Starting phenix.real_space_refine on Sat Dec 28 06:13:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i6r_35204/12_2024/8i6r_35204.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i6r_35204/12_2024/8i6r_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8i6r_35204/12_2024/8i6r_35204.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i6r_35204/12_2024/8i6r_35204.map" model { file = "/net/cci-nas-00/data/ceres_data/8i6r_35204/12_2024/8i6r_35204.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i6r_35204/12_2024/8i6r_35204.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 5.15, per 1000 atoms: 0.66 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: 2.13 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.81 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: 2.09 Time building geometry restraints manager: 2.40 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 222 or resid 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.120 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 20.830 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.520 ------------------------------------------------------------------------------- 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 : 0.006 0.108 7889 Z= 0.400 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (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 TRP 0.034 0.003 TRP C 322 HIS 0.006 0.001 HIS D 88 PHE 0.017 0.002 PHE B 180 TYR 0.013 0.002 TYR D 11 ARG 0.000 0.000 ARG B 171 *********************** 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 : 0.916 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: 0.1571 time to fit residues: 20.1278 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 : 0.920 ------------------------------------------------------------------------------- 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 83 optimal weight: 0.0070 chunk 75 optimal weight: 0.3980 chunk 41 optimal weight: 8.9990 chunk 25 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 chunk 40 optimal weight: 0.3980 chunk 77 optimal weight: 10.0000 chunk 30 optimal weight: 0.0470 chunk 47 optimal weight: 6.9990 chunk 57 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 overall best weight: 0.3096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 167 ASN C 82 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7889 Z= 0.198 Angle : 0.745 8.860 10670 Z= 0.376 Chirality : 0.043 0.204 1278 Planarity : 0.005 0.075 1309 Dihedral : 11.262 82.264 1142 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.81 % Favored : 94.09 % Rotamer: Outliers : 1.55 % Allowed : 12.01 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.27), residues: 999 helix: 1.41 (0.22), residues: 581 sheet: -1.88 (0.53), residues: 78 loop : -2.34 (0.31), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 322 HIS 0.008 0.001 HIS B 205 PHE 0.021 0.002 PHE D 180 TYR 0.012 0.002 TYR D 11 ARG 0.000 0.000 ARG D 185 *********************** 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 86 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.896 Fit side-chains revert: symmetry clash REVERT: B 1 MET cc_start: 0.3832 (tpp) cc_final: 0.3436 (tpp) REVERT: B 87 ASN cc_start: 0.9560 (t0) cc_final: 0.8512 (t0) REVERT: B 109 MET cc_start: 0.8183 (mmm) cc_final: 0.7885 (mmm) REVERT: B 207 MET cc_start: 0.8869 (mtm) cc_final: 0.8524 (mtm) REVERT: C 62 THR cc_start: 0.8804 (p) cc_final: 0.8436 (t) REVERT: D 87 ASN cc_start: 0.9555 (t0) cc_final: 0.9300 (t0) REVERT: D 167 ASN cc_start: 0.8090 (m-40) cc_final: 0.7607 (m-40) REVERT: D 207 MET cc_start: 0.7557 (mpp) cc_final: 0.7185 (mpp) outliers start: 13 outliers final: 10 residues processed: 85 average time/residue: 0.1571 time to fit residues: 19.9368 Evaluate side-chains 66 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.965 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 9.9990 chunk 27 optimal weight: 0.9990 chunk 74 optimal weight: 7.9990 chunk 61 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 90 optimal weight: 9.9990 chunk 97 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 chunk 89 optimal weight: 8.9990 chunk 30 optimal weight: 7.9990 chunk 72 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN ** C 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 7889 Z= 0.303 Angle : 0.728 7.615 10670 Z= 0.375 Chirality : 0.041 0.180 1278 Planarity : 0.005 0.070 1309 Dihedral : 10.388 81.544 1118 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.41 % Favored : 93.49 % Rotamer: Outliers : 2.97 % Allowed : 18.31 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.27), residues: 999 helix: 1.37 (0.22), residues: 577 sheet: -2.28 (0.48), residues: 96 loop : -2.47 (0.32), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 