Starting phenix.real_space_refine on Sun Jun 8 07:24:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j1p_61077/06_2025/9j1p_61077.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j1p_61077/06_2025/9j1p_61077.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9j1p_61077/06_2025/9j1p_61077.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j1p_61077/06_2025/9j1p_61077.map" model { file = "/net/cci-nas-00/data/ceres_data/9j1p_61077/06_2025/9j1p_61077.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j1p_61077/06_2025/9j1p_61077.cif" } resolution = 2.99 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= -0.001 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 64 5.16 5 C 5973 2.51 5 N 1620 2.21 5 O 1728 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 9385 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1941 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 228} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "B" Number of atoms: 2586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2586 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "G" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 396 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 4, 'TRANS': 46} Chain: "N" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 947 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 5, 'TRANS': 118} Chain: "P" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 353 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 4, 'TRANS': 44} Chain: "R" Number of atoms: 3162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 3162 Classifications: {'peptide': 389} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 14, 'TRANS': 374} Chain breaks: 1 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 34 Time building chain proxies: 6.24, per 1000 atoms: 0.66 Number of scatterers: 9385 At special positions: 0 Unit cell: (80.325, 96.39, 174.573, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 64 16.00 O 1728 8.00 N 1620 7.00 C 5973 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS P 21 " - pdb=" SG CYS P 47 " distance=2.03 Simple disulfide: pdb=" SG CYS P 29 " - pdb=" SG CYS P 43 " distance=2.03 Simple disulfide: pdb=" SG CYS P 33 " - pdb=" SG CYS P 39 " distance=2.03 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 71 " distance=2.03 Simple disulfide: pdb=" SG CYS R 62 " - pdb=" SG CYS R 104 " distance=2.03 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 126 " distance=2.03 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.58 Conformation dependent library (CDL) restraints added in 1.2 seconds 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2236 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 11 sheets defined 43.1% alpha, 15.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 13 through 39 removed outlier: 3.651A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 51 No H-bonds generated for 'chain 'A' and resid 49 through 51' Processing helix chain 'A' and resid 52 through 64 removed outlier: 3.508A pdb=" N ILE A 62 " --> pdb=" O LYS A 58 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N HIS A 64 " --> pdb=" O MET A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 240 removed outlier: 4.585A pdb=" N ASP A 240 " --> pdb=" O CYS A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 279 Processing helix chain 'A' and resid 280 through 283 removed outlier: 3.663A pdb=" N ARG A 283 " --> pdb=" O ARG A 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 280 through 283' Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.643A pdb=" N VAL A 301 " --> pdb=" O LEU A 297 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU A 302 " --> pdb=" O ALA A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.953A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 26 removed outlier: 3.616A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.548A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 24 removed outlier: 3.533A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 45 removed outlier: 3.543A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.976A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 65 removed outlier: 3.534A pdb=" N LYS N 65 " --> pdb=" O GLY N 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 62 through 65' Processing helix chain 'N' and resid 87 through 91 removed outlier: 4.179A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 28 Processing helix chain 'P' and resid 28 through 33 removed outlier: 3.676A pdb=" N CYS P 33 " --> pdb=" O CYS P 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 40 through 44 Processing helix chain 'R' and resid 31 through 53 removed outlier: 3.637A pdb=" N THR R 51 " --> pdb=" O GLN R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 136 through 169 removed outlier: 4.488A pdb=" N GLN R 140 " --> pdb=" O SER R 136 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N LEU R 141 " --> pdb=" O PRO R 137 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 205 removed outlier: 3.589A pdb=" N TYR R 205 " --> pdb=" O LEU R 201 " (cutoff:3.500A) Processing helix chain 'R' and resid 206 through 216 Processing helix chain 'R' and resid 219 through 223 Processing helix chain 'R' and resid 224 through 256 removed outlier: 3.785A pdb=" N PHE R 230 " --> pdb=" O CYS R 226 " (cutoff:3.500A) Processing helix chain 'R' and resid 261 through 276 removed outlier: 3.962A pdb=" N ARG R 267 " --> pdb=" O GLN R 263 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU R 268 " --> pdb=" O TRP R 264 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL R 276 " --> pdb=" O ILE R 272 " (cutoff:3.500A) Processing helix chain 'R' and resid 277 through 291 removed outlier: 3.663A pdb=" N VAL R 282 " --> pdb=" O