Starting phenix.real_space_refine on Wed Sep 17 15:16:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j1p_61077/09_2025/9j1p_61077.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j1p_61077/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9j1p_61077/09_2025/9j1p_61077.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j1p_61077/09_2025/9j1p_61077.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9j1p_61077/09_2025/9j1p_61077.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j1p_61077/09_2025/9j1p_61077.map" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ARG:plan': 1, 'GLU:plan': 1, 'GLN:plan1': 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: {'ASP:plan': 4, 'GLU:plan': 1, 'GLN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 34 Time building chain proxies: 2.01, per 1000 atoms: 0.21 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: 0.74 Conformation dependent library (CDL) restraints added in 290.7 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.30 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: 1.36 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3050 1.34 - 1.46: 2042 1.46 - 1.58: 4425 1.58 - 1.70: 0 1.70 - 1.82: 85 Bond restraints: 9602 Sorted by residual: bond pdb=" N ASN B 16 " pdb=" CA ASN B 16 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.21e-02 6.83e+03 6.10e+00 bond pdb=" N LEU B 14 " pdb=" CA LEU B 14 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.35e-02 5.49e+03 4.37e+00 bond pdb=" N GLU B 12 " pdb=" CA GLU B 12 " ideal model delta sigma weight residual 1.459 1.485 -0.027 1.28e-02 6.10e+03 4.31e+00 bond pdb=" N GLN B 13 " pdb=" CA GLN B 13 " ideal model delta sigma weight residual 1.459 1.484 -0.024 1.19e-02 7.06e+03 4.14e+00 bond pdb=" N LYS B 15 " pdb=" CA LYS B 15 " ideal model delta sigma weight residual 1.458 1.483 -0.026 1.27e-02 6.20e+03 4.04e+00 ... (remaining 9597 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 12867 1.94 - 3.87: 139 3.87 - 5.81: 18 5.81 - 7.75: 5 7.75 - 9.69: 3 Bond angle restraints: 13032 Sorted by residual: angle pdb=" N LEU B 14 " pdb=" CA LEU B 14 " pdb=" C LEU B 14 " ideal model delta sigma weight residual 113.01 108.74 4.27 1.20e+00 6.94e-01 1.26e+01 angle pdb=" N ASN B 16 " pdb=" CA ASN B 16 " pdb=" C ASN B 16 " ideal model delta sigma weight residual 111.28 107.62 3.66 1.09e+00 8.42e-01 1.13e+01 angle pdb=" CA GLU A 299 " pdb=" CB GLU A 299 " pdb=" CG GLU A 299 " ideal model delta sigma weight residual 114.10 120.66 -6.56 2.00e+00 2.50e-01 1.07e+01 angle pdb=" CB MET B 217 " pdb=" CG MET B 217 " pdb=" SD MET B 217 " ideal model delta sigma weight residual 112.70 122.39 -9.69 3.00e+00 1.11e-01 1.04e+01 angle pdb=" CB MET R 397 " pdb=" CG MET R 397 " pdb=" SD MET R 397 " ideal model delta sigma weight residual 112.70 122.34 -9.64 3.00e+00 1.11e-01 1.03e+01 ... (remaining 13027 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 4773 17.65 - 35.31: 667 35.31 - 52.96: 194 52.96 - 70.61: 42 70.61 - 88.26: 16 Dihedral angle restraints: 5692 sinusoidal: 2232 harmonic: 3460 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 2.26 -88.26 1 1.00e+01 1.00e-02 9.31e+01 dihedral pdb=" CB CYS R 46 " pdb=" SG CYS R 46 " pdb=" SG CYS R 71 " pdb=" CB CYS R 71 " ideal model delta sinusoidal sigma weight residual -86.00 -163.67 77.67 1 1.00e+01 1.00e-02 7.55e+01 dihedral pdb=" CB CYS R 62 " pdb=" SG CYS R 62 " pdb=" SG CYS R 104 " pdb=" CB CYS R 104 " ideal model delta sinusoidal sigma weight residual 93.00 163.68 -70.68 1 1.00e+01 1.00e-02 6.42e+01 ... (remaining 5689 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 942 0.030 - 0.060: 312 0.060 - 0.090: 123 0.090 - 0.120: 60 0.120 - 0.150: 7 Chirality restraints: 1444 Sorted by residual: chirality pdb=" CG LEU B 14 " pdb=" CB LEU B 14 " pdb=" CD1 LEU B 14 " pdb=" CD2 LEU B 14 " both_signs ideal model delta sigma weight residual False -2.59 -2.74 0.15 2.00e-01 2.50e+01 5.60e-01 chirality pdb=" CA ILE B 93 " pdb=" N ILE B 93 " pdb=" C ILE B 93 " pdb=" CB ILE B 93 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.48e-01 chirality pdb=" CA TYR R 88 " pdb=" N TYR R 88 " pdb=" C TYR R 88 " pdb=" CB TYR R 88 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.29e-01 ... (remaining 1441 not shown) Planarity restraints: 1661 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG R 48 " 0.133 9.50e-02 1.11e+02 6.05e-02 3.33e+00 pdb=" NE ARG R 48 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG R 48 " 0.017 2.00e-02 2.50e+03 pdb=" NH1 ARG R 48 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG R 48 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL R 276 " -0.025 5.00e-02 4.00e+02 