Starting phenix.real_space_refine on Fri Oct 23 05:00:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9t8c_55684/10_2026/9t8c_55684.cif Found real_map, /net/cci-nas-00/data/ceres_data/9t8c_55684/10_2026/9t8c_55684.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9t8c_55684/10_2026/9t8c_55684.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9t8c_55684/10_2026/9t8c_55684.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9t8c_55684/10_2026/9t8c_55684.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9t8c_55684/10_2026/9t8c_55684.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.030 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 63 5.16 5 Cl 2 4.86 5 C 5310 2.51 5 N 1425 2.21 5 O 1559 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-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8359 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 1974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1974 Classifications: {'peptide': 271} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 9, 'TRANS': 261} Chain breaks: 1 Unresolved non-hydrogen bonds: 153 Unresolved non-hydrogen angles: 193 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3, 'HIS:plan': 3, 'GLN:plan1': 4, 'ARG:plan': 3, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 96 Chain: "A" Number of atoms: 1667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1667 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 4, 'TRANS': 212} Chain breaks: 1 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "B" Number of atoms: 2564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2564 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 5, 'TRANS': 335} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 1, 'GLN:plan1': 3, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 44 Chain: "C" Number of atoms: 398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 398 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 21 Chain: "S" Number of atoms: 1728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1728 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 5, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 38 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'7RU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.63, per 1000 atoms: 0.19 Number of scatterers: 8359 At special positions: 0 Unit cell: (98.5491, 115.395, 126.345, 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 2 17.00 S 63 16.00 O 1559 8.00 N 1425 7.00 C 5310 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 103 " - pdb=" SG CYS R 181 " distance=2.03 Simple disulfide: pdb=" SG CYS R 355 " - pdb=" SG CYS R 358 " distance=2.03 Simple disulfide: pdb=" SG CYS S 23 " - pdb=" SG CYS S 97 " distance=2.03 Simple disulfide: pdb=" SG CYS S 160 " - pdb=" SG CYS S 230 " distance=2.04 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: 0.83 Conformation dependent library (CDL) restraints added in 423.3 milliseconds 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2088 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 12 sheets defined 38.7% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'R' and resid 32 through 57 removed outlier: 3.611A pdb=" N TYR R 36 " --> pdb=" O TYR R 32 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLY R 48 " --> pdb=" O VAL R 44 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N CYS R 51 " --> pdb=" O ASN R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 58 through 61 Processing helix chain 'R' and resid 62 through 93 removed outlier: 4.245A pdb=" N LEU R 67 " --> pdb=" O THR R 63 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N VAL R 68 " --> pdb=" O THR R 64 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N MET R 83 " --> pdb=" O ALA R 79 " (cutoff:3.500A) Proline residue: R 84 - end of helix Processing helix chain 'R' and resid 99 through 134 removed outlier: 3.637A pdb=" N LEU R 121 " --> pdb=" O SER R 117 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N CYS R 122 " --> pdb=" O ILE R 118 " (cutoff:3.500A) Processing helix chain 'R' and resid 134 through 139 Processing helix chain 'R' and resid 145 through 170 Proline residue: R 167 - end of helix Processing helix chain 'R' and resid 187 through 197 Processing helix chain 'R' and resid 197 through 223 Processing helix chain 'R' and resid 324 through 355 Proline residue: R 344 - end of helix removed outlier: 3.683A pdb=" N VAL R 350 " --> pdb=" O PHE R 346 " (cutoff:3.500A) Processing helix chain 'R' and resid 361 through 385 removed outlier: 3.864A pdb=" N SER R 376 " --> pdb=" O GLY R 372 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA R 377 " --> pdb=" O TYR R 373 " (cutoff:3.500A) Proline residue: R 380 - end of helix Processing helix chain 'R' and resid 387 through 399 removed outlier: 4.015A pdb=" N SER R 399 " --> pdb=" O LEU R 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 4 through 29 Processing helix chain 'A' and resid 43 through 47 removed outlier: 3.563A pdb=" N THR A 46 " --> pdb=" O GLY A 43 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ILE A 47 " --> pdb=" O LYS A 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 43 through 47' Processing helix chain 'A' and resid 90 through 99 removed outlier: 4.328A pdb=" N ILE A 95 " --> pdb=" O LYS A 92 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N HIS A 96 " --> pdb=" O LYS A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 128 Processing helix chain 'A' and resid 143 through 154 removed outlier: 3.556A pdb=" N PHE A 147 " --> pdb=" O LYS A 143 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LYS A 152 " --> pdb=" O GLY A 148 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LYS A 153 " --> pdb=" O GLU A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 159 removed outlier: 3.543A pdb=" N ILE A 158 " --> pdb=" O PRO