Starting phenix.real_space_refine on Thu Jul 2 12:50:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8e9z_27969/07_2026/8e9z_27969.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e9z_27969/07_2026/8e9z_27969.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8e9z_27969/07_2026/8e9z_27969.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e9z_27969/07_2026/8e9z_27969.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8e9z_27969/07_2026/8e9z_27969.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e9z_27969/07_2026/8e9z_27969.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8e9z_27969/07_2026/8e9z_27969.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8e9z_27969/07_2026/8e9z_27969.cif" } resolution = 2.69 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.021 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: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 5488 2.51 5 N 1443 2.21 5 O 1581 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8566 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2173 Classifications: {'peptide': 278} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 9, 'TRANS': 268} Chain breaks: 1 Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TRP:plan': 1, 'GLN:plan1': 2, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "B" Number of atoms: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1698 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 6, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 7, 'ARG:plan': 6, 'ASP:plan': 5, 'GLN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 83 Chain: "C" Number of atoms: 2504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2504 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 6, 'GLN:plan1': 3, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 72 Chain: "D" Number of atoms: 397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 397 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "E" Number of atoms: 1745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1745 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 6, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "A" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {'IXO': 1, 'Y01': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.10, per 1000 atoms: 0.25 Number of scatterers: 8566 At special positions: 0 Unit cell: (88, 120.56, 124.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 1581 8.00 N 1443 7.00 C 5488 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 141 " - pdb=" SG CYS A 221 " distance=2.03 Simple disulfide: pdb=" SG CYS A 517 " - pdb=" SG CYS A 520 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.68 Conformation dependent library (CDL) restraints added in 521.7 milliseconds 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2118 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 12 sheets defined 35.9% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 68 through 96 removed outlier: 3.866A pdb=" N ALA A 72 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL A 89 " --> pdb=" O GLY A 85 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE A 90 " --> pdb=" O ASN A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 100 Processing helix chain 'A' and resid 104 through 120 removed outlier: 3.615A pdb=" N ILE A 116 " --> pdb=" O CYS A 112 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE A 117 " --> pdb=" O ALA A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.815A pdb=" N THR A 127 " --> pdb=" O ASN A 123 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR A 128 " --> pdb=" O LEU A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 172 removed outlier: 4.089A pdb=" N ASP A 142 " --> pdb=" O ASN A 138 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N LEU A 143 " --> pdb=" O LEU A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 206 removed outlier: 3.830A pdb=" N VAL A 187 " --> pdb=" O LYS A 183 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET A 188 " --> pdb=" O ARG A 184 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N SER A 196 " --> pdb=" O ALA A 192 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TRP A 200 " --> pdb=" O SER A 196 " (cutoff:3.500A) Proline residue: A 202 - end of helix Processing helix chain 'A' and resid 231 through 238 Processing helix chain 'A' and resid 240 through 265 Processing helix chain 'A' and resid 487 through 502 removed outlier: 3.953A pdb=" N GLN A 491 " --> pdb=" O LYS A 487 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE A 500 " --> pdb=" O ILE A 496 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE A 501 " --> pdb=" O LEU A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 517 removed outlier: 3.875A pdb=" N LEU A 512 " --> pdb=" O ASN A 508 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL A 513 " --> pdb=" O ILE A 509 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN A 514 " --> pdb=" O MET A 510 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR A 515 " --> pdb=" O VAL A 511 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N PHE A 516 " --> pdb=" O LEU A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 532 removed outlier: 3.544A pdb=" N LEU A 528 " --> pdb=" O THR A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 544 Proline residue: A 541 - end of helix Processing helix chain 'A' and resid 548 through 561 Processing helix chain 'B' and resid 6 through 31 removed outlier: 3.961A pdb=" N ASP B 26 " --> pdb=" O ASN B 22 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY B 27 " --> pdb=" O LEU B 23 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS B 29 " --> pdb=" O GLU B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 49 removed outlier: 3.744A pdb=" N ILE B 49 " --> pdb=" O LYS B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 102 removed outlier: 3.604A pdb=" N ILE B 97 " --> pdb=" O ARG B 94 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLN B 98 " --> pdb=" O LYS B 95 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASN B 101 " --> pdb=" O GLN B 98 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ASP B 102 " --> pdb=" O CYS B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 130 Processing helix chain 'B' and resid 147 through 155 removed outlier: 3.743A pdb=" N GLU B 151 " --> pdb=" O ASP B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 164 removed outlier: 4.159A pdb=" N TYR B 163 " --> pdb=" O LYS B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 202 removed outlier: 3.550A pdb=" N ILE B 193 " --> pdb=" O ALA B 189 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE B 197 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ILE B 200 " --> pdb=" O GLU B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 242 removed outlier: 3.573A pdb=" N GLU B 242 " --> pdb=" O MET B 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 24 removed outlier: 3.534A pdb=" N GLU C 10 " --> pdb=" O GLN C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'D' and resid 7 through 24 removed outlier: 3.582A pdb=" N ASN D 24 " --> pdb=" O LYS D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 43 removed outlier: 3.649A pdb=" N CYS D 41 " --> pdb=" O LEU D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 48 removed outlier: 3.527A pdb=" N ASP D 48 " --> pdb=" O ALA D 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.512A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 69 through 75 removed outlier: 3.648A pdb=" N PHE B 74 " --> pdb=" O PHE B 81 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N VAL B 86 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N GLY B 40 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ARG B 35 " --> pdb=" O ALA B 105 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N ILE B 107 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU B 37 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N VAL B 109 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N LEU B 39 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 8.636A pdb=" N ASP B 111 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ILE B 106 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N PHE B 142 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N PHE B 108 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ASN B 144 " --> pdb=" O PHE B 108 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N VAL B 110 " --> pdb=" O ASN B 144 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 51 removed outlier: 3.718A pdb=" N ARG C 49 " --> pdb=" O ILE C 338 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY C 330 " --> pdb=" O CYS C 317 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N CYS C 317 " --> pdb=" O GLY C 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.683A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.891A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 151 removed outlier: 3.544A pdb=" N CYS C 148 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 192 removed outlier: 3.554A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.260A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.521A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N CYS C 294 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N VAL C 307 " --> pdb=" O CYS C 294 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N VAL C 296 " --> pdb=" O ALA C 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.886A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR E 115 " --> pdb=" O TYR E 94 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 134 through 136 removed outlier: 6.632A pdb=" N LEU E 162 " --> pdb=" O TYR E 178 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N TYR E 178 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 143 through 148 400 hydrogen bonds defined for protein. 