318 HIS 0.006 0.001 HIS D 88 PHE 0.017 0.002 PHE C 60 TYR 0.013 0.002 TYR D 11 ARG 0.000 0.000 ARG B 171 *********************** 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 83 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 58 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 109 MET cc_start: 0.8249 (mmm) cc_final: 0.7968 (mmm) REVERT: B 207 MET cc_start: 0.8940 (mtm) cc_final: 0.8608 (mtm) REVERT: C 258 MET cc_start: 0.8774 (OUTLIER) cc_final: 0.8427 (ppp) REVERT: D 45 LEU cc_start: 0.9693 (pp) cc_final: 0.9491 (pt) REVERT: D 160 LEU cc_start: 0.9740 (mt) cc_final: 0.9291 (tt) REVERT: D 207 MET cc_start: 0.7764 (mpp) cc_final: 0.7523 (mpp) outliers start: 25 outliers final: 19 residues processed: 80 average time/residue: 0.1636 time to fit residues: 20.1430 Evaluate side-chains 75 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 55 time to evaluate : 0.993 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain D residue 206 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 2.9990 chunk 67 optimal weight: 10.0000 chunk 46 optimal weight: 6.9990 chunk 9 optimal weight: 30.0000 chunk 42 optimal weight: 2.9990 chunk 60 optimal weight: 50.0000 chunk 90 optimal weight: 8.9990 chunk 95 optimal weight: 8.9990 chunk 47 optimal weight: 6.9990 chunk 85 optimal weight: 8.9990 chunk 25 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 ASN ** C 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 144 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.102 7889 Z= 0.391 Angle : 0.802 8.879 10670 Z= 0.408 Chirality : 0.043 0.182 1278 Planarity : 0.005 0.068 1309 Dihedral : 10.080 79.297 1114 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 19.10 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.31 % Favored : 92.59 % Rotamer: Outliers : 3.80 % Allowed : 20.33 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.26), residues: 999 helix: 1.10 (0.21), residues: 577 sheet: -2.29 (0.52), residues: 78 loop : -2.52 (0.30), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 318 HIS 0.009 0.002 HIS D 88 PHE 0.040 0.002 PHE D 180 TYR 0.016 0.002 TYR D 11 ARG 0.000 0.000 ARG A 335 *********************** 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 87 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 55 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 GLU cc_start: 0.9091 (OUTLIER) cc_final: 0.8864 (pp20) REVERT: B 109 MET cc_start: 0.8170 (mmm) cc_final: 0.7908 (mmm) REVERT: B 207 MET cc_start: 0.8941 (mtm) cc_final: 0.8594 (mtm) REVERT: C 258 MET cc_start: 0.8770 (OUTLIER) cc_final: 0.8490 (ppp) REVERT: C 282 ASN cc_start: 0.8686 (OUTLIER) cc_final: 0.7805 (m-40) REVERT: D 160 LEU cc_start: 0.9715 (mt) cc_final: 0.9259 (tp) outliers start: 32 outliers final: 23 residues processed: 83 average time/residue: 0.1565 time to fit residues: 19.7152 Evaluate side-chains 80 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 54 time to evaluate : 1.003 ------------------------------------------------------------------------------- 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 118 ARG 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 195 GLU Chi-restraints excluded: chain A residue 239 GLU Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 212 ARG Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain C residue 62 THR 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 273 LEU Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 335 ARG Chi-restraints excluded: chain D residue 51 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 79 optimal weight: 20.0000 chunk 54 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 39 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 chunk 24 optimal weight: 7.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 ASN C 82 ASN D 144 GLN ** D 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 7889 Z= 0.212 Angle : 0.708 9.567 10670 Z= 0.355 Chirality : 0.041 0.183 1278 Planarity : 0.004 0.066 1309 Dihedral : 9.479 83.526 1110 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.41 % Favored : 93.49 % Rotamer: Outliers : 4.16 % Allowed : 22.00 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.27), residues: 999 helix: 1.40 (0.22), residues: 580 sheet: -2.48 (0.47), residues: 94 loop : -2.49 (0.32), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 318 HIS 0.010 0.001 HIS A 230 PHE 0.046 0.002 PHE D 180 TYR 0.015 0.002 TYR D 11 ARG 0.000 0.000 ARG D 219 *********************** 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 95 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 60 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 109 MET cc_start: 0.8203 (mmm) cc_final: 0.7951 (mmm) REVERT: B 207 MET cc_start: 0.8933 (mtm) cc_final: 