Starting phenix.real_space_refine on Mon May 12 21:26:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j1p_61077/05_2025/9j1p_61077.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j1p_61077/05_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_61077/05_2025/9j1p_61077.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j1p_61077/05_2025/9j1p_61077.map" model { file = "/net/cci-nas-00/data/ceres_data/9j1p_61077/05_2025/9j1p_61077.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j1p_61077/05_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-5687/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: 5.83, per 1000 atoms: 0.62 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: 2.20 Conformation dependent library (CDL) restraints added in 1.1 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: 0.91 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: 2.68 Time building geometry restraints manager: 2.60 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: 1.580 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: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 23.330 Find NCS groups from input model: 0.110 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:11.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.240 ------------------------------------------------------------------------------- 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 : 1.014 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: 0.9977 time to fit residues: 130.6020 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 : 1.026 ------------------------------------------------------------------------------- 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 = 0.158979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.095030 restraints weight = 12468.956| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.79 r_work: 0.2964 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 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 0.038 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 59.221 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 4.30179 ( 1287) SS BOND : bond 0.00199 ( 9) SS BOND : angle 0.66662 ( 18) covalent geometry : bond 0.00360 ( 9602) covalent geometry : angle 0.50850 (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 : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 GLN cc_start: 0.8052 (tm-30) cc_final: 0.7430 (tm-30) REVERT: A 380 ARG cc_start: 0.7697 (OUTLIER) cc_final: 0.6328 (tpm-80) REVERT: B 12 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8288 (pm20) REVERT: B 14 LEU cc_start: 0.7081 (OUTLIER) cc_final: 0.6716 (pt) REVERT: B 76 ASP cc_start: 0.8492 (p0) cc_final: 0.8268 (p0) REVERT: B 175 GLN cc_start: 0.8327 (mm110) cc_final: 0.8069 (mm110) REVERT: B 228 ASP cc_start: 0.8686 (m-30) cc_final: 0.8405 (m-30) REVERT: G 48 ASP cc_start: 0.8392 (t0) cc_final: 0.8073 (t0) REVERT: P 45 ASN cc_start: 0.6906 (OUTLIER) cc_final: 0.6395 (p0) REVERT: R 213 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.8609 (mt0) REVERT: R 326 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.7339 (mmm160) outliers start: 57 outliers final: 26 residues processed: 148 average time/residue: 0.9233 time to fit residues: 149.0560 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 : 1.069 ------------------------------------------------------------------------------- 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: 0.2980 chunk 1 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 96 optimal weight: 0.5980 chunk 108 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 42 optimal weight: 0.0870 overall best weight: 0.4958 ------------------------------------------------------------------------------- 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 = 0.3960 r_free = 0.3960 target = 0.160074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.095952 restraints weight = 12617.287| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 2.85 r_work: 0.2976 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.0839 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= 0.116 Angle : 0.489 6.261 13050 Z= 0.260 Chirality : 0.039 0.134 1444 Planarity : 0.004 0.040 1661 Dihedral : 5.483 59.792 1316 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 5.48 % Allowed : 29.68 % 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: 0.97 (0.26), residues: 1170 helix: 2.71 (0.25), residues: 444 sheet: 0.40 (0.35), residues: 218 loop : -1.20 (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 0.012 0.001 PHE R 230 TYR 0.021 0.001 TYR R 148 ARG 0.008 0.000 ARG R 48 Details of bonding type rmsd hydrogen bonds : bond 0.04009 ( 452) hydrogen bonds : angle 4.08694 ( 1287) SS BOND : bond 0.00169 ( 9) SS BOND : angle 0.55689 ( 18) covalent geometry : bond 0.00266 ( 9602) covalent geometry : angle 0.48926 (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: 