A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 183 removed outlier: 4.140A pdb=" N LYS A 183 " --> pdb=" O GLN A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 223 Processing helix chain 'B' and resid 3 through 25 Processing helix chain 'B' and resid 28 through 33 Processing helix chain 'C' and resid 8 through 24 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 45 through 48 Processing helix chain 'C' and resid 55 through 59 Processing helix chain 'S' and resid 54 through 57 Processing helix chain 'S' and resid 88 through 92 Processing helix chain 'S' and resid 221 through 225 Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 53 removed outlier: 3.556A pdb=" N LYS A 52 " --> pdb=" O HIS A 71 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N HIS A 71 " --> pdb=" O LYS A 52 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA A 103 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ILE A 104 " --> pdb=" O ILE A 138 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N PHE A 140 " --> pdb=" O ILE A 104 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N PHE A 106 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N ASN A 142 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N VAL A 108 " --> pdb=" O ASN A 142 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 44 through 51 removed outlier: 6.785A pdb=" N ILE B 337 " --> pdb=" O ARG B 47 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N THR B 49 " --> pdb=" O LEU B 335 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU B 335 " --> pdb=" O THR B 49 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N PHE B 334 " --> pdb=" O SER B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 57 through 62 removed outlier: 6.811A pdb=" N ALA B 72 " --> pdb=" O TYR B 58 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N MET B 60 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL B 70 " --> pdb=" O MET B 60 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N TRP B 62 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N LEU B 68 " --> pdb=" O TRP B 62 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS B 77 " --> pdb=" O SER B 73 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ASP B 82 " --> pdb=" O LYS B 88 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N LYS B 88 " --> pdb=" O ASP B 82 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 99 through 104 removed outlier: 6.930A pdb=" N GLY B 114 " --> pdb=" O MET B 100 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N CYS B 102 " --> pdb=" O ALA B 112 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ALA B 112 " --> pdb=" O CYS B 102 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N TYR B 104 " --> pdb=" O TYR B 110 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N TYR B 110 " --> pdb=" O TYR B 104 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLY B 115 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ILE B 119 " --> pdb=" O GLY B 115 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ASN B 124 " --> pdb=" O VAL B 134 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N VAL B 134 " --> pdb=" O ASN B 124 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 145 through 152 removed outlier: 6.528A pdb=" N GLN B 155 " --> pdb=" O LEU B 151 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER B 160 " --> pdb=" O THR B 164 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N THR B 164 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ASP B 169 " --> pdb=" O GLN B 175 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N GLN B 175 " --> pdb=" O ASP B 169 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 186 through 191 removed outlier: 3.807A pdb=" N GLN B 219 " --> pdb=" O LEU B 209 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ASP B 211 " --> pdb=" O CYS B 217 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N CYS B 217 " --> pdb=" O ASP B 211 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 228 through 233 removed outlier: 3.542A pdb=" N ALA B 230 " --> pdb=" O GLY B 243 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ASP B 253 " --> pdb=" O GLU B 259 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N GLU B 259 " --> pdb=" O ASP B 253 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 272 through 277 removed outlier: 6.560A pdb=" N GLY B 287 " --> pdb=" O THR B 273 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N VAL B 275 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LEU B 285 " --> pdb=" O VAL B 275 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N PHE B 277 " --> pdb=" O LEU B 283 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N LEU B 283 " --> pdb=" O PHE B 277 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ASP B 297 " --> pdb=" O ARG B 303 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ARG B 303 " --> pdb=" O ASP B 297 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 4 through 8 Processing sheet with id=AB1, first strand: chain 'S' and resid 11 through 13 removed outlier: 5.881A pdb=" N GLY S 11 " --> pdb=" O THR S 119 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N ARG S 39 " --> pdb=" O TRP S 48 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N TRP S 48 " --> pdb=" O ARG S 39 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 141 through 142 Processing sheet with id=AB3, first strand: chain 'S' and resid 187 through 190 removed outlier: 5.281A pdb=" N LEU S 188 " --> pdb=" O LEU S 179 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N LEU S 179 " --> pdb=" O LEU S 188 " (cutoff:3.500A) 447 hydrogen bonds defined for protein. 1251 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: 1.30 Time building geometry restraints manager: 1.