LEU R 278 " (cutoff:3.500A) Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 302 through 336 removed outlier: 3.559A pdb=" N TRP R 306 " --> pdb=" O ASN R 302 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE R 308 " --> pdb=" O ASN R 304 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ILE R 309 " --> pdb=" O TYR R 305 " (cutoff:3.500A) Proline residue: R 312 - end of helix Processing helix chain 'R' and resid 344 through 360 Proline residue: R 358 - end of helix Processing helix chain 'R' and resid 364 through 369 removed outlier: 4.563A pdb=" N PHE R 369 " --> pdb=" O VAL R 365 " (cutoff:3.500A) Processing helix chain 'R' and resid 377 through 404 removed outlier: 4.152A pdb=" N GLY R 395 " --> pdb=" O THR R 391 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N LEU R 396 " --> pdb=" O SER R 392 " (cutoff:3.500A) Processing helix chain 'R' and resid 406 through 423 removed outlier: 3.596A pdb=" N LEU R 422 " --> pdb=" O GLU R 418 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU R 423 " --> pdb=" O ARG R 419 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 219 through 223 removed outlier: 6.328A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N ASP A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.037A 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: 3.575A 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: 3.574A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.951A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 4.395A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.538A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 232 removed outlier: 3.603A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.545A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 58 through 60 removed outlier: 6.623A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 65 through 66 452 hydrogen bonds defined for protein. 1287 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: 2.65 Time building geometry restraints manager: 3.05 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: 3050 1.34 - 1.46: 2042 1.46 - 1.58: 4425 1.58 - 1.70: 0 1.70 - 1.82: 85 Bond restraints: 9602 Sorted by residual: bond pdb=" N ASN B 16 " pdb=" CA ASN B 16 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.21e-02 6.83e+03 6.10e+00 bond pdb=" N LEU B 14 " pdb=" CA LEU B 14 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.35e-02 5.49e+03 4.37e+00 bond pdb=" N GLU B 12 " pdb=" CA GLU B 12 " ideal model delta sigma weight residual 1.459 1.485 -0.027 1.28e-02 6.10e+03 4.31e+00 bond pdb=" N GLN B 13 " pdb=" CA GLN B 13 " ideal model delta sigma weight residual 1.459 1.484 -0.024 1.19e-02 7.06e+03 4.14e+00 bond pdb=" N LYS B 15 " pdb=" CA LYS B 15 " ideal model delta sigma weight residual 1.458 1.483 -0.026 1.27e-02 6.20e+03 4.04e+00 ... (remaining 9597 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 12867 1.94 - 3.87: 139 3.87 - 5.81: 18 5.81 - 7.75: 5 7.75 - 9.69: 3 Bond angle restraints: 13032 Sorted by residual: angle pdb=" N LEU B 14 " pdb=" CA LEU B 14 " pdb=" C LEU B 14 " ideal model delta sigma weight residual 113.01 108.74 4.27 1.20e+00 6.94e-01 1.26e+01 angle pdb=" N ASN B 16 " pdb=" CA ASN B 16 " pdb=" C ASN B 16 " ideal model delta sigma weight residual 111.28 107.62 3.66 1.09e+00 8.42e-01 1.13e+01 angle pdb=" CA GLU A 299 " pdb=" CB GLU A 299 " pdb=" CG GLU A 299 " ideal model delta sigma weight residual 114.10 120.66 -6.56 2.00e+00 2.50e-01 1.07e+01 angle pdb=" CB MET B 217 " pdb=" CG MET B 217 " pdb=" SD MET B 217 " ideal model delta sigma weight residual 112.70 122.39 -9.69 3.00e+00 1.11e-01 1.04e+01 angle pdb=" CB MET R 397 " pdb=" CG MET R 397 " pdb=" SD MET R 397 " ideal model delta sigma weight residual 112.70 122.34 -9.64 3.00e+00 1.11e-01 1.03e+01 ... (remaining 13027 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 4773 17.65 - 35.31: 667 35.31 - 52.96: 194 52.96 - 70.61: 42 70.61 - 88.26: 16 Dihedral angle restraints: 5692 sinusoidal: 2232 harmonic: 3460 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 2.26 -88.26 1 1.00e+01 1.00e-02 9.31e+01 dihedral pdb=" CB CYS R 46 " pdb=" SG CYS R 46 " pdb=" SG CYS R 71 " pdb=" CB CYS R 71 " ideal model delta sinusoidal sigma weight residual -86.00 -163.67 77.67 1 1.00e+01 1.00e-02 7.55e+01 dihedral pdb=" CB CYS R 62 " pdb=" SG CYS R 62 " pdb=" SG CYS R 104 " pdb=" CB CYS R 104 " ideal model delta sinusoidal sigma weight residual 93.00 163.68 -70.68 1 1.00e+01 1.00e-02 6.42e+01 ... (remaining 5689 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 942 0.030 - 0.060: 312 0.060 - 0.090: 123 0.090 - 0.120: 60 0.120 - 0.150: 7 Chirality restraints: 1444 Sorted by residual: chirality pdb=" CG LEU B 14 " pdb=" CB LEU B 14 " pdb=" CD1 LEU B 14 " pdb=" CD2 LEU B 14 " both_signs ideal model delta sigma weight residual False -2.59 -2.74 0.15 2.00e-01 2.50e+01 5.60e-01 chirality pdb=" CA ILE B 93 " pdb=" N ILE B 93 " pdb=" C ILE B 93 " pdb=" CB ILE B 93 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.48e-01 chirality pdb=" CA TYR R 88 " pdb=" N TYR R 88 " pdb=" C TYR R 88 " pdb=" CB TYR R 88 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.29e-01 ... (remaining 1441 not shown) Planarity restraints: 1661 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG R 48 " 0.133 9.50e-02 1.11e+02 6.05e-02 3.33e+00 pdb=" NE ARG R 48 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG R 48 " 0.017 2.00e-02 2.50e+03 pdb=" NH1 ARG R 48 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG R 48 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL R 276 " -0.025 5.00e-02 4.00e+02 3.77e-02 2.27e+00 pdb=" N PRO R 277 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO R 277 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO R 277 