Starting phenix.real_space_refine on Sun Dec 29 14:21:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f23_31426/12_2024/7f23_31426.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f23_31426/12_2024/7f23_31426.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7f23_31426/12_2024/7f23_31426.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f23_31426/12_2024/7f23_31426.map" model { file = "/net/cci-nas-00/data/ceres_data/7f23_31426/12_2024/7f23_31426.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f23_31426/12_2024/7f23_31426.cif" } resolution = 3.58 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= 0.003 sd= 0.090 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3063 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 53 5.16 5 C 5196 2.51 5 N 1440 2.21 5 O 1519 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 8211 Number of models: 1 Model: "" Number of chains: 7 Chain: "F" Number of atoms: 2197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2197 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 9, 'TRANS': 266} Chain breaks: 3 Chain: "A" Number of atoms: 1937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1937 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 228} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 2629 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 341, 2605 Classifications: {'peptide': 341} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 335} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 341, 2605 Classifications: {'peptide': 341} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 335} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 2624 Chain: "E" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 971 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 434 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "F" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'LDP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AASP B 27 " occ=0.45 ... (14 atoms not shown) pdb=" OD2BASP B 27 " occ=0.55 Time building chain proxies: 6.28, per 1000 atoms: 0.76 Number of scatterers: 8211 At special positions: 0 Unit cell: (84.786, 95.656, 126.092, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 53 16.00 P 3 15.00 O 1519 8.00 N 1440 7.00 C 5196 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS F 96 " - pdb=" SG CYS F 186 " distance=2.02 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 99 " - pdb=" SG CYS E 107 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.41 Conformation dependent library (CDL) restraints added in 1.2 seconds 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1964 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 10 sheets defined 43.8% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'F' and resid 20 through 51 Processing helix chain 'F' and resid 58 through 88 Proline residue: F 79 - end of helix Processing helix chain 'F' and resid 94 through 127 removed outlier: 4.325A pdb=" N ILE F 98 " --> pdb=" O SER F 94 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR F 108 " --> pdb=" O ILE F 104 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ILE F 111 " --> pdb=" O SER F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 135 Processing helix chain 'F' and resid 136 through 161 Proline residue: F 158 - end of helix Processing helix chain 'F' and resid 191 through 203 Processing helix chain 'F' and resid 203 through 237 removed outlier: 3.601A pdb=" N ALA F 208 " --> pdb=" O TYR F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 265 through 298 Proline residue: F 287 - end of helix Proline residue: F 296 - end of helix Processing helix chain 'F' and resid 309 through 332 removed outlier: 3.777A pdb=" N GLY F 320 " --> pdb=" O PHE F 316 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TRP F 321 " --> pdb=" O VAL F 317 " (cutoff:3.500A) Proline residue: F 328 - end of helix Processing helix chain 'F' and resid 334 through 346 Processing helix chain 'A' and resid 13 through 39 Processing helix chain 'A' and resid 52 through 64 Processing helix chain 'A' and resid 233 through 238 Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 307 through 312 removed outlier: 3.773A pdb=" N PHE A 312 " --> pdb=" O GLU A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 318 removed outlier: 4.264A pdb=" N ARG A 317 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 353 removed outlier: 4.051A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N GLY A 353 " --> pdb=" O SER A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 391 Processing helix chain 'B' and resid 2 through 25 removed outlier: 3.984A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.507A pdb=" N TYR E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 24 removed outlier: 3.772A pdb=" N ASN D 24 " --> pdb=" O LYS