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1456 1.32 - 1.45: 2283 1.45 - 1.57: 4699 1.57 - 1.69: 2 1.69 - 1.81: 90 Bond restraints: 8530 Sorted by residual: bond pdb=" C12 7RU R 601 " pdb=" N3 7RU R 601 " ideal model delta sigma weight residual 1.445 1.302 0.143 2.00e-02 2.50e+03 5.14e+01 bond pdb=" C3 7RU R 601 " pdb=" N1 7RU R 601 " ideal model delta sigma weight residual 1.363 1.502 -0.139 2.00e-02 2.50e+03 4.81e+01 bond pdb=" C15 7RU R 601 " pdb=" N3 7RU R 601 " ideal model delta sigma weight residual 1.446 1.313 0.133 2.00e-02 2.50e+03 4.41e+01 bond pdb=" C3 7RU R 601 " pdb=" N2 7RU R 601 " ideal model delta sigma weight residual 1.362 1.486 -0.124 2.00e-02 2.50e+03 3.83e+01 bond pdb=" C16 7RU R 601 " pdb=" N4 7RU R 601 " ideal model delta sigma weight residual 1.398 1.496 -0.098 2.00e-02 2.50e+03 2.39e+01 ... (remaining 8525 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 11473 2.25 - 4.51: 119 4.51 - 6.76: 13 6.76 - 9.02: 4 9.02 - 11.27: 2 Bond angle restraints: 11611 Sorted by residual: angle pdb=" N1 7RU R 601 " pdb=" C3 7RU R 601 " pdb=" N2 7RU R 601 " ideal model delta sigma weight residual 116.34 127.61 -11.27 3.00e+00 1.11e-01 1.41e+01 angle pdb=" C10 7RU R 601 " pdb=" C7 7RU R 601 " pdb=" C8 7RU R 601 " ideal model delta sigma weight residual 112.51 123.28 -10.77 3.00e+00 1.11e-01 1.29e+01 angle pdb=" C SER R 361 " pdb=" N PRO R 362 " pdb=" CA PRO R 362 " ideal model delta sigma weight residual 119.28 115.52 3.76 1.10e+00 8.26e-01 1.17e+01 angle pdb=" N THR R 368 " pdb=" CA THR R 368 " pdb=" C THR R 368 " ideal model delta sigma weight residual 111.07 107.48 3.59 1.07e+00 8.73e-01 1.12e+01 angle pdb=" CA TYR S 191 " pdb=" CB TYR S 191 " pdb=" CG TYR S 191 " ideal model delta sigma weight residual 113.90 119.67 -5.77 1.80e+00 3.09e-01 1.03e+01 ... (remaining 11606 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.99: 4572 15.99 - 31.98: 360 31.98 - 47.97: 70 47.97 - 63.95: 20 63.95 - 79.94: 11 Dihedral angle restraints: 5033 sinusoidal: 1795 harmonic: 3238 Sorted by residual: dihedral pdb=" CB CYS R 355 " pdb=" SG CYS R 355 " pdb=" SG CYS R 358 " pdb=" CB CYS R 358 " ideal model delta sinusoidal sigma weight residual -86.00 -160.47 74.47 1 1.00e+01 1.00e-02 7.03e+01 dihedral pdb=" CB CYS S 23 " pdb=" SG CYS S 23 " pdb=" SG CYS S 97 " pdb=" CB CYS S 97 " ideal model delta sinusoidal sigma weight residual 93.00 162.34 -69.34 1 1.00e+01 1.00e-02 6.21e+01 dihedral pdb=" CB CYS R 103 " pdb=" SG CYS R 103 " pdb=" SG CYS R 181 " pdb=" CB CYS R 181 " ideal model delta sinusoidal sigma weight residual -86.00 -142.77 56.77 1 1.00e+01 1.00e-02 4.34e+01 ... (remaining 5030 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.363: 1362 0.363 - 0.726: 0 0.726 - 1.089: 0 1.089 - 1.452: 0 1.452 - 1.815: 1 Chirality restraints: 1363 Sorted by residual: chirality pdb=" C7 7RU R 601 " pdb=" C10 7RU R 601 " pdb=" C6 7RU R 601 " pdb=" C8 7RU R 601 " both_signs ideal model delta sigma weight residual False -2.59 -0.77 -1.81 2.00e-01 2.50e+01 8.23e+01 chirality pdb=" C4 7RU R 601 " pdb=" C5 7RU R 601 " pdb=" C9 7RU R 601 " pdb=" N2 7RU R 601 " both_signs ideal model delta sigma weight residual False -2.46 -2.75 0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" CA SER S 32 " pdb=" N SER S 32 " pdb=" C SER S 32 " pdb=" CB SER S 32 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 1360 not shown) Planarity restraints: 1466 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR S 191 " -0.019 2.00e-02 2.50e+03 1.24e-02 3.05e+00 pdb=" CG TYR S 191 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR S 191 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR S 191 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR S 191 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR S 191 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR S 191 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR S 191 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET R 83 " 0.025 5.00e-02 4.00e+02 3.85e-02 2.37e+00 pdb=" N PRO R 84 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO R 84 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO R 84 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 92 " -0.008 2.00e-02 2.50e+03 1.53e-02 2.33e+00 pdb=" C LYS A 92 " 0.026 2.00e-02 2.50e+03 pdb=" O LYS A 92 " -0.010 2.00e-02 2.50e+03 pdb=" N LYS A 93 " -0.009 2.00e-02 2.50e+03 ... (remaining 1463 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 2816 2.84 - 3.35: 8136 3.35 - 3.87: 13586 3.87 - 4.38: 15857 4.38 - 4.90: 27922 Nonbonded interactions: 68317 Sorted by model distance: nonbonded pdb=" O ASP B 332 " pdb=" OG SER B 333 " model vdw 2.322 3.040 nonbonded pdb=" O ASP A 134 " pdb=" OD1 ASP A 134 " model vdw 2.329 3.040 nonbonded pdb=" O LEU R 378 " pdb=" CG1 VAL R 381 " model vdw 2.365 3.460 nonbonded pdb=" OG SER B 160 " pdb=" OD1 ASP B 162 " model vdw 2.397 3.040 nonbonded pdb=" OG SER B 330 " pdb=" OD1 ASP B 332 " model vdw 2.433 3.040 ... (remaining 68312 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.350 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:5.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 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 : 0.005 0.143 8534 Z= 0.268 Angle : 0.595 11.274 11619 Z= 0.324 Chirality : 0.065 1.815 1363 Planarity : 0.004 0.038 1466 Dihedral : 12.932 79.943 2933 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.23 % Allowed : 1.74 % Favored : 98.