1128 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: 1.31 Time building geometry restraints manager: 0.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1374 1.31 - 1.43: 2450 1.43 - 1.56: 4851 1.56 - 1.68: 3 1.68 - 1.81: 76 Bond restraints: 8754 Sorted by residual: bond pdb=" C TYR E 178 " pdb=" N ARG E 179 " ideal model delta sigma weight residual 1.333 1.419 -0.086 1.39e-02 5.18e+03 3.85e+01 bond pdb=" N PRO B 173 " pdb=" CA PRO B 173 " ideal model delta sigma weight residual 1.467 1.424 0.043 1.21e-02 6.83e+03 1.27e+01 bond pdb=" C ARG E 179 " pdb=" N MET E 180 " ideal model delta sigma weight residual 1.332 1.289 0.043 1.40e-02 5.10e+03 9.62e+00 bond pdb=" C TYR E 95 " pdb=" N CYS E 96 " ideal model delta sigma weight residual 1.330 1.368 -0.038 1.32e-02 5.74e+03 8.27e+00 bond pdb=" N PHE B 167 " pdb=" CA PHE B 167 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.19e-02 7.06e+03 8.20e+00 ... (remaining 8749 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 11570 2.03 - 4.05: 285 4.05 - 6.08: 56 6.08 - 8.11: 17 8.11 - 10.13: 6 Bond angle restraints: 11934 Sorted by residual: angle pdb=" CA TYR E 223 " pdb=" C TYR E 223 " pdb=" O TYR E 223 " ideal model delta sigma weight residual 120.25 110.12 10.13 1.08e+00 8.57e-01 8.80e+01 angle pdb=" CA TYR E 223 " pdb=" C TYR E 223 " pdb=" N PRO E 224 " ideal model delta sigma weight residual 118.23 125.10 -6.87 9.20e-01 1.18e+00 5.57e+01 angle pdb=" N ASP B 175 " pdb=" CA ASP B 175 " pdb=" C ASP B 175 " ideal model delta sigma weight residual 111.28 103.98 7.30 1.09e+00 8.42e-01 4.48e+01 angle pdb=" N PRO B 173 " pdb=" CA PRO B 173 " pdb=" C PRO B 173 " ideal model delta sigma weight residual 111.14 101.09 10.05 1.56e+00 4.11e-01 4.15e+01 angle pdb=" N ALA B 176 " pdb=" CA ALA B 176 " pdb=" C ALA B 176 " ideal model delta sigma weight residual 109.23 99.98 9.25 1.55e+00 4.16e-01 3.56e+01 ... (remaining 11929 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.39: 4496 16.39 - 32.77: 446 32.77 - 49.16: 129 49.16 - 65.55: 33 65.55 - 81.94: 5 Dihedral angle restraints: 5109 sinusoidal: 1829 harmonic: 3280 Sorted by residual: dihedral pdb=" CB CYS A 517 " pdb=" SG CYS A 517 " pdb=" SG CYS A 520 " pdb=" CB CYS A 520 " ideal model delta sinusoidal sigma weight residual -86.00 -147.99 61.99 1 1.00e+01 1.00e-02 5.09e+01 dihedral pdb=" C CYS C 233 " pdb=" N CYS C 233 " pdb=" CA CYS C 233 " pdb=" CB CYS C 233 " ideal model delta harmonic sigma weight residual -122.60 -111.46 -11.14 0 2.50e+00 1.60e-01 1.98e+01 dihedral pdb=" C ARG E 179 " pdb=" N ARG E 179 " pdb=" CA ARG E 179 " pdb=" CB ARG E 179 " ideal model delta harmonic sigma weight residual -122.60 -133.30 10.70 0 2.50e+00 1.60e-01 1.83e+01 ... (remaining 5106 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1189 0.066 - 0.132: 177 0.132 - 0.199: 14 0.199 - 0.265: 9 0.265 - 0.331: 3 Chirality restraints: 1392 Sorted by residual: chirality pdb=" CBG Y01 A 802 " pdb=" CAQ Y01 A 802 " pdb=" CBD Y01 A 802 " pdb=" CBI Y01 A 802 " both_signs ideal model delta sigma weight residual False -2.33 -2.66 0.33 2.00e-01 2.50e+01 2.74e+00 chirality pdb=" CBF Y01 A 802 " pdb=" CAS Y01 A 802 " pdb=" CBD Y01 A 802 " pdb=" CBH Y01 A 802 " both_signs ideal model delta sigma weight residual False -2.45 -2.77 0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" CA ARG B 169 " pdb=" N ARG B 169 " pdb=" C ARG B 169 " pdb=" CB ARG B 169 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.37e+00 ... (remaining 1389 not shown) Planarity restraints: 1500 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR E 223 " -0.021 2.00e-02 2.50e+03 4.16e-02 1.73e+01 pdb=" C TYR E 223 " 0.072 2.00e-02 2.50e+03 pdb=" O TYR E 223 " -0.025 2.00e-02 2.50e+03 pdb=" N PRO E 224 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 165 " 0.018 2.00e-02 2.50e+03 3.62e-02 1.31e+01 pdb=" C PRO B 165 " -0.063 2.00e-02 2.50e+03 pdb=" O PRO B 165 " 0.024 2.00e-02 2.50e+03 pdb=" N GLU B 166 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 