Starting phenix.real_space_refine on Wed Jan 15 22:06:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xjn_38402/01_2025/8xjn_38402.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xjn_38402/01_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_38402/01_2025/8xjn_38402.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xjn_38402/01_2025/8xjn_38402.map" model { file = "/net/cci-nas-00/data/ceres_data/8xjn_38402/01_2025/8xjn_38402.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xjn_38402/01_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-5571/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: 5.24, per 1000 atoms: 0.59 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: 2.53 Conformation dependent library (CDL) restraints added in 1.1 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: 1.21 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: 2.95 Time building geometry restraints manager: 2.88 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: 0.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 24.030 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.150 ------------------------------------------------------------------------------- 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 9133 Z= 0.261 Angle : 0.428 12.955 12393 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 *********************** 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 : 0.934 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: 0.2826 time to fit residues: 96.8506 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 : 0.966 ------------------------------------------------------------------------------- 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 = 64)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.114111 restraints weight = 10473.119| |-----------------------------------------------------------------------------| 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: 0.8046 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 9133 Z= 0.202 Angle : 0.526 6.414 12393 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 *********************** 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 : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 GLN cc_start: 0.8342 (tp40) cc_final: 0.8133 (tp-100) REVERT: A 75 GLN cc_start: 0.8196 (tt0) cc_final: 0.7963 (tt0) REVERT: A 126 LYS cc_start: 0.8326 (ttmt) cc_final: 0.7746 (tttm) REVERT: A 161 GLU cc_start: 0.7725 (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: 0.8398 (m-80) cc_final: 0.7645 (m-80) REVERT: B 137 ARG cc_start: 0.7682 (mmt-90) cc_final: 0.7276 (mmt180) REVERT: B 214 ARG cc_start: 0.7683 (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: 0.8094 (ttp80) REVERT: E 213 THR cc_start: 0.8062 (m) cc_final: 0.7805 (p) REVERT: E 215 THR cc_start: 0.8000 (m) cc_final: 0.7388 (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: 0.2653 time to fit residues: 75.0408 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 : 0.987 ------------------------------------------------------------------------------- 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: 4.9990 chunk 75 optimal weight: 7.9990 chunk 39 optimal weight: 0.9980 chunk 78 optimal weight: 0.3980 chunk 69 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.159683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.111164 restraints weight = 10760.609| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.42 r_work: 0.2975 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9133 Z= 0.178 Angle : 0.485 6.262 12393 Z= 0.257 Chirality : 0.040 0.145 1412 Planarity : 0.003 0.043 1582 Dihedral : 6.137 75.254 1298 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.33 % Allowed : 11.84 % Favored : 85.84 % 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: 1.79 (0.25), residues: 1148 helix: 2.36 (0.26), residues: 408 sheet: 0.56 (0.31), residues: 275 loop : 0.66 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.005 0.001 HIS A 209 PHE 0.009 0.001 PHE A 74 TYR 0.012 0.001 TYR E 190 ARG 0.006 0.001 ARG