D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 44 Processing helix chain 'D' and resid 45 through 48 Processing helix chain 'D' and resid 55 through 59 removed outlier: 3.571A pdb=" N ASN D 59 " --> pdb=" O ALA D 56 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 214 removed outlier: 9.365A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.487A pdb=" N ASP A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.690A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.904A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN B 88 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.866A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.645A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.783A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.361A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.127A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 58 through 60 removed outlier: 4.817A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) 435 hydrogen bonds defined for protein. 1251 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.66 Time building geometry restraints manager: 2.59 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: 2681 1.34 - 1.46: 2060 1.46 - 1.58: 3567 1.58 - 1.71: 5 1.71 - 1.83: 72 Bond restraints: 8385 Sorted by residual: bond pdb=" N CYS F 96 " pdb=" CA CYS F 96 " ideal model delta sigma weight residual 1.458 1.427 0.030 1.33e-02 5.65e+03 5.13e+00 bond pdb=" CA SER F 110 " pdb=" C SER F 110 " ideal model delta sigma weight residual 1.525 1.498 0.027 1.25e-02 6.40e+03 4.68e+00 bond pdb=" CB TRP B 99 " pdb=" CG TRP B 99 " ideal model delta sigma weight residual 1.498 1.434 0.064 3.10e-02 1.04e+03 4.22e+00 bond pdb=" CG LEU F 66 " pdb=" CD1 LEU F 66 " ideal model delta sigma weight residual 1.521 1.454 0.067 3.30e-02 9.18e+02 4.15e+00 bond pdb=" C3 LDP F 501 " pdb=" C4 LDP F 501 " ideal model delta sigma weight residual 1.400 1.361 0.039 2.00e-02 2.50e+03 3.87e+00 ... (remaining 8380 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 11016 2.51 - 5.01: 312 5.01 - 7.52: 33 7.52 - 10.02: 9 10.02 - 12.53: 1 Bond angle restraints: 11371 Sorted by residual: angle pdb=" CA CYS E 99 " pdb=" CB CYS E 99 " pdb=" SG CYS E 99 " ideal model delta sigma weight residual 114.40 126.93 -12.53 2.30e+00 1.89e-01 2.97e+01 angle pdb=" C LYS A 233 " pdb=" N TRP A 234 " pdb=" CA TRP A 234 " ideal model delta sigma weight residual 121.58 113.52 8.06 1.95e+00 2.63e-01 1.71e+01 angle pdb=" C THR F 108 " pdb=" N ALA F 109 " pdb=" CA ALA F 109 " ideal model delta sigma weight residual 120.72 114.50 6.22 1.67e+00 3.59e-01 1.39e+01 angle pdb=" C SER B 334 " pdb=" CA SER B 334 " pdb=" CB SER B 334 " ideal model delta sigma weight residual 111.63 106.58 5.05 1.36e+00 5.41e-01 1.38e+01 angle pdb=" C GLY B 131 " pdb=" N ASN B 132 " pdb=" CA ASN B 132 " ideal model delta sigma weight residual 122.81 128.33 -5.52 1.57e+00 4.06e-01 1.24e+01 ... (remaining 11366 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.60: 4895 34.60 - 69.20: 87 69.20 - 103.80: 4 103.80 - 138.40: 1 138.40 - 173.00: 2 Dihedral angle restraints: 4989 sinusoidal: 1958 harmonic: 3031 Sorted by residual: dihedral pdb=" CB CYS E 99 " pdb=" SG CYS E 99 " pdb=" SG CYS E 107 " pdb=" CB CYS E 107 " ideal model delta sinusoidal sigma weight residual -86.00 -18.21 -67.79 1 1.00e+01 1.00e-02 5.97e+01 dihedral pdb=" C5' GTP A 401 " pdb=" O5' GTP A 401 " pdb=" PA GTP A 401 " pdb=" O3A GTP A 401 " ideal model delta sinusoidal sigma weight residual 69.27 -117.73 -173.00 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" C8 GTP A 401 " pdb=" C1' GTP A 401 " pdb=" N9 GTP A 401 " pdb=" O4' GTP A 401 " ideal model delta sinusoidal sigma weight residual 104.59 -36.16 140.75 1 2.00e+01 2.50e-03 4.26e+01 ... (remaining 4986 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 956 0.062 - 0.125: 272 0.125 - 0.187: 48 0.187 - 0.250: 1 0.250 - 0.312: 1 Chirality restraints: 1278 Sorted by residual: chirality pdb=" CA CYS E 99 " pdb=" N CYS E 99 " pdb=" C CYS E 99 " pdb=" CB CYS E 99 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" CA PRO F 206 " pdb=" N PRO F 206 " pdb=" C PRO F 206 " pdb=" CB PRO F 206 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 9.53e-01 chirality pdb=" CA PHE A 222 " pdb=" N PHE A 222 " pdb=" C PHE A 222 " pdb=" CB PHE A 222 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.19 2.00e-01 2.50e+01 8.58e-01 ... (remaining 1275 not shown) Planarity restraints: 1444 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA F 109 " -0.043 2.00e-02 2.50e+03 8.57e-02 7.34e+01 pdb=" C ALA F 109 " 0.148 2.00e-02 2.50e+03 pdb=" O ALA F 109 " -0.054 2.00e-02 2.50e+03 pdb=" N SER F 110 " -0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER F 94 " -0.030 2.00e-02 2.50e+03 6.06e-02 3.68e+01 pdb=" C SER F 94 " 0.105 2.00e-02 