131 " -0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C MET A 131 " 0.055 2.00e-02 2.50e+03 pdb=" O MET A 131 " -0.021 2.00e-02 2.50e+03 pdb=" N ASN A 132 " -0.019 2.00e-02 2.50e+03 ... (remaining 1497 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1861 2.78 - 3.31: 7462 3.31 - 3.84: 14339 3.84 - 4.37: 16774 4.37 - 4.90: 29326 Nonbonded interactions: 69762 Sorted by model distance: nonbonded pdb=" OE2 GLU B 8 " pdb=" OH TYR E 163 " model vdw 2.248 3.040 nonbonded pdb=" O ILE C 58 " pdb=" OG SER C 316 " model vdw 2.262 3.040 nonbonded pdb=" OG1 THR C 128 " pdb=" O ARG C 129 " model vdw 2.278 3.040 nonbonded pdb=" OD1 ASP E 211 " pdb=" OH TYR E 215 " model vdw 2.280 3.040 nonbonded pdb=" O GLN C 75 " pdb=" OG SER C 98 " model vdw 2.313 3.040 ... (remaining 69757 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: 2.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 8.940 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 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 0.086 8757 Z= 0.249 Angle : 0.799 10.132 11940 Z= 0.488 Chirality : 0.052 0.331 1392 Planarity : 0.006 0.071 1500 Dihedral : 15.120 81.937 2982 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.34 % Allowed : 14.56 % Favored : 85.09 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 2.94 % 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: -1.79 (0.23), residues: 1111 helix: -2.53 (0.18), residues: 364 sheet: 0.50 (0.31), residues: 286 loop : -0.96 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG C 219 TYR 0.034 0.002 TYR B 170 PHE 0.016 0.001 PHE C 234 TRP 0.012 0.001 TRP A 531 HIS 0.009 0.002 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.25 ( 8754) covalent geometry : angle 0.79954 / 0.49 (11934) SS BOND : bond 0.00228 / 0.12 ( 3) SS BOND : angle 0.25368 / 0.14 ( 6) hydrogen bonds : bond 0.27231 / 17.91 ( 400) hydrogen bonds : angle 8.97325 / 6.56 ( 1128) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 168 time to evaluate : 0.218 Fit side-chains REVERT: C 283 ARG cc_start: 0.8430 (tpt-90) cc_final: 0.8079 (tpt90) REVERT: E 68 PHE cc_start: 0.8234 (m-10) cc_final: 0.7832 (m-10) REVERT: E 211 ASP cc_start: 0.7398 (t0) cc_final: 0.7043 (t0) outliers start: 3 outliers final: 0 residues processed: 169 average time/residue: 0.4019 time to fit residues: 73.4890 Evaluate side-chains 163 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 0.0570 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 0.0170 chunk 106 optimal weight: 1.9990 overall best weight: 0.5540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 514 ASN A 536 ASN C 230 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.139350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.120737 restraints weight = 11958.525| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 1.82 r_work: 0.3492 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3350 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8757 Z= 0.150 Angle : 0.543 6.161 11940 Z= 0.295 Chirality : 0.042 0.179 1392 Planarity : 0.004 0.051 1500 Dihedral : 5.311 52.869 1231 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.29 % Allowed : 15.48 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: -0.12 (0.25), residues: 1111 helix: 0.15 (0.26), residues: 369 sheet: 0.55 (0.30), residues: 290 loop : -0.57 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 219 TYR 0.012 0.001 TYR A 128 PHE 0.017 0.002 PHE A 225 TRP 0.019 0.001 TRP C 169 HIS 0.004 0.001 HIS B 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 ( 8754) covalent geometry : angle 0.54276 / 0.29 (11934) SS BOND : bond 0.00492 / 0.22 ( 3) SS BOND : angle 0.91682 / 0.53 ( 6) hydrogen bonds : bond 0.05291 / 3.55 ( 400) hydrogen bonds : angle 5.24885 / 3.84 ( 1128) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 178 time to evaluate : 0.211 Fit side-chains REVERT: A 193 TRP cc_start: 0.8213 (m100) cc_final: 0.7981 (m100) REVERT: B 220 ASP cc_start: 0.7583 (t0) cc_final: 0.7379 (t0) REVERT: E 68 PHE cc_start: 0.8170 (m-10) cc_final: 0.7865 (m-10) outliers start: 20 outliers final: 9 residues processed: 187 average time/residue: 0.3730 time to fit residues: 75.4542 Evaluate side-chains 184 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 175 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 83 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 45 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 21 optimal weight: 0.2980 chunk 58 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 54 optimal weight: 0.5980 chunk 96 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 