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TRP R 87 " -0.007 2.00e-02 2.50e+03 1.47e-02 2.17e+00 pdb=" C TRP R 87 " 0.025 2.00e-02 2.50e+03 pdb=" O TRP R 87 " -0.010 2.00e-02 2.50e+03 pdb=" N TYR R 88 " -0.009 2.00e-02 2.50e+03 ... (remaining 1658 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 655 2.73 - 3.27: 9380 3.27 - 3.82: 16039 3.82 - 4.36: 18308 4.36 - 4.90: 32227 Nonbonded interactions: 76609 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.191 3.040 nonbonded pdb=" OG1 THR B 321 " pdb=" O ALA B 326 " model vdw 2.199 3.040 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.219 3.040 nonbonded pdb=" OH TYR P 13 " pdb=" OE1 GLU R 138 " model vdw 2.224 3.040 nonbonded pdb=" N GLU G 47 " pdb=" OE1 GLU G 47 " model vdw 2.228 3.120 ... (remaining 76604 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.080 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: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 24.660 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: 0.000 Load rotamer database and sin/cos tables:13.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 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 : 0.003 0.036 9611 Z= 0.130 Angle : 0.533 9.687 13050 Z= 0.289 Chirality : 0.039 0.150 1444 Planarity : 0.004 0.060 1661 Dihedral : 18.166 87.197 3429 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 2.89 % Allowed : 35.06 % Favored : 62.05 % 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: 0.94 (0.26), residues: 1170 helix: 2.74 (0.25), residues: 436 sheet: 0.51 (0.35), residues: 217 loop : -1.27 (0.28), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP R 420 HIS 0.003 0.000 HIS R 212 PHE 0.011 0.001 PHE R 230 TYR 0.021 0.001 TYR R 148 ARG 0.018 0.001 ARG R 48 Details of bonding type rmsd hydrogen bonds : bond 0.15099 ( 452) hydrogen bonds : angle 5.40995 ( 1287) SS BOND : bond 0.00205 ( 9) SS BOND : angle 1.03228 ( 18) covalent geometry : bond 0.00269 ( 9602) covalent geometry : angle 0.53225 (13032) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 95 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLN cc_start: 0.7978 (tm-30) cc_final: 0.7319 (tm-30) REVERT: B 12 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.8289 (pm20) REVERT: B 14 LEU cc_start: 0.7180 (OUTLIER) cc_final: 0.6784 (pt) REVERT: B 175 GLN cc_start: 0.8314 (mm110) cc_final: 0.7969 (mm110) REVERT: B 228 ASP cc_start: 0.8745 (m-30) cc_final: 0.8439 (m-30) REVERT: B 291 ASP cc_start: 0.7327 (p0) cc_final: 0.7117 (p0) outliers start: 29 outliers final: 24 residues processed: 120 average time/residue: 1.0347 time to fit residues: 135.4075 Evaluate side-chains 119 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 93 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 15 LYS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain R residue 126 CYS Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 197 LYS Chi-restraints excluded: chain R residue 217 LEU Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 271 SER Chi-restraints excluded: chain R residue 340 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 0.3980 chunk 87 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 54 optimal weight: 0.5980 chunk 67 optimal weight: 9.9990 chunk 104 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 212 HIS ** R 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.158978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.095025 restraints weight = 12469.224| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.80 r_work: 0.2960 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.0709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9611 Z= 0.154 Angle : 0.509 7.405 13050 Z= 0.275 Chirality : 0.040 0.142 1444 Planarity : 0.004 0.041 1661 Dihedral : 6.233 59.220 1342 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 5.68 % Allowed : 29.58 % Favored : 64.74 % 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: 0.88 (0.26), residues: 1170 helix: 2.62 (0.25), residues: 444 sheet: 0.20 (0.35), residues: 227 loop : -1.18 (0.29), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.002 0.001 HIS A 357 PHE 0.015 0.001 PHE R 230 TYR 0.021 0.001 TYR R 148 ARG 0.007 0.000 ARG R 48 Details of bonding type rmsd hydrogen bonds : bond 0.04489 ( 452) hydrogen bonds : angle 4.30177 ( 1287) SS BOND : bond 0.00199 ( 9) SS BOND : angle 0.66662 ( 18) covalent geometry : bond 0.00360 ( 9602) covalent geometry : angle 0.50851 (13032) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 100 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 GLN cc_start: 0.8050 (tm-30) cc_final: 0.7429 (tm-30) REVERT: A 380 ARG cc_start: 0.7692 (OUTLIER) cc_final: 0.6323 (tpm-80) REVERT: B 12 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8290 (pm20) REVERT: B 14 LEU cc_start: 0.7080 (OUTLIER) cc_final: 0.6714 (pt) REVERT: B 76 ASP cc_start: 0.8491 (p0) cc_final: 0.8266 (p0) REVERT: B 175 GLN cc_start: 0.8323 (mm110) cc_final: 0.8067 (mm110) REVERT: B 228 ASP cc_start: 0.8689 (m-30) cc_final: 0.8410 (m-30) REVERT: G 48 ASP cc_start: 0.8391 (t0) cc_final: 0.8073 (t0) REVERT: P 45 ASN cc_start: 0.6901 (OUTLIER) cc_final: 0.6392 (p0) REVERT: R 213 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.8603 (mt0) REVERT: R 326 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7334 (mmm160) outliers start: 57 outliers final: 26 residues processed: 148 average time/residue: 0.9801 time to fit residues: 158.1787 Evaluate side-chains 121 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 89 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 64 HIS Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 297 TRP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain P residue 27 ILE Chi-restraints excluded: chain P residue 45 ASN Chi-restraints excluded: chain P residue 46 THR Chi-restraints excluded: chain R residue 126 CYS Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 213 GLN Chi-restraints excluded: chain R residue 217 LEU Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 326 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 71 optimal weight: 0.0670 chunk 1 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 108 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 78 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 320 ASN ** 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 = 0.3952 r_free = 0.3952 target = 0.159270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.094921 restraints weight = 12617.391| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 2.85 r_work: 0.2960 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.0817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9611 Z= 0.133 Angle : 0.498 6.058 13050 Z= 0.265 Chirality : 0.040 0.136 1444 Planarity : 0.004 0.041 1661 Dihedral : 5.527 59.877 1316 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 5.58 % Allowed : 29.58 % Favored : 64.84 % 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: 0.92 (0.26), residues: 1170 helix: 2.65 (0.25), residues: 444 sheet: 0.39 (0.35), residues: 218 loop : -1.21 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 420 HIS 0.002 0.000 HIS A 357 PHE 0.013 0.001 PHE R 230 TYR 0.021 0.001 TYR R 148 ARG 0.007 0.000 ARG R 48 Details of bonding type rmsd hydrogen bonds : bond 0.04165 ( 452) hydrogen bonds : angle 4.13393 ( 1287) SS BOND : bond 0.00181 ( 9) SS BOND : angle 0.58341 ( 18) covalent geometry : bond 0.00312 ( 9602) covalent geometry : angle 0.49780 (13032) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 101 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 LYS cc_start: 0.7457 (OUTLIER) cc_final: 0.6685 (mtpp) REVERT: A 380 ARG cc_start: 0.7569 (OUTLIER) cc_final: 0.6170 (tpm-80) REVERT: B 12 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8351 (pm20) REVERT: B 14 LEU cc_start: 0.7108 (OUTLIER) cc_final: 0.6805 (pt) REVERT: B 146 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8083 (mp) REVERT: B 175 GLN cc_start: 0.8333 (mm110) cc_final: 0.8048 (mm110) REVERT: B 228 ASP cc_start: 0.8595 (m-30) cc_final: 0.8253 (m-30) REVERT: G 48 ASP cc_start: 0.8264 (t0) cc_final: 0.7865 (t0) REVERT: P 45 ASN cc_start: 0.6889 (OUTLIER) cc_final: 0.6436 (p0) REVERT: R 288 LYS cc_start: 0.7954 (OUTLIER) cc_final: 0.7741 (mptm) REVERT: R 326 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7207 (mmm160) REVERT: R 351 LYS cc_start: 0.7681 (tttm) cc_final: 0.7447 (tmtt) outliers start: 56 outliers final: 27 residues processed: 148 average time/residue: 1.0143 time to fit residues: 162.7284 Evaluate side-chains 125 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 90 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 64 HIS Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 297 TRP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain N residue 67 ARG Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain P residue 45 ASN Chi-restraints excluded: chain R residue 126 CYS Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 217 LEU Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 288 LYS Chi-restraints excluded: chain R residue 326 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 54 optimal weight: 0.9980 chunk 113 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 110 optimal weight: 0.5980 chunk 79 optimal weight: 20.0000 chunk 59 optimal weight: 0.8980 chunk 100 optimal weight: 0.5980 chunk 86 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 103 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 213 GLN ** R 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.158704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.094416 restraints weight = 12491.571| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.83 r_work: 0.2951 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.1008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9611 Z= 0.150 Angle : 0.508 5.949 13050 Z= 0.272 Chirality : 0.040 0.170 1444 Planarity : 0.004 0.042 1661 Dihedral : 5.520 59.655 1316 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 5.78 % Allowed : 29.28 % Favored : 64.94 % 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: 0.85 (0.26), residues: 1170 helix: 2.61 (0.24), residues: 444 sheet: 0.15 (0.34), residues: 227 loop : -1.19 (0.29), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP R 420 HIS 0.002 0.001 HIS A 357 PHE 0.015 0.001 PHE R 230 TYR 0.021 0.001 TYR R 148 ARG 0.010 0.000 ARG R 48 Details of bonding type rmsd hydrogen bonds : bond 0.04154 ( 452) hydrogen bonds : angle 4.06393 ( 1287) SS BOND : bond 0.00189 ( 9) SS BOND : angle 0.59520 ( 18) covalent geometry : bond 0.00355 ( 9602) covalent geometry : angle 0.50798 (13032) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 97 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 LYS cc_start: 0.7447 (OUTLIER) cc_final: 0.6686 (mtpp) REVERT: A 327 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8343 (mp0) REVERT: A 380 ARG cc_start: 0.7585 (OUTLIER) cc_final: 0.6159 (tpm-80) REVERT: B 12 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.8367 (pm20) REVERT: B 14 LEU cc_start: 0.7231 (OUTLIER) cc_final: 0.6845 (pt) REVERT: B 76 ASP cc_start: 0.8572 (p0) cc_final: 0.8302 (p0) REVERT: B 146 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8127 (mp) REVERT: B 175 GLN cc_start: 0.8390 (mm110) cc_final: 0.8096 (mm110) REVERT: B 228 ASP cc_start: 0.8599 (m-30) cc_final: 0.8337 (m-30) REVERT: G 48 ASP cc_start: 0.8258 (t0) cc_final: 0.7848 (t0) REVERT: P 45 ASN cc_start: 0.6841 (OUTLIER) cc_final: 