2.50e+03 pdb=" O SER F 94 " -0.039 2.00e-02 2.50e+03 pdb=" N PHE F 95 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 347 " -0.021 2.00e-02 2.50e+03 4.26e-02 1.81e+01 pdb=" C ARG A 347 " 0.074 2.00e-02 2.50e+03 pdb=" O ARG A 347 " -0.027 2.00e-02 2.50e+03 pdb=" N ILE A 348 " -0.025 2.00e-02 2.50e+03 ... (remaining 1441 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 216 2.65 - 3.21: 8278 3.21 - 3.77: 13082 3.77 - 4.34: 17654 4.34 - 4.90: 29033 Nonbonded interactions: 68263 Sorted by model distance: nonbonded pdb=" OG SER F 65 " pdb=" ND2 ASN F 113 " model vdw 2.087 3.120 nonbonded pdb=" OG SER B 331 " pdb=" OD2 ASP B 333 " model vdw 2.135 3.040 nonbonded pdb=" OG SER A 54 " pdb=" O1G GTP A 401 " model vdw 2.142 3.040 nonbonded pdb=" NE2 HIS B 54 " pdb=" OG SER B 72 " model vdw 2.163 3.120 nonbonded pdb=" OG1 THR A 55 " pdb=" O1A GTP A 401 " model vdw 2.164 3.040 ... (remaining 68258 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.38 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: 0.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 24.000 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 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 : 0.010 0.068 8385 Z= 0.675 Angle : 1.006 12.527 11371 Z= 0.572 Chirality : 0.057 0.312 1278 Planarity : 0.007 0.086 1444 Dihedral : 15.075 172.997 3016 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 17.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.57 % Allowed : 10.99 % Favored : 88.45 % 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: -2.63 (0.23), residues: 1025 helix: -1.68 (0.21), residues: 416 sheet: -1.41 (0.30), residues: 245 loop : -1.74 (0.29), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 99 HIS 0.014 0.002 HIS A 357 PHE 0.032 0.003 PHE F 333 TYR 0.018 0.002 TYR E 95 ARG 0.004 0.001 ARG F 226 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 209 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 86 ILE cc_start: 0.8784 (mm) cc_final: 0.8539 (mt) REVERT: F 194 TYR cc_start: 0.8868 (t80) cc_final: 0.8660 (t80) REVERT: F 225 ILE cc_start: 0.8842 (mt) cc_final: 0.8642 (mp) REVERT: A 20 ARG cc_start: 0.8359 (mtt180) cc_final: 0.8067 (mtt-85) REVERT: A 33 ASP cc_start: 0.8447 (t0) cc_final: 0.8115 (t0) REVERT: A 35 GLN cc_start: 0.8451 (tm-30) cc_final: 0.7814 (tm-30) REVERT: B 214 ARG cc_start: 0.7145 (mtm180) cc_final: 0.6755 (ttp-170) REVERT: B 269 ILE cc_start: 0.9095 (mt) cc_final: 0.8793 (mm) REVERT: E 29 PHE cc_start: 0.9027 (t80) cc_final: 0.8697 (t80) REVERT: E 80 TYR cc_start: 0.7366 (m-80) cc_final: 0.7081 (m-80) REVERT: E 82 GLN cc_start: 0.7631 (tp40) cc_final: 0.7293 (tp40) REVERT: E 83 MET cc_start: 0.7743 (ptp) cc_final: 0.7524 (ptp) REVERT: D 47 GLU cc_start: 0.7750 (pm20) cc_final: 0.6941 (pm20) outliers start: 2 outliers final: 0 residues processed: 210 average time/residue: 0.2362 time to fit residues: 65.0101 Evaluate side-chains 160 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 9.9990 chunk 76 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 51 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 91 optimal weight: 7.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 41 ASN F 113 ASN F 164 HIS A 14 ASN A 267 GLN ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN B 110 ASN B 119 ASN B 220 GLN B 266 HIS E 13 GLN E 77 ASN ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8385 Z= 0.194 Angle : 0.641 12.510 11371 Z= 0.334 Chirality : 0.045 0.191 1278 Planarity : 0.004 0.040 1444 Dihedral : 9.576 177.611 1155 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.15 % Allowed : 15.74 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.45 % 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: -0.58 (0.25), residues: 1025 helix: 0.42 (0.24), residues: 414 sheet: -0.88 (0.33), residues: 218 loop : -0.78 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 169 HIS 0.008 0.001 HIS F 53 PHE 0.019 0.001 PHE E 108 TYR 0.013 0.001 TYR F 122 ARG 0.004 0.000 ARG E 98 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 202 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 210 MET cc_start: 0.6345 (mtp) cc_final: 0.5756 (ttm) REVERT: F 211 ILE cc_start: 0.7801 (OUTLIER) cc_final: 0.7598 (mt) REVERT: F 271 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8915 (mm) REVERT: F 333 PHE cc_start: 0.8176 (OUTLIER) cc_final: 0.7806 (m-10) REVERT: A 33 ASP cc_start: 0.8300 (t0) cc_final: 0.7921 (t0) REVERT: A 249 ASP cc_start: 0.8111 (OUTLIER) cc_final: 0.7686 (p0) REVERT: A 356 ARG cc_start: 0.8481 (mtm-85) cc_final: 0.8230 (mtm180) REVERT: B 46 ARG cc_start: 0.7462 (mtp85) cc_final: 0.7029 (mtm110) REVERT: B 211 TRP cc_start: 0.7741 (m100) cc_final: 0.7436 (m100) REVERT: B 214 ARG cc_start: 0.7093 (mtm180) cc_final: 0.6761 (ptp-170) REVERT: B 289 TYR cc_start: 0.8998 (m-80) cc_final: 0.8776 (m-80) REVERT: E 4 LEU cc_start: 0.8085 (mt) cc_final: 0.7881 (mt) REVERT: E 82 GLN cc_start: 0.7599 (tp40) cc_final: 0.7293 (tp40) REVERT: E 83 MET cc_start: 0.7912 (ptp) cc_final: 0.7703 (ptp) REVERT: D 47 GLU cc_start: 0.8093 (pm20) cc_final: 0.7762 (pm20) outliers start: 16 outliers final: 9 residues processed: 211 average time/residue: 0.2217 time to fit residues: 63.0083 Evaluate side-chains 179 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 166 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 185 ASN Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 211 ILE Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 290 ILE Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 125 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 20.0000 chunk 28 optimal weight: 7.9990 chunk 76 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 chunk 91 optimal weight: 10.0000 chunk 99 optimal weight: 10.0000 chunk 81 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 90 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN B 266 HIS ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.051 8385 Z= 0.497 Angle : 0.750 11.745 11371 Z= 0.395 Chirality : 0.049 0.189 1278 Planarity : 0.005 0.051 1444 Dihedral : 9.684 177.091 1155 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 5.78 % Allowed : 18.35 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.45 % 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: -0.28 (0.26), residues: 1025 helix: 0.73 (0.25), residues: 423 sheet: -0.85 (0.32), residues: 238 loop : -0.61 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.009 0.002 HIS F 53 PHE 0.023 0.002 PHE E 108 TYR 0.012 0.002 TYR F 194 ARG 0.007 0.001 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 169 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 160 GLN cc_start: 0.8345 (tm-30) cc_final: 0.7921 (tm-30) REVERT: F 271 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.8840 (mm) REVERT: F 333 PHE cc_start: 0.8424 (OUTLIER) cc_final: 0.8110 (m-10) REVERT: A 33 ASP cc_start: 0.8445 (t0) cc_final: 0.8022 (t0) REVERT: A 249 ASP cc_start: 0.8375 (OUTLIER) cc_final: 0.7808 (p0) REVERT: B 214 ARG cc_start: 0.7101 (mtm180) cc_final: 0.6750 (ttp-170) REVERT: B 264 TYR cc_start: 0.8623 (m-10) cc_final: 0.8267 (m-10) REVERT: E 4 LEU cc_start: 0.8098 (mt) cc_final: 0.7819 (mt) REVERT: E 82 GLN cc_start: 0.7602 (tp40) cc_final: 0.7283 (tp40) REVERT: E 83 MET cc_start: 0.7826 (ptp) cc_final: 0.7546 (ptp) REVERT: E 98 ARG cc_start: 0.8645 (ttp80) cc_final: 0.8078 (tmm-80) REVERT: D 47 GLU cc_start: 0.8208 (pm20) cc_final: 0.7736 (pm20) outliers start: 48 outliers final: 32 residues processed: 202 average time/residue: 0.2233 time to fit residues: 60.2805 Evaluate side-chains 187 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 152 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 132 GLU Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 185 ASN Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 280 VAL Chi-restraints excluded: chain F residue 323 ASN Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain D residue 50 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 7.9990 chunk 47 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 43 optimal weight: 8.9990 chunk 61 optimal weight: 0.9990 chunk 92 optimal weight: 6.9990 chunk 97 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 87 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN B 266 HIS ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8385 Z= 0.219 Angle : 0.621 11.597 11371 Z= 0.323 Chirality : 0.044 0.145 1278 Planarity : 0.004 0.042 1444 Dihedral : 9.542 178.001 1155 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 4.53 % Allowed : 21.06 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.45 % 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: 1025 helix: 1.15 (0.26), residues: 423 sheet: -0.47 (0.34), residues: 213 loop : -0.55 (0.33), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.011 0.001 HIS A 357 PHE 0.021 0.002 PHE B 235 TYR 0.018 0.001 TYR F 194 ARG 0.005 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 175 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 76 LEU cc_start: 0.8411 (mt) cc_final: 0.8180 (mp) REVERT: F 160 GLN cc_start: 0.8265 (tm-30) cc_final: 0.7840 (tm-30) REVERT: F 210 MET cc_start: 0.6651 (mtp) cc_final: 0.6209 (ttm) REVERT: F 214 TYR cc_start: 0.8352 (OUTLIER) cc_final: 0.7129 (m-80) REVERT: F 271 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8842 (mm) REVERT: F 333 PHE cc_start: 0.8211 (OUTLIER) cc_final: 0.7827 (m-10) REVERT: A 33 ASP cc_start: 0.8321 (t0) cc_final: 0.7877 (t0) REVERT: A 249 ASP cc_start: 0.8167 (OUTLIER) cc_final: 0.7541 (p0) REVERT: B 45 MET cc_start: 0.8701 (mtm) cc_final: 0.8441 (mtm) REVERT: B 124 TYR cc_start: 0.8922 (m-80) cc_final: 0.8658 (m-80) REVERT: B 188 MET cc_start: 0.8282 (mmm) cc_final: 0.7971 (mmt) REVERT: B 211 TRP cc_start: 0.7604 (m100) cc_final: 0.7335 (m100) REVERT: B 214 ARG cc_start: 0.7068 (mtm180) cc_final: 0.6773 (ptp-170) REVERT: B 234 PHE cc_start: 0.8424 (OUTLIER) cc_final: 0.8208 (t80) REVERT: B 264 TYR cc_start: 0.8615 (m-10) cc_final: 0.8324 (m-10) REVERT: E 77 ASN cc_start: 0.7434 (t0) cc_final: 0.7201 (t0) REVERT: E 83 MET cc_start: 0.7799 (ptp) cc_final: 0.7436 (ptp) REVERT: E 98 ARG cc_start: 0.8357 (ttp80) cc_final: 0.7862 (tmm-80) REVERT: E 106 ASP cc_start: 0.8286 (p0) cc_final: 0.8061 (p0) REVERT: D 47 GLU cc_start: 0.8149 (pm20) cc_final: 0.7727 (pm20) outliers start: 37 outliers final: 26 residues processed: 196 average time/residue: 0.2166 time to fit residues: 57.8714 Evaluate side-chains 195 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 164 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 214 TYR Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 323 ASN Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 33 LYS Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain D residue 44 HIS Chi-restraints excluded: chain D residue 50 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 72 optimal weight: 10.0000 chunk 40 optimal weight: 0.7980 chunk 83 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 87 optimal weight: 6.9990 chunk 24 optimal weight: 0.7980 chunk 32 optimal weight: 10.0000 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN B B 266 HIS E 35 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8385 Z= 0.188 Angle : 0.602 10.933 11371 Z= 0.310 Chirality : 0.044 0.218 1278 Planarity : 0.004 0.043 1444 Dihedral : 9.411 178.405 1155 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 4.08 % Allowed : 22.65 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.45 % 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: 0.37 (0.27), residues: 1025 helix: 1.41 (0.26), residues: 419 sheet: -0.45 (0.34), residues: 215 loop : -0.52 (0.33), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.008 0.001 HIS F 53 PHE 0.021 0.001 PHE B 235 TYR 0.021 0.001 TYR F 194 ARG 0.004 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 186 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 76 LEU cc_start: 0.8470 (mt) cc_final: 0.8237 (mp) REVERT: F 160 GLN cc_start: 0.8254 (tm-30) cc_final: 0.7879 (tm-30) REVERT: F 210 MET cc_start: 0.6584 (mtp) cc_final: 0.6238 (ttm) REVERT: F 214 TYR cc_start: 0.8280 (OUTLIER) cc_final: 0.6969 (m-10) REVERT: F 271 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8844 (mm) REVERT: F 333 PHE cc_start: 0.8096 (OUTLIER) cc_final: 0.7781 (m-10) REVERT: A 33 ASP cc_start: 0.8315 (t0) cc_final: 0.7903 (t0) REVERT: A 249 ASP cc_start: 0.8116 (OUTLIER) cc_final: 0.7487 (p0) REVERT: B 37 ILE cc_start: 0.8268 (OUTLIER) cc_final: 0.7950 (mp) REVERT: B 124 TYR cc_start: 0.8844 (m-80) cc_final: 0.8587 (m-80) REVERT: B 188 MET cc_start: 0.8270 (mmm) cc_final: 0.8046 (mmt) REVERT: B 211 TRP cc_start: 0.7631 (m100) cc_final: 0.7330 (m100) REVERT: B 214 ARG cc_start: 0.7069 (mtm180) cc_final: 0.6798 (ptp-170) REVERT: B 254 ASP cc_start: 0.8342 (t70) cc_final: 0.8078 (t0) REVERT: B 262 MET cc_start: 0.6698 (ttm) cc_final: 0.6412 (ttm) REVERT: B 297 TRP cc_start: 0.8236 (m100) cc_final: 0.7907 (m-10) REVERT: E 43 LYS cc_start: 0.7828 (mtmm) cc_final: 0.7488 (ptpt) REVERT: E 77 ASN cc_start: 0.7358 (t0) cc_final: 0.7090 (t0) REVERT: E 83 MET cc_start: 0.7787 (ptp) cc_final: 0.7447 (ptp) REVERT: E 90 ASP cc_start: 0.7120 (m-30) cc_final: 0.6797 (m-30) REVERT: D 47 GLU cc_start: 0.8142 (pm20) cc_final: 0.7691 (pm20) outliers start: 33 outliers final: 22 residues processed: 204 average time/residue: 0.1921 time to fit residues: 53.5711 Evaluate side-chains 201 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 174 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 214 TYR Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 323 ASN Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain D residue 44 HIS Chi-restraints excluded: chain D residue 50 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 97 optimal weight: 20.0000 chunk 81 optimal weight: 7.9990 chunk 45 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 94 optimal weight: 0.0970 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS E 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8385 Z= 0.241 Angle : 0.625 11.115 11371 Z= 0.320 Chirality : 0.045 0.233 1278 Planarity : 0.004 0.046 1444 Dihedral : 9.424 178.522 1155 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 4.30 % Allowed : 24.46 % Favored : 71.