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 12 optimal weight: 7.9990 chunk 64 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 = 0.3853 r_free = 0.3853 target = 0.156740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.111188 restraints weight = 11052.316| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.40 r_work: 0.3067 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 9137 Z= 0.203 Angle : 0.533 8.783 12401 Z= 0.278 Chirality : 0.042 0.149 1412 Planarity : 0.004 0.043 1582 Dihedral : 5.899 76.186 1300 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.96 % Allowed : 13.95 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.60 (0.25), residues: 1148 helix: 2.35 (0.26), residues: 414 sheet: 0.20 (0.30), residues: 279 loop : 0.56 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 160 TYR 0.012 0.001 TYR R 226 PHE 0.012 0.001 PHE E 27 TRP 0.017 0.002 TRP B 169 HIS 0.006 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00477 ( 9133) covalent geometry : angle 0.53341 (12393) SS BOND : bond 0.00220 ( 4) SS BOND : angle 0.64382 ( 8) hydrogen bonds : bond 0.03728 ( 452) hydrogen bonds : angle 4.35421 ( 1299) *********************** 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 203 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 175 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 VAL cc_start: 0.8672 (OUTLIER) cc_final: 0.8454 (p) REVERT: A 126 LYS cc_start: 0.8524 (ttmt) cc_final: 0.7972 (tttm) REVERT: A 161 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7486 (mm-30) REVERT: A 195 LYS cc_start: 0.8630 (tptp) cc_final: 0.8352 (tptp) REVERT: B 59 TYR cc_start: 0.8502 (m-80) cc_final: 0.8048 (m-80) REVERT: B 75 GLN cc_start: 0.8683 (mt0) cc_final: 0.8468 (mt0) REVERT: B 137 ARG cc_start: 0.7788 (mmt-90) cc_final: 0.7278 (mmt180) REVERT: B 215 GLU cc_start: 0.8573 (mp0) cc_final: 0.8248 (mp0) REVERT: B 266 HIS cc_start: 0.8623 (t70) cc_final: 0.8271 (t70) REVERT: C 17 GLU cc_start: 0.9114 (tp30) cc_final: 0.8892 (tp30) REVERT: C 20 LYS cc_start: 0.9132 (ttmm) cc_final: 0.8706 (mtmm) REVERT: E 201 ASP cc_start: 0.7732 (OUTLIER) cc_final: 0.7407 (t0) REVERT: R 30 PHE cc_start: 0.7510 (OUTLIER) cc_final: 0.7116 (t80) REVERT: R 108 MET cc_start: 0.7023 (tpt) cc_final: 0.6686 (tpt) REVERT: R 163 LEU cc_start: 0.8170 (tp) cc_final: 0.7846 (tp) REVERT: R 203 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7720 (tp) outliers start: 28 outliers final: 19 residues processed: 189 average time/residue: 0.1187 time to fit residues: 30.1008 Evaluate side-chains 195 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 172 time to evaluate : 0.355 ------------------------------------------------------------------------------- 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 110 VAL Chi-restraints excluded: chain A residue 120 GLU 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 331 SER Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 201 ASP 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 110 VAL 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 Chi-restraints excluded: chain R residue 259 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 101 optimal weight: 0.2980 chunk 37 optimal weight: 0.6980 chunk 102 optimal weight: 9.9990 chunk 83 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 114 optimal weight: 0.9990 chunk 13 optimal weight: 0.1980 chunk 29 optimal weight: 0.7980 chunk 80 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3862 r_free = 0.3862 target = 0.157775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.110979 restraints weight = 10951.781| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.37 r_work: 0.3129 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.3064 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= 0.094 Angle : 0.459 8.584 12401 Z= 0.240 Chirality : 0.040 0.145 1412 Planarity : 0.003 0.050 1582 Dihedral : 5.885 75.673 1300 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.22 % Allowed : 15.01 