E 218 *********************** 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 220 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 198 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 GLN cc_start: 0.8169 (tt0) cc_final: 0.7963 (tt0) REVERT: A 126 LYS cc_start: 0.8294 (ttmt) cc_final: 0.7745 (tttm) REVERT: A 161 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7523 (mm-30) REVERT: A 195 LYS cc_start: 0.8607 (tptp) cc_final: 0.8050 (tptp) REVERT: A 196 GLU cc_start: 0.8022 (tp30) cc_final: 0.7713 (tp30) REVERT: A 233 ASP cc_start: 0.8797 (t0) cc_final: 0.8394 (t0) REVERT: B 59 TYR cc_start: 0.8456 (m-80) cc_final: 0.7808 (m-80) REVERT: B 137 ARG cc_start: 0.7675 (mmt-90) cc_final: 0.7259 (mmt180) REVERT: B 189 SER cc_start: 0.9324 (p) cc_final: 0.8860 (t) REVERT: B 266 HIS cc_start: 0.8565 (t70) cc_final: 0.8109 (t70) REVERT: B 304 ARG cc_start: 0.8610 (ttm170) cc_final: 0.8183 (mtp-110) REVERT: C 20 LYS cc_start: 0.9099 (ttmm) cc_final: 0.8724 (mtmm) REVERT: E 144 THR cc_start: 0.7845 (m) cc_final: 0.7507 (p) REVERT: E 160 ARG cc_start: 0.8421 (ttp80) cc_final: 0.8195 (ttp80) REVERT: R 30 PHE cc_start: 0.7393 (OUTLIER) cc_final: 0.7060 (t80) REVERT: R 108 MET cc_start: 0.6740 (tpt) cc_final: 0.6423 (tpt) REVERT: R 163 LEU cc_start: 0.8105 (tp) cc_final: 0.7723 (tp) REVERT: R 203 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7532 (tp) REVERT: R 271 ARG cc_start: 0.7448 (ttp80) cc_final: 0.7132 (ttp-170) outliers start: 22 outliers final: 13 residues processed: 211 average time/residue: 0.2661 time to fit residues: 73.7747 Evaluate side-chains 196 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 181 time to evaluate : 1.082 ------------------------------------------------------------------------------- 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 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: 0.6980 chunk 26 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 3 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 100 optimal weight: 9.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- 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 = 0.3815 r_free = 0.3815 target = 0.153320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.113634 restraints weight = 11027.454| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.50 r_work: 0.3060 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9133 Z= 0.361 Angle : 0.557 7.215 12393 Z= 0.292 Chirality : 0.043 0.150 1412 Planarity : 0.004 0.044 1582 Dihedral : 5.944 77.414 1298 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.64 % Allowed : 13.32 % Favored : 84.04 % 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: 1.54 (0.25), residues: 1148 helix: 2.25 (0.26), residues: 412 sheet: 0.20 (0.29), residues: 282 loop : 0.56 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 169 HIS 0.007 0.001 HIS A 209 PHE 0.013 0.002 PHE E 27 TYR 0.012 0.001 TYR R 226 ARG 0.006 0.001 ARG E 218 *********************** 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 212 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 187 time to evaluate : 1.070 Fit side-chains revert: symmetry clash REVERT: A 29 VAL cc_start: 0.8664 (OUTLIER) cc_final: 0.8430 (p) REVERT: A 126 LYS cc_start: 0.8525 (ttmt) cc_final: 0.7936 (tttm) REVERT: A 161 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7503 (mm-30) REVERT: A 199 ASP cc_start: 0.8494 (m-30) cc_final: 0.8205 (m-30) REVERT: B 59 TYR cc_start: 0.8484 (m-80) cc_final: 0.7960 (m-80) REVERT: B 137 ARG cc_start: 0.7809 (mmt-90) cc_final: 0.7314 (mmt180) REVERT: B 215 GLU cc_start: 0.8563 (mp0) cc_final: 0.8256 (mp0) REVERT: B 266 HIS cc_start: 0.8538 (t70) cc_final: 0.8157 (t70) REVERT: B 304 ARG cc_start: 0.8624 (ttm170) cc_final: 0.8115 (mtp180) REVERT: C 20 LYS cc_start: 0.9111 (ttmm) cc_final: 0.8682 (mtmm) REVERT: E 201 ASP cc_start: 0.7769 (p0) cc_final: 0.7476 (t0) REVERT: R 30 PHE cc_start: 0.7512 (OUTLIER) cc_final: 0.7114 (t80) REVERT: R 106 ARG cc_start: 0.8129 (mpp80) cc_final: 0.7787 (mpp80) REVERT: R 108 MET cc_start: 0.7061 (tpt) cc_final: 0.6659 (tpt) REVERT: R 163 LEU cc_start: 0.8237 (tp) cc_final: 0.7904 (tp) REVERT: R 203 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7792 (tp) REVERT: R 271 ARG cc_start: 0.7618 (ttp80) cc_final: 0.7259 (ttp-170) outliers start: 25 outliers final: 18 residues processed: 199 average time/residue: 0.2530 time to fit residues: 66.7763 Evaluate side-chains 200 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 179 time to evaluate : 1.118 ------------------------------------------------------------------------------- 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 155 VAL 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 259 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 37 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 100 optimal weight: 0.0970 chunk 82 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 86 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 87 optimal weight: 6.9990 chunk 111 optimal weight: 5.9990 overall best weight: 0.7578 ------------------------------------------------------------------------------- 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 = 0.3847 r_free = 0.3847 target = 0.156311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.117025 restraints weight = 10876.693| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.47 r_work: 0.3125 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9133 Z= 0.161 Angle : 0.473 9.276 12393 Z= 0.248 Chirality : 0.040 0.143 1412 Planarity : 0.003 0.044 1582 Dihedral : 5.778 74.175 1298 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.54 % Allowed : 14.48 % Favored : 82.98 % 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: 1.76 (0.25), residues: 1148 helix: 2.53 (0.26), residues: 413 sheet: 0.29 (0.30), residues: 276 loop : 0.59 (0.30), residues: 459 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 0.010 0.001 PHE B 151 TYR 0.013 0.001 TYR E 190 ARG 0.007 0.000 ARG E 218 *********************** 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 213 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 189 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 VAL cc_start: 0.8664 (OUTLIER) cc_final: 0.8455 (p) REVERT: A 126 LYS cc_start: 0.8499 (ttmt) cc_final: 0.7979 (tttm) REVERT: A 161 GLU cc_start: 0.7761 (mm-30) cc_final: 0.7467 (mm-30) REVERT: A 199 ASP cc_start: 0.8398 (m-30) cc_final: 0.8073 (m-30) REVERT: A 233 ASP cc_start: 0.8840 (t0) cc_final: 0.8506 (t0) REVERT: B 57 LYS cc_start: 0.8524 (mtmm) cc_final: 0.8258 (mtmm) REVERT: B 59 TYR cc_start: 0.8327 (m-80) cc_final: 0.8021 (m-80) REVERT: B 130 GLU cc_start: 0.8908 (mp0) cc_final: 0.8691 (mp0) REVERT: B 303 ASP cc_start: 0.8011 (m-30) cc_final: 0.7698 (m-30) REVERT: B 304 ARG cc_start: 0.8375 (ttm170) cc_final: 0.7977 (mtp-110) REVERT: E 201 ASP cc_start: 0.7604 (p0) cc_final: 0.7358 (t0) REVERT: R 30 PHE cc_start: 0.7457 (OUTLIER) cc_final: 0.7029 (t80) REVERT: R 108 MET cc_start: 0.6989 (tpt) cc_final: 0.6677 (tpt) REVERT: R 163 LEU cc_start: 0.8188 (tp) cc_final: 0.7758 (tp) REVERT: R 203 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7674 (tp) REVERT: R 271 ARG cc_start: 0.7630 (ttp80) cc_final: 0.7374 (ttp80) outliers start: 24 outliers final: 14 residues processed: 201 average time/residue: 0.2523 time to fit residues: 67.2266 Evaluate side-chains 195 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 178 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 98 GLN 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 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 R residue 30 PHE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 19 optimal weight: 0.2980 chunk 21 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 105 optimal weight: 0.7980 chunk 110 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 = 0.3844 r_free = 0.3844 target = 0.156182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.116318 restraints weight = 10890.308| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.46 r_work: 0.3133 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9133 