94 optimal weight: 0.0050 chunk 31 optimal weight: 0.7980 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 508 ASN A 514 ASN A 536 ASN B 123 ASN C 230 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.141134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.123415 restraints weight = 12095.925| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 1.78 r_work: 0.3511 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3371 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8757 Z= 0.131 Angle : 0.517 6.437 11940 Z= 0.275 Chirality : 0.042 0.184 1392 Planarity : 0.004 0.043 1500 Dihedral : 5.254 59.778 1231 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.33 % Allowed : 16.28 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.51 (0.26), residues: 1111 helix: 1.21 (0.28), residues: 355 sheet: 0.47 (0.30), residues: 297 loop : -0.36 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 219 TYR 0.010 0.001 TYR A 128 PHE 0.014 0.001 PHE A 225 TRP 0.016 0.001 TRP C 82 HIS 0.005 0.001 HIS B 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 8754) covalent geometry : angle 0.51651 / 0.28 (11934) SS BOND : bond 0.00414 / 0.19 ( 3) SS BOND : angle 0.71118 / 0.41 ( 6) hydrogen bonds : bond 0.04025 / 2.69 ( 400) hydrogen bonds : angle 4.73435 / 3.45 ( 1128) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 177 time to evaluate : 0.327 Fit side-chains REVERT: A 493 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7617 (mm) REVERT: B 245 LEU cc_start: 0.7896 (mt) cc_final: 0.7655 (mp) REVERT: E 68 PHE cc_start: 0.8191 (m-10) cc_final: 0.7880 (m-10) outliers start: 29 outliers final: 9 residues processed: 191 average time/residue: 0.3811 time to fit residues: 78.9894 Evaluate side-chains 186 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 176 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain B residue 145 LYS Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 63 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 9 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 31 optimal weight: 0.0170 chunk 96 optimal weight: 0.9980 chunk 91 optimal weight: 0.5980 chunk 101 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 78 optimal weight: 0.5980 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 514 ASN A 536 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.140421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.122647 restraints weight = 12251.725| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 1.79 r_work: 0.3501 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8757 Z= 0.140 Angle : 0.512 5.918 11940 Z= 0.274 Chirality : 0.042 0.177 1392 Planarity : 0.004 0.041 1500 Dihedral : 5.276 58.971 1231 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.33 % Allowed : 18.12 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.67 (0.26), residues: 1111 helix: 1.45 (0.28), residues: 367 sheet: 0.51 (0.30), residues: 295 loop : -0.37 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 219 TYR 0.010 0.001 TYR D 40 PHE 0.016 0.001 PHE A 225 TRP 0.014 0.001 TRP C 82 HIS 0.005 0.001 HIS B 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 8754) covalent geometry : angle 0.51224 / 0.27 (11934) SS BOND : bond 0.00403 / 0.19 ( 3) SS BOND : angle 0.70134 / 0.40 ( 6) hydrogen bonds : bond 0.03745 / 2.50 ( 400) hydrogen bonds : angle 4.59945 / 3.33 ( 1128) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 181 time to evaluate : 0.321 Fit side-chains REVERT: A 493 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7695 (mm) REVERT: B 245 LEU cc_start: 0.7885 (mt) cc_final: 0.7658 (mp) REVERT: C 186 ASP cc_start: 0.7786 (m-30) cc_final: 0.7542 (m-30) REVERT: E 68 PHE cc_start: 0.8200 (m-10) cc_final: 0.7926 (m-10) outliers start: 29 outliers final: 11 residues processed: 193 average time/residue: 0.3903 time to fit residues: 81.9801 Evaluate side-chains 192 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 180 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain B residue 145 LYS Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 63 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 42 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 93 optimal weight: 0.3980 chunk 56 optimal weight: 0.3980 chunk 34 optimal weight: 0.4980 chunk 29 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 514 ASN A 536 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.140537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.122687 restraints weight = 12287.845| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 1.80 r_work: 0.3500 