55 poor density : 102 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 LYS cc_start: 0.7440 (OUTLIER) cc_final: 0.6667 (mtpp) REVERT: A 380 ARG cc_start: 0.7546 (OUTLIER) cc_final: 0.6153 (tpm-80) REVERT: B 12 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8340 (pm20) REVERT: B 14 LEU cc_start: 0.7106 (OUTLIER) cc_final: 0.6806 (pt) REVERT: B 146 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8140 (mp) REVERT: B 175 GLN cc_start: 0.8352 (mm110) cc_final: 0.8057 (mm110) REVERT: B 228 ASP cc_start: 0.8569 (m-30) cc_final: 0.8202 (m-30) REVERT: G 48 ASP cc_start: 0.8229 (t0) cc_final: 0.7808 (t0) REVERT: P 45 ASN cc_start: 0.6883 (OUTLIER) cc_final: 0.6422 (p0) REVERT: R 288 LYS cc_start: 0.7932 (OUTLIER) cc_final: 0.7698 (mptm) REVERT: R 326 ARG cc_start: 0.8157 (OUTLIER) cc_final: 0.7151 (mmm160) REVERT: R 351 LYS cc_start: 0.7653 (tttm) cc_final: 0.7425 (tmtt) outliers start: 55 outliers final: 25 residues processed: 148 average time/residue: 0.9664 time to fit residues: 155.5206 Evaluate side-chains 125 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 92 time to evaluate : 1.042 ------------------------------------------------------------------------------- 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 325 THR 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 146 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 234 PHE 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 172 LEU Chi-restraints excluded: chain R residue 193 SER 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: 0.5980 chunk 113 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 110 optimal weight: 0.9980 chunk 79 optimal weight: 20.0000 chunk 59 optimal weight: 0.9980 chunk 100 optimal weight: 0.6980 chunk 86 optimal weight: 9.9990 chunk 112 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 chunk 103 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3949 r_free = 0.3949 target = 0.159040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.094751 restraints weight = 12489.707| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 2.85 r_work: 0.2961 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.1012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9611 Z= 0.142 Angle : 0.503 5.960 13050 Z= 0.269 Chirality : 0.040 0.182 1444 Planarity : 0.004 0.041 1661 Dihedral : 5.483 59.497 1316 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 5.58 % Allowed : 29.48 % 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: 0.89 (0.26), residues: 1170 helix: 2.65 (0.25), residues: 444 sheet: 0.16 (0.34), residues: 227 loop : -1.17 (0.29), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 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 0.04057 ( 452) hydrogen bonds : angle 4.04047 ( 1287) SS BOND : bond 0.00183 ( 9) SS BOND : angle 0.60090 ( 18) covalent geometry : bond 0.00337 ( 9602) covalent geometry : angle 0.50252 (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 153 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 97 time to evaluate : 0.978 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: 0.7459 (OUTLIER) cc_final: 0.6685 (mtpp) REVERT: A 327 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8369 (mp0) REVERT: A 380 ARG cc_start: 0.7576 (OUTLIER) cc_final: 0.6176 (tpm-80) REVERT: B 12 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8371 (pm20) REVERT: B 14 LEU cc_start: 0.7221 (OUTLIER) cc_final: 0.6854 (pt) REVERT: B 76 ASP cc_start: 0.8576 (p0) cc_final: 0.8291 (p0) REVERT: B 146 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8120 (mp) REVERT: B 228 ASP cc_start: 0.8530 (m-30) cc_final: 0.8231 (m-30) REVERT: G 48 ASP cc_start: 0.8240 (t0) cc_final: 0.7818 (t0) REVERT: P 45 ASN cc_start: 0.6889 (OUTLIER) cc_final: 0.6493 (p0) REVERT: R 288 LYS cc_start: 0.7984 (OUTLIER) cc_final: 0.7764 (mptm) REVERT: R 326 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7220 (mmm160) REVERT: R 351 LYS cc_start: 0.7669 (tttm) cc_final: 0.7448 (tmtt) outliers start: 56 outliers final: 32 residues processed: 144 average time/residue: 0.9754 time to fit residues: 152.6449 Evaluate side-chains 130 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 89 time to evaluate : 1.050 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 110 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 37 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 24 optimal weight: 9.9990 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 = 0.3949 r_free = 0.3949 target = 0.159079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.094914 restraints weight = 12534.604| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.86 r_work: 0.2954 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.1028 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= 0.135 Angle : 0.503 6.344 13050 Z= 0.268 Chirality : 0.040 0.167 1444 Planarity : 