Z= 0.210 Angle : 0.499 8.381 12393 Z= 0.258 Chirality : 0.041 0.143 1412 Planarity : 0.003 0.042 1582 Dihedral : 6.042 78.728 1298 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.22 % Allowed : 15.22 % 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: 1.74 (0.25), residues: 1148 helix: 2.52 (0.26), residues: 413 sheet: 0.22 (0.30), residues: 281 loop : 0.63 (0.30), residues: 454 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 160 *********************** 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 208 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 187 time to evaluate : 1.127 Fit side-chains revert: symmetry clash REVERT: A 126 LYS cc_start: 0.8519 (ttmt) cc_final: 0.7998 (tttm) REVERT: A 161 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7457 (mm-30) REVERT: A 222 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7610 (mp0) REVERT: B 57 LYS cc_start: 0.8548 (mtmm) cc_final: 0.8296 (mtmm) REVERT: B 59 TYR cc_start: 0.8394 (m-80) cc_final: 0.8077 (m-80) REVERT: B 137 ARG cc_start: 0.7782 (mmt-90) cc_final: 0.7318 (mmt180) REVERT: B 214 ARG cc_start: 0.7640 (mmp80) cc_final: 0.7426 (mmt-90) REVERT: B 215 GLU cc_start: 0.8579 (mp0) cc_final: 0.8226 (mp0) REVERT: B 266 HIS cc_start: 0.8586 (t70) cc_final: 0.8229 (t70) REVERT: B 304 ARG cc_start: 0.8379 (ttm170) cc_final: 0.7979 (mtp-110) REVERT: C 20 LYS cc_start: 0.9116 (ttmm) cc_final: 0.8741 (tttm) REVERT: E 201 ASP cc_start: 0.7696 (p0) cc_final: 0.7451 (t0) REVERT: R 30 PHE cc_start: 0.7539 (OUTLIER) cc_final: 0.7109 (t80) REVERT: R 106 ARG cc_start: 0.8020 (mpp80) cc_final: 0.7813 (mpp80) REVERT: R 108 MET cc_start: 0.7057 (tpt) cc_final: 0.6738 (tpt) REVERT: R 112 MET cc_start: 0.7664 (ttm) cc_final: 0.7425 (ttm) REVERT: R 163 LEU cc_start: 0.8145 (tp) cc_final: 0.7717 (tp) REVERT: R 203 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7675 (tp) REVERT: R 271 ARG cc_start: 0.7644 (ttp80) cc_final: 0.7393 (ttp80) outliers start: 21 outliers final: 17 residues processed: 198 average time/residue: 0.2740 time to fit residues: 72.1283 Evaluate side-chains 199 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 180 time to evaluate : 1.033 ------------------------------------------------------------------------------- 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 184 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 255 LEU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 67 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 52 optimal weight: 7.9990 chunk 98 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 88 optimal weight: 9.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3881 r_free = 0.3881 target = 0.159295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.112122 restraints weight = 10894.618| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.38 r_work: 0.3117 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9133 Z= 0.164 Angle : 0.477 8.017 12393 Z= 0.249 Chirality : 0.040 0.142 1412 Planarity : 0.003 0.044 1582 Dihedral : 6.037 80.947 1298 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.33 % Allowed : 15.43 % Favored : 82.24 % 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: 1.84 (0.26), residues: 1148 helix: 2.66 (0.26), residues: 413 sheet: 0.20 (0.30), residues: 281 loop : 0.67 (0.30), residues: 454 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 0.012 0.001 PHE R 184 TYR 0.012 0.001 TYR E 190 ARG 0.008 0.000 ARG E 218 *********************** 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 214 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 192 time to evaluate : 1.029 Fit side-chains revert: symmetry clash REVERT: A 126 LYS cc_start: 0.8481 (ttmt) cc_final: 0.7970 (tttm) REVERT: A 161 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7457 (mm-30) REVERT: A 222 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7586 (mp0) REVERT: A 233 ASP cc_start: 0.8865 (t0) cc_final: 0.8492 (t0) REVERT: B 59 TYR cc_start: 0.8357 (m-80) cc_final: 0.8090 (m-80) REVERT: B 130 GLU cc_start: 0.8880 (mp0) cc_final: 0.8677 (mp0) REVERT: B 214 ARG cc_start: 0.7679 (mmp80) cc_final: 0.7429 (mmt-90) REVERT: B 215 GLU cc_start: 0.8527 (mp0) cc_final: 0.8154 (mp0) REVERT: B 258 ASP cc_start: 0.8318 (t70) cc_final: 0.7848 (t0) REVERT: B 266 HIS cc_start: 0.8504 (t70) cc_final: 0.8124 (t70) REVERT: B 304 ARG cc_start: 0.8327 (ttm170) cc_final: 0.7932 (mtp-110) REVERT: C 20 LYS cc_start: 0.9105 (ttmm) cc_final: 0.8559 (mtmm) REVERT: E 201 ASP cc_start: 0.7690 (p0) cc_final: 0.7430 (t0) REVERT: E 218 ARG cc_start: 0.7143 (ttp-110) cc_final: 0.6737 (tmm-80) REVERT: R 30 PHE cc_start: 0.7499 (OUTLIER) cc_final: 0.7021 (t80) REVERT: R 108 MET cc_start: 0.7034 (tpt) cc_final: 0.6729 (tpt) REVERT: R 112 MET cc_start: 0.7614 (ttm) cc_final: 0.7377 (ttm) REVERT: R 163 LEU cc_start: 0.8135 (tp) cc_final: 0.7653 (tp) REVERT: R 203 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7621 (tp) outliers start: 22 outliers final: 16 residues processed: 203 average time/residue: 0.2545 time to fit residues: 68.4566 Evaluate side-chains 201 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 183 time to evaluate : 1.061 ------------------------------------------------------------------------------- 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 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 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: 0.9980 chunk 111 optimal weight: 0.0870 chunk 70 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 97 optimal weight: 9.9990 chunk 4 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 overall best weight: 0.7760 ------------------------------------------------------------------------------- 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 = 0.157801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.118429 restraints weight = 11087.937| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.55 r_work: 0.3128 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 9133 Z= 0.163 Angle : 0.484 10.268 12393 Z= 0.251 Chirality : 0.040 0.149 1412 Planarity : 0.003 0.044 1582 Dihedral : 6.042 82.168 1298 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.11 % Allowed : 15.96 % Favored : 81.92 % 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: 1.89 (0.26), residues: 1148 helix: 2.79 (0.27), residues: 407 sheet: 0.17 (0.30), residues: 276 loop : 0.67 (0.30), residues: 465 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 0.012 0.001 TYR E 190 ARG 0.007 0.000 ARG E 160 *********************** 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 203 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 183 time to evaluate : 1.138 Fit side-chains revert: symmetry clash REVERT: A 120 GLU cc_start: 0.7790 (mp0) cc_final: 0.7561 (mp0) REVERT: A 126 LYS cc_start: 0.8490 (ttmt) cc_final: 0.7986 (tttm) REVERT: A 161 GLU cc_start: 0.7784 (mm-30) cc_final: 0.7450 (mm-30) REVERT: A 233 ASP cc_start: 0.8888 (t0) cc_final: 0.8511 (t0) REVERT: B 59 TYR cc_start: 0.8305 (m-80) cc_final: 0.8097 (m-80) REVERT: B 130 GLU cc_start: 0.8860 (mp0) cc_final: 0.8652 (mp0) REVERT: B 214 ARG cc_start: 0.7662 (mmp80) cc_final: 0.7448 (mmt-90) REVERT: B 215 GLU cc_start: 0.8509 (mp0) cc_final: 0.8165 (mp0) REVERT: B 258 ASP cc_start: 0.8220 (t70) cc_final: 0.7917 (t0) REVERT: B 266 HIS cc_start: 0.8497 (t70) cc_final: 0.8103 (t70) REVERT: B 303 ASP cc_start: 0.8115 (m-30) cc_final: 0.7754 (m-30) REVERT: B 304 ARG cc_start: 0.8277 (ttm170) cc_final: 0.7908 (mtp-110) REVERT: C 17 GLU cc_start: 0.9165 (tp30) cc_final: 0.8913 (tp30) REVERT: C 20 LYS cc_start: 0.9104 (ttmm) cc_final: 0.8566 (mtmm) REVERT: E 201 ASP cc_start: 0.7650 (p0) cc_final: 0.7393 (t0) REVERT: R 30 PHE cc_start: 0.7524 (OUTLIER) cc_final: 0.7053 (t80) REVERT: R 108 MET cc_start: 0.7035 (tpt) cc_final: 0.6713 (tpt) REVERT: R 112 MET cc_start: 0.7674 (ttm) cc_final: 0.7440 (ttm) REVERT: R 163 LEU cc_start: 0.8113 (tp) cc_final: 0.7637 (tp) REVERT: R 203 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7619 (tp) REVERT: R 312 ARG cc_start: 0.7821 (mmp80) cc_final: 0.6416 (mmp80) outliers start: 20 outliers final: 