Starting phenix.real_space_refine on Tue Feb 3 23:32:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i6r_35204/02_2026/8i6r_35204.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i6r_35204/02_2026/8i6r_35204.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8i6r_35204/02_2026/8i6r_35204.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i6r_35204/02_2026/8i6r_35204.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8i6r_35204/02_2026/8i6r_35204.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i6r_35204/02_2026/8i6r_35204.map" } resolution = 4.0 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= 0.002 sd= 0.031 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 1 5.21 5 S 20 5.16 5 C 5027 2.51 5 N 1275 2.21 5 O 1428 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7757 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2210 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 11, 'TRANS': 277} Chain breaks: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'ARG:plan': 20} Unresolved non-hydrogen planarities: 41 Chain: "B" Number of atoms: 1680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1680 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 10, 'TRANS': 211} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 22} Unresolved non-hydrogen planarities: 44 Chain: "C" Number of atoms: 2128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2128 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 9, 'TRANS': 268} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'ARG:plan': 20} Unresolved non-hydrogen planarities: 40 Chain: "D" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1676 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 211} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'ARG:plan': 22} Unresolved non-hydrogen planarities: 44 Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.38, per 1000 atoms: 0.18 Number of scatterers: 7757 At special positions: 0 Unit cell: (67.782, 80.652, 145.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 20 16.00 P 6 15.00 Mg 1 11.99 O 1428 8.00 N 1275 7.00 C 5027 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.81 Conformation dependent library (CDL) restraints added in 276.9 milliseconds 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1834 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 8 sheets defined 61.2% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 35 through 54 removed outlier: 4.328A pdb=" N GLU A 39 " --> pdb=" O SER A 35 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N HIS A 41 " --> pdb=" O TYR A 37 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA A 43 " --> pdb=" O GLU A 39 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL A 46 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 86 removed outlier: 3.558A pdb=" N SER A 59 " --> pdb=" O HIS A 55 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU A 72 " --> pdb=" O ILE A 68 " (cutoff:3.500A) Proline residue: A 73 - end of helix removed outlier: 3.739A pdb=" N LEU A 79 " --> pdb=" O GLY A 75 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU A 80 " --> pdb=" O LEU A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 91 Processing helix chain 'A' and resid 105 through 118 removed outlier: 4.226A pdb=" N GLU A 114 " --> pdb=" O GLN A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 141 removed outlier: 3.598A pdb=" N SER A 135 " --> pdb=" O GLU A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 179 Processing helix chain 'A' and resid 190 through 233 removed outlier: 3.719A pdb=" N LYS A 202 " --> pdb=" O SER A 198 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A 203 " --> pdb=" O ALA A 199 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY A 204 " --> pdb=" O ILE A 200 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU A 217 " --> pdb=" O ILE A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 245 Processing helix chain 'A' and resid 247 through 293 Proline residue: A 254 - end of helix removed outlier: 4.146A pdb=" N GLY A 283 " --> pdb=" O ASN A 279 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N SER A 284 " --> pdb=" O TRP A 280 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N VAL A 285 " --> pdb=" O LEU A 281 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL A 286 " --> pdb=" O ASN A 282 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ASN A 287 " --> pdb=" O GLY A 283 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A 288 " --> pdb=" O SER A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 332 removed outlier: 3.837A pdb=" N HIS A 328 " --> pdb=" O ALA A 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 49 removed outlier: 3.570A pdb=" N ILE B 48 " --> pdb=" O LEU B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 80 removed outlier: 3.802A pdb=" N GLN B 80 " --> pdb=" O PHE B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 107 Proline residue: B 103 - end of helix Processing helix chain 'B' and resid 110 through 125 removed outlier: 3.665A pdb=" N ILE B 114 " --> pdb=" O PRO B 110 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA B 115 " --> pdb=" O LYS B 111 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LYS B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU B 123 " --> pdb=" O ALA B 119 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG B 124 " --> pdb=" O SER B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 138 Processing helix chain 'B' and resid 139 through 153 Processing helix chain 'B' and resid 169 through 186 Processing helix chain 'B' and resid 197 through 202 removed outlier: 3.810A pdb=" N ARG B 202 " --> pdb=" O ALA B 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 54 removed outlier: 3.614A pdb=" N HIS C 41 " --> pdb=" O TYR C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 86 removed outlier: 3.743A pdb=" N VAL C 65 " --> pdb=" O PHE C 61 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N MET C 66 " --> pdb=" O THR C 62 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU C 72 " --> pdb=" O ILE C 68 " (cutoff:3.500A) Proline residue: C 73 - end of helix removed outlier: 3.661A pdb=" N LEU C 86 " --> pdb=" O ASN C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 119 removed outlier: 3.601A pdb=" N GLY C 109 " --> pdb=" O SER C 105 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLU C 114 " --> pdb=" O GLN C 110 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N GLN C 115 " --> pdb=" O ASP C 111 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ILE C 116 " --> pdb=" O LEU C 112 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLU C 117 " --> pdb=" O ARG C 113 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG C 118 " --> pdb=" O GLU C 114 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU C 119 " --> pdb=" O GLN C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 179 Processing helix chain 'C' and resid 191 through 201 Processing helix chain 'C' and resid 202 through 233 Processing helix chain 'C' and resid 235 through 245 removed outlier: 3.928A pdb=" N GLU C 239 " --> pdb=" O ARG C 235 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS C 242 " --> pdb=" O ILE C 238 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL C 244 " --> pdb=" O VAL C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 292 Proline residue: C 254 - end of helix removed outlier: 3.586A pdb=" N TRP C 271 " --> pdb=" O GLY C 267 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA C 272 " --> pdb=" O ILE C 268 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLY C 283 " --> pdb=" O ASN C 279 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N SER C 284 " --> pdb=" O TRP C 280 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL C 285 " --> pdb=" O LEU C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 332 removed outlier: 3.585A pdb=" N SER C 308 " --> pdb=" O ASP C 304 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG C 327 " --> pdb=" O LEU C 323 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N HIS C 328 " --> pdb=" O ALA C 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 50 removed outlier: 3.846A pdb=" N ILE D 48 " --> pdb=" O LEU D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 79 removed outlier: 4.642A pdb=" N PHE D 76 " --> pdb=" O ALA D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 108 Proline residue: D 103 - end of helix Processing helix chain 'D' and resid 110 through 124 removed outlier: 3.554A pdb=" N GLU D 123 " --> pdb=" O ALA D 119 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG D 124 " --> pdb=" O SER D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 138 Processing helix chain 'D' and resid 139 through 153 removed outlier: 3.800A pdb=" N GLN D 144 " --> pdb=" O THR D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 185 removed outlier: 3.692A pdb=" N SER D 174 " --> pdb=" O PRO D 170 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLU D 175 " --> pdb=" O ARG D 171 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE D 176 " --> pdb=" O LEU D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 202 removed outlier: 3.580A pdb=" N LEU D 199 " --> pdb=" O ASP D 196 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALA D 201 " --> pdb=" O ALA D 198 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG D 202 " --> pdb=" O LEU D 199 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 125 through 127 removed outlier: 3.524A pdb=" N SER A 160 " --> pdb=" O GLN A 126 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU A 98 " --> pdb=" O ILE A 159 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 16 through 25 removed outlier: 5.596A pdb=" N GLY B 17 " --> pdb=" O ARG B 10 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ARG B 10 " --> pdb=" O GLY B 17 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N HIS B 19 " --> pdb=" O GLY B 8 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLY B 8 " --> pdb=" O HIS B 19 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N VAL B 21 " --> pdb=" O GLN B 6 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N PHE B 4 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N LEU B 60 " --> pdb=" O PHE B 4 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N GLN B 6 " --> pdb=" O LYS B 58 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS B 58 " --> pdb=" O GLN B 6 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 30 through 31 Processing sheet with id=AA4, first strand: chain 'B' and resid 34 through 35 removed outlier: 7.082A pdb=" N THR B 34 " --> pdb=" O LEU B 210 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 98 through 99 removed outlier: 3.707A pdb=" N SER C 160 " --> pdb=" O GLN C 126 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 4 through 5 removed outlier: 3.621A pdb=" N GLU D 5 " --> pdb=" O LYS D 58 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 30 through 31 removed outlier: 3.612A pdb=" N GLY D 82 " --> pdb=" O LEU D 158 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 33 through 35 removed outlier: 6.852A pdb=" N THR D 34 " --> pdb=" O LEU D 210 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 429 hydrogen bonds defined for protein. 