0.8538 (mtm) REVERT: C 282 ASN cc_start: 0.8728 (OUTLIER) cc_final: 0.7781 (m110) REVERT: D 45 LEU cc_start: 0.9686 (pp) cc_final: 0.9481 (pt) REVERT: D 47 LEU cc_start: 0.9719 (OUTLIER) cc_final: 0.9505 (mt) REVERT: D 160 LEU cc_start: 0.9716 (mt) cc_final: 0.9321 (tt) REVERT: D 207 MET cc_start: 0.7345 (mpp) cc_final: 0.6796 (mpp) outliers start: 35 outliers final: 20 residues processed: 92 average time/residue: 0.1474 time to fit residues: 20.4689 Evaluate side-chains 79 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 57 time to evaluate : 1.151 ------------------------------------------------------------------------------- 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 239 GLU 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 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 32 optimal weight: 1.9990 chunk 86 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 56 optimal weight: 50.0000 chunk 23 optimal weight: 5.9990 chunk 95 optimal weight: 8.9990 chunk 79 optimal weight: 1.9990 chunk 44 optimal weight: 0.0030 chunk 7 optimal weight: 1.9990 chunk 31 optimal weight: 9.9990 chunk 50 optimal weight: 9.9990 overall best weight: 2.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN B 26 HIS C 82 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 7889 Z= 0.219 Angle : 0.739 12.150 10670 Z= 0.367 Chirality : 0.043 0.406 1278 Planarity : 0.004 0.063 1309 Dihedral : 9.093 83.828 1102 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.81 % Favored : 93.09 % Rotamer: Outliers : 3.45 % Allowed : 23.66 % Favored : 72.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.27), residues: 999 helix: 1.34 (0.22), residues: 581 sheet: -2.54 (0.45), residues: 94 loop : -2.47 (0.32), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 318 HIS 0.007 0.001 HIS A 230 PHE 0.017 0.002 PHE C 60 TYR 0.014 0.002 TYR D 11 ARG 0.000 0.000 ARG B 202 *********************** 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 88 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 59 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 109 MET cc_start: 0.8219 (mmm) cc_final: 0.7969 (mmm) REVERT: B 207 MET cc_start: 0.8940 (mtm) cc_final: 0.8552 (mtm) REVERT: C 282 ASN cc_start: 0.8724 (OUTLIER) cc_final: 0.7770 (m110) REVERT: D 47 LEU cc_start: 0.9711 (OUTLIER) cc_final: 0.9507 (mt) REVERT: D 207 MET cc_start: 0.7396 (mpp) cc_final: 0.6539 (mpp) outliers start: 29 outliers final: 23 residues processed: 85 average time/residue: 0.1441 time to fit residues: 18.7370 Evaluate side-chains 83 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 58 time to evaluate : 1.120 ------------------------------------------------------------------------------- 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 96 ILE 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 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 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 99 ASN Chi-restraints excluded: chain D residue 124 ARG Chi-restraints excluded: chain D residue 143 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 3.9990 chunk 10 optimal weight: 20.0000 chunk 54 optimal weight: 8.9990 chunk 69 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 59 optimal weight: 40.0000 chunk 58 optimal weight: 9.9990 chunk 44 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 7889 Z= 0.209 Angle : 0.724 11.068 10670 Z= 0.360 Chirality : 0.042 0.291 1278 Planarity : 0.004 0.064 1309 Dihedral : 8.931 85.716 1102 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.61 % Favored : 93.29 % Rotamer: Outliers : 4.40 % Allowed : 23.31 % Favored : 72.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.27), residues: 999 helix: 1.43 (0.22), residues: 581 sheet: -2.59 (0.44), residues: 94 loop : -2.44 (0.32), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 318 HIS 0.004 0.001 HIS D 154 PHE 0.016 0.001 PHE C 60 TYR 0.014 0.001 TYR D 11 ARG 0.000 0.000 ARG B 202 *********************** 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 97 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 60 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.4120 (tpp) cc_final: 0.3717 (tpp) REVERT: B 109 MET cc_start: 0.8238 (mmm) cc_final: 0.7986 (mmm) REVERT: B 207 MET cc_start: 0.8943 (mtm) cc_final: 0.8555 (mtm) REVERT: C 282 ASN cc_start: 0.8687 (OUTLIER) cc_final: 0.7729 (m110) REVERT: D 47 LEU cc_start: 0.9696 (OUTLIER) cc_final: 0.9491 (mt) REVERT: D 207 MET cc_start: 0.7374 (mpp) cc_final: 0.6653 (mpp) outliers start: 37 outliers final: 25 residues processed: 94 average time/residue: 0.1422 time to fit residues: 20.3242 Evaluate side-chains 87 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 60 time to evaluate : 0.809 ------------------------------------------------------------------------------- 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 96 ILE 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 A residue 285 VAL 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 55 HIS 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 31 LEU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 143 GLN 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 56 optimal weight: 50.0000 chunk 28 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 60 optimal weight: 8.9990 chunk 65 optimal weight: 3.9990 chunk 47 optimal weight: 7.9990 chunk 8 optimal weight: 20.0000 chunk 75 optimal weight: 6.9990 chunk 86 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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** D 144 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 7889 Z= 0.295 Angle : 0.770 11.209 10670 Z= 0.384 Chirality : 0.043 0.237 1278 Planarity : 0.005 0.063 1309 Dihedral : 8.796 83.271 1094 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.51 % Favored : 92.39 % Rotamer: Outliers : 3.80 % Allowed : 24.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.27), residues: 999 helix: 1.31 (0.22), residues: 580 sheet: -2.74 (0.43), residues: 94 loop : -2.44 (0.32), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 318 HIS 0.006 0.001 HIS D 88 PHE 0.037 0.002 PHE D 180 TYR 0.014 0.002 TYR D 11 ARG 0.000 0.000 ARG A 234 *********************** 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 90 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 58 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 109 MET cc_start: 0.8181 (mmm) cc_final: 0.7932 (mmm) REVERT: C 282 ASN cc_start: 0.8554 (OUTLIER) cc_final: 0.8226 (m-40) REVERT: D 47 LEU cc_start: 0.9706 (OUTLIER) cc_final: 0.9506 (mt) REVERT: D 207 MET cc_start: 0.7411 (mpp) cc_final: 0.6751 (mpp) outliers start: 32 outliers final: 27 residues processed: 87 average time/residue: 0.1514 time to fit residues: 20.0123 Evaluate side-chains 86 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 57 time to evaluate : 1.031 ------------------------------------------------------------------------------- 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 96 ILE Chi-restraints excluded: chain A residue 113 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 239 GLU Chi-restraints excluded: chain A residue 285 VAL 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 55 HIS Chi-restraints excluded: chain C residue 118 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 99 ASN Chi-restraints excluded: chain D residue 143 GLN Chi-restraints excluded: chain D residue 206 ARG Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 219 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 6.9990 chunk 91 optimal weight: 0.4980 chunk 53 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 84 optimal weight: 0.0670 chunk 58 optimal weight: 6.9990 chunk 94 optimal weight: 4.9990 chunk 57 optimal weight: 50.0000 overall best weight: 2.5124 ------------------------------------------------------------------------------- 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** A 225 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 7889 Z= 0.219 Angle : 0.747 11.566 10670 Z= 0.367 Chirality : 0.042 0.225 1278 Planarity : 0.004 0.061 1309 Dihedral : 8.638 85.231 1094 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.41 % Favored : 93.49 % Rotamer: Outliers : 3.57 % Allowed : 24.26 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.27), residues: 999 helix: 1.47 (0.22), residues: 577 sheet: -2.69 (0.44), residues: 94 loop : -2.32 (0.32), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 318 HIS 0.004 0.001 HIS B 154 PHE 0.041 0.002 PHE D 180 TYR 0.014 0.001 TYR D 11 ARG 0.000 0.000 ARG D 185 *********************** 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 91 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 61 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.4327 (tpp) cc_final: 0.3910 (tpp) REVERT: B 109 MET cc_start: 0.8203 (mmm) cc_final: 0.7946 (mmm) REVERT: B 207 MET cc_start: 0.8939 (mtm) cc_final: 0.8441 (mtm) REVERT: C 49 LEU cc_start: 0.9677 (OUTLIER) cc_final: 0.9459 (mt) REVERT: C 282 ASN cc_start: 0.8612 (OUTLIER) cc_final: 0.7663 (m110) REVERT: D 123 GLU cc_start: 0.9472 (OUTLIER) cc_final: 0.9238 (pm20) REVERT: D 207 MET cc_start: 0.7386 (mpp) cc_final: 0.6757 (mpp) outliers start: 30 outliers final: 24 residues processed: 89 average time/residue: 0.1546 time to fit residues: 20.6097 Evaluate side-chains 84 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 57 time to evaluate : 0.944 ------------------------------------------------------------------------------- 