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.81 (0.26), residues: 1148 helix: 2.61 (0.26), residues: 412 sheet: 0.28 (0.30), residues: 272 loop : 0.61 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 312 TYR 0.013 0.001 TYR E 190 PHE 0.009 0.001 PHE B 151 TRP 0.016 0.001 TRP B 169 HIS 0.003 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00205 ( 9133) covalent geometry : angle 0.45934 (12393) SS BOND : bond 0.00181 ( 4) SS BOND : angle 0.47811 ( 8) hydrogen bonds : bond 0.03090 ( 452) hydrogen bonds : angle 4.06207 ( 1299) *********************** 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 215 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 194 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 126 LYS cc_start: 0.8445 (ttmt) cc_final: 0.7921 (tttm) REVERT: A 161 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7472 (mm-30) REVERT: A 195 LYS cc_start: 0.8470 (tptp) cc_final: 0.8206 (tptp) REVERT: A 222 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7567 (mp0) REVERT: A 233 ASP cc_start: 0.8891 (t0) cc_final: 0.8523 (t0) REVERT: B 59 TYR cc_start: 0.8390 (m-80) cc_final: 0.7925 (m-80) REVERT: B 75 GLN cc_start: 0.8498 (mt0) cc_final: 0.8285 (mt0) REVERT: B 215 GLU cc_start: 0.8546 (mp0) cc_final: 0.8196 (mp0) REVERT: B 266 HIS cc_start: 0.8489 (t70) cc_final: 0.8109 (t70) REVERT: C 17 GLU cc_start: 0.9110 (tp30) cc_final: 0.8646 (tp30) REVERT: C 20 LYS cc_start: 0.9142 (ttmm) cc_final: 0.8704 (mtmm) REVERT: C 21 MET cc_start: 0.8602 (mtp) cc_final: 0.8057 (mtp) REVERT: E 201 ASP cc_start: 0.7642 (OUTLIER) cc_final: 0.7328 (t0) REVERT: R 30 PHE cc_start: 0.7467 (OUTLIER) cc_final: 0.7013 (t80) REVERT: R 108 MET cc_start: 0.6981 (tpt) cc_final: 0.6673 (tpt) REVERT: R 163 LEU cc_start: 0.8040 (tp) cc_final: 0.7557 (tp) REVERT: R 203 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7612 (tp) outliers start: 21 outliers final: 12 residues processed: 205 average time/residue: 0.1130 time to fit residues: 31.4863 Evaluate side-chains 186 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 171 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 115 TYR Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain E residue 201 ASP 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 42 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 chunk 79 optimal weight: 10.0000 chunk 49 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 14 optimal weight: 0.0030 chunk 110 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 overall best weight: 0.8994 ------------------------------------------------------------------------------- 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 = 0.156989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.110146 restraints weight = 11009.317| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.37 r_work: 0.3115 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.3144 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= 0.116 Angle : 0.474 7.821 12401 Z= 0.249 Chirality : 0.040 0.146 1412 Planarity : 0.003 0.043 1582 Dihedral : 5.829 76.120 1298 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.01 % Allowed : 16.28 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.81 (0.26), residues: 1148 helix: 2.73 (0.26), residues: 405 sheet: 0.20 (0.30), residues: 282 loop : 0.60 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 160 TYR 0.011 0.001 TYR E 190 PHE 0.009 0.001 PHE B 151 TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 9133) covalent geometry : angle 0.47381 (12393) SS BOND : bond 0.00170 ( 4) SS BOND : angle 0.54949 ( 8) hydrogen bonds : bond 0.03165 ( 452) hydrogen bonds : angle 4.07578 ( 1299) *********************** 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 204 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 185 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 126 LYS cc_start: 0.8458 (ttmt) cc_final: 0.7973 (tttm) REVERT: A 161 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7453 (mm-30) REVERT: A 233 ASP cc_start: 0.8862 (t0) cc_final: 0.8501 (t0) REVERT: B 59 TYR cc_start: 0.8396 (m-80) cc_final: 0.7803 (m-80) REVERT: B 75 GLN cc_start: 0.8571 (mt0) cc_final: 0.7500 (mt0) REVERT: B 197 ARG cc_start: 0.7979 (mtp85) cc_final: 0.7688 (mmm160) REVERT: B 215 GLU cc_start: 0.8482 (mp0) cc_final: 0.8133 (mp0) REVERT: B 258 ASP cc_start: 0.8217 (t70) cc_final: 0.7925 (t70) REVERT: C 17 GLU cc_start: 0.9114 (tp30) cc_final: 0.8638 (tp30) REVERT: C 20 LYS cc_start: 0.9139 (ttmm) cc_final: 0.8666 (mtmm) REVERT: C 21 MET cc_start: 0.8525 (mtp) cc_final: 0.7980 (mtp) REVERT: E 201 ASP cc_start: 0.7629 (OUTLIER) cc_final: 0.7376 (t0) REVERT: R 30 PHE cc_start: 0.7543 (OUTLIER) cc_final: 0.7085 (t80) REVERT: R 108 MET cc_start: 0.6950 (tpt) cc_final: 0.6634 (tpt) REVERT: R 163 LEU cc_start: 0.8101 (tp) cc_final: 0.7616 (tp) REVERT: R 203 LEU cc_start: 0.7868 (OUTLIER) cc_final: 0.7589 (tp) outliers start: 19 outliers final: 13 residues processed: 192 average time/residue: 0.1152 time to fit residues: 30.0112 Evaluate side-chains 191 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 175 time to evaluate : 0.360 ------------------------------------------------------------------------------- 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 115 TYR Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain B residue 184 THR 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 7 optimal weight: 0.4980 chunk 107 optimal weight: 5.9990 chunk 39 optimal weight: 0.0030 chunk 38 optimal weight: 2.9990 overall best weight: 1.0592 ------------------------------------------------------------------------------- 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 = 0.3850 r_free = 0.3850 target = 0.156549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.109594 restraints weight = 10990.261| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.37 r_work: 0.3110 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.3215 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= 0.127 Angle : 0.481 7.916 12401 Z= 0.252 Chirality : 0.040 0.145 1412 Planarity : 0.003 0.045 1582 Dihedral : 5.830 76.204 1298 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.90 % Allowed : 16.60 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.84 (0.25), residues: 1148 helix: 2.83 (0.26), residues: 399 sheet: 0.16 (0.30), residues: 277 loop : 0.59 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 160 TYR 0.011 0.001 TYR R 226 PHE 0.011 0.001 PHE R 184 TRP 0.015 0.001 TRP B 169 HIS 0.004 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 9133) covalent geometry : angle 0.48091 (12393) SS BOND : bond 0.00195 ( 4) SS BOND : angle 0.54796 ( 8) hydrogen bonds : bond 0.03165 ( 452) hydrogen bonds : angle 4.06737 ( 1299) *********************** 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 205 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 187 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 126 LYS cc_start: 0.8451 (ttmt) cc_final: 0.7967 (tttm) REVERT: A 161 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7449 (mm-30) REVERT: A 233 ASP cc_start: 0.8866 (t0) cc_final: 0.8549 (t0) REVERT: B 59 TYR cc_start: 0.8424 (m-80) cc_final: 0.8202 (m-80) REVERT: B 130 GLU cc_start: 0.8904 (mp0) cc_final: 0.8688 (mp0) REVERT: B 197 ARG cc_start: 0.7975 (mtp85) cc_final: 0.7683 (mmm160) REVERT: B 215 GLU cc_start: 0.8486 (mp0) cc_final: 0.8139 (mp0) REVERT: C 17 GLU cc_start: 0.9109 (tp30) cc_final: 0.8535 (tp30) REVERT: C 21 MET cc_start: 0.8540 (mtp) cc_final: 0.8026 (mtp) REVERT: E 201 ASP cc_start: 0.7675 (OUTLIER) cc_final: 0.7430 (t0) REVERT: R 30 PHE cc_start: 0.7541 (OUTLIER) cc_final: 0.7084 (t80) REVERT: R 108 MET cc_start: 0.6936 (tpt) cc_final: 0.6638 (tpt) REVERT: R 163 LEU cc_start: 0.8107 (tp) cc_final: 0.7624 (tp) REVERT: R 203 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7586 (tp) outliers start: 18 outliers final: 14 residues processed: 194 average time/residue: 0.1085 time to fit residues: 28.5815 Evaluate side-chains 200 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 