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.45 % 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: 1025 helix: 1.41 (0.26), residues: 418 sheet: -0.35 (0.35), residues: 214 loop : -0.53 (0.33), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.007 0.001 HIS F 53 PHE 0.020 0.001 PHE B 235 TYR 0.022 0.001 TYR F 194 ARG 0.005 0.000 ARG E 98 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 173 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 76 LEU cc_start: 0.8493 (mt) cc_final: 0.8260 (mp) REVERT: F 160 GLN cc_start: 0.8263 (tm-30) cc_final: 0.8000 (tm-30) REVERT: F 210 MET cc_start: 0.6583 (mtp) cc_final: 0.6205 (ttm) REVERT: F 214 TYR cc_start: 0.8297 (OUTLIER) cc_final: 0.7127 (m-80) REVERT: F 271 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8831 (mm) REVERT: F 333 PHE cc_start: 0.8095 (OUTLIER) cc_final: 0.7781 (m-10) REVERT: A 33 ASP cc_start: 0.8367 (t0) cc_final: 0.7907 (t0) REVERT: A 249 ASP cc_start: 0.8151 (OUTLIER) cc_final: 0.7502 (p0) REVERT: B 37 ILE cc_start: 0.8274 (OUTLIER) cc_final: 0.8004 (mp) REVERT: B 188 MET cc_start: 0.8423 (mmm) cc_final: 0.8170 (mmt) REVERT: B 211 TRP cc_start: 0.7688 (m100) cc_final: 0.7462 (m100) REVERT: B 235 PHE cc_start: 0.8942 (t80) cc_final: 0.8689 (t80) REVERT: B 254 ASP cc_start: 0.8346 (t70) cc_final: 0.8064 (t0) REVERT: B 264 TYR cc_start: 0.8449 (OUTLIER) cc_final: 0.8027 (m-80) REVERT: E 43 LYS cc_start: 0.7865 (mtmm) cc_final: 0.7540 (ptpt) REVERT: E 77 ASN cc_start: 0.7470 (t0) cc_final: 0.7188 (t0) REVERT: E 83 MET cc_start: 0.7738 (ptp) cc_final: 0.7165 (ptp) REVERT: E 90 ASP cc_start: 0.7220 (m-30) cc_final: 0.6977 (m-30) REVERT: D 47 GLU cc_start: 0.8113 (pm20) cc_final: 0.7661 (pm20) outliers start: 35 outliers final: 25 residues processed: 190 average time/residue: 0.2126 time to fit residues: 54.8462 Evaluate side-chains 195 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 164 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 214 TYR Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 323 ASN Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 264 TYR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain D residue 44 HIS Chi-restraints excluded: chain D residue 50 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 71 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 54 optimal weight: 7.9990 chunk 97 optimal weight: 6.9990 chunk 60 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN B B 266 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8385 Z= 0.270 Angle : 0.642 11.598 11371 Z= 0.329 Chirality : 0.045 0.242 1278 Planarity : 0.004 0.045 1444 Dihedral : 9.419 178.380 1155 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 5.21 % Allowed : 24.35 % Favored : 70.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.45 % 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: 0.45 (0.27), residues: 1025 helix: 1.46 (0.26), residues: 418 sheet: -0.21 (0.36), residues: 208 loop : -0.58 (0.32), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 281 HIS 0.007 0.001 HIS A 357 PHE 0.021 0.002 PHE B 235 TYR 0.020 0.001 TYR F 194 ARG 0.004 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 176 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 76 LEU cc_start: 0.8606 (mt) cc_final: 0.8376 (mp) REVERT: F 160 GLN cc_start: 0.8304 (tm-30) cc_final: 0.7915 (tm-30) REVERT: F 210 MET cc_start: 0.6640 (mtp) cc_final: 0.6387 (ttm) REVERT: F 214 TYR cc_start: 0.8323 (OUTLIER) cc_final: 0.7131 (m-80) REVERT: F 271 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8837 (mm) REVERT: F 333 PHE cc_start: 0.8188 (OUTLIER) cc_final: 0.7838 (m-10) REVERT: A 33 ASP cc_start: 0.8346 (t0) cc_final: 0.7882 (t0) REVERT: A 60 MET cc_start: 0.8365 (mmm) cc_final: 0.8053 (mmm) REVERT: A 249 ASP cc_start: 0.8179 (OUTLIER) cc_final: 0.7527 (p0) REVERT: B 188 MET cc_start: 0.8497 (mmm) cc_final: 0.8244 (mmt) REVERT: B 211 TRP cc_start: 0.7755 (m100) cc_final: 0.7498 (m100) REVERT: B 254 ASP cc_start: 0.8368 (t70) cc_final: 0.8091 (t0) REVERT: B 264 TYR cc_start: 0.8444 (OUTLIER) cc_final: 0.8109 (m-80) REVERT: E 65 LYS cc_start: 0.8182 (tppt) cc_final: 0.7762 (mmmt) REVERT: E 77 ASN cc_start: 0.7450 (t0) cc_final: 0.7147 (t0) REVERT: E 86 LEU cc_start: 0.7330 (mp) cc_final: 0.7059 (mp) REVERT: D 47 GLU cc_start: 0.8075 (pm20) cc_final: 0.7609 (pm20) outliers start: 43 outliers final: 35 residues processed: 200 average time/residue: 0.1977 time to fit residues: 53.9827 Evaluate side-chains 206 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 166 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 214 TYR Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 323 ASN Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 264 TYR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain E residue 33 LYS Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain D residue 44 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 66 optimal weight: 10.0000 chunk 48 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 76 optimal weight: 7.9990 chunk 88 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 85 optimal weight: 5.