17 residues processed: 192 average time/residue: 0.2523 time to fit residues: 64.6244 Evaluate side-chains 197 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 178 time to evaluate : 1.050 ------------------------------------------------------------------------------- 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 176 GLN 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 B residue 318 LEU Chi-restraints excluded: chain C residue 25 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 255 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 43 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 96 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 15 optimal weight: 0.0980 chunk 8 optimal weight: 0.8980 chunk 109 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 106 optimal weight: 9.9990 chunk 45 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.157919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.111106 restraints weight = 10978.177| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.36 r_work: 0.3128 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9133 Z= 0.161 Angle : 0.481 10.226 12393 Z= 0.249 Chirality : 0.040 0.144 1412 Planarity : 0.003 0.044 1582 Dihedral : 6.041 83.391 1298 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.01 % Allowed : 16.17 % Favored : 81.82 % 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: 1.92 (0.26), residues: 1148 helix: 2.86 (0.27), residues: 407 sheet: 0.09 (0.29), residues: 284 loop : 0.74 (0.31), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.004 0.001 HIS A 209 PHE 0.019 0.001 PHE R 184 TYR 0.011 0.001 TYR E 190 ARG 0.009 0.000 ARG E 218 *********************** 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 212 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 193 time to evaluate : 1.105 Fit side-chains revert: symmetry clash REVERT: A 28 GLN cc_start: 0.8396 (mm-40) cc_final: 0.8188 (mm110) REVERT: A 120 GLU cc_start: 0.7807 (mp0) cc_final: 0.7572 (mp0) REVERT: A 126 LYS cc_start: 0.8441 (ttmt) cc_final: 0.7922 (tttm) REVERT: A 161 GLU cc_start: 0.7761 (mm-30) cc_final: 0.7438 (mm-30) REVERT: A 196 GLU cc_start: 0.7740 (tp30) cc_final: 0.7531 (tp30) REVERT: A 233 ASP cc_start: 0.8844 (t0) cc_final: 0.8489 (t0) REVERT: B 59 TYR cc_start: 0.8342 (m-80) cc_final: 0.8103 (m-80) REVERT: B 130 GLU cc_start: 0.8863 (mp0) cc_final: 0.8656 (mp0) REVERT: B 214 ARG cc_start: 0.7684 (mmp80) cc_final: 0.7459 (mmt-90) REVERT: B 215 GLU cc_start: 0.8506 (mp0) cc_final: 0.8151 (mp0) REVERT: B 259 GLN cc_start: 0.8896 (pt0) cc_final: 0.8479 (pt0) REVERT: B 266 HIS cc_start: 0.8506 (t70) cc_final: 0.8100 (t70) REVERT: B 303 ASP cc_start: 0.8074 (m-30) cc_final: 0.7776 (m-30) REVERT: C 17 GLU cc_start: 0.9169 (tp30) cc_final: 0.8896 (tp30) REVERT: C 20 LYS cc_start: 0.9106 (ttmm) cc_final: 0.8596 (mtmm) REVERT: E 201 ASP cc_start: 0.7651 (p0) cc_final: 0.7387 (t0) REVERT: E 218 ARG cc_start: 0.7073 (ttp-110) cc_final: 0.6539 (tmm-80) REVERT: E 220 GLU cc_start: 0.8354 (mt-10) cc_final: 0.8009 (mt-10) REVERT: R 30 PHE cc_start: 0.7470 (OUTLIER) cc_final: 0.6949 (t80) REVERT: R 108 MET cc_start: 0.6951 (tpt) cc_final: 0.6665 (tpt) REVERT: R 112 MET cc_start: 0.7679 (ttm) cc_final: 0.7454 (ttm) REVERT: R 163 LEU cc_start: 0.8075 (tp) cc_final: 0.7691 (tp) REVERT: R 203 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7557 (tp) REVERT: R 312 ARG cc_start: 0.7839 (mmp80) cc_final: 0.6484 (mmp80) outliers start: 19 outliers final: 14 residues processed: 202 average time/residue: 0.2443 time to fit residues: 66.3507 Evaluate side-chains 199 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 183 time to evaluate : 1.010 ------------------------------------------------------------------------------- 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 176 GLN 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 35 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 48 optimal weight: 0.0040 chunk 20 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 84 optimal weight: 30.0000 overall