183 time to evaluate : 0.321 ------------------------------------------------------------------------------- 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 184 THR 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 4 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 85 optimal weight: 0.0870 chunk 28 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 overall best weight: 1.5964 ------------------------------------------------------------------------------- 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 = 0.3846 r_free = 0.3846 target = 0.156289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.115726 restraints weight = 10945.569| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.56 r_work: 0.3059 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9137 Z= 0.169 Angle : 0.522 10.698 12401 Z= 0.271 Chirality : 0.041 0.145 1412 Planarity : 0.004 0.046 1582 Dihedral : 5.863 77.267 1298 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.01 % Allowed : 17.44 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.70 (0.25), residues: 1148 helix: 2.62 (0.26), residues: 403 sheet: 0.12 (0.29), residues: 280 loop : 0.57 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 134 TYR 0.011 0.001 TYR R 226 PHE 0.022 0.001 PHE R 184 TRP 0.016 0.001 TRP B 339 HIS 0.005 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 9133) covalent geometry : angle 0.52235 (12393) SS BOND : bond 0.00206 ( 4) SS BOND : angle 0.63045 ( 8) hydrogen bonds : bond 0.03368 ( 452) hydrogen bonds : angle 4.14646 ( 1299) *********************** 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 210 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 191 time to evaluate : 0.348 Fit side-chains revert: symmetry clash REVERT: A 126 LYS cc_start: 0.8458 (ttmt) cc_final: 0.7964 (tttm) REVERT: A 161 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7449 (mm-30) REVERT: B 59 TYR cc_start: 0.8536 (m-80) cc_final: 0.8209 (m-80) REVERT: B 99 TRP cc_start: 0.8552 (m100) cc_final: 0.8279 (m100) REVERT: B 130 GLU cc_start: 0.8927 (mp0) cc_final: 0.8714 (mp0) REVERT: B 197 ARG cc_start: 0.8032 (mtp85) cc_final: 0.7779 (mmm160) REVERT: B 215 GLU cc_start: 0.8489 (mp0) cc_final: 0.8116 (mp0) REVERT: C 17 GLU cc_start: 0.9095 (tp30) cc_final: 0.8626 (tp30) REVERT: C 20 LYS cc_start: 0.9129 (ttmm) cc_final: 0.8608 (mtmm) REVERT: C 21 MET cc_start: 0.8556 (mtp) cc_final: 0.7963 (mtp) REVERT: E 201 ASP cc_start: 0.7708 (OUTLIER) cc_final: 0.7504 (t0) REVERT: E 220 GLU cc_start: 0.8473 (mt-10) cc_final: 0.8200 (mt-10) REVERT: R 30 PHE cc_start: 0.7548 (OUTLIER) cc_final: 0.7220 (t80) REVERT: R 108 MET cc_start: 0.7010 (tpt) cc_final: 0.6697 (tpt) REVERT: R 163 LEU cc_start: 0.8066 (tp) cc_final: 0.7623 (tp) REVERT: R 203 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7623 (tp) outliers start: 19 outliers final: 14 residues processed: 198 average time/residue: 0.1152 time to fit residues: 30.7528 Evaluate side-chains 205 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 188 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER 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 184 THR 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 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 270 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 69 optimal weight: 4.9990 chunk 66 optimal weight: 0.0370 chunk 53 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 74 optimal weight: 8.9990 chunk 51 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 22 optimal weight: 0.0570 chunk 79 optimal weight: 0.2980 overall best weight: 0.4176 ------------------------------------------------------------------------------- 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 = 0.3882 r_free = 0.3882 target = 0.159576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.112542 restraints weight = 10919.408| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.40 r_work: 0.3146 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9137 