0.004 0.041 1661 Dihedral : 5.421 59.071 1316 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 5.78 % Allowed : 29.68 % Favored : 64.54 % 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: 0.93 (0.26), residues: 1170 helix: 2.70 (0.25), residues: 444 sheet: 0.30 (0.35), residues: 220 loop : -1.21 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 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 0.010 0.000 ARG R 48 Details of bonding type rmsd hydrogen bonds : bond 0.03968 ( 452) hydrogen bonds : angle 3.98162 ( 1287) SS BOND : bond 0.00174 ( 9) SS BOND : angle 0.64924 ( 18) covalent geometry : bond 0.00319 ( 9602) covalent geometry : angle 0.50263 (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 158 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 100 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 LYS cc_start: 0.7441 (OUTLIER) cc_final: 0.6644 (mtpp) REVERT: A 327 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8371 (mp0) REVERT: A 380 ARG cc_start: 0.7575 (OUTLIER) cc_final: 0.6173 (tpm-80) REVERT: B 12 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8445 (pm20) REVERT: B 14 LEU cc_start: 0.7143 (OUTLIER) cc_final: 0.6816 (pt) REVERT: B 76 ASP cc_start: 0.8594 (p0) cc_final: 0.8280 (p0) REVERT: B 134 ARG cc_start: 0.7267 (mtp85) cc_final: 0.7047 (mtp85) REVERT: B 146 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8113 (mp) REVERT: B 228 ASP cc_start: 0.8576 (m-30) cc_final: 0.8318 (m-30) REVERT: G 48 ASP cc_start: 0.8238 (t0) cc_final: 0.7840 (t0) REVERT: P 45 ASN cc_start: 0.6846 (OUTLIER) cc_final: 0.6416 (p0) REVERT: R 288 LYS cc_start: 0.7988 (OUTLIER) cc_final: 0.7760 (mptm) REVERT: R 326 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7226 (mmm160) REVERT: R 351 LYS cc_start: 0.7656 (tttm) cc_final: 0.7439 (tmtt) outliers start: 58 outliers final: 35 residues processed: 148 average time/residue: 1.0605 time to fit residues: 169.7376 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 : 1.103 ------------------------------------------------------------------------------- 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 0.5980 chunk 7 optimal weight: 0.4980 chunk 87 optimal weight: 0.0040 chunk 1 optimal weight: 0.5980 chunk 69 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 10 optimal weight: 0.4980 chunk 95 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 overall best weight: 0.4392 ------------------------------------------------------------------------------- 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 = 0.3959 r_free = 0.3959 target = 0.160005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.096594 restraints weight = 12481.526| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 2.81 r_work: 0.2990 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.1133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9611 Z= 0.111 Angle : 0.494 6.563 13050 Z= 0.263 Chirality : 0.039 0.160 1444 Planarity : 0.003 0.040 1661 Dihedral : 5.371 59.029 1316 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 4.98 % Allowed : 30.88 % Favored : 64.14 % 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: 0.97 (0.26), residues: 1170 helix: 2.75 (0.25), residues: 445 sheet: 0.39 (0.35), residues: 218 loop : -1.25 (0.28), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.002 0.000 HIS A 357 PHE 0.011 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 0.03738 ( 452) hydrogen bonds : angle 3.88723 ( 1287) SS BOND : bond 0.00156 ( 9) SS BOND : angle 0.58474 ( 18) covalent geometry : bond 0.00259 ( 9602) covalent geometry : angle 0.49349 (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 149 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 99 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 LYS cc_start: 0.7444 (OUTLIER) cc_final: 0.6615 (mtpp) REVERT: A 327 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8414 (mp0) REVERT: A 380 ARG cc_start: 0.7648 (OUTLIER) cc_final: 0.6341 (tpm-80) REVERT: B 12 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8505 (pm20) REVERT: B 14 LEU cc_start: 0.7020 (OUTLIER) cc_final: 0.6746 (pt) REVERT: B 76 ASP cc_start: 0.8693 (p0) cc_final: 0.8433 (p0) REVERT: B 134 ARG cc_start: 0.7343 (mtp85) cc_final: 0.7130 (mtp85) REVERT: B 146 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8228 (mp) REVERT: B 228 ASP cc_start: 0.8616 (m-30) cc_final: 0.8226 (m-30) REVERT: P 45 ASN cc_start: 0.6801 (OUTLIER) cc_final: 0.6387 (p0) REVERT: R 41 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8058 (tm-30) REVERT: R 44 ARG cc_start: 0.8562 (tmm160) cc_final: 0.8326 (tmm160) REVERT: R 288 LYS cc_start: 0.8002 (OUTLIER) cc_final: 0.7769 (mptm) REVERT: R 326 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7327 (mmm160) REVERT: R 420 TRP cc_start: 0.8084 (t60) cc_final: 0.7813 (t60) outliers start: 50 outliers final: 30 residues processed: 140 average