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.26), residues: 1102 helix: 2.36 (0.28), residues: 382 sheet: 0.05 (0.30), residues: 274 loop : -0.58 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 218 TYR 0.028 0.002 TYR S 191 PHE 0.015 0.001 PHE B 233 TRP 0.024 0.001 TRP S 48 HIS 0.003 0.001 HIS S 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.27 ( 8530) covalent geometry : angle 0.59498 / 0.32 (11611) SS BOND : bond 0.00509 / 0.26 ( 4) SS BOND : angle 0.94280 / 0.56 ( 8) hydrogen bonds : bond 0.14170 / 9.70 ( 447) hydrogen bonds : angle 5.69773 / 4.09 ( 1251) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 147 time to evaluate : 0.329 Fit side-chains REVERT: R 134 MET cc_start: 0.7106 (mtm) cc_final: 0.6814 (tmm) REVERT: R 218 ARG cc_start: 0.8024 (mtt-85) cc_final: 0.5686 (ptt180) REVERT: R 330 MET cc_start: 0.7442 (mmm) cc_final: 0.7216 (mmm) REVERT: A 22 LYS cc_start: 0.7850 (tttm) cc_final: 0.7228 (tppt) REVERT: A 185 ARG cc_start: 0.7734 (mtt180) cc_final: 0.7397 (mtt180) REVERT: B 19 ASP cc_start: 0.8479 (m-30) cc_final: 0.8141 (m-30) REVERT: B 97 SER cc_start: 0.8698 (p) cc_final: 0.8474 (p) REVERT: B 174 GLN cc_start: 0.8260 (mt0) cc_final: 0.7876 (mm-40) outliers start: 2 outliers final: 0 residues processed: 148 average time/residue: 0.4162 time to fit residues: 66.5702 Evaluate side-chains 110 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: [108, 49, 97, 53, 5, 33, 65, 62, 51, 100, 106] chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.5980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 0.0970 chunk 106 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 173 ASN R 375 ASN A 219 ASN B 16 GLN B 31 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.181170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.133559 restraints weight = 9875.839| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.23 r_work: 0.3448 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8534 Z= 0.152 Angle : 0.599 11.838 11619 Z= 0.309 Chirality : 0.044 0.226 1363 Planarity : 0.004 0.044 1466 Dihedral : 5.365 67.357 1229 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.62 % Allowed : 11.12 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.26), residues: 1102 helix: 2.55 (0.26), residues: 387 sheet: 0.30 (0.31), residues: 269 loop : -0.69 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 133 TYR 0.031 0.002 TYR S 191 PHE 0.016 0.002 PHE B 233 TRP 0.014 0.001 TRP B 81 HIS 0.004 0.001 HIS R 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 ( 8530) covalent geometry : angle 0.59856 / 0.31 (11611) SS BOND : bond 0.00301 / 0.15 ( 4) SS BOND : angle 0.83422 / 0.55 ( 8) hydrogen bonds : bond 0.04049 / 2.75 ( 447) hydrogen bonds : angle 4.62693 / 3.36 ( 1251) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 124 time to evaluate : 0.295 Fit side-chains REVERT: R 112 MET cc_start: 0.7957 (tmt) cc_final: 0.7497 (tmm) REVERT: R 113 MET cc_start: 0.8373 (mpp) cc_final: 0.7063 (mpp) REVERT: R 134 MET cc_start: 0.7574 (mtm) cc_final: 0.6791 (tmm) REVERT: A 22 LYS cc_start: 0.7979 (tttm) cc_final: 0.7337 (tppt) REVERT: A 185 ARG cc_start: 0.7664 (mtt180) cc_final: 0.7330 (mtt180) REVERT: A 195 MET cc_start: 0.8162 (mpt) cc_final: 0.7326 (mpt) REVERT: B 19 ASP cc_start: 0.8451 (m-30) cc_final: 0.8113 (m-30) REVERT: B 174 GLN cc_start: 0.8263 (mt0) cc_final: 0.7910 (mm-40) REVERT: S 83 GLN cc_start: 0.8130 (tp40) cc_final: 0.7883 (tp40) outliers start: 14 outliers final: 6 residues processed: 131 average time/residue: 0.4417 time to fit residues: 62.6784 Evaluate side-chains 119 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 113 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 125 SER Chi-restraints excluded: chain R residue 196 SER Chi-restraints excluded: chain R residue 369 THR Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain B residue 64 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: [79, 109, 93, 34, 40, 11, 12, 98, 19, 82, 106] chunk 79 optimal weight: 0.5980 chunk 109 optimal weight: 0.9990 chunk 93 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 19 optimal weight: 10.0000 chunk 82 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 16 GLN B 31 GLN B 74 GLN B 175 GLN B 258 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.181922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.132439 restraints weight = 9771.287| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 2.29 r_work: 0.3439 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8534 Z= 0.146 Angle : 0.589 11.331 11619 Z= 0.302 Chirality : 0.043 0.232 1363 Planarity : 0.004 0.044 1466 Dihedral : 5.364 60.816 1229 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.62 % Allowed : 14.83 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.26), residues: 1102 helix: 2.57 (0.26), residues: 390 sheet: 0.27 (0.31), residues: 269 loop : -0.76 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 133 TYR 0.031 0.002 TYR S 191 PHE 0.014 0.002 PHE B 233 TRP 0.015 0.001 TRP B 81 HIS 0.003 0.001 HIS A 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 ( 8530) covalent geometry : angle 0.58925 / 0.30 (11611) SS BOND : bond 0.00246 / 0.12 ( 4) SS BOND : angle 0.80842 / 0.54 ( 8) hydrogen bonds : bond 0.03823 / 2.60 ( 447) hydrogen bonds : angle 4.46563 / 3.24 ( 1251) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 120 time to evaluate : 0.195 Fit side-chains revert: symmetry clash REVERT: R 112 MET cc_start: 0.7949 (tmt) cc_final: 0.7734 (tmm) REVERT: R 134 MET cc_start: 0.7580 (mtm) cc_final: 0.6872 (tmm) REVERT: R 369 THR cc_start: 0.7999 (OUTLIER) cc_final: 0.7561 (p) REVERT: A 22 LYS cc_start: 0.7933 (tttm) cc_final: 0.7244 (tppt) REVERT: A 133 ILE cc_start: 0.7988 (OUTLIER) cc_final: 0.7368 (pp) REVERT: A 185 ARG cc_start: 0.7687 (mtt180) cc_final: 0.7310 (mtt180) REVERT: B 19 ASP cc_start: 0.8401 (m-30) cc_final: 0.8063 (m-30) REVERT: B 37 ASP cc_start: 0.8395 (m-30) cc_final: 0.8181 (m-30) REVERT: B 174 GLN cc_start: 0.8249 (mt0) cc_final: 0.7885 (mm-40) outliers start: 14 outliers final: 6 residues processed: 126 average time/residue: 0.4411 time to fit residues: 60.0674 Evaluate side-chains 121 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 113 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 103 CYS Chi-restraints excluded: chain R residue 125 SER