1242 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: 1.02 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2517 1.34 - 1.46: 1318 1.46 - 1.58: 4006 1.58 - 1.69: 10 1.69 - 1.81: 38 Bond restraints: 7889 Sorted by residual: bond pdb=" C6 ATP D 301 " pdb=" N6 ATP D 301 " ideal model delta sigma weight residual 1.337 1.445 -0.108 1.10e-02 8.26e+03 9.66e+01 bond pdb=" C6 ATP B 301 " pdb=" N6 ATP B 301 " ideal model delta sigma weight residual 1.337 1.445 -0.108 1.10e-02 8.26e+03 9.60e+01 bond pdb=" C5 ATP D 301 " pdb=" N7 ATP D 301 " ideal model delta sigma weight residual 1.387 1.471 -0.084 1.00e-02 1.00e+04 6.99e+01 bond pdb=" C5 ATP B 301 " pdb=" N7 ATP B 301 " ideal model delta sigma weight residual 1.387 1.465 -0.078 1.00e-02 1.00e+04 6.07e+01 bond pdb=" O5' ATP B 301 " pdb=" PA ATP B 301 " ideal model delta sigma weight residual 1.579 1.645 -0.066 1.10e-02 8.26e+03 3.55e+01 ... (remaining 7884 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.29: 10568 4.29 - 8.58: 81 8.58 - 12.87: 14 12.87 - 17.16: 4 17.16 - 21.45: 3 Bond angle restraints: 10670 Sorted by residual: angle pdb=" PB ATP B 301 " pdb=" O3B ATP B 301 " pdb=" PG ATP B 301 " ideal model delta sigma weight residual 139.87 118.42 21.45 1.00e+00 1.00e+00 4.60e+02 angle pdb=" PB ATP D 301 " pdb=" O3B ATP D 301 " pdb=" PG ATP D 301 " ideal model delta sigma weight residual 139.87 120.57 19.30 1.00e+00 1.00e+00 3.73e+02 angle pdb=" PA ATP B 301 " pdb=" O3A ATP B 301 " pdb=" PB ATP B 301 " ideal model delta sigma weight residual 136.83 117.70 19.13 1.00e+00 1.00e+00 3.66e+02 angle pdb=" PA ATP D 301 " pdb=" O3A ATP D 301 " pdb=" PB ATP D 301 " ideal model delta sigma weight residual 136.83 121.83 15.00 1.00e+00 1.00e+00 2.25e+02 angle pdb=" C4 ATP D 301 " pdb=" N9 ATP D 301 " pdb=" C8 ATP D 301 " ideal model delta sigma weight residual 105.72 115.00 -9.28 1.00e+00 1.00e+00 8.61e+01 ... (remaining 10665 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 4267 17.94 - 35.87: 424 35.87 - 53.81: 84 53.81 - 71.75: 23 71.75 - 89.68: 6 Dihedral angle restraints: 4804 sinusoidal: 1952 harmonic: 2852 Sorted by residual: dihedral pdb=" CA ILE D 216 " pdb=" C ILE D 216 " pdb=" N ALA D 217 " pdb=" CA ALA D 217 " ideal model delta harmonic sigma weight residual 180.00 152.65 27.35 0 5.00e+00 4.00e-02 2.99e+01 dihedral pdb=" CA ILE B 216 " pdb=" C ILE B 216 " pdb=" N ALA B 217 " pdb=" CA ALA B 217 " ideal model delta harmonic sigma weight residual 180.00 155.09 24.91 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CG ARG A 130 " pdb=" CD ARG A 130 " pdb=" NE ARG A 130 " pdb=" CZ ARG A 130 " ideal model delta sinusoidal sigma weight residual -90.00 -24.85 -65.15 2 1.50e+01 4.44e-03 1.76e+01 ... (remaining 4801 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 841 0.035 - 0.070: 294 0.070 - 0.105: 110 0.105 - 0.140: 26 0.140 - 0.175: 7 Chirality restraints: 1278 Sorted by residual: chirality pdb=" CB ILE D 2 " pdb=" CA ILE D 2 " pdb=" CG1 ILE D 2 " pdb=" CG2 ILE D 2 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.18 2.00e-01 2.50e+01 7.68e-01 chirality pdb=" C2' ATP D 301 " pdb=" C1' ATP D 301 " pdb=" C3' ATP D 301 " pdb=" O2' ATP D 301 " both_signs ideal model delta sigma weight residual False -2.68 -2.51 -0.17 2.00e-01 2.50e+01 7.65e-01 chirality pdb=" C2' ATP B 301 " pdb=" C1' ATP B 301 " pdb=" C3' ATP B 301 " pdb=" O2' ATP B 301 " both_signs ideal model delta sigma weight residual False -2.68 -2.51 -0.17 2.00e-01 2.50e+01 7.17e-01 ... (remaining 1275 not shown) Planarity restraints: 1309 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS C 202 " 0.015 2.00e-02 2.50e+03 3.02e-02 9.12e+00 pdb=" C LYS C 202 " -0.052 2.00e-02 2.50e+03 pdb=" O LYS C 202 " 0.020 2.00e-02 2.50e+03 pdb=" N LEU C 203 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 192 " -0.015 2.00e-02 2.50e+03 2.86e-02 8.19e+00 pdb=" C VAL A 192 " 0.050 2.00e-02 2.50e+03 pdb=" O VAL A 192 " -0.018 2.00e-02 2.50e+03 pdb=" N TRP A 193 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET D 109 " -0.035 5.00e-02 4.00e+02 5.33e-02 4.54e+00 pdb=" N PRO D 110 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO D 110 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 110 " -0.029 5.00e-02 4.00e+02 ... (remaining 1306 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 51 2.42 - 3.04: 5400 3.04 - 3.66: 12868 3.66 - 4.28: 17341 4.28 - 4.90: 26589 Nonbonded interactions: 62249 Sorted by model distance: nonbonded pdb=" O1B ATP B 301 " pdb="MG MG B 302 " model vdw 1.797 2.170 nonbonded pdb=" O2B ATP B 301 " pdb="MG MG B 302 " model vdw 1.963 2.170 nonbonded pdb=" O ILE C 68 " pdb=" OG SER C 71 " model vdw 2.120 3.040 nonbonded pdb=" NE2 GLN A 95 " pdb=" OE2 GLU A 124 " model vdw 2.148 3.120 nonbonded pdb=" O ARG C 92 " pdb=" NE2 GLN C 95 " model vdw 2.166 3.120 ... (remaining 62244 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 35 through 131 or resid 157 through 335)) selection = (chain 'C' and (resid 35 through 249 or (resid 250 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name \ CE2 or name CZ )) or resid 251 through 335)) } ncs_group { reference = (chain 'B' and (resid 1 through 8 or (resid 9 and (name N or name CA or name C o \ r name O or name CB )) or resid 10 through 301)) selection = chain 'D' } 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 group one per residue 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: 2.150 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: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.870 Find NCS groups from input model: 0.070 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: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 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 : 0.012 0.901 7891 Z= 1.091 Angle : 1.029 21.451 10670 Z= 0.672 Chirality : 0.043 0.175 1278 Planarity : 0.005 0.053 1309 Dihedral : 15.432 89.684 2970 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 22.17 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.81 % Favored : 93.09 % Rotamer: Outliers : 1.66 % Allowed : 1.55 % Favored : 96.