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS E 35 ASN ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8385 Z= 0.184 Angle : 0.635 11.025 11371 Z= 0.324 Chirality : 0.045 0.269 1278 Planarity : 0.004 0.043 1444 Dihedral : 9.379 179.786 1155 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 4.08 % Allowed : 25.82 % Favored : 70.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.45 % 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: 0.54 (0.27), residues: 1025 helix: 1.55 (0.26), residues: 419 sheet: -0.12 (0.36), residues: 205 loop : -0.59 (0.32), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 281 HIS 0.007 0.001 HIS F 53 PHE 0.032 0.001 PHE B 235 TYR 0.025 0.001 TYR F 194 ARG 0.004 0.000 ARG E 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 186 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 160 GLN cc_start: 0.8315 (tm-30) cc_final: 0.8016 (tm-30) REVERT: F 210 MET cc_start: 0.6435 (mtp) cc_final: 0.6205 (ttm) REVERT: F 214 TYR cc_start: 0.8236 (OUTLIER) cc_final: 0.6956 (m-10) REVERT: F 269 LYS cc_start: 0.8081 (tptt) cc_final: 0.7576 (ttpt) REVERT: F 271 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8823 (mt) REVERT: F 333 PHE cc_start: 0.8155 (OUTLIER) cc_final: 0.7904 (m-10) REVERT: A 249 ASP cc_start: 0.8082 (OUTLIER) cc_final: 0.7719 (p0) REVERT: B 124 TYR cc_start: 0.8909 (m-80) cc_final: 0.8578 (m-80) REVERT: B 234 PHE cc_start: 0.8274 (OUTLIER) cc_final: 0.7691 (t80) REVERT: B 254 ASP cc_start: 0.8387 (t70) cc_final: 0.8142 (t0) REVERT: B 264 TYR cc_start: 0.8265 (OUTLIER) cc_final: 0.7917 (m-80) REVERT: B 289 TYR cc_start: 0.8952 (m-80) cc_final: 0.8512 (m-80) REVERT: E 33 LYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7783 (ptpt) REVERT: E 77 ASN cc_start: 0.7438 (t0) cc_final: 0.7126 (t0) REVERT: E 87 LYS cc_start: 0.7197 (mtmt) cc_final: 0.6577 (mptt) REVERT: E 90 ASP cc_start: 0.7279 (m-30) cc_final: 0.6604 (m-30) REVERT: D 47 GLU cc_start: 0.7998 (pm20) cc_final: 0.7786 (pm20) outliers start: 33 outliers final: 21 residues processed: 201 average time/residue: 0.2076 time to fit residues: 56.6937 Evaluate side-chains 201 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 173 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 145 SER Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 214 TYR Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 323 ASN Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 264 TYR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain E residue 33 LYS Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 74 ASN Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain D residue 44 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 9.9990 chunk 93 optimal weight: 5.9990 chunk 54 optimal weight: 8.9990 chunk 39 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 81 optimal weight: 7.9990 chunk 85 optimal weight: 10.0000 chunk 59 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 58 optimal weight: 0.5980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8385 Z= 0.193 Angle : 0.653 12.135 11371 Z= 0.330 Chirality : 0.044 0.277 1278 Planarity : 0.004 0.067 1444 Dihedral : 9.317 178.790 1155 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.74 % Allowed : 27.07 % Favored : 69.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.45 % 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: 0.62 (0.27), residues: 1025 helix: 1.58 (0.26), residues: 419 sheet: 0.01 (0.36), residues: 203 loop : -0.56 (0.33), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 281 HIS 0.007 0.001 HIS F 53 PHE 0.029 0.001 PHE B 235 TYR 0.023 0.001 TYR F 194 ARG 0.008 0.000 ARG E 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 174 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 160 GLN cc_start: 0.8203 (tm-30) cc_final: 0.7970 (tm-30) REVERT: F 214 TYR cc_start: 0.8244 (OUTLIER) cc_final: 0.6834 (m-10) REVERT: F 269 LYS cc_start: 0.8211 (tptt) cc_final: 0.7844 (ttpt) REVERT: F 271 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8863 (mt) REVERT: A 249 ASP cc_start: 0.8020 (OUTLIER) cc_final: 0.7666 (p0) REVERT: B 124 TYR cc_start: 0.8915 (m-80) cc_final: 0.8560 (m-80) REVERT: B 211 TRP cc_start: 0.7713 (m100) cc_final: 0.7419 (m100) REVERT: B 234 PHE cc_start: 0.8279 (OUTLIER) cc_final: 0.7634 (t80) REVERT: B 254 ASP cc_start: 0.8379 (t70) cc_final: 0.8133 (t0) REVERT: B 289 TYR cc_start: 0.8865 (m-80) cc_final: 0.8342 (m-80) REVERT: E 33 LYS cc_start: 0.8007 (OUTLIER) cc_final: 0.7647 (ptpt) REVERT: E 65 LYS cc_start: 0.8158 (tppt) cc_final: 0.7920 (mmmt) REVERT: E 77 ASN cc_start: 0.7426 (t0) cc_final: 0.7101 (t0) REVERT: E 87 LYS cc_start: 0.7014 (mtmt) cc_final: 0.6488 (mptt) REVERT: E 90 ASP cc_start: 0.7239 (m-30) cc_final: 0.6666 (m-30) outliers start: 