Chi-restraints excluded: chain R residue 196 SER Chi-restraints excluded: chain R residue 369 THR Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 133 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: [85, 63, 52, 57, 19, 6, 90, 47, 109, 42, 12] chunk 85 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 chunk 57 optimal weight: 0.0050 chunk 19 optimal weight: 8.9990 chunk 6 optimal weight: 8.9990 chunk 90 optimal weight: 0.6980 chunk 47 optimal weight: 0.1980 chunk 109 optimal weight: 0.6980 chunk 42 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 16 GLN B 31 GLN B 74 GLN B 258 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.183070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.135967 restraints weight = 9950.436| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 2.21 r_work: 0.3490 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3365 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8534 Z= 0.109 Angle : 0.540 11.395 11619 Z= 0.277 Chirality : 0.042 0.213 1363 Planarity : 0.004 0.046 1466 Dihedral : 5.080 58.840 1229 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.97 % Allowed : 16.11 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.26), residues: 1102 helix: 2.70 (0.27), residues: 384 sheet: 0.34 (0.31), residues: 269 loop : -0.80 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 133 TYR 0.025 0.001 TYR S 191 PHE 0.010 0.001 PHE B 233 TRP 0.016 0.001 TRP B 81 HIS 0.003 0.001 HIS S 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 ( 8530) covalent geometry : angle 0.53978 / 0.28 (11611) SS BOND : bond 0.00257 / 0.13 ( 4) SS BOND : angle 0.73159 / 0.50 ( 8) hydrogen bonds : bond 0.03325 / 2.26 ( 447) hydrogen bonds : angle 4.24224 / 3.08 ( 1251) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 0.311 Fit side-chains revert: symmetry clash REVERT: R 112 MET cc_start: 0.8029 (tmt) cc_final: 0.7766 (ttp) REVERT: R 134 MET cc_start: 0.7630 (mtm) cc_final: 0.6746 (tmm) REVERT: R 330 MET cc_start: 0.7567 (mmm) cc_final: 0.7367 (mmp) REVERT: R 369 THR cc_start: 0.7967 (OUTLIER) cc_final: 0.7535 (p) REVERT: A 22 LYS cc_start: 0.7948 (tttm) cc_final: 0.7282 (tppt) REVERT: A 122 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7968 (tt) REVERT: A 133 ILE cc_start: 0.8035 (tp) cc_final: 0.7531 (pp) REVERT: A 185 ARG cc_start: 0.7731 (mtt180) cc_final: 0.7438 (mtt180) REVERT: B 19 ASP cc_start: 0.8414 (m-30) cc_final: 0.8089 (m-30) REVERT: B 37 ASP cc_start: 0.8394 (m-30) cc_final: 0.8174 (m-30) REVERT: B 174 GLN cc_start: 0.8275 (mt0) cc_final: 0.7903 (mm-40) REVERT: C 62 ARG cc_start: 0.8027 (ptp90) cc_final: 0.7723 (ptp90) outliers start: 17 outliers final: 6 residues processed: 135 average time/residue: 0.4658 time to fit residues: 67.8919 Evaluate side-chains 122 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 114 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 103 CYS Chi-restraints excluded: chain R residue 125 SER Chi-restraints excluded: chain R residue 196 SER Chi-restraints excluded: chain R residue 369 THR Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain S residue 98 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: [51, 29, 47, 37, 100, 21, 54, 44, 91, 101, 99] chunk 51 optimal weight: 0.5980 chunk 29 optimal weight: 0.1980 chunk 47 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 100 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 101 optimal weight: 0.5980 chunk 99 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 179 GLN A 194 HIS B 16 GLN B 31 GLN B 74 GLN B 258 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.180768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.132935 restraints weight = 9851.692| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 2.23 r_work: 0.3435 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8534 Z= 0.146 Angle : 0.587 11.309 11619 Z= 0.299 Chirality : 0.043 0.233 1363 Planarity : 0.004 0.044 1466 Dihedral : 5.104 57.753 1229 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.78 % Allowed : 16.34 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.26), residues: 1102 helix: 2.58 (0.27), residues: 389 sheet: 0.33 (0.31), residues: 269 loop : -0.81 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 133 TYR 0.032 0.002 TYR S 191 PHE 0.014 0.002 PHE B 240 TRP 0.014 0.001 TRP B 81 HIS 0.011 0.001 HIS A 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 ( 8530) covalent geometry : angle 0.58682 / 0.30 (11611) SS BOND : bond 0.00251 / 0.13 ( 4) SS BOND : angle 0.85340 / 0.59 ( 8) hydrogen bonds : bond 0.03703 / 2.52 ( 447) hydrogen bonds : angle 4.35878 / 3.17 ( 1251) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 121 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: R 112 MET cc_start: 0.8109 (tmt) cc_final: 0.7856 (ttp) REVERT: R 134 MET cc_start: 0.7790 (mtm) cc_final: 0.6918 (tmm) REVERT: R 330 MET cc_start: 0.7639 (mmm) cc_final: 0.7428 (mmp) REVERT: R 369 THR cc_start: 0.8031 (OUTLIER) cc_final: 0.7600 (p) REVERT: A 22 LYS cc_start: 0.8027 (tttm) cc_final: 0.7360 (tppt) REVERT: A 133 ILE cc_start: 0.8086 (tp) cc_final: 0.7579 (pp) REVERT: A 185 ARG cc_start: 0.7792 (mtt180) cc_final: 0.7498 (mtt180) REVERT: B 19 ASP cc_start: 0.8451 (m-30) cc_final: 0.8107 (m-30) REVERT: B 37 ASP cc_start: 0.8402 (m-30) cc_final: 0.8187 (m-30) REVERT: B 174 GLN cc_start: 0.8254 (mt0) cc_final: 0.7941 (mm-40) REVERT: B 261 MET cc_start: 0.8840 (tpp) cc_final: 0.8627 (ttm) REVERT: C 62 ARG cc_start: 0.8098 (ptp90) cc_final: 0.7771 (ptp90) REVERT: S 94 MET cc_start: 0.7376 (OUTLIER) cc_final: 0.7019 (ttt) REVERT: S 193 MET cc_start: 0.7761 (OUTLIER) cc_final: 0.7478 (ptt) outliers start: 24 outliers final: 11 residues processed: 133 average time/residue: 0.4602 time to fit residues: 66.0040 Evaluate side-chains 129 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 103 CYS