3.77e-02 2.27e+00 pdb=" N PRO R 277 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO R 277 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO R 277 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TRP R 87 " -0.007 2.00e-02 2.50e+03 1.47e-02 2.17e+00 pdb=" C TRP R 87 " 0.025 2.00e-02 2.50e+03 pdb=" O TRP R 87 " -0.010 2.00e-02 2.50e+03 pdb=" N TYR R 88 " -0.009 2.00e-02 2.50e+03 ... (remaining 1658 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 655 2.73 - 3.27: 9380 3.27 - 3.82: 16039 3.82 - 4.36: 18308 4.36 - 4.90: 32227 Nonbonded interactions: 76609 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.191 3.040 nonbonded pdb=" OG1 THR B 321 " pdb=" O ALA B 326 " model vdw 2.199 3.040 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.219 3.040 nonbonded pdb=" OH TYR P 13 " pdb=" OE1 GLU R 138 " model vdw 2.224 3.040 nonbonded pdb=" N GLU G 47 " pdb=" OE1 GLU G 47 " model vdw 2.228 3.120 ... (remaining 76604 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.250 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.960 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.580 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.018 0.001 ARG R 48 TYR 0.021 0.001 TYR R 148 PHE 0.011 0.001 PHE R 230 TRP 0.024 0.001 TRP R 420 HIS 0.003 0.000 HIS R 212 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 9602) covalent geometry : angle 0.53225 (13032) SS BOND : bond 0.00205 ( 9) SS BOND : angle 1.03228 ( 18) hydrogen bonds : bond 0.15099 ( 452) hydrogen bonds : angle 5.40995 ( 1287) *********************** 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 : 0.333 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: 0.4610 time to fit residues: 59.9231 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 : 0.345 ------------------------------------------------------------------------------- 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 108 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.3980 chunk 113 optimal weight: 0.5980 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.0070 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 overall best weight: 0.4598 ------------------------------------------------------------------------------- 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 = 0.3969 r_free = 0.3969 target = 0.160536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.096536 restraints weight = 12506.230| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 2.84 r_work: 0.2972 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.0673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9611 Z= 0.118 Angle : 0.494 7.378 13050 Z= 0.266 Chirality : 0.040 0.142 1444 Planarity : 0.004 0.039 1661 Dihedral : 6.104 59.518 1342 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 4.88 % Allowed : 30.28 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.26), residues: 1170 helix: 2.72 (0.25), residues: 444 sheet: 0.39 (0.36), residues: 219 loop : -1.19 (0.28), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 48 TYR 0.021 0.001 TYR R 148 PHE 0.012 0.001 PHE R 230 TRP 0.017 0.001 TRP B 82 HIS 0.002 0.001 HIS R 212 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 9602) covalent geometry : angle 0.49340 (13032) SS BOND : bond 0.00166 ( 9) SS BOND : angle 0.61378 ( 18) hydrogen bonds : bond 0.04241 ( 452) hydrogen bonds : angle 4.28024 ( 1287) *********************** 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 151 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 102 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 GLN cc_start: 0.7974 (tm-30) cc_final: 0.7331 (tm-30) REVERT: A 380 ARG cc_start: 0.7586 (OUTLIER) cc_final: 0.6201 (tpm-80) REVERT: B 12 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8304 (pm20) REVERT: B 14 LEU cc_start: 0.7052 (OUTLIER) cc_final: 0.6681 (pt) REVERT: B 76 ASP cc_start: 0.8317 (p0) cc_final: 0.8062 (p0) REVERT: B 175 GLN cc_start: 0.8340 (mm110) cc_final: 0.7980 (mm110) REVERT: B 222 PHE cc_start: 0.8446 (m-80) cc_final: 0.8242 (m-80) REVERT: B 228 ASP cc_start: 0.8574 (m-30) cc_final: 0.8231 (m-30) REVERT: B 291 ASP cc_start: 0.7322 (p0) cc_final: 0.7103 (p0) REVERT: R 326 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7201 (mmm160) outliers start: 49 outliers final: 24 residues processed: 142 average time/residue: 0.4474 time to fit residues: 68.7622 Evaluate side-chains 123 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 95 time to evaluate : 0.400 ------------------------------------------------------------------------------- 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 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 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 326 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 71 optimal weight: 8.9990 chunk 107 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 chunk 58 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 67 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 97 optimal weight: 0.0980 chunk 23 optimal weight: 5.