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.44 (0.27), residues: 999 helix: 1.19 (0.22), residues: 568 sheet: -2.34 (0.49), residues: 89 loop : -2.30 (0.31), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG B 171 TYR 0.013 0.002 TYR D 11 PHE 0.017 0.002 PHE B 180 TRP 0.034 0.003 TRP C 322 HIS 0.006 0.001 HIS D 88 Details of bonding type rmsd covalent geometry : bond 0.00623 ( 7889) covalent geometry : angle 1.02912 (10670) hydrogen bonds : bond 0.18885 ( 429) hydrogen bonds : angle 7.14988 ( 1242) Misc. bond : bond 0.63686 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.192 Fit side-chains revert: symmetry clash REVERT: B 1 MET cc_start: 0.4617 (tpp) cc_final: 0.4203 (tpp) REVERT: D 85 PHE cc_start: 0.9092 (m-80) cc_final: 0.8672 (m-80) REVERT: D 87 ASN cc_start: 0.9616 (t0) cc_final: 0.9407 (t0) REVERT: D 109 MET cc_start: 0.8676 (mmt) cc_final: 0.8186 (mmm) REVERT: D 160 LEU cc_start: 0.9731 (mt) cc_final: 0.9519 (tt) REVERT: D 207 MET cc_start: 0.7413 (mpp) cc_final: 0.6937 (mpp) outliers start: 14 outliers final: 14 residues processed: 85 average time/residue: 0.0525 time to fit residues: 6.8303 Evaluate side-chains 65 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 51 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain A residue 113 ARG Chi-restraints excluded: chain A residue 118 ARG Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 168 ARG Chi-restraints excluded: chain A residue 175 ARG Chi-restraints excluded: chain C residue 92 ARG Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain C residue 118 ARG Chi-restraints excluded: chain C residue 168 ARG Chi-restraints excluded: chain C residue 175 ARG Chi-restraints excluded: chain C residue 335 ARG Chi-restraints excluded: chain D residue 124 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 0.0040 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 20.0000 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 overall best weight: 0.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN B 167 ASN C 82 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.044490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.031622 restraints weight = 64809.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.032357 restraints weight = 45368.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.032888 restraints weight = 35170.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.033282 restraints weight = 29214.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.033565 restraints weight = 25370.736| |-----------------------------------------------------------------------------| r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7891 Z= 0.147 Angle : 0.733 7.915 10670 Z= 0.371 Chirality : 0.043 0.203 1278 Planarity : 0.005 0.074 1309 Dihedral : 11.202 81.700 1142 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.01 % Favored : 93.89 % Rotamer: Outliers : 1.78 % Allowed : 12.01 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.19 (0.27), residues: 999 helix: 1.40 (0.22), residues: 583 sheet: -2.16 (0.48), residues: 96 loop : -2.41 (0.32), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG B 202 TYR 0.013 0.002 TYR D 11 PHE 0.020 0.002 PHE D 180 TRP 0.020 0.002 TRP C 322 HIS 0.006 0.001 HIS A 41 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 7889) covalent geometry : angle 0.73294 (10670) hydrogen bonds : bond 0.05634 ( 429) hydrogen bonds : angle 5.73644 ( 1242) Misc. bond : bond 0.00364 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.306 Fit side-chains REVERT: B 1 MET cc_start: 0.4064 (tpp) cc_final: 0.3585 (tpp) REVERT: B 87 ASN cc_start: 0.9565 (t0) cc_final: 0.8614 (t0) REVERT: B 207 MET cc_start: 0.8822 (mtm) cc_final: 0.8495 (mtm) REVERT: C 62 THR cc_start: 0.8930 (p) cc_final: 0.8503 (t) REVERT: D 87 ASN cc_start: 0.9574 (t0) cc_final: 0.9309 (t0) REVERT: D 167 ASN cc_start: 0.8226 (m-40) cc_final: 0.7678 (m-40) REVERT: D 207 MET cc_start: 0.7670 (mpp) cc_final: 0.7209 (mpp) outliers start: 15 outliers final: 11 residues processed: 81 average time/residue: 0.0632 time to fit residues: 7.6427 Evaluate side-chains 66 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain A residue 118 ARG Chi-restraints excluded: chain A residue 168 ARG Chi-restraints excluded: chain A residue 175 ARG Chi-restraints excluded: chain C residue 92 ARG Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain C residue 175 ARG Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain D residue 124 ARG Chi-restraints excluded: chain D residue 206 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 4 optimal weight: 2.9990 chunk 19 optimal weight: 0.3980 chunk 27 optimal weight: 4.9990 chunk 39 optimal weight: 6.9990 chunk 9 optimal weight: 30.0000 chunk 85 optimal weight: 6.9990 chunk 24 optimal weight: 0.6980 chunk 2 optimal weight: 5.9990 chunk 73 optimal weight: 9.9990 chunk 57 optimal weight: 30.0000 chunk 48 optimal weight: 7.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 ASN A 225 ASN ** C 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.043471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.030962 restraints weight = 66498.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.031670 restraints weight = 47186.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.032177 restraints weight = 36876.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.032541 restraints weight = 30592.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.032793 restraints weight = 26611.323| |-----------------------------------------------------------------------------| r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 7891 Z= 0.174 Angle : 0.697 8.062 10670 Z= 0.358 Chirality : 0.041 0.191 1278 Planarity : 0.005 0.069 1309 Dihedral : 10.280 82.214 1118 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.11 % Favored : 93.79 % Rotamer: Outliers : 3.09 % Allowed : 17.60 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.21 (0.27), residues: 999 helix: 1.45 (0.22), residues: 577 sheet: -2.27 (0.48), residues: 96 loop : -2.45 (0.32), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG B 219 TYR 0.013 0.002 TYR D 11 PHE 0.055 0.002 PHE D 180 TRP 0.015 0.001 TRP A 318 HIS 0.005 0.001 HIS D 88 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 7889) covalent geometry : angle 0.69691 (10670) hydrogen bonds : bond 0.05247 ( 429) hydrogen bonds : angle 5.63251 ( 1242) Misc. bond : bond 0.00226 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 56 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.4376 (tpp) cc_final: 0.3840 (tpp) REVERT: B 207 MET cc_start: 0.8804 (mtm) cc_final: 0.8475 (mtm) REVERT: C 258 MET cc_start: 0.8721 (OUTLIER) cc_final: 0.8422 (ppp) REVERT: D 160 LEU cc_start: 0.9628 (mt) cc_final: 0.9224 (tt) REVERT: D 207 MET cc_start: 0.7838 (mpp) cc_final: 0.7497 (mpp) outliers start: 26 outliers final: 19 residues processed: 79 