0.6407 (p0) REVERT: R 288 LYS cc_start: 0.7972 (OUTLIER) cc_final: 0.7737 (mptm) REVERT: R 326 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7218 (mmm160) REVERT: R 351 LYS cc_start: 0.7665 (tttm) cc_final: 0.7440 (tmtt) outliers start: 58 outliers final: 35 residues processed: 144 average time/residue: 0.9777 time to fit residues: 153.4706 Evaluate side-chains 135 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 91 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 64 HIS Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 297 TRP Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain N residue 67 ARG Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain P residue 27 ILE Chi-restraints excluded: chain P residue 45 ASN Chi-restraints excluded: chain R residue 41 GLU Chi-restraints excluded: chain R residue 126 CYS Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain R residue 202 LYS Chi-restraints excluded: chain R residue 217 LEU Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 288 LYS Chi-restraints excluded: chain R residue 326 ARG Chi-restraints excluded: chain R residue 340 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 110 optimal weight: 0.2980 chunk 13 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 37 optimal weight: 0.6980 chunk 47 optimal weight: 0.3980 chunk 36 optimal weight: 0.9980 chunk 24 optimal weight: 10.0000 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN N 1 GLN ** R 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.159271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.095066 restraints weight = 12546.062| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.85 r_work: 0.2957 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.1036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9611 Z= 0.128 Angle : 0.497 6.343 13050 Z= 0.265 Chirality : 0.040 0.166 1444 Planarity : 0.004 0.040 1661 Dihedral : 5.433 59.140 1316 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 5.58 % Allowed : 29.78 % Favored : 64.64 % 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: 0.92 (0.26), residues: 1170 helix: 2.70 (0.25), residues: 444 sheet: 0.29 (0.35), residues: 220 loop : -1.21 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP R 420 HIS 0.002 0.000 HIS A 357 PHE 0.013 0.001 PHE R 230 TYR 0.021 0.001 TYR R 148 ARG 0.011 0.000 ARG R 48 Details of bonding type rmsd hydrogen bonds : bond 0.03958 ( 452) hydrogen bonds : angle 3.98094 ( 1287) SS BOND : bond 0.00228 ( 9) SS BOND : angle 0.63462 ( 18) covalent geometry : bond 0.00301 ( 9602) covalent geometry : angle 0.49702 (13032) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 101 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 LYS cc_start: 0.7430 (OUTLIER) cc_final: 0.6640 (mtpp) REVERT: A 380 ARG cc_start: 0.7574 (OUTLIER) cc_final: 0.6176 (tpm-80) REVERT: B 12 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.8421 (pm20) REVERT: B 14 LEU cc_start: 0.7160 (OUTLIER) cc_final: 0.6838 (pt) REVERT: B 76 ASP cc_start: 0.8502 (p0) cc_final: 0.8217 (p0) REVERT: B 134 ARG cc_start: 0.7276 (mtp85) cc_final: 0.7056 (mtp85) REVERT: B 146 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8111 (mp) REVERT: B 175 GLN cc_start: 0.8381 (mm110) cc_final: 0.8166 (mm110) REVERT: B 228 ASP cc_start: 0.8612 (m-30) cc_final: 0.8333 (m-30) REVERT: G 48 ASP cc_start: 0.8241 (t0) cc_final: 0.7848 (t0) REVERT: P 45 ASN cc_start: 0.6831 (OUTLIER) cc_final: 0.6401 (p0) REVERT: R 41 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.7905 (tm-30) REVERT: R 44 ARG cc_start: 0.8513 (tmm160) cc_final: 0.8281 (tmm160) REVERT: R 288 LYS cc_start: 0.7980 (OUTLIER) cc_final: 0.7725 (mptm) REVERT: R 326 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7221 (mmm160) REVERT: R 351 LYS cc_start: 0.7661 (tttm) cc_final: 0.7442 (tmtt) outliers start: 56 outliers final: 33 residues processed: 146 average time/residue: 1.1395 time to fit residues: 180.3581 Evaluate side-chains 135 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 93 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 297 TRP Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain N residue 67 ARG Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain P residue 27 ILE Chi-restraints excluded: chain P residue 45 ASN Chi-restraints excluded: chain R residue 41 GLU Chi-restraints excluded: chain R residue 126 CYS Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 217 LEU Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 288 LYS Chi-restraints excluded: chain R residue 326 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 0.6980 chunk 7 optimal weight: 0.4980 chunk 87 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 69 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 65 optimal weight: 7.9990 chunk 10 optimal weight: 0.5980 chunk 95 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN ** R 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.159186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.094845 restraints weight = 12523.121| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.86 r_work: 0.2955 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9611 Z= 0.135 Angle : 0.504 6.577 13050 Z= 0.268 Chirality : 0.040 0.161 1444 Planarity : 0.004 0.041 1661 Dihedral : 5.434 58.970 1316 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 5.78 % Allowed : 29.98 % Favored : 64.24 % 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: 0.88 (0.26), residues: 1170 helix: 2.67 (0.25), residues: 444 sheet: 0.21 (0.35), residues: 222 loop : -1.23 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP R 420 HIS 0.002 0.000 HIS A 357 PHE 0.014 0.001 PHE R 230 TYR 0.021 0.001 TYR R 148 ARG 0.010 0.000 ARG R 48 Details of bonding type