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN R 213 GLN ** R 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.158047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.093365 restraints weight = 12565.535| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.82 r_work: 0.2936 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.0864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9611 Z= 0.177 Angle : 0.524 6.407 13050 Z= 0.279 Chirality : 0.041 0.147 1444 Planarity : 0.004 0.041 1661 Dihedral : 5.567 59.531 1316 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 5.98 % Allowed : 29.08 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.26), residues: 1170 helix: 2.58 (0.25), residues: 444 sheet: 0.28 (0.35), residues: 222 loop : -1.21 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 48 TYR 0.022 0.001 TYR R 148 PHE 0.016 0.001 PHE R 230 TRP 0.015 0.001 TRP B 82 HIS 0.002 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00421 ( 9602) covalent geometry : angle 0.52428 (13032) SS BOND : bond 0.00209 ( 9) SS BOND : angle 0.65026 ( 18) hydrogen bonds : bond 0.04440 ( 452) hydrogen bonds : angle 4.18593 ( 1287) *********************** 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 158 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 98 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 LYS cc_start: 0.7519 (OUTLIER) cc_final: 0.6755 (mtpp) REVERT: A 380 ARG cc_start: 0.7650 (OUTLIER) cc_final: 0.6088 (tpm-80) REVERT: B 12 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8327 (pm20) REVERT: B 14 LEU cc_start: 0.7118 (OUTLIER) cc_final: 0.6800 (pt) REVERT: B 76 ASP cc_start: 0.8380 (p0) cc_final: 0.8179 (p0) REVERT: B 146 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8089 (mp) REVERT: B 175 GLN cc_start: 0.8341 (mm110) cc_final: 0.8064 (mm110) REVERT: B 228 ASP cc_start: 0.8625 (m-30) cc_final: 0.8321 (m-30) REVERT: G 48 ASP cc_start: 0.8346 (t0) cc_final: 0.7942 (t0) REVERT: P 45 ASN cc_start: 0.6852 (OUTLIER) cc_final: 0.6337 (p0) REVERT: R 288 LYS cc_start: 0.7988 (OUTLIER) cc_final: 0.7751 (mptm) REVERT: R 326 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7235 (mmm160) REVERT: R 420 TRP cc_start: 0.8133 (t60) cc_final: 0.7851 (t60) outliers start: 60 outliers final: 28 residues processed: 147 average time/residue: 0.4470 time to fit residues: 71.0292 Evaluate side-chains 128 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 92 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU 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 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 55 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 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 51 LEU Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain N residue 67 ARG Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain P residue 45 ASN Chi-restraints excluded: chain R residue 126 CYS Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 217 LEU Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 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 21 optimal weight: 0.5980 chunk 101 optimal weight: 0.9980 chunk 79 optimal weight: 0.3980 chunk 68 optimal weight: 9.9990 chunk 69 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 92 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 chunk 24 optimal weight: 9.9990 chunk 3 optimal weight: 0.0970 chunk 105 optimal weight: 0.6980 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 = 0.3950 r_free = 0.3950 target = 0.159152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.095712 restraints weight = 12635.278| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 2.80 r_work: 0.2978 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.0988 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= 0.121 Angle : 0.492 6.069 13050 Z= 0.263 Chirality : 0.040 0.135 1444 Planarity : 0.004 0.040 1661 Dihedral : 5.479 59.634 1316 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 5.28 % Allowed : 29.48 % Favored : 65.