time/residue: 1.0387 time to fit residues: 157.4969 Evaluate side-chains 131 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 91 time to evaluate : 0.979 ------------------------------------------------------------------------------- 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 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 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 296 VAL Chi-restraints excluded: chain B residue 297 TRP 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 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 172 LEU Chi-restraints excluded: chain R residue 193 SER 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: 0.5980 chunk 45 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 98 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 62 optimal weight: 0.0980 chunk 3 optimal weight: 0.0270 chunk 25 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.4638 ------------------------------------------------------------------------------- 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 = 0.3964 r_free = 0.3964 target = 0.160288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.096452 restraints weight = 12616.321| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 2.87 r_work: 0.2982 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.1160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9611 Z= 0.115 Angle : 0.500 7.014 13050 Z= 0.265 Chirality : 0.039 0.168 1444 Planarity : 0.003 0.050 1661 Dihedral : 5.255 58.645 1314 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 5.28 % Allowed : 30.98 % 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: 0.96 (0.26), residues: 1170 helix: 2.76 (0.25), residues: 445 sheet: 0.31 (0.34), residues: 223 loop : -1.25 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.002 0.000 HIS A 357 PHE 0.014 0.001 PHE N 103 TYR 0.021 0.001 TYR R 148 ARG 0.013 0.000 ARG R 48 Details of bonding type rmsd hydrogen bonds : bond 0.03699 ( 452) hydrogen bonds : angle 3.85589 ( 1287) SS BOND : bond 0.00149 ( 9) SS BOND : angle 0.56013 ( 18) covalent geometry : bond 0.00269 ( 9602) covalent geometry : angle 0.49970 (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 155 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 102 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 327 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8372 (mp0) REVERT: A 380 ARG cc_start: 0.7568 (OUTLIER) cc_final: 0.6174 (tpm-80) REVERT: B 12 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.8572 (pm20) REVERT: B 14 LEU cc_start: 0.7005 (OUTLIER) cc_final: 0.6722 (pt) REVERT: B 76 ASP cc_start: 0.8492 (p0) cc_final: 0.8232 (p0) REVERT: B 134 ARG cc_start: 0.7278 (mtp85) cc_final: 0.7056 (mtp85) REVERT: B 146 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8125 (mp) REVERT: B 228 ASP cc_start: 0.8520 (m-30) cc_final: 0.8121 (m-30) REVERT: N 83 MET cc_start: 0.6766 (ptp) cc_final: 0.5406 (ptm) REVERT: P 45 ASN cc_start: 0.6872 (OUTLIER) cc_final: 0.6481 (p0) REVERT: R 41 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.7966 (tm-30) REVERT: R 44 ARG cc_start: 0.8517 (tmm160) cc_final: 0.8273 (tmm160) REVERT: R 288 LYS cc_start: 0.7979 (OUTLIER) cc_final: 0.7725 (mptm) REVERT: R 326 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.7201 (mmm160) outliers start: 53 outliers final: 37 residues processed: 144 average time/residue: 1.0197 time to fit residues: 159.1788 Evaluate side-chains 140 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 94 time to evaluate : 1.017 ------------------------------------------------------------------------------- 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 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 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 41 GLU Chi-restraints excluded: chain R residue 126 CYS Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain R residue 193 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 76 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 67 optimal weight: 8.9990 chunk 110 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 81 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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** B 44 GLN N 1 GLN R 263 GLN ** R 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.156847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.091948 restraints weight = 12792.323| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 2.87 r_work: 0.2916 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 9611 Z= 0.225 Angle : 0.574 7.847 13050 Z= 0.305 Chirality : 0.042 0.175 1444 Planarity : 0.004 0.058 1661 Dihedral : 5.457 58.467 1314 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 5.78 % Allowed : 30.18 % Favored : 64.04 % 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: 0.69 (0.25), residues: 1170 helix: 2.39 (0.24), residues: 449 