rmsd hydrogen bonds : bond 0.03966 ( 452) hydrogen bonds : angle 3.94280 ( 1287) SS BOND : bond 0.00172 ( 9) SS BOND : angle 0.61537 ( 18) covalent geometry : bond 0.00321 ( 9602) covalent geometry : angle 0.50349 (13032) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 101 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 LYS cc_start: 0.7433 (OUTLIER) cc_final: 0.6641 (mtpp) REVERT: A 327 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.8388 (mp0) REVERT: A 380 ARG cc_start: 0.7563 (OUTLIER) cc_final: 0.6166 (tpm-80) REVERT: B 12 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.8443 (pm20) REVERT: B 14 LEU cc_start: 0.7054 (OUTLIER) cc_final: 0.6780 (pt) REVERT: B 76 ASP cc_start: 0.8542 (p0) cc_final: 0.8253 (p0) REVERT: B 134 ARG cc_start: 0.7267 (mtp85) cc_final: 0.7042 (mtp85) REVERT: B 146 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8119 (mp) REVERT: B 175 GLN cc_start: 0.8377 (mm110) cc_final: 0.8160 (mm110) REVERT: B 228 ASP cc_start: 0.8607 (m-30) cc_final: 0.8326 (m-30) REVERT: G 48 ASP cc_start: 0.8205 (t0) cc_final: 0.7753 (t0) REVERT: P 45 ASN cc_start: 0.6840 (OUTLIER) cc_final: 0.6413 (p0) REVERT: R 41 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.7938 (tm-30) REVERT: R 44 ARG cc_start: 0.8502 (tmm160) cc_final: 0.8269 (tmm160) REVERT: R 288 LYS cc_start: 0.7974 (OUTLIER) cc_final: 0.7750 (mptm) REVERT: R 326 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7215 (mmm160) REVERT: R 351 LYS cc_start: 0.7646 (tttm) cc_final: 0.7436 (tmtt) outliers start: 58 outliers final: 38 residues processed: 148 average time/residue: 1.0552 time to fit residues: 169.2592 Evaluate side-chains 141 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 93 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 64 HIS Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 297 TRP Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain N residue 67 ARG Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain P residue 27 ILE Chi-restraints excluded: chain P residue 45 ASN Chi-restraints excluded: chain R residue 41 GLU Chi-restraints excluded: chain R residue 126 CYS Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 217 LEU Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 288 LYS Chi-restraints excluded: chain R residue 326 ARG Chi-restraints excluded: chain R residue 340 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 2 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 chunk 39 optimal weight: 6.9990 chunk 98 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 62 optimal weight: 0.0060 chunk 3 optimal weight: 0.6980 chunk 25 optimal weight: 4.9990 chunk 94 optimal weight: 0.0980 chunk 29 optimal weight: 0.7980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN ** R 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.160206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.096557 restraints weight = 12632.544| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.83 r_work: 0.2981 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9611 Z= 0.112 Angle : 0.505 7.099 13050 Z= 0.267 Chirality : 0.039 0.156 1444 Planarity : 0.004 0.052 1661 Dihedral : 5.336 58.883 1316 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 5.28 % Allowed : 30.88 % Favored : 63.84 % 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: 0.94 (0.26), residues: 1170 helix: 2.77 (0.25), residues: 445 sheet: 0.30 (0.35), residues: 223 loop : -1.28 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 420 HIS 0.002 0.000 HIS B 91 PHE 0.011 0.001 PHE R 230 TYR 0.021 0.001 TYR R 148 ARG 0.013 0.000 ARG R 48 Details of bonding type rmsd hydrogen bonds : bond 0.03717 ( 452) hydrogen bonds : angle 3.87642 ( 1287) SS BOND : bond 0.00147 ( 9) SS BOND : angle 0.53909 ( 18) covalent geometry : bond 0.00261 ( 9602) covalent geometry : angle 0.50463 (13032) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 103 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8374 (mp0) REVERT: A 380 ARG cc_start: 0.7567 (OUTLIER) cc_final: 0.6176 (tpm-80) REVERT: B 12 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8541 (pm20) REVERT: B 14 LEU cc_start: 0.7013 (OUTLIER) cc_final: 0.6720 (pt) REVERT: B 76 ASP cc_start: 0.8533 (p0) cc_final: 0.8278 (p0) REVERT: B 134 ARG cc_start: 0.7274 (mtp85) cc_final: 0.7053 (mtp85) REVERT: B 146 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8123 (mp) REVERT: B 175 GLN cc_start: 0.8384 (mm110) cc_final: 0.8085 (mm110) REVERT: B 228 ASP cc_start: 0.8534 (m-30) cc_final: 0.8178 (m-30) REVERT: N 83 MET cc_start: 0.6777 (ptp) cc_final: 0.5415 (ptm) REVERT: P 45 ASN cc_start: 0.6830 (OUTLIER) cc_final: 0.6408 (p0) REVERT: R 41 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.7957 (tm-30) REVERT: R 44 ARG cc_start: 0.8514 (tmm160) cc_final: 0.8269 (tmm160) REVERT: R 288 LYS cc_start: 0.7984 (OUTLIER) cc_final: 0.7734 (mptm) REVERT: R 326 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7209 (mmm160) REVERT: R 351 LYS cc_start: 0.7644 (tttm) cc_final: 0.7442 (tmtt) outliers start: 53 outliers final: 33 residues processed: 145 average time/residue: 1.0974 time to fit residues: 172.6022 Evaluate side-chains 132 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 90 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 64 HIS Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 297 TRP Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain P residue 27 ILE Chi-restraints excluded: chain P residue 45 ASN Chi-restraints excluded: chain R residue 41 GLU Chi-restraints excluded: chain R residue 126 CYS Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 217 LEU Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 288 LYS Chi-restraints excluded: chain R residue 326 ARG Chi-restraints excluded: chain R residue 340 MET Chi-restraints excluded: chain R residue 365 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 76 optimal weight: 0.0670 chunk 71 optimal weight: 3.9990 chunk 67 optimal weight: 7.9990 chunk 110 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 93 optimal weight: 0.6980 chunk 25 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 31 optimal weight: 0.0870 chunk 86 optimal weight: 0.4980 chunk 53 optimal weight: 3.