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.26), residues: 1170 helix: 2.67 (0.25), residues: 444 sheet: 0.41 (0.35), residues: 218 loop : -1.24 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG R 48 TYR 0.021 0.001 TYR R 148 PHE 0.013 0.001 PHE R 230 TRP 0.015 0.001 TRP B 82 HIS 0.002 0.000 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 9602) covalent geometry : angle 0.49162 (13032) SS BOND : bond 0.00163 ( 9) SS BOND : angle 0.56339 ( 18) hydrogen bonds : bond 0.03987 ( 452) hydrogen bonds : angle 4.02546 ( 1287) *********************** 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 152 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 99 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 LYS cc_start: 0.7452 (OUTLIER) cc_final: 0.6672 (mtpp) REVERT: A 327 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8401 (mp0) REVERT: A 380 ARG cc_start: 0.7637 (OUTLIER) cc_final: 0.6330 (tpm-80) REVERT: B 12 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.8346 (pm20) REVERT: B 14 LEU cc_start: 0.7246 (OUTLIER) cc_final: 0.6871 (pt) REVERT: B 175 GLN cc_start: 0.8368 (mm110) cc_final: 0.8072 (mm110) REVERT: B 228 ASP cc_start: 0.8662 (m-30) cc_final: 0.8379 (m-30) REVERT: G 48 ASP cc_start: 0.8292 (t0) cc_final: 0.7893 (t0) REVERT: P 45 ASN cc_start: 0.6734 (OUTLIER) cc_final: 0.6297 (p0) REVERT: R 41 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.7997 (tm-30) REVERT: R 44 ARG cc_start: 0.8575 (tmm160) cc_final: 0.8359 (tmm160) REVERT: R 326 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7350 (mmm160) REVERT: R 351 LYS cc_start: 0.7687 (tttm) cc_final: 0.7481 (tmtt) outliers start: 53 outliers final: 28 residues processed: 143 average time/residue: 0.4478 time to fit residues: 69.1989 Evaluate side-chains 126 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 90 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 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 181 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 297 TRP Chi-restraints excluded: chain B residue 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 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 326 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 16 optimal weight: 2.9990 chunk 63 optimal weight: 9.9990 chunk 57 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 47 optimal weight: 0.0770 chunk 78 optimal weight: 0.7980 chunk 3 optimal weight: 0.2980 chunk 64 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 overall best weight: 0.5538 ------------------------------------------------------------------------------- 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 = 0.3954 r_free = 0.3954 target = 0.159535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.095806 restraints weight = 12626.489| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.82 r_work: 0.2970 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.1040 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= 0.121 Angle : 0.497 6.295 13050 Z= 0.264 Chirality : 0.040 0.170 1444 Planarity : 0.003 0.040 1661 Dihedral : 5.397 59.188 1316 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 5.28 % Allowed : 30.18 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.26), residues: 1170 helix: 2.73 (0.25), residues: 444 sheet: 0.40 (0.35), residues: 218 loop : -1.26 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG R 48 TYR 0.021 0.001 TYR R 148 PHE 0.012 0.001 PHE R 230 TRP 0.019 0.001 TRP R 420 HIS 0.002 0.000 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 9602) covalent geometry : angle 0.49675 (13032) SS BOND : bond 0.00167 ( 9) SS BOND : angle 0.62109 ( 18) hydrogen bonds : bond 0.03877 ( 452) hydrogen bonds : angle 3.96939 ( 1287) *********************** 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 155 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 102 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 LYS cc_start: 0.7453 (OUTLIER) cc_final: 0.6642 (mtpp) REVERT: A 380 ARG cc_start: 0.7587 (OUTLIER) cc_final: 0.6185 (tpm-80) REVERT: B 12 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8448 (pm20) REVERT: B 14 LEU cc_start: 0.7196 (OUTLIER) cc_final: 0.6868 (pt) REVERT: B 76 ASP cc_start: 0.8649 (p0) cc_final: 0.8347 (p0) REVERT: B 134 ARG cc_start: 0.7284 (mtp85) cc_final: 0.7063 (mtp85) REVERT: B 146 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8116 (mp) REVERT: B 175 GLN cc_start: 0.8386 (mm110) cc_final: 0.8168 (mm110) REVERT: B 228 ASP cc_start: 0.8593 (m-30) cc_final: 0.8279 (m-30) REVERT: G 48 ASP cc_start: 0.8231 (t0) cc_final: 0.7804 (t0) REVERT: P 45 ASN cc_start: 0.6831 (m110) cc_final: 0.6399 (p0) REVERT: R 41 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.7842 (tm-30) REVERT: R 44 ARG cc_start: 0.8506 (tmm160) cc_final: 0.8244 (tmm160) REVERT: R 288 LYS cc_start: 0.7990 (OUTLIER) cc_final: 0.7736 (mptm) REVERT: R 