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 8757 Z= 0.135 Angle : 0.518 8.609 11940 Z= 0.274 Chirality : 0.042 0.178 1392 Planarity : 0.004 0.039 1500 Dihedral : 5.229 59.110 1231 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.67 % Allowed : 17.89 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.83 (0.26), residues: 1111 helix: 1.67 (0.28), residues: 368 sheet: 0.59 (0.30), residues: 285 loop : -0.33 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 219 TYR 0.010 0.001 TYR A 507 PHE 0.015 0.001 PHE A 225 TRP 0.014 0.001 TRP C 82 HIS 0.005 0.001 HIS B 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 ( 8754) covalent geometry : angle 0.51803 / 0.27 (11934) SS BOND : bond 0.00401 / 0.19 ( 3) SS BOND : angle 0.70093 / 0.40 ( 6) hydrogen bonds : bond 0.03577 / 2.38 ( 400) hydrogen bonds : angle 4.50938 / 3.26 ( 1128) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 186 time to evaluate : 0.338 Fit side-chains REVERT: A 493 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7691 (mm) REVERT: B 245 LEU cc_start: 0.7908 (mt) cc_final: 0.7667 (mp) REVERT: E 68 PHE cc_start: 0.8201 (m-10) cc_final: 0.7920 (m-10) outliers start: 32 outliers final: 15 residues processed: 198 average time/residue: 0.3894 time to fit residues: 83.8568 Evaluate side-chains 197 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 181 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 145 LYS Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 118 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 7 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 108 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 132 ASN A 514 ASN A 536 ASN ** B 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.139702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.121882 restraints weight = 12185.794| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 1.79 r_work: 0.3490 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8757 Z= 0.170 Angle : 0.534 6.252 11940 Z= 0.284 Chirality : 0.043 0.180 1392 Planarity : 0.004 0.038 1500 Dihedral : 5.287 59.276 1231 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.33 % Allowed : 19.61 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.84 (0.26), residues: 1111 helix: 1.70 (0.28), residues: 368 sheet: 0.58 (0.30), residues: 287 loop : -0.34 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 219 TYR 0.011 0.001 TYR A 507 PHE 0.019 0.002 PHE A 225 TRP 0.012 0.001 TRP C 82 HIS 0.005 0.001 HIS B 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 ( 8754) covalent geometry : angle 0.53370 / 0.28 (11934) SS BOND : bond 0.00451 / 0.21 ( 3) SS BOND : angle 0.80203 / 0.46 ( 6) hydrogen bonds : bond 0.03748 / 2.50 ( 400) hydrogen bonds : angle 4.52596 / 3.27 ( 1128) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 186 time to evaluate : 0.318 Fit side-chains REVERT: A 493 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7722 (mm) REVERT: B 245 LEU cc_start: 0.7919 (mt) cc_final: 0.7692 (mp) REVERT: E 68 PHE cc_start: 0.8234 (m-10) cc_final: 0.7982 (m-10) REVERT: E 93 MET cc_start: 0.8499 (OUTLIER) cc_final: 0.8008 (ttp) outliers start: 29 outliers final: 20 residues processed: 195 average time/residue: 0.4106 time to fit residues: 87.0660 Evaluate side-chains 206 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 184 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 508 ASN Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 145 LYS Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 118 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 48 optimal weight: 1.9990 chunk 107 optimal weight: 0.0970 chunk 10 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 527 ASN A 536 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.139922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.122120 restraints weight = 12299.002| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 1.79 r_work: 0.3493 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3350 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8757 Z= 0.159 Angle : 0.530 6.163 11940 Z= 0.282 Chirality : 0.042 0.180 1392 Planarity : 0.004 0.038 1500 Dihedral : 5.307 59.186 1231 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.67 % Allowed : 19.61 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.86 (0.26), residues: 1111 helix: 1.79 (0.28), residues: 367 sheet: 0.57 (0.30), residues: 288 loop : -0.38 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 219 TYR 0.010 0.001 TYR A 507 PHE 0.018 0.002 PHE A 225 TRP 0.012 0.001 TRP C 169 HIS 0.005 0.001 HIS B 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 ( 8754) covalent geometry : angle 0.52999 / 0.28 (11934) SS BOND : bond 0.00407 / 0.19 ( 3) SS BOND : angle 0.75064 / 0.43 ( 6) hydrogen bonds : bond 0.03662 / 2.43 ( 400) hydrogen bonds : angle 4.51973 / 3.27 ( 1128) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 186 time to evaluate : 0.313 Fit side-chains REVERT: A 493 LEU cc_start: 0.8001 (OUTLIER) cc_final: 0.7729 (mm) REVERT: B 245 LEU cc_start: 0.7934 (mt) cc_final: 0.7704 (mp) REVERT: E 68 PHE cc_start: 0.8207 (m-10) cc_final: 0.7956 (m-10) REVERT: E 93 MET cc_start: 0.8502 (OUTLIER) cc_final: 0.8007 (ttp) outliers start: 32 outliers final: 18 residues processed: 199 average time/residue: 0.3956 time to fit residues: 85.7966 Evaluate side-chains 203 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 183 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 145 LYS Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 118 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 23 optimal weight: 0.5980 chunk 88 optimal weight: 0.4980 chunk 72 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 101 optimal weight: 0.3980 chunk 76 optimal weight: 0.7980 chunk 85 optimal weight: 0.3980 chunk 48 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 75 optimal weight: 0.0770 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 536 ASN C 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.140951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.123180 restraints weight = 12140.014| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 1.78 r_work: 0.3512 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8757 Z= 0.116 Angle : 0.514 9.515 11940 Z= 0.269 Chirality : 0.041 0.173 1392 Planarity : 0.003 0.040 1500 Dihedral : 5.188 57.768 1231 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.75 % Allowed : 20.76 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.94 (0.26), residues: 1111 helix: 1.93 (0.29), residues: 368 sheet: 0.56 (0.30), residues: 286 loop : -0.37 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 219 TYR 0.011 0.001 TYR A 507 PHE 0.012 0.001 PHE B 74 TRP 0.015 0.001 TRP C 169 HIS 0.004 0.001 HIS B 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 ( 8754) covalent geometry : angle 0.51418 / 0.27 (11934) SS BOND : bond 0.00319 / 0.15 ( 3) SS BOND : angle 0.59688 / 0.34 ( 6) hydrogen bonds : bond 0.03276 / 2.18 ( 400) hydrogen bonds : angle 4.35915 / 3.15 ( 1128) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 185 time to evaluate : 0.278 Fit side-chains REVERT: A 493 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7678 (mm) REVERT: B 20 ASP cc_start: 0.7956 (m-30) cc_final: 0.7550 (m-30) REVERT: B 245 LEU cc_start: 0.7904 (mt) cc_final: 0.7665 (mp) REVERT: E 68 PHE cc_start: 0.8205 (m-10) cc_final: 0.7918 (m-10) outliers start: 24 outliers final: 17 residues processed: 194 average time/residue: 0.4054 time to fit residues: 85.5166 Evaluate side-chains 201 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 183 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 118 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 28 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 57 optimal weight: 0.2980 chunk 97 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 chunk 105 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 26 optimal weight: 0.4980 chunk 95 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 508 ASN A 536 ASN ** B 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.140646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.122849 restraints weight = 12035.701| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 1.78 r_work: 0.3505 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8757 Z= 0.137 Angle : 0.527 7.268 11940 Z= 0.277 Chirality : 0.042 0.177 1392 Planarity : 0.004 0.038 1500 Dihedral : 5.187 56.784 1231 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.41 % Allowed : 21.10 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.98 (0.26), residues: 1111 helix: 1.97 (0.29), residues: 368 sheet: 0.57 (0.30), residues: 288 loop : -0.35 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 219 TYR 0.012 0.001 TYR A 149 PHE 0.015 0.001 PHE A 225 TRP 0.013 0.001 TRP C 82 HIS 0.004 0.001 HIS B 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 ( 8754) covalent geometry : angle 0.52649 / 0.28 (11934) SS BOND : bond 0.00358 / 0.17 ( 3) SS BOND : angle 0.66227 / 0.37 ( 6) hydrogen bonds : bond 0.03406 / 2.26 ( 400) hydrogen bonds : angle 4.37781 / 3.17 ( 1128) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 183 time to evaluate : 0.322 Fit side-chains