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN ** R 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.159346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.095526 restraints weight = 12691.563| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.82 r_work: 0.2966 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9611 Z= 0.138 Angle : 0.524 7.766 13050 Z= 0.277 Chirality : 0.040 0.174 1444 Planarity : 0.004 0.058 1661 Dihedral : 5.288 58.906 1314 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 4.78 % Allowed : 31.47 % Favored : 63.75 % 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: 0.85 (0.26), residues: 1170 helix: 2.69 (0.25), residues: 445 sheet: 0.13 (0.34), residues: 230 loop : -1.28 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 420 HIS 0.003 0.000 HIS R 363 PHE 0.013 0.001 PHE R 230 TYR 0.021 0.001 TYR R 148 ARG 0.015 0.000 ARG R 48 Details of bonding type rmsd hydrogen bonds : bond 0.03872 ( 452) hydrogen bonds : angle 3.89391 ( 1287) SS BOND : bond 0.00176 ( 9) SS BOND : angle 0.57786 ( 18) covalent geometry : bond 0.00329 ( 9602) covalent geometry : angle 0.52442 (13032) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 100 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 LYS cc_start: 0.7466 (OUTLIER) cc_final: 0.6686 (mtpp) REVERT: A 327 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8397 (mp0) REVERT: A 380 ARG cc_start: 0.7577 (OUTLIER) cc_final: 0.6178 (tpm-80) REVERT: B 14 LEU cc_start: 0.7009 (OUTLIER) cc_final: 0.6712 (pt) REVERT: B 76 ASP cc_start: 0.8491 (p0) cc_final: 0.8265 (p0) REVERT: B 134 ARG cc_start: 0.7308 (mtp85) cc_final: 0.7076 (mtp85) REVERT: B 146 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8143 (mp) REVERT: B 175 GLN cc_start: 0.8399 (mm110) cc_final: 0.8190 (mm110) REVERT: B 228 ASP cc_start: 0.8546 (m-30) cc_final: 0.8192 (m-30) REVERT: G 48 ASP cc_start: 0.8201 (t0) cc_final: 0.7790 (t0) REVERT: N 83 MET cc_start: 0.6680 (ptp) cc_final: 0.5377 (ptm) REVERT: P 45 ASN cc_start: 0.6819 (OUTLIER) cc_final: 0.6423 (p0) REVERT: R 44 ARG cc_start: 0.8517 (tmm160) cc_final: 0.8221 (tmm160) REVERT: R 288 LYS cc_start: 0.8007 (OUTLIER) cc_final: 0.7775 (mptm) REVERT: R 326 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7228 (mmm160) REVERT: R 351 LYS cc_start: 0.7666 (tttm) cc_final: 0.7457 (tmtt) outliers start: 48 outliers final: 33 residues processed: 137 average time/residue: 1.1056 time to fit residues: 164.1425 Evaluate side-chains 131 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 90 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 297 TRP Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain P residue 27 ILE Chi-restraints excluded: chain P residue 45 ASN Chi-restraints excluded: chain R residue 126 CYS Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 217 LEU Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 288 LYS Chi-restraints excluded: chain R residue 326 ARG Chi-restraints excluded: chain R residue 340 MET Chi-restraints excluded: chain R residue 365 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 113 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 67 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 98 optimal weight: 0.5980 chunk 24 optimal weight: 7.9990 chunk 73 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 263 GLN ** R 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.158781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.094208 restraints weight = 12581.410| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 2.87 r_work: 0.2950 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 9611 Z= 0.160 Angle : 0.542 8.090 13050 Z= 0.287 Chirality : 0.041 0.167 1444 Planarity : 0.004 0.072 1661 Dihedral : 5.196 59.296 1311 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 4.78 % Allowed : 31.37 % Favored : 63.84 % 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: 0.78 (0.26), residues: 1170 helix: 2.60 (0.25), residues: 445 sheet: 0.11 (0.34), residues: 227 loop : -1.29 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP R 420 HIS 0.002 0.001 HIS R 363 PHE 0.015 0.001 PHE R 230 TYR 0.021 0.001 TYR R 148 ARG 0.018 0.001 ARG R 48 Details of bonding type rmsd hydrogen bonds : bond 0.04072 ( 452) hydrogen bonds : angle 3.92882 ( 1287) SS BOND : bond 0.00184 ( 9) SS BOND : angle 0.60099 ( 18) covalent geometry : bond 0.00389 ( 9602) covalent geometry : angle 0.54166 (13032) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 95 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 LYS cc_start: 0.7476 (OUTLIER) cc_final: 0.6683 (mtpp) REVERT: A 380 ARG cc_start: 0.7592 (OUTLIER) cc_final: 0.6192 (tpm-80) REVERT: B 14 LEU cc_start: 0.6973 (OUTLIER) cc_final: 0.6712 (pt) REVERT: B 76 ASP cc_start: 0.8410 (p0) cc_final: 0.8194 (p0) REVERT: B 134 ARG cc_start: 0.7299 (mtp85) cc_final: 0.7064 (mtp85) REVERT: B 146 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8179 (mp) REVERT: B 175 GLN cc_start: 0.8396 (mm110) cc_final: 0.8186 (mm110) REVERT: B 228 ASP cc_start: 0.8630 (m-30) cc_final: 0.8333 (m-30) REVERT: G 48 ASP cc_start: 0.8267 (t0) cc_final: 0.7811 (t0) REVERT: N 83 MET cc_start: 0.6616 (ptp) cc_final: 0.5210 (ptm) REVERT: P 45 ASN cc_start: 0.6768 (OUTLIER) cc_final: 0.6355 (p0) REVERT: R 44 ARG cc_start: 