average time/residue: 0.0500 time to fit residues: 6.1956 Evaluate side-chains 74 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 54 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain A residue 118 ARG Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 168 ARG Chi-restraints excluded: chain A residue 175 ARG Chi-restraints excluded: chain A residue 239 GLU Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 212 ARG Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain C residue 175 ARG Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 258 MET Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 335 ARG Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 124 ARG Chi-restraints excluded: chain D residue 143 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 7.9990 chunk 25 optimal weight: 10.0000 chunk 96 optimal weight: 20.0000 chunk 47 optimal weight: 20.0000 chunk 89 optimal weight: 0.0370 chunk 98 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 86 optimal weight: 3.9990 chunk 73 optimal weight: 8.9990 chunk 44 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 overall best weight: 1.9664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 82 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.044098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.031651 restraints weight = 66887.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.032379 restraints weight = 47526.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.032890 restraints weight = 36839.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.033276 restraints weight = 30658.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.033575 restraints weight = 26585.845| |-----------------------------------------------------------------------------| r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 7891 Z= 0.136 Angle : 0.668 9.013 10670 Z= 0.340 Chirality : 0.041 0.183 1278 Planarity : 0.004 0.066 1309 Dihedral : 9.791 83.740 1114 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.01 % Favored : 93.89 % Rotamer: Outliers : 3.92 % Allowed : 19.26 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.10 (0.28), residues: 999 helix: 1.54 (0.22), residues: 581 sheet: -2.29 (0.48), residues: 96 loop : -2.41 (0.32), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG B 185 TYR 0.013 0.002 TYR D 11 PHE 0.039 0.002 PHE B 180 TRP 0.015 0.001 TRP A 318 HIS 0.005 0.001 HIS A 230 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 7889) covalent geometry : angle 0.66763 (10670) hydrogen bonds : bond 0.04720 ( 429) hydrogen bonds : angle 5.34352 ( 1242) Misc. bond : bond 0.00251 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 60 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 GLU cc_start: 0.8979 (OUTLIER) cc_final: 0.8620 (pp20) REVERT: B 1 MET cc_start: 0.4555 (tpp) cc_final: 0.4068 (tpp) REVERT: B 207 MET cc_start: 0.8825 (mtm) cc_final: 0.8487 (mtm) REVERT: C 258 MET cc_start: 0.8680 (OUTLIER) cc_final: 0.8479 (ppp) REVERT: C 282 ASN cc_start: 0.8551 (OUTLIER) cc_final: 0.7603 (m110) REVERT: D 45 LEU cc_start: 0.9671 (pp) cc_final: 0.9428 (pt) REVERT: D 160 LEU cc_start: 0.9649 (mt) cc_final: 0.9231 (tt) outliers start: 33 outliers final: 19 residues processed: 89 average time/residue: 0.0528 time to fit residues: 7.3918 Evaluate side-chains 80 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 58 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 168 ARG Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 239 GLU Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 212 ARG Chi-restraints excluded: chain C residue 175 ARG Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 258 MET Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 335 ARG Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 124 ARG Chi-restraints excluded: chain D residue 143 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 1 optimal weight: 0.9990 chunk 87 optimal weight: 6.9990 chunk 4 optimal weight: 8.9990 chunk 94 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 62 optimal weight: 50.0000 chunk 96 optimal weight: 20.0000 chunk 19 optimal weight: 0.6980 chunk 64 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.044002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.031637 restraints weight = 66275.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.032324 restraints weight = 46706.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.032844 restraints weight = 36361.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.033224 restraints weight = 30184.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.033383 restraints weight = 26240.956| |-----------------------------------------------------------------------------| r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 7891 Z= 0.132 Angle : 0.698 10.795 10670 Z= 0.346 Chirality : 0.041 0.359 1278 Planarity : 0.004 0.063 1309 Dihedral : 9.305 83.494 1102 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.51 % Favored : 93.39 % Rotamer: Outliers : 3.57 % Allowed : 21.40 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.14 (0.28), residues: 999 helix: 1.51 (0.23), residues: 581 sheet: -2.34 (0.47), residues: 96 loop : -2.42 (0.32), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG D 206 TYR 0.013 0.001 TYR D 11 PHE 0.049 0.002 PHE D 180 TRP 0.013 0.001 TRP A 318 HIS 0.008 0.001 HIS A 230 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 7889) covalent geometry : angle 0.69760 (10670) hydrogen bonds : bond 0.04579 ( 429) hydrogen bonds : angle 5.28293 ( 1242) Misc. bond : bond 0.00249 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 63 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 GLU cc_start: 0.8941 (OUTLIER) cc_final: 0.8590 (pp20) REVERT: B 1 MET cc_start: 0.4530 (tpp) cc_final: 0.4067 (tpp) REVERT: B 109 MET cc_start: 0.8213 (mmm) cc_final: 0.7839 (mmm) REVERT: B 207 MET cc_start: 0.8839 (mtm) cc_final: 0.8506 (mtm) REVERT: C 282 ASN cc_start: 0.8561 (OUTLIER) cc_final: 0.7629 (m110) REVERT: D 45 LEU cc_start: 0.9646 (pp) cc_final: 0.9441 (pt) REVERT: D 47 LEU cc_start: 0.9723 (OUTLIER) cc_final: 0.9490 (mt) REVERT: D 160 LEU cc_start: 0.9650 (mt) cc_final: 0.9276 (tt) outliers start: 30 outliers final: 21 residues processed: 90 average time/residue: 0.0585 time to fit residues: 8.0424 Evaluate side-chains 82 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 58 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 168 ARG Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 239 GLU Chi-restraints excluded: chain B residue 4 PHE Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 212 ARG Chi-restraints excluded: chain C residue 175 ARG Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 335 ARG Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 124 ARG Chi-restraints excluded: chain D residue 143 GLN Chi-restraints excluded: chain D residue 206 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 76 optimal weight: 8.9990 chunk 9 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 50 optimal weight: 9.9990 chunk 87 optimal weight: 7.9990 chunk 32 optimal weight: 8.9990 chunk 22 optimal weight: 6.9990 chunk 11 optimal weight: 30.0000 chunk 72 optimal weight: 0.9980 chunk 95 optimal weight: 7.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 86 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.042410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.029791 restraints weight = 67924.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.030428 restraints weight = 48099.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.030884 restraints weight = 37849.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.031225 restraints weight = 31746.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.031482 restraints weight = 27988.235| |-----------------------------------------------------------------------------| r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 7891 Z= 0.209 Angle : 0.742 8.478 10670 Z= 0.377 Chirality : 0.041 0.241 1278 Planarity : 0.005 0.063 1309 Dihedral : 9.295 81.831 1102 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.71 % Favored : 93.19 % Rotamer: Outliers : 3.33 % Allowed : 22.71 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.29 (0.27), residues: 999 helix: 1.36 (0.22), residues: 578 sheet: -2.50 (0.46), residues: 96 loop : -2.36 (0.32), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG B 185 TYR 0.014 0.002 TYR D 11 PHE 0.038 0.002 PHE B 180 TRP 0.012 0.001 TRP A 318 HIS 0.010 0.001 HIS A 230 Details of bonding type rmsd covalent geometry : bond 0.00441 ( 7889) covalent geometry : angle 0.74161 (10670) hydrogen bonds : bond 0.04790 ( 429) hydrogen bonds : angle 5.50934 ( 1242) Misc. bond : bond 0.00221 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 56 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 GLU cc_start: 0.8919 (OUTLIER) cc_final: 0.8567 (pp20) REVERT: B 1 MET cc_start: 0.4883 (tpp) cc_final: 0.4675 (tpp) REVERT: B 109 MET cc_start: 0.8220 (mmm) cc_final: 0.7905 (mmm) REVERT: B 207 MET cc_start: 0.8794 (mtm) cc_final: 0.8423 (mtm) REVERT: C 282 ASN cc_start: 0.8592 (OUTLIER) cc_final: 0.7717 (m-40) REVERT: D 47 LEU cc_start: 0.9717 (OUTLIER) cc_final: 0.9488 (mt) REVERT: D 160 LEU cc_start: 0.9634 (mt) cc_final: 0.9229 (tp) outliers start: 28 outliers final: 22 residues processed: 80 average time/residue: 0.0564 time to fit residues: 6.8770 Evaluate side-chains 78 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 53 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 168 ARG Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 239 GLU Chi-restraints excluded: chain B residue 4 PHE Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 212 ARG Chi-restraints excluded: chain C residue 175 ARG Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 258 MET Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 335 ARG Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 124 ARG Chi-restraints excluded: chain D residue 143 GLN Chi-restraints excluded: chain D residue 206 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 34 optimal weight: 10.0000 chunk 45 optimal weight: 0.9990 chunk 8 optimal weight: 30.0000 chunk 3 optimal weight: 2.9990 chunk 58 optimal weight: 0.4980 chunk 54 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 56 optimal weight: 50.0000 chunk 86 optimal weight: 4.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.043440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.030838 restraints weight = 66363.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.031508 restraints weight = 47371.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.032011 restraints weight = 37273.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.032393 restraints weight = 31067.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.032624 restraints weight = 27144.181| |-----------------------------------------------------------------------------| r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7891 Z= 0.132 Angle : 0.716 10.994 10670 Z= 0.353 Chirality : 0.041 0.190 1278 Planarity : 0.004 0.061 1309 Dihedral : 8.872 84.338 1098 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.71 % Favored : 93.19 % Rotamer: Outliers : 3.33 % Allowed : 22.95 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.10 (0.28), residues: 999 helix: 1.53 (0.23), residues: 578 sheet: -2.44 (0.46), residues: 96 loop : -2.31 (0.32), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG D 219 TYR 0.014 0.001 TYR D 11 PHE 0.042 0.002 PHE B 180 TRP 0.013 0.001 TRP A 318 HIS 0.005 0.001 HIS D 154 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 7889) covalent geometry : angle 0.71565 (10670) hydrogen bonds : bond 0.04569 ( 429) hydrogen bonds : angle 5.21766 ( 1242) Misc. bond : bond 0.00261 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 59 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.4601 (tpp) cc_final: 0.4107 (tpp) REVERT: B 4 PHE cc_start: 0.9164 (OUTLIER) cc_final: 0.8715 (t80) REVERT: B 109 MET cc_start: 0.8231 (mmm) cc_final: 0.7935 (mmm) REVERT: B 207 MET cc_start: 0.8831 (mtm) cc_final: 0.8458 (mtm) REVERT: C 237 GLU cc_start: 0.9564 (mp0) cc_final: 0.9177 (pm20) REVERT: C 282 ASN cc_start: 0.8533 (OUTLIER) cc_final: 0.7557 (m110) REVERT: D 45 LEU cc_start: 0.9667 (pp) cc_final: 0.9419 (pt) REVERT: D 47 LEU cc_start: 0.9710 (OUTLIER) cc_final: 0.9479 (mt) REVERT: D 160 LEU cc_start: 0.9675 (mt) cc_final: 0.9270 (tt) outliers start: 28 outliers final: 18 residues processed: 83 average time/residue: 0.0501 time to fit residues: 6.5457 Evaluate side-chains 77 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 56 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 168 ARG Chi-restraints excluded: chain A residue 239 GLU Chi-restraints excluded: chain B residue 4 PHE Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 212 ARG Chi-restraints excluded: chain C residue 175 ARG Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 335 ARG Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 124 ARG Chi-restraints excluded: chain D residue 206 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 3 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 29 optimal weight: 40.0000 chunk 11 optimal weight: 9.9990 chunk 97 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 63 optimal weight: 0.0670 chunk 19 optimal weight: 1.9990 chunk 78 optimal weight: 9.9990 chunk 77 optimal weight: 9.9990 overall best weight: 3.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.042760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.030338 restraints weight = 69179.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.030987 restraints weight = 49399.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.031489 restraints weight = 38897.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.031859 restraints weight = 32307.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.032023 restraints weight = 28357.822| |-----------------------------------------------------------------------------| r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 7891 Z= 0.173 Angle : 0.744 10.651 10670 Z= 0.371 Chirality : 0.041 0.184 1278 Planarity : 0.004 0.060 1309 Dihedral : 8.829 83.662 1098 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.81 % Favored : 93.09 % Rotamer: Outliers : 2.97 % Allowed : 23.54 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.20 (0.27), residues: 999 helix: 1.47 (0.22), residues: 578 sheet: -2.58 (0.44), residues: 96 loop : -2.35 (0.32), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG B 171 TYR 0.013 0.001 TYR D 11 PHE 0.041 0.002 PHE B 180 TRP 0.011 0.001 TRP A 318 HIS 0.007 0.001 HIS A 230 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 7889) covalent geometry : angle 0.74357 (10670) hydrogen bonds : bond 0.04665 ( 429) hydrogen bonds : angle 5.40702 ( 1242) Misc. bond : bond 0.00227 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 57 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 4 PHE cc_start: 0.9087 (OUTLIER) cc_final: 0.8671 (t80) REVERT: B 109 MET cc_start: 0.8146 (mmm) cc_final: 0.7844 (mmm) REVERT: B 207 MET cc_start: 0.8792 (mtm) cc_final: 0.8362 (mtm) REVERT: C 282 ASN cc_start: 0.8516 (OUTLIER) cc_final: 0.7613 (m-40) REVERT: D 45 LEU cc_start: 0.9690 (pp) cc_final: 0.9413 (pt) REVERT: D 47 LEU cc_start: 0.9706 (OUTLIER) cc_final: 0.9448 (mt) REVERT: D 160 LEU cc_start: 0.9657 (mt) cc_final: 0.9243 (tp) outliers start: 25 outliers final: 19 residues processed: 80 average time/residue: 0.0564 time to fit residues: 7.0190 Evaluate side-chains 77 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 55 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain A residue 113 ARG Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 168 ARG Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 239 GLU Chi-restraints excluded: chain B residue 4 PHE Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 212 ARG Chi-restraints excluded: chain C residue 175 ARG Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 335 ARG Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 99 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 59 optimal weight: 9.9990 chunk 44 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.043517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.030995 restraints weight = 66151.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.031657 restraints weight = 47194.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.032166 restraints weight = 37045.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.032533 restraints weight = 30859.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.032711 restraints weight = 27028.790| |-----------------------------------------------------------------------------| r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7891 Z= 0.134 Angle : 0.759 11.726 10670 Z= 0.369 Chirality : 0.041 0.188 1278 Planarity : 0.004 0.057 1309 Dihedral : 8.555 85.638 1094 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.81 % Favored : 93.09 % Rotamer: Outliers : 2.62 % Allowed : 24.61 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.13 (0.28), residues: 999 helix: 1.53 (0.23), residues: 578 sheet: -2.56 (0.44), residues: 96 loop : -2.33 (0.32), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG B 206 TYR 0.013 0.001 TYR D 11 PHE 0.041 0.002 PHE B 180 TRP 0.012 0.001 TRP A 318 HIS 0.005 0.001 HIS A 230 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 7889) covalent geometry : angle 0.75879 (10670) hydrogen bonds : bond 0.04563 ( 429) hydrogen bonds : angle 5.23836 ( 1242) Misc. bond : bond 0.00251 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 63 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 4 PHE cc_start: 0.9141 (OUTLIER) cc_final: 0.8724 (t80) REVERT: B 109 MET cc_start: 0.8203 (mmm) cc_final: 0.7905 (mmm) REVERT: B 207 MET cc_start: 0.8826 (mtm) cc_final: 0.8348 (mtm) REVERT: C 237 GLU cc_start: 0.9597 (mp0) cc_final: 0.9253 (pm20) REVERT: C 282 ASN cc_start: 0.8474 (OUTLIER) cc_final: 0.7462 (m110) REVERT: D 45 LEU cc_start: 0.9667 (pp) cc_final: 0.9442 (pt) REVERT: D 47 LEU cc_start: 0.9695 (OUTLIER) cc_final: 0.9431 (mt) REVERT: D 109 MET cc_start: 0.8713 (mmm) cc_final: 0.8391 (mmm) REVERT: D 160 LEU cc_start: 0.9664 (mt) cc_final: 0.9301 (tt) outliers start: 22 outliers final: 17 residues processed: 83 average time/residue: 0.0526 time to fit residues: 6.7612 Evaluate side-chains 79 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 59 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 168 ARG Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 239 GLU Chi-restraints excluded: chain B residue 4 PHE Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 212 ARG Chi-restraints excluded: chain C residue 175 ARG Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 335 ARG Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 47 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 44 optimal weight: 7.9990 chunk 78 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 13 optimal weight: 6.9990 chunk 77 optimal weight: 8.9990 chunk 91 optimal weight: 0.9990 chunk 57 optimal weight: 30.0000 chunk 16 optimal weight: 0.6980 chunk 12 optimal weight: 7.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.043855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.031635 restraints weight = 66509.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.032346 restraints weight = 47047.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.032831 restraints weight = 36501.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.033216 restraints weight = 30265.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.033399 restraints weight = 26460.820| |-----------------------------------------------------------------------------| r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7891 Z= 0.130 Angle : 0.758 11.418 10670 Z= 0.368 Chirality : 0.041 0.187 1278 Planarity : 0.004 0.057 1309 Dihedral : 8.464 85.822 1094 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.61 % Favored : 93.29 % Rotamer: Outliers : 2.50 % Allowed : 25.33 % Favored : 72.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.18 (0.27), residues: 999 helix: 1.49 (0.23), residues: 579 sheet: -2.52 (0.46), residues: 89 loop : -2.40 (0.31), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG D 204 TYR 0.013 0.001 TYR D 11 PHE 0.044 0.002 PHE B 180 TRP 0.012 0.001 TRP C 271 HIS 0.005 0.001 HIS A 230 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 7889) covalent geometry : angle 0.75770 (10670) hydrogen bonds : bond 0.04418 ( 429) hydrogen bonds : angle 5.21603 ( 1242) Misc. bond : bond 0.00244 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 63 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 LEU cc_start: 0.9685 (mp) cc_final: 0.9455 (tp) REVERT: B 1 MET cc_start: 0.4296 (tpp) cc_final: 0.3983 (mmt) REVERT: B 4 PHE cc_start: 0.9125 (OUTLIER) cc_final: 0.8730 (t80) REVERT: B 109 MET cc_start: 0.8227 (mmm) cc_final: 0.7934 (mmm) REVERT: B 207 MET cc_start: 0.8795 (mtm) cc_final: 0.8359 (mtm) REVERT: C 237 GLU cc_start: 0.9604 (mp0) cc_final: 0.9264 (pm20) REVERT: C 282 ASN cc_start: 0.8460 (OUTLIER) cc_final: 0.7460 (m110) REVERT: D 45 LEU cc_start: 0.9666 (pp) cc_final: 0.9403 (pt) REVERT: D 47 LEU cc_start: 0.9706 (OUTLIER) cc_final: 0.9438 (mt) REVERT: D 109 MET cc_start: 0.8745 (mmm) cc_final: 0.8423 (mmm) REVERT: D 160 LEU cc_start: 0.9671 (mt) cc_final: 0.9289 (tt) outliers start: 21 outliers final: 17 residues processed: 82 average time/residue: 0.0580 time to fit residues: 7.4074 Evaluate side-chains 83 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 63 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 55 HIS Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 168 ARG Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 239 GLU Chi-restraints excluded: chain B residue 4 PHE Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 212 ARG Chi-restraints excluded: chain C residue 175 ARG Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 217 LEU Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 335 ARG Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 206 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 28 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 chunk 15 optimal weight: 10.0000 chunk 32 optimal weight: 0.0970 chunk 9 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 69 optimal weight: 0.0270 chunk 53 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 overall best weight: 2.0242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.043441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.030937 restraints weight = 65889.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.031596 restraints weight = 47662.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.032093 restraints weight = 37633.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.032460 restraints weight = 31604.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.032713 restraints weight = 27532.732| |-----------------------------------------------------------------------------| r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 7891 Z= 0.140 Angle : 0.758 11.051 10670 Z= 0.370 Chirality : 0.041 0.187 1278 Planarity : 0.004 0.056 1309 Dihedral : 8.443 85.216 1094 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.41 % Favored : 93.49 % Rotamer: Outliers : 2.50 % Allowed : 25.33 % Favored : 72.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.19 (0.27), residues: 999 helix: 1.48 (0.23), residues: 581 sheet: -2.56 (0.45), residues: 89 loop : -2.43 (0.31), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG B 185 TYR 0.013 0.001 TYR D 11 PHE 0.044 0.002 PHE B 180 TRP 0.011 0.001 TRP A 318 HIS 0.005 0.001 HIS A 230 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 7889) covalent geometry : angle 0.75821 (10670) hydrogen bonds : bond 0.04393 ( 429) hydrogen bonds : angle 5.21850 ( 1242) Misc. bond : bond 0.00229 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1126.96 seconds wall clock time: 20 minutes 12.07 seconds (1212.07 seconds total)