REVERT: A 493 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7667 (mm) REVERT: B 20 ASP cc_start: 0.7950 (m-30) cc_final: 0.7542 (m-30) REVERT: B 245 LEU cc_start: 0.7952 (mt) cc_final: 0.7710 (mp) REVERT: C 258 ASP cc_start: 0.6972 (t0) cc_final: 0.6641 (t0) REVERT: C 283 ARG cc_start: 0.8625 (tpt-90) cc_final: 0.8277 (tpt90) REVERT: E 68 PHE cc_start: 0.8204 (m-10) cc_final: 0.7934 (m-10) outliers start: 21 outliers final: 15 residues processed: 191 average time/residue: 0.4176 time to fit residues: 86.5645 Evaluate side-chains 198 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 182 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 118 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 34 optimal weight: 0.4980 chunk 38 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 52 optimal weight: 0.4980 chunk 102 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 103 optimal weight: 0.3980 chunk 35 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 82 optimal weight: 5.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 536 ASN ** B 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.140541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.122780 restraints weight = 12106.430| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 1.78 r_work: 0.3491 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8757 Z= 0.137 Angle : 0.527 7.268 11940 Z= 0.277 Chirality : 0.042 0.177 1392 Planarity : 0.004 0.038 1500 Dihedral : 5.187 56.784 1231 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.83 % Allowed : 22.02 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 0.98 (0.26), residues: 1111 helix: 1.97 (0.29), residues: 368 sheet: 0.57 (0.30), residues: 288 loop : -0.35 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 219 TYR 0.012 0.001 TYR A 149 PHE 0.015 0.001 PHE A 225 TRP 0.013 0.001 TRP C 82 HIS 0.004 0.001 HIS B 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 ( 8754) covalent geometry : angle 0.52649 / 0.28 (11934) SS BOND : bond 0.00358 / 0.17 ( 3) SS BOND : angle 0.66227 / 0.37 ( 6) hydrogen bonds : bond 0.03406 / 2.26 ( 400) hydrogen bonds : angle 4.37781 / 3.17 ( 1128) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 182 time to evaluate : 0.313 Fit side-chains REVERT: A 493 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.7685 (mm) REVERT: B 20 ASP cc_start: 0.7954 (m-30) cc_final: 0.7550 (m-30) REVERT: B 245 LEU cc_start: 0.7942 (mt) cc_final: 0.7713 (mp) REVERT: C 258 ASP cc_start: 0.6975 (t0) cc_final: 0.6644 (t0) REVERT: C 283 ARG cc_start: 0.8641 (tpt-90) cc_final: 0.8299 (tpt90) REVERT: E 68 PHE cc_start: 0.8203 (m-10) cc_final: 0.7939 (m-10) outliers start: 16 outliers final: 15 residues processed: 189 average time/residue: 0.4133 time to fit residues: 84.8525 Evaluate side-chains 198 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 182 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 222 PHE Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 277 SER Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 118 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 39 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 64 optimal weight: 0.0470 chunk 88 optimal weight: 0.4980 chunk 108 optimal weight: 0.9980 chunk 35 optimal weight: 0.1980 chunk 5 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 536 ASN ** B 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.140894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.123162 restraints weight = 12070.756| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 1.77 r_work: 0.3496 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8757 Z= 0.123 Angle : 0.525 8.225 11940 Z= 0.276 Chirality : 0.041 0.174 1392 Planarity : 0.004 0.039 1500 Dihedral : 5.162 57.635 1231 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.95 % Allowed : 21.79 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % 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: 1111 helix: 2.01 (0.29), residues: 367 sheet: 0.57 (0.30), residues: 286 loop : -0.35 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 219 TYR 0.012 0.001 TYR A 507 PHE 0.014 0.001 PHE A 225 TRP 0.014 0.001 TRP C 169 HIS 0.004 0.001 HIS B 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 8754) covalent geometry : angle 0.52462 / 0.28 (11934) SS BOND : bond 0.00329 / 0.16 ( 3) SS BOND : angle 0.62676 / 0.35 ( 6) hydrogen bonds : bond 0.03333 / 2.21 ( 400) hydrogen bonds : angle 4.35603 / 3.15 ( 1128) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3236.26 seconds wall clock time: 55 minutes 49.26 seconds (3349.26 seconds total)