Chi-restraints excluded: chain R residue 125 SER Chi-restraints excluded: chain R residue 196 SER Chi-restraints excluded: chain R residue 340 VAL Chi-restraints excluded: chain R residue 369 THR Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain A residue 16 MET Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain S residue 58 THR Chi-restraints excluded: chain S residue 94 MET Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 193 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: [42, 1, 37, 64, 52, 17, 95, 19, 12, 70, 81] chunk 42 optimal weight: 8.9990 chunk 1 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 95 optimal weight: 0.8980 chunk 19 optimal weight: 10.0000 chunk 12 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 81 optimal weight: 0.5980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 16 GLN B 31 GLN B 74 GLN B 258 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.180436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.132697 restraints weight = 9838.699| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 2.22 r_work: 0.3435 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8534 Z= 0.146 Angle : 0.587 11.383 11619 Z= 0.299 Chirality : 0.043 0.230 1363 Planarity : 0.004 0.045 1466 Dihedral : 5.098 57.583 1229 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.67 % Allowed : 17.27 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.26), residues: 1102 helix: 2.57 (0.27), residues: 389 sheet: 0.37 (0.31), residues: 264 loop : -0.85 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 133 TYR 0.031 0.002 TYR S 191 PHE 0.015 0.001 PHE B 240 TRP 0.015 0.001 TRP B 81 HIS 0.003 0.001 HIS A 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 ( 8530) covalent geometry : angle 0.58623 / 0.30 (11611) SS BOND : bond 0.00283 / 0.14 ( 4) SS BOND : angle 0.90061 / 0.62 ( 8) hydrogen bonds : bond 0.03692 / 2.51 ( 447) hydrogen bonds : angle 4.35597 / 3.16 ( 1251) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 0.313 Fit side-chains revert: symmetry clash REVERT: R 61 GLN cc_start: 0.7761 (OUTLIER) cc_final: 0.6441 (mp10) REVERT: R 112 MET cc_start: 0.8022 (tmt) cc_final: 0.7735 (ttp) REVERT: R 134 MET cc_start: 0.7715 (mtm) cc_final: 0.6835 (tmm) REVERT: R 330 MET cc_start: 0.7653 (mmm) cc_final: 0.7392 (mmp) REVERT: R 369 THR cc_start: 0.8053 (OUTLIER) cc_final: 0.7636 (p) REVERT: A 22 LYS cc_start: 0.8034 (tttm) cc_final: 0.7364 (tppt) REVERT: A 133 ILE cc_start: 0.8064 (tp) cc_final: 0.7549 (pp) REVERT: A 185 ARG cc_start: 0.7760 (mtt180) cc_final: 0.7445 (mtt180) REVERT: B 19 ASP cc_start: 0.8463 (m-30) cc_final: 0.8123 (m-30) REVERT: B 37 ASP cc_start: 0.8421 (m-30) cc_final: 0.8206 (m-30) REVERT: B 174 GLN cc_start: 0.8259 (mt0) cc_final: 0.7946 (mm-40) REVERT: S 40 GLN cc_start: 0.7702 (OUTLIER) cc_final: 0.7382 (tt0) REVERT: S 94 MET cc_start: 0.7425 (OUTLIER) cc_final: 0.7110 (ttt) REVERT: S 193 MET cc_start: 0.7784 (OUTLIER) cc_final: 0.7509 (ptt) outliers start: 23 outliers final: 11 residues processed: 132 average time/residue: 0.4638 time to fit residues: 65.9389 Evaluate side-chains 130 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 61 GLN Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 103 CYS Chi-restraints excluded: chain R residue 125 SER Chi-restraints excluded: chain R residue 196 SER Chi-restraints excluded: chain R residue 340 VAL Chi-restraints excluded: chain R residue 369 THR Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain S residue 40 GLN Chi-restraints excluded: chain S residue 58 THR Chi-restraints excluded: chain S residue 94 MET Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 193 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: [96, 47, 72, 13, 56, 19, 40, 24, 41, 18, 102] chunk 96 optimal weight: 3.9990 chunk 47 optimal weight: 0.4980 chunk 72 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 40 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 16 GLN B 31 GLN B 74 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.180735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.130671 restraints weight = 9923.965| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 2.32 r_work: 0.3421 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8534 Z= 0.161 Angle : 0.605 11.454 11619 Z= 0.309 Chirality : 0.044 0.236 1363 Planarity : 0.004 0.044 1466 Dihedral : 5.136 57.650 1229 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.90 % Allowed : 17.61 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.26), residues: 1102 helix: 2.52 (0.27), residues: 389 sheet: 0.31 (0.31), residues: 269 loop : -0.82 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 133 TYR 0.033 0.002 TYR S 191 PHE 0.015 0.002 PHE B 240 TRP 0.014 0.001 TRP B 81 HIS 0.004 0.001 HIS A 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 ( 8530) covalent geometry : angle 0.60426 / 0.31 (11611) SS BOND : bond 0.00301 / 0.15 ( 4) SS BOND : angle 0.93343 / 0.65 ( 8) hydrogen bonds : bond 0.03837 / 2.61 ( 447) hydrogen bonds : angle 4.40397 / 3.20 ( 1251) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 117 time to evaluate : 0.228 Fit side-chains revert: symmetry clash REVERT: R 61 GLN cc_start: 0.7762 (OUTLIER) cc_final: 0.6443 (mp10) REVERT: R 112 MET cc_start: 0.8029 (tmt) cc_final: 0.7733 (ttp) REVERT: R 134 MET cc_start: 0.7701 (mtm) cc_final: 0.6804 (tmm) REVERT: R 330 MET cc_start: 0.7672 (mmm) cc_final: 0.7399 (mmp) REVERT: R 369 THR cc_start: 0.8014 (OUTLIER) cc_final: 0.7599 (p) REVERT: A 22 LYS cc_start: 0.8049 (tttm) cc_final: 0.7379 (tppt) REVERT: A 133 ILE cc_start: 0.8097 (tp) cc_final: 0.7550 (pp) REVERT: A 185 ARG cc_start: 0.7704 (mtt180) cc_final: 0.7362 (mtt180) REVERT: B 19 ASP cc_start: 0.8508 (m-30) cc_final: 0.8168 (m-30) REVERT: B 37 ASP cc_start: 0.8463 (m-30) cc_final: 0.8252 (m-30) REVERT: B 174 GLN cc_start: 