sheet: 0.10 (0.34), residues: 225 loop : -1.25 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 420 HIS 0.002 0.001 HIS R 180 PHE 0.019 0.001 PHE R 230 TYR 0.022 0.002 TYR R 148 ARG 0.014 0.001 ARG R 48 Details of bonding type rmsd hydrogen bonds : bond 0.04552 ( 452) hydrogen bonds : angle 4.07427 ( 1287) SS BOND : bond 0.00250 ( 9) SS BOND : angle 0.70897 ( 18) covalent geometry : bond 0.00541 ( 9602) covalent geometry : angle 0.57422 (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 154 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 96 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 LYS cc_start: 0.7557 (OUTLIER) cc_final: 0.6801 (mtpp) REVERT: A 317 ARG cc_start: 0.8450 (mtm-85) cc_final: 0.8249 (mtm-85) REVERT: A 323 ASP cc_start: 0.8985 (t0) cc_final: 0.8723 (t0) REVERT: A 380 ARG cc_start: 0.7671 (OUTLIER) cc_final: 0.6098 (tpm-80) REVERT: B 14 LEU cc_start: 0.7039 (OUTLIER) cc_final: 0.6737 (pt) REVERT: B 76 ASP cc_start: 0.8501 (p0) cc_final: 0.8235 (p0) REVERT: B 134 ARG cc_start: 0.7298 (mtp85) cc_final: 0.7049 (mtp85) REVERT: B 146 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8204 (mp) REVERT: B 228 ASP cc_start: 0.8690 (m-30) cc_final: 0.8361 (m-30) REVERT: G 48 ASP cc_start: 0.8289 (t0) cc_final: 0.7867 (t0) REVERT: P 45 ASN cc_start: 0.6834 (OUTLIER) cc_final: 0.6415 (p0) REVERT: R 44 ARG cc_start: 0.8521 (tmm160) cc_final: 0.8148 (tmm160) REVERT: R 288 LYS cc_start: 0.7985 (OUTLIER) cc_final: 0.7772 (mptm) REVERT: R 326 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7270 (mmm160) outliers start: 58 outliers final: 31 residues processed: 143 average time/residue: 1.0951 time to fit residues: 169.3013 Evaluate side-chains 128 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 90 time to evaluate : 1.063 ------------------------------------------------------------------------------- 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 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 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 186 ASP Chi-restraints excluded: chain B residue 234 PHE 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 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 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 Chi-restraints excluded: chain R residue 340 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 113 optimal weight: 0.5980 chunk 88 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 63 optimal weight: 9.9990 chunk 98 optimal weight: 0.5980 chunk 24 optimal weight: 7.9990 chunk 73 optimal weight: 0.7980 chunk 48 optimal weight: 0.0010 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN B 44 GLN R 263 GLN ** R 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.159322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.095081 restraints weight = 12530.335| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 2.86 r_work: 0.2963 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 9611 Z= 0.130 Angle : 0.540 8.245 13050 Z= 0.287 Chirality : 0.040 0.164 1444 Planarity : 0.004 0.071 1661 Dihedral : 5.228 59.538 1311 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 4.48 % Allowed : 31.87 % 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: 0.79 (0.26), residues: 1170 helix: 2.62 (0.25), residues: 445 sheet: 0.16 (0.34), residues: 223 loop : -1.31 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP R 420 HIS 0.001 0.000 HIS A 357 PHE 0.012 0.001 PHE R 230 TYR 0.021 0.001 TYR R 148 ARG 0.019 0.000 ARG R 48 Details of bonding type rmsd hydrogen bonds : bond 0.03996 ( 452) hydrogen bonds : angle 3.93876 ( 1287) SS BOND : bond 0.00153 ( 9) SS BOND : angle 0.60086 ( 18) covalent geometry : bond 0.00311 ( 9602) covalent geometry : angle 0.54025 (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 142 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 97 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 327 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.8406 (mp0) REVERT: A 380 ARG cc_start: 0.7566 (OUTLIER) cc_final: 0.6162 (tpm-80) REVERT: B 14 LEU cc_start: 0.6996 (OUTLIER) cc_final: 0.6689 (pt) REVERT: B 76 ASP cc_start: 0.8354 (p0) cc_final: 0.8130 (p0) REVERT: B 134 ARG cc_start: 0.7263 (mtp85) cc_final: 0.7025 (mtp85) REVERT: B 146 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8121 (mp) REVERT: B 228 ASP cc_start: 0.8596 (m-30) cc_final: 0.8200 (m-30) REVERT: G 48 ASP cc_start: 0.8214 (t0) cc_final: 0.7778 (t0) REVERT: N 83 MET cc_start: 0.6476 (ptp) cc_final: 0.5115 (ptm) REVERT: P 45 ASN cc_start: 0.6783 (OUTLIER) cc_final: 0.6375 (p0) REVERT: R 44 ARG cc_start: 0.8517 (tmm160) cc_final: 0.8224 (tmm160) REVERT: R 48 ARG cc_start: 0.7539 (ttp80) cc_final: 0.7333 (ttp80) REVERT: R 288 LYS cc_start: 0.7977 (OUTLIER) cc_final: 0.7736 (mptm) REVERT: R 326 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7228 (mmm160) outliers start: 45 