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 96 ILE 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 239 GLU Chi-restraints excluded: chain A residue 285 VAL 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 49 LEU Chi-restraints excluded: chain C residue 55 HIS 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 99 ASN Chi-restraints excluded: chain D residue 123 GLU Chi-restraints excluded: chain D residue 143 GLN Chi-restraints excluded: chain D residue 206 ARG Chi-restraints excluded: chain D residue 215 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 44 optimal weight: 0.0670 chunk 65 optimal weight: 1.9990 chunk 98 optimal weight: 9.9990 chunk 90 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 8 optimal weight: 8.9990 chunk 60 optimal weight: 50.0000 chunk 48 optimal weight: 5.9990 chunk 62 optimal weight: 40.0000 chunk 83 optimal weight: 7.9990 chunk 24 optimal weight: 6.9990 overall best weight: 2.6124 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 7889 Z= 0.228 Angle : 0.759 11.395 10670 Z= 0.371 Chirality : 0.042 0.230 1278 Planarity : 0.004 0.059 1309 Dihedral : 8.637 88.352 1094 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.91 % Favored : 92.99 % Rotamer: Outliers : 3.45 % Allowed : 24.26 % Favored : 72.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.27), residues: 999 helix: 1.48 (0.22), residues: 577 sheet: -2.68 (0.44), residues: 94 loop : -2.30 (0.32), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 318 HIS 0.004 0.001 HIS D 88 PHE 0.041 0.002 PHE D 180 TYR 0.014 0.001 TYR D 11 ARG 0.000 0.000 ARG D 171 ********************** 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 88 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 59 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 109 MET cc_start: 0.8230 (mmm) cc_final: 0.7972 (mmm) REVERT: B 207 MET cc_start: 0.8940 (mtm) cc_final: 0.8442 (mtm) REVERT: C 49 LEU cc_start: 0.9676 (OUTLIER) cc_final: 0.9458 (mm) REVERT: C 282 ASN cc_start: 0.8522 (OUTLIER) cc_final: 0.7505 (m110) REVERT: D 109 MET cc_start: 0.8838 (mmm) cc_final: 0.8526 (mmm) REVERT: D 123 GLU cc_start: 0.9466 (OUTLIER) cc_final: 0.9228 (pm20) REVERT: D 207 MET cc_start: 0.7366 (mpp) cc_final: 0.6744 (mpp) outliers start: 29 outliers final: 25 residues processed: 86 average time/residue: 0.1516 time to fit residues: 19.8108 Evaluate side-chains 86 residues out of total 842 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 58 time to evaluate : 0.928 ------------------------------------------------------------------------------- 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 96 ILE 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 217 LEU Chi-restraints excluded: chain A residue 239 GLU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 212 ARG Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 55 HIS 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 123 GLU Chi-restraints excluded: chain D residue 143 GLN Chi-restraints excluded: chain D residue 206 ARG Chi-restraints excluded: chain D residue 219 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 72 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 chunk 78 optimal weight: 0.8980 chunk 32 optimal weight: 7.9990 chunk 80 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 14 optimal weight: 7.9990 chunk 69 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 56 optimal weight: 40.0000 overall best weight: 3.3788 ------------------------------------------------------------------------------- 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 = 0.3127 r_free = 0.3127 target = 0.042092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.029982 restraints weight = 67906.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.030653 restraints weight = 48044.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.031147 restraints weight = 37499.529| |-----------------------------------------------------------------------------| r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 7889 Z= 0.262 Angle : 0.778 11.140 10670 Z= 0.382 Chirality : 0.044 0.278 1278 Planarity : 0.004 0.059 1309 Dihedral : 8.736 87.040 1094 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.31 % Favored : 92.59 % Rotamer: Outliers : 3.33 % Allowed : 24.61 % Favored : 72.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.27), residues: 999 helix: 1.42 (0.22), residues: 577 sheet: -2.70 (0.44), residues: 94 loop : -2.31 (0.32), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 318 HIS 0.005 0.001 HIS D 88 PHE 0.041 0.002 PHE D 180 TYR 0.014 0.001 TYR D 11 ARG 0.000 0.000 ARG B 202 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1505.85 seconds wall clock time: 28 minutes 31.81 seconds (1711.81 seconds total)