best weight: 1.4000 ------------------------------------------------------------------------------- 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 = 0.3851 r_free = 0.3851 target = 0.156763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.109036 restraints weight = 10966.743| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.41 r_work: 0.3094 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9133 Z= 0.236 Angle : 0.516 10.120 12393 Z= 0.267 Chirality : 0.041 0.144 1412 Planarity : 0.004 0.050 1582 Dihedral : 6.078 80.395 1298 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.01 % Allowed : 17.23 % Favored : 80.76 % 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: 1.85 (0.26), residues: 1148 helix: 2.77 (0.27), residues: 407 sheet: 0.07 (0.29), residues: 286 loop : 0.71 (0.31), residues: 455 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 0.021 0.001 PHE R 184 TYR 0.011 0.001 TYR R 226 ARG 0.014 0.001 ARG B 134 ********************** 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 197 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 178 time to evaluate : 1.069 Fit side-chains revert: symmetry clash REVERT: A 120 GLU cc_start: 0.7860 (mp0) cc_final: 0.7610 (mp0) REVERT: A 126 LYS cc_start: 0.8484 (ttmt) cc_final: 0.7973 (tttm) REVERT: A 161 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7441 (mm-30) REVERT: B 59 TYR cc_start: 0.8475 (m-80) cc_final: 0.8207 (m-80) REVERT: B 130 GLU cc_start: 0.8891 (mp0) cc_final: 0.8685 (mp0) REVERT: B 214 ARG cc_start: 0.7677 (mmp80) cc_final: 0.7447 (mmt-90) REVERT: B 215 GLU cc_start: 0.8528 (mp0) cc_final: 0.8125 (mp0) REVERT: B 303 ASP cc_start: 0.8061 (m-30) cc_final: 0.7725 (m-30) REVERT: C 17 GLU cc_start: 0.9180 (tp30) cc_final: 0.8974 (tp30) REVERT: C 20 LYS cc_start: 0.9117 (ttmm) cc_final: 0.8588 (mtmm) REVERT: E 201 ASP cc_start: 0.7664 (p0) cc_final: 0.7416 (t0) REVERT: E 218 ARG cc_start: 0.7062 (ttp-110) cc_final: 0.6687 (tmm-80) REVERT: R 30 PHE cc_start: 0.7489 (OUTLIER) cc_final: 0.7073 (t80) REVERT: R 108 MET cc_start: 0.7047 (tpt) cc_final: 0.6719 (tpt) REVERT: R 112 MET cc_start: 0.7688 (ttm) cc_final: 0.7452 (ttm) REVERT: R 163 LEU cc_start: 0.8150 (tp) cc_final: 0.7705 (tp) REVERT: R 203 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7614 (tp) REVERT: R 312 ARG cc_start: 0.7926 (mmp80) cc_final: 0.6525 (mmp80) outliers start: 19 outliers final: 17 residues processed: 187 average time/residue: 0.2430 time to fit residues: 61.1827 Evaluate side-chains 193 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 174 time to evaluate : 1.182 ------------------------------------------------------------------------------- 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 176 GLN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 318 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 5 optimal weight: 0.9990 chunk 18 optimal weight: 7.9990 chunk 113 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 58 optimal weight: 9.9990 chunk 111 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 104 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.157624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.110795 restraints weight = 10963.825| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.36 r_work: 0.3122 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9133 Z= 0.163 Angle : 0.489 9.917 12393 Z= 0.253 Chirality : 0.040 0.143 1412 Planarity : 0.003 0.043 1582 Dihedral : 6.081 83.195 1298 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.90 % Allowed : 17.86 % 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 (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: 1.92 (0.26), residues: 1148 helix: 2.85 (0.27), residues: 407 sheet: 0.05 (0.29), residues: 286 loop : 0.77 (0.31), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.004 0.001 HIS A 209 PHE 0.018 0.001 PHE R 184 TYR 0.011 0.001 TYR E 190 ARG 0.008 0.000 ARG E 218 Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 6202.89 seconds wall clock time: 109 minutes 57.72 seconds (6597.72 seconds total)