30 outliers final: 22 residues processed: 191 average time/residue: 0.2017 time to fit residues: 53.0153 Evaluate side-chains 194 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 167 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 145 SER Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 214 TYR Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 323 ASN Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain E residue 33 LYS Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 74 ASN Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 125 THR Chi-restraints excluded: chain D residue 44 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 1.9990 chunk 66 optimal weight: 9.9990 chunk 100 optimal weight: 8.9990 chunk 92 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 8 optimal weight: 0.7980 chunk 61 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 63 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 24 optimal weight: 0.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 35 ASN B 230 ASN B 266 HIS E 35 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 8385 Z= 0.301 Angle : 0.709 10.828 11371 Z= 0.363 Chirality : 0.047 0.311 1278 Planarity : 0.005 0.083 1444 Dihedral : 9.422 178.425 1155 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.62 % Allowed : 28.31 % Favored : 68.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.45 % 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: 1025 helix: 1.43 (0.26), residues: 418 sheet: -0.25 (0.37), residues: 186 loop : -0.61 (0.32), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 281 HIS 0.007 0.001 HIS F 53 PHE 0.028 0.002 PHE B 235 TYR 0.024 0.002 TYR F 194 ARG 0.008 0.000 ARG E 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 165 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 214 TYR cc_start: 0.8411 (OUTLIER) cc_final: 0.7156 (m-80) REVERT: F 269 LYS cc_start: 0.8399 (tptt) cc_final: 0.7998 (ttpt) REVERT: F 271 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8811 (mm) REVERT: A 249 ASP cc_start: 0.8126 (OUTLIER) cc_final: 0.7555 (p0) REVERT: B 211 TRP cc_start: 0.7810 (m100) cc_final: 0.7523 (m100) REVERT: B 234 PHE cc_start: 0.8336 (OUTLIER) cc_final: 0.7636 (t80) REVERT: B 254 ASP cc_start: 0.8407 (t70) cc_final: 0.8157 (t0) REVERT: B 289 TYR cc_start: 0.9031 (m-80) cc_final: 0.8556 (m-80) REVERT: E 77 ASN cc_start: 0.7442 (t0) cc_final: 0.7112 (t0) outliers start: 29 outliers final: 24 residues processed: 182 average time/residue: 0.1963 time to fit residues: 49.0947 Evaluate side-chains 185 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 157 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 145 SER Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 214 TYR Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 323 ASN Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain E residue 33 LYS Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 74 ASN Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 125 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 0.0870 chunk 11 optimal weight: 10.0000 chunk 22 optimal weight: 0.2980 chunk 80 optimal weight: 8.9990 chunk 33 optimal weight: 4.9990 chunk 82 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 20.0000 chunk 70 optimal weight: 9.9990 chunk 4 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 overall best weight: 0.8162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 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 = 0.4001 r_free = 0.4001 target = 0.158272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.111722 restraints weight = 36525.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.117069 restraints weight = 12206.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.120586 restraints weight = 7291.877| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3541 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3541 r_free = 0.3541 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3541 r_free = 0.3541 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3541 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.112 8385 Z= 0.333 Angle : 1.037 59.196 11371 Z= 0.585 Chirality : 0.048 0.414 1278 Planarity : 0.005 0.082 1444 Dihedral : 9.439 178.262 1155 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.62 % Allowed : 28.54 % Favored : 67.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.45 % 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: 1025 helix: 1.45 (0.26), residues: 418 sheet: -0.20 (0.37), residues: 192 loop : -0.60 (0.32), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 281 HIS 0.010 0.002 HIS A 64 PHE 0.028 0.002 PHE B 235 TYR 0.023 0.002 TYR F 194 ARG 0.007 0.000 ARG E 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1968.10 seconds wall clock time: 39 minutes 4.81 seconds (2344.81 seconds total)