0.8526 (tmm160) cc_final: 0.8235 (tmm160) REVERT: R 48 ARG cc_start: 0.7536 (ttp80) cc_final: 0.7325 (ttp80) REVERT: R 288 LYS cc_start: 0.8016 (OUTLIER) cc_final: 0.7765 (mptm) REVERT: R 326 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7240 (mmm160) REVERT: R 351 LYS cc_start: 0.7668 (tttm) cc_final: 0.7455 (tmtt) outliers start: 48 outliers final: 35 residues processed: 132 average time/residue: 1.1425 time to fit residues: 162.9213 Evaluate side-chains 133 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 91 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 297 TRP Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain P residue 45 ASN Chi-restraints excluded: chain R residue 126 CYS Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 217 LEU Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 288 LYS Chi-restraints excluded: chain R residue 326 ARG Chi-restraints excluded: chain R residue 340 MET Chi-restraints excluded: chain R residue 365 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 14 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 98 optimal weight: 0.5980 chunk 95 optimal weight: 1.9990 chunk 0 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 5 optimal weight: 0.0170 chunk 34 optimal weight: 0.7980 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN R 263 GLN ** R 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.159172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.095435 restraints weight = 12711.322| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.83 r_work: 0.2970 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9611 Z= 0.134 Angle : 0.534 8.482 13050 Z= 0.282 Chirality : 0.040 0.164 1444 Planarity : 0.004 0.063 1661 Dihedral : 5.188 59.556 1311 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 4.88 % Allowed : 31.47 % Favored : 63.65 % 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: 0.83 (0.26), residues: 1170 helix: 2.65 (0.25), residues: 445 sheet: 0.15 (0.34), residues: 228 loop : -1.28 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP R 420 HIS 0.002 0.000 HIS A 357 PHE 0.013 0.001 PHE R 230 TYR 0.021 0.001 TYR R 148 ARG 0.017 0.000 ARG R 48 Details of bonding type rmsd hydrogen bonds : bond 0.03920 ( 452) hydrogen bonds : angle 3.89077 ( 1287) SS BOND : bond 0.00166 ( 9) SS BOND : angle 0.54899 ( 18) covalent geometry : bond 0.00319 ( 9602) covalent geometry : angle 0.53388 (13032) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 98 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 LYS cc_start: 0.7469 (OUTLIER) cc_final: 0.6676 (mtpp) REVERT: A 380 ARG cc_start: 0.7590 (OUTLIER) cc_final: 0.6193 (tpm-80) REVERT: B 14 LEU cc_start: 0.7014 (OUTLIER) cc_final: 0.6753 (pt) REVERT: B 134 ARG cc_start: 0.7312 (mtp85) cc_final: 0.7077 (mtp85) REVERT: B 146 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8148 (mp) REVERT: B 175 GLN cc_start: 0.8415 (mm110) cc_final: 0.8208 (mm110) REVERT: B 228 ASP cc_start: 0.8640 (m-30) cc_final: 0.8332 (m-30) REVERT: G 48 ASP cc_start: 0.8242 (t0) cc_final: 0.7789 (t0) REVERT: N 83 MET cc_start: 0.6678 (ptp) cc_final: 0.5276 (ptm) REVERT: P 45 ASN cc_start: 0.6798 (OUTLIER) cc_final: 0.6400 (p0) REVERT: R 44 ARG cc_start: 0.8526 (tmm160) cc_final: 0.8235 (tmm160) REVERT: R 288 LYS cc_start: 0.8015 (OUTLIER) cc_final: 0.7757 (mptm) REVERT: R 326 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7254 (mmm160) REVERT: R 351 LYS cc_start: 0.7665 (tttm) cc_final: 0.7455 (tmtt) outliers start: 49 outliers final: 35 residues processed: 136 average time/residue: 1.0122 time to fit residues: 150.3988 Evaluate side-chains 133 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 91 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 297 TRP Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain N residue 67 ARG Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain P residue 45 ASN Chi-restraints excluded: chain R residue 126 CYS Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 217 LEU Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 288 LYS Chi-restraints excluded: chain R residue 326 ARG Chi-restraints excluded: chain R residue 340 MET Chi-restraints excluded: chain R residue 365 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 44 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 77 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 81 optimal weight: 6.9990 chunk 56 optimal weight: 10.0000 chunk 29 optimal weight: 0.1980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 263 GLN ** R 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.159450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.095209 restraints weight = 12632.522| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 2.89 r_work: 0.2962 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 9611 Z= 0.139 Angle : 0.546 8.096 13050 Z= 0.288 Chirality : 0.040 0.163 1444 Planarity : 0.004 0.056 1661 Dihedral : 5.176 59.859 1311 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 4.08 % Allowed : 32.37 % Favored : 63.55 % 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: 0.83 (0.26), residues: 1170 helix: 2.65 (0.25), residues: 445 sheet: 0.04 (0.34), residues: 232 loop : -1.23 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP R 420 HIS 0.002 0.000 HIS A 357 PHE 0.013 0.001 PHE R 230 TYR 0.021 0.001 TYR R 148 ARG 0.015 0.000 ARG R 48 Details of bonding type rmsd hydrogen bonds : bond 0.03925 ( 452) hydrogen bonds : angle 3.88788 ( 1287) SS BOND : bond 0.00170 ( 9) SS BOND : angle 0.55425 ( 18) covalent geometry : bond 0.00337 ( 9602) covalent geometry : angle 0.54604 (13032) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7165.91 seconds wall clock time: 124 minutes 6.56 seconds (7446.56 seconds total)