Z= 0.093 Angle : 0.487 10.683 12401 Z= 0.252 Chirality : 0.040 0.144 1412 Planarity : 0.004 0.045 1582 Dihedral : 5.877 76.079 1298 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.37 % Allowed : 18.39 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.95 (0.26), residues: 1148 helix: 2.92 (0.27), residues: 399 sheet: 0.24 (0.30), residues: 271 loop : 0.64 (0.30), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 60 TYR 0.013 0.001 TYR E 190 PHE 0.020 0.001 PHE R 184 TRP 0.014 0.001 TRP B 169 HIS 0.003 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00204 ( 9133) covalent geometry : angle 0.48732 (12393) SS BOND : bond 0.00204 ( 4) SS BOND : angle 0.47692 ( 8) hydrogen bonds : bond 0.02941 ( 452) hydrogen bonds : angle 3.96351 ( 1299) ********************** 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 204 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 191 time to evaluate : 0.286 Fit side-chains revert: symmetry clash REVERT: A 126 LYS cc_start: 0.8426 (ttmt) cc_final: 0.7953 (tttm) REVERT: A 161 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7431 (mm-30) REVERT: A 233 ASP cc_start: 0.8848 (t0) cc_final: 0.8504 (t0) REVERT: B 59 TYR cc_start: 0.8438 (m-80) cc_final: 0.8174 (m-80) REVERT: B 130 GLU cc_start: 0.8866 (mp0) cc_final: 0.8664 (mp0) REVERT: B 197 ARG cc_start: 0.7956 (mtp85) cc_final: 0.7738 (mmm160) REVERT: B 215 GLU cc_start: 0.8499 (mp0) cc_final: 0.8151 (mp0) REVERT: C 17 GLU cc_start: 0.9083 (tp30) cc_final: 0.8605 (tp30) REVERT: C 20 LYS cc_start: 0.9124 (ttmm) cc_final: 0.8603 (mtmm) REVERT: C 21 MET cc_start: 0.8604 (mtp) cc_final: 0.8008 (mtp) REVERT: E 201 ASP cc_start: 0.7701 (p0) cc_final: 0.7472 (t0) REVERT: E 220 GLU cc_start: 0.8450 (mt-10) cc_final: 0.8188 (mt-10) REVERT: R 30 PHE cc_start: 0.7426 (OUTLIER) cc_final: 0.7045 (t80) REVERT: R 108 MET cc_start: 0.7095 (tpt) cc_final: 0.6766 (tpt) REVERT: R 163 LEU cc_start: 0.8079 (tp) cc_final: 0.7679 (tp) REVERT: R 203 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7517 (tp) outliers start: 13 outliers final: 9 residues processed: 197 average time/residue: 0.1096 time to fit residues: 29.5603 Evaluate side-chains 193 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 182 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain B residue 270 ILE 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 270 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 13 optimal weight: 0.3980 chunk 54 optimal weight: 5.9990 chunk 53 optimal weight: 0.5980 chunk 60 optimal weight: 0.0980 chunk 6 optimal weight: 0.7980 chunk 75 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 10 optimal weight: 0.0980 chunk 41 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 overall best weight: 0.3980 ------------------------------------------------------------------------------- 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 = 0.3916 r_free = 0.3916 target = 0.162379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.119405 restraints weight = 10868.828| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.46 r_work: 0.3166 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9137 Z= 0.095 Angle : 0.487 10.745 12401 Z= 0.252 Chirality : 0.039 0.144 1412 Planarity : 0.004 0.043 1582 Dihedral : 5.822 76.934 1298 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.37 % Allowed : 18.60 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.98 (0.26), residues: 1148 helix: 2.99 (0.27), residues: 400 sheet: 0.29 (0.31), residues: 265 loop : 0.58 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 312 TYR 0.012 0.001 TYR E 190 PHE 0.020 0.001 PHE R 184 TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00206 ( 9133) covalent geometry : angle 0.48727 (12393) SS BOND : bond 0.00177 ( 4) SS BOND : angle 0.48667 ( 8) hydrogen bonds : bond 0.02857 ( 452) hydrogen bonds : angle 3.89426 ( 1299) Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 3332.30 seconds wall clock time: 57 minutes 18.16 seconds (3438.16 seconds total)