0.8267 (mt0) cc_final: 0.7944 (mm-40) REVERT: C 62 ARG cc_start: 0.8088 (ptp90) cc_final: 0.7755 (ptp90) REVERT: S 40 GLN cc_start: 0.7724 (OUTLIER) cc_final: 0.7354 (tt0) REVERT: S 94 MET cc_start: 0.7454 (OUTLIER) cc_final: 0.7142 (ttt) REVERT: S 193 MET cc_start: 0.7837 (OUTLIER) cc_final: 0.7582 (ptt) outliers start: 25 outliers final: 12 residues processed: 133 average time/residue: 0.4606 time to fit residues: 65.9112 Evaluate side-chains 127 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 61 GLN Chi-restraints excluded: chain R residue 62 THR Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 103 CYS Chi-restraints excluded: chain R residue 125 SER Chi-restraints excluded: chain R residue 196 SER Chi-restraints excluded: chain R residue 369 THR Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 113 CYS Chi-restraints excluded: chain S residue 40 GLN Chi-restraints excluded: chain S residue 58 THR Chi-restraints excluded: chain S residue 94 MET Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 193 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: [53, 15, 14, 78, 62, 22, 56, 87, 29, 74, 66] chunk 53 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 14 optimal weight: 9.9990 chunk 78 optimal weight: 0.0970 chunk 62 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 56 optimal weight: 0.4980 chunk 87 optimal weight: 2.9990 chunk 29 optimal weight: 0.0770 chunk 74 optimal weight: 0.0670 chunk 66 optimal weight: 1.9990 overall best weight: 0.3074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 GLN B 31 GLN B 74 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.185112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.135965 restraints weight = 9843.338| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.30 r_work: 0.3507 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8534 Z= 0.096 Angle : 0.538 11.581 11619 Z= 0.272 Chirality : 0.041 0.191 1363 Planarity : 0.003 0.046 1466 Dihedral : 4.806 58.668 1229 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.43 % Allowed : 18.08 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.26), residues: 1102 helix: 2.70 (0.27), residues: 389 sheet: 0.33 (0.31), residues: 267 loop : -0.76 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 133 TYR 0.021 0.001 TYR S 191 PHE 0.008 0.001 PHE B 198 TRP 0.019 0.001 TRP B 81 HIS 0.003 0.001 HIS S 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.10 ( 8530) covalent geometry : angle 0.53818 / 0.27 (11611) SS BOND : bond 0.00173 / 0.09 ( 4) SS BOND : angle 0.53973 / 0.32 ( 8) hydrogen bonds : bond 0.03051 / 2.08 ( 447) hydrogen bonds : angle 4.09808 / 2.99 ( 1251) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 0.266 Fit side-chains revert: symmetry clash REVERT: R 112 MET cc_start: 0.7882 (OUTLIER) cc_final: 0.7628 (ttp) REVERT: R 134 MET cc_start: 0.7734 (mtm) cc_final: 0.6713 (tmm) REVERT: R 330 MET cc_start: 0.7519 (mmm) cc_final: 0.7267 (mmp) REVERT: R 369 THR cc_start: 0.7986 (OUTLIER) cc_final: 0.7596 (p) REVERT: A 18 GLU cc_start: 0.8679 (mt-10) cc_final: 0.8429 (mt-10) REVERT: A 22 LYS cc_start: 0.7917 (tttm) cc_final: 0.7245 (tppt) REVERT: A 133 ILE cc_start: 0.8029 (tp) cc_final: 0.7563 (pp) REVERT: A 185 ARG cc_start: 0.7730 (mtt180) cc_final: 0.7426 (mtt180) REVERT: B 19 ASP cc_start: 0.8406 (m-30) cc_final: 0.7956 (m-30) REVERT: B 37 ASP cc_start: 0.8408 (m-30) cc_final: 0.8204 (m-30) REVERT: B 97 SER cc_start: 0.8681 (p) cc_final: 0.8454 (p) REVERT: B 174 GLN cc_start: 0.8286 (mt0) cc_final: 0.7884 (mm110) REVERT: S 193 MET cc_start: 0.7502 (OUTLIER) cc_final: 0.7195 (ptt) outliers start: 21 outliers final: 10 residues processed: 139 average time/residue: 0.4459 time to fit residues: 66.8678 Evaluate side-chains 127 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 103 CYS Chi-restraints excluded: chain R residue 112 MET Chi-restraints excluded: chain R residue 125 SER Chi-restraints excluded: chain R residue 369 THR Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain B residue 233 PHE Chi-restraints excluded: chain S residue 58 THR Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 156 VAL Chi-restraints excluded: chain S residue 193 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: [96, 87, 83, 1, 30, 16, 71, 17, 91, 24, 9] chunk 96 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 16 GLN B 31 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.181040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.133162 restraints weight = 9831.894| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.20 r_work: 0.3442 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8534 Z= 0.145 Angle : 0.593 11.504 11619 Z= 0.302 Chirality : 0.043 0.226 1363 Planarity : 0.004 0.045 1466 Dihedral : 4.933 57.951 1229 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.20 % Allowed : 18.42 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.26), residues: 1102 helix: 2.62 (0.27), residues: 385 sheet: 0.40 (0.31), residues: 269 loop : -0.86 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 133 TYR 0.032 0.002 TYR S 191 PHE 0.020 0.002 PHE R 201 TRP 0.014 0.001 TRP B 81 HIS 0.004 0.001 HIS A 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 ( 8530) covalent geometry : angle 0.59233 / 0.30 (11611) SS BOND : bond 0.00266 / 0.13 ( 4) SS BOND : angle 0.86500 / 0.60 ( 8) hydrogen bonds : bond 0.03656 / 2.49 ( 447) hydrogen bonds : angle 4.33440 / 3.15 ( 1251) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 0.321 Fit side-chains revert: symmetry clash REVERT: R 44 VAL cc_start: 0.8537 (t) cc_final: 0.8321 (m) REVERT: R 112 MET cc_start: 0.7988 (OUTLIER) cc_final: 0.7726 (ttp) REVERT: R 134 MET cc_start: 0.7832 (mtm) cc_final: 0.6874 (tmm) REVERT: R 330 MET cc_start: 0.7702 (mmm) cc_final: 0.7409 (mmp) REVERT: R 369 THR cc_start: 0.8051 (OUTLIER) cc_final: 0.7636 (p) REVERT: A 22 LYS cc_start: 0.8058 (tttm) cc_final: 0.7387 (tppt) REVERT: A 133 ILE cc_start: 0.8104 (tp) cc_final: 0.7585 (pp) REVERT: A 185 ARG cc_start: 0.7807 (mtt180) cc_final: 0.7500 (mtt180) REVERT: B 18 ARG cc_start: 0.7541 (ttp80) cc_final: 0.7330 (ttp80) REVERT: B 19 ASP cc_start: 0.8560 (m-30) cc_final: 0.8186 (m-30) REVERT: B 37 ASP cc_start: 0.8459 (m-30) cc_final: 0.8252 (m-30) REVERT: B 174 GLN cc_start: 0.8269 (mt0) cc_final: 0.7961 (mm-40) REVERT: S 40 GLN cc_start: 0.7708 (OUTLIER) cc_final: 0.7320 (tt0) REVERT: S 193 MET cc_start: 0.7683 (OUTLIER) cc_final: 0.7437 (ptt) outliers start: 19 outliers final: 10 residues processed: 131 average time/residue: 0.4405 time to fit residues: 62.3673 Evaluate side-chains 129 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 103 CYS Chi-restraints excluded: chain R residue 112 MET Chi-restraints excluded: chain R residue 125 SER Chi-restraints excluded: chain R residue 369 THR Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain S residue 40 GLN Chi-restraints excluded: chain S residue 58 THR Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 193 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: [102, 11, 24, 95, 35, 66, 48, 96, 77, 82, 75] chunk 102 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 35 optimal weight: 0.0980 chunk 66 optimal weight: 1.9990 chunk 48 optimal weight: 9.9990 chunk 96 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 75 optimal weight: 0.2980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 GLN B 31 GLN B 74 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.182586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.132509 restraints weight = 9895.082| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 2.33 r_work: 0.3455 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8534 Z= 0.122 Angle : 0.574 11.545 11619 Z= 0.291 Chirality : 0.042 0.215 1363 Planarity : 0.004 0.045 1466 Dihedral : 4.879 57.810 1229 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.20 % Allowed : 18.66 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.26), residues: 1102 helix: 2.63 (0.27), residues: 385 sheet: 0.47 (0.31), residues: 264 loop : -0.88 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 133 TYR 0.027 0.001 TYR S 191 PHE 0.019 0.001 PHE R 201 TRP 0.017 0.001 TRP B 81 HIS 0.003 0.001 HIS S 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 ( 8530) covalent geometry : angle 0.57396 / 0.29 (11611) SS BOND : bond 0.00291 / 0.15 ( 4) SS BOND : angle 0.85302 / 0.59 ( 8) hydrogen bonds : bond 0.03431 / 2.33 ( 447) hydrogen bonds : angle 4.28027 / 3.11 ( 1251) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 0.307 Fit side-chains revert: symmetry clash REVERT: R 44 VAL cc_start: 0.8481 (t) cc_final: 0.8270 (m) REVERT: R 112 MET cc_start: 0.7910 (OUTLIER) cc_final: 0.7645 (ttp) REVERT: R 134 MET cc_start: 0.7799 (mtm) cc_final: 0.6791 (tmm) REVERT: R 330 MET cc_start: 0.7583 (mmm) cc_final: 0.7287 (mmp) REVERT: R 369 THR cc_start: 0.8015 (OUTLIER) cc_final: 0.7604 (p) REVERT: A 18 GLU cc_start: 0.8704 (mt-10) cc_final: 0.8388 (mt-10) REVERT: A 22 LYS cc_start: 0.7975 (tttm) cc_final: 0.7304 (tppt) REVERT: A 133 ILE cc_start: 0.8053 (tp) cc_final: 0.7548 (pp) REVERT: A 185 ARG cc_start: 0.7799 (mtt180) cc_final: 0.7491 (mtt180) REVERT: B 19 ASP cc_start: 0.8530 (m-30) cc_final: 0.8117 (m-30) REVERT: B 37 ASP cc_start: 0.8430 (m-30) cc_final: 0.8224 (m-30) REVERT: B 174 GLN cc_start: 0.8271 (mt0) cc_final: 0.7942 (mm-40) REVERT: S 193 MET cc_start: 0.7637 (OUTLIER) cc_final: 0.7346 (ptt) outliers start: 19 outliers final: 11 residues processed: 129 average time/residue: 0.4469 time to fit residues: 62.4263 Evaluate side-chains 127 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 113 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 69 VAL Chi-restraints excluded: chain R residue 103 CYS Chi-restraints excluded: chain R residue 112 MET Chi-restraints excluded: chain R residue 125 SER Chi-restraints excluded: chain R residue 196 SER Chi-restraints excluded: chain R residue 369 THR Chi-restraints excluded: chain R residue 385 THR Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 188 SER Chi-restraints excluded: chain S residue 58 THR Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 193 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: [15, 46, 24, 10, 27, 75, 0, 64, 84, 49, 93] chunk 15 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 64 optimal weight: 0.7980 chunk 84 optimal weight: 0.1980 chunk 49 optimal weight: 6.9990 chunk 93 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 16 GLN B 31 GLN B 74 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.182167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.131891 restraints weight = 9880.050| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 2.35 r_work: 0.3446 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8534 Z= 0.130 Angle : 0.574 11.558 11619 Z= 0.293 Chirality : 0.042 0.220 1363 Planarity : 0.004 0.045 1466 Dihedral : 4.873 57.774 1229 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.20 % Allowed : 19.12 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.26), residues: 1102 helix: 2.64 (0.27), residues: 385 sheet: 0.42 (0.31), residues: 269 loop : -0.88 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 133 TYR 0.029 0.001 TYR S 191 PHE 0.019 0.001 PHE R 201 TRP 0.016 0.001 TRP B 81 HIS 0.003 0.001 HIS A 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 8530) covalent geometry : angle 0.57406 / 0.29 (11611) SS BOND : bond 0.00264 / 0.13 ( 4) SS BOND : angle 0.81871 / 0.56 ( 8) hydrogen bonds : bond 0.03524 / 2.39 ( 447) hydrogen bonds : angle 4.29342 / 3.13 ( 1251) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3300.41 seconds wall clock time: 56 minutes 48.52 seconds (3408.52 seconds total)