outliers final: 30 residues processed: 131 average time/residue: 1.0489 time to fit residues: 148.6790 Evaluate side-chains 132 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 95 time to evaluate : 0.976 ------------------------------------------------------------------------------- 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 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 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 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 14 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 98 optimal weight: 0.5980 chunk 95 optimal weight: 2.9990 chunk 0 optimal weight: 0.7980 chunk 49 optimal weight: 0.0010 chunk 53 optimal weight: 1.9990 chunk 62 optimal weight: 0.0980 chunk 5 optimal weight: 0.0970 chunk 34 optimal weight: 1.9990 overall best weight: 0.3184 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.161235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.097342 restraints weight = 12720.970| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.91 r_work: 0.2999 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 9611 Z= 0.110 Angle : 0.530 8.846 13050 Z= 0.279 Chirality : 0.040 0.159 1444 Planarity : 0.004 0.065 1661 Dihedral : 5.117 59.233 1311 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 3.29 % Allowed : 32.97 % 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: 0.93 (0.26), residues: 1170 helix: 2.80 (0.25), residues: 445 sheet: 0.15 (0.34), residues: 228 loop : -1.26 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP R 420 HIS 0.001 0.000 HIS P 1 PHE 0.009 0.001 PHE R 230 TYR 0.022 0.001 TYR R 148 ARG 0.017 0.000 ARG R 48 Details of bonding type rmsd hydrogen bonds : bond 0.03591 ( 452) hydrogen bonds : angle 3.82202 ( 1287) SS BOND : bond 0.00156 ( 9) SS BOND : angle 0.57990 ( 18) covalent geometry : bond 0.00260 ( 9602) covalent geometry : angle 0.52986 (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 138 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 105 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 293 LYS cc_start: 0.7430 (OUTLIER) cc_final: 0.6623 (mtpp) REVERT: A 380 ARG cc_start: 0.7545 (OUTLIER) cc_final: 0.6164 (tpm-80) REVERT: B 14 LEU cc_start: 0.7007 (OUTLIER) cc_final: 0.6748 (pt) REVERT: B 61 MET cc_start: 0.9241 (ppp) cc_final: 0.9024 (ptm) REVERT: B 134 ARG cc_start: 0.7274 (mtp85) cc_final: 0.7045 (mtp85) REVERT: B 228 ASP cc_start: 0.8517 (m-30) cc_final: 0.8191 (m-30) REVERT: B 297 TRP cc_start: 0.8224 (OUTLIER) cc_final: 0.7880 (m-10) REVERT: N 83 MET cc_start: 0.6624 (ptp) cc_final: 0.5181 (ptm) REVERT: P 45 ASN cc_start: 0.6806 (m110) cc_final: 0.6414 (p0) REVERT: R 44 ARG cc_start: 0.8532 (tmm160) cc_final: 0.8243 (tmm160) REVERT: R 326 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.7194 (mmm160) outliers start: 33 outliers final: 24 residues processed: 128 average time/residue: 0.9491 time to fit residues: 132.3249 Evaluate side-chains 123 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 94 time to evaluate : 1.045 ------------------------------------------------------------------------------- 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 181 THR Chi-restraints excluded: chain B residue 232 ILE 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 331 SER Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 126 CYS 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 326 ARG Chi-restraints excluded: chain R residue 340 MET 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: 0.5980 chunk 58 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 81 optimal weight: 0.3980 chunk 56 optimal weight: 20.0000 chunk 29 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 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 = 0.3953 r_free = 0.3953 target = 0.159246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.095449 restraints weight = 12570.243| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 2.85 r_work: 0.2966 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9611 Z= 0.142 Angle : 0.546 7.763 13050 Z= 0.288 Chirality : 0.041 0.160 1444 Planarity : 0.004 0.056 1661 Dihedral : 4.882 47.898 1309 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 3.29 % Allowed : 33.17 % 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: 0.88 (0.26), residues: 1170 helix: 2.72 (0.25), residues: 445 sheet: 0.18 (0.34), residues: 223 loop : -1.27 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP R 420 HIS 0.001 0.000 HIS A 387 PHE 0.014 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 0.03881 ( 452) hydrogen bonds : angle 3.85151 ( 1287) SS BOND : bond 0.00168 ( 9) SS BOND : angle 0.56441 ( 18) covalent geometry : bond 0.00341 ( 9602) covalent geometry : angle 0.54603 (13032) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6963.09 seconds wall clock time: 120 minutes 34.23 seconds (7234.23 seconds total)