326 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7240 (mmm160) REVERT: R 351 LYS cc_start: 0.7667 (tttm) cc_final: 0.7458 (tmtt) outliers start: 53 outliers final: 34 residues processed: 146 average time/residue: 0.5019 time to fit residues: 78.8807 Evaluate side-chains 135 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 93 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 64 HIS Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 297 TRP Chi-restraints excluded: chain B residue 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 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 217 LEU Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 288 LYS Chi-restraints excluded: chain R residue 326 ARG Chi-restraints excluded: chain R residue 340 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 51 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 86 optimal weight: 0.5980 chunk 110 optimal weight: 0.5980 chunk 80 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 73 optimal weight: 1.9990 chunk 68 optimal weight: 7.9990 chunk 52 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN N 1 GLN ** R 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 263 GLN ** R 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.158716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.094791 restraints weight = 12610.192| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.81 r_work: 0.2950 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9611 Z= 0.150 Angle : 0.508 6.480 13050 Z= 0.271 Chirality : 0.040 0.168 1444 Planarity : 0.004 0.041 1661 Dihedral : 5.453 58.989 1316 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 5.38 % Allowed : 30.48 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.26), residues: 1170 helix: 2.63 (0.24), residues: 444 sheet: 0.21 (0.35), residues: 224 loop : -1.23 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG R 48 TYR 0.021 0.001 TYR R 148 PHE 0.014 0.001 PHE R 230 TRP 0.015 0.001 TRP R 420 HIS 0.002 0.000 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 9602) covalent geometry : angle 0.50812 (13032) SS BOND : bond 0.00183 ( 9) SS BOND : angle 0.61003 ( 18) hydrogen bonds : bond 0.04049 ( 452) hydrogen bonds : angle 3.97204 ( 1287) *********************** 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 153 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 99 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 LYS cc_start: 0.7471 (OUTLIER) cc_final: 0.6674 (mtpp) REVERT: A 327 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8368 (mp0) REVERT: A 380 ARG cc_start: 0.7595 (OUTLIER) cc_final: 0.6193 (tpm-80) REVERT: B 12 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8429 (pm20) REVERT: B 14 LEU cc_start: 0.7010 (OUTLIER) cc_final: 0.6737 (pt) REVERT: B 76 ASP cc_start: 0.8634 (p0) cc_final: 0.8309 (p0) REVERT: B 134 ARG cc_start: 0.7289 (mtp85) cc_final: 0.7062 (mtp85) REVERT: B 146 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8132 (mp) REVERT: B 175 GLN cc_start: 0.8399 (mm110) cc_final: 0.8183 (mm110) REVERT: B 228 ASP cc_start: 0.8627 (m-30) cc_final: 0.8350 (m-30) REVERT: G 48 ASP cc_start: 0.8228 (t0) cc_final: 0.7834 (t0) REVERT: P 45 ASN cc_start: 0.6862 (OUTLIER) cc_final: 0.6368 (p0) REVERT: R 44 ARG cc_start: 0.8506 (tmm160) cc_final: 0.8226 (tmm160) REVERT: R 288 LYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7773 (mptm) REVERT: R 326 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7236 (mmm160) REVERT: R 351 LYS cc_start: 0.7681 (tttm) cc_final: 0.7468 (tmtt) outliers start: 54 outliers final: 36 residues processed: 142 average time/residue: 0.5031 time to fit residues: 77.0086 Evaluate side-chains 137 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 92 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 64 HIS Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 297 TRP Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain N residue 67 ARG Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain P residue 27 ILE Chi-restraints excluded: chain P residue 45 ASN Chi-restraints excluded: chain R residue 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 2 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 104 optimal weight: 0.2980 chunk 110 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 69 optimal weight: 7.9990 chunk 103 optimal weight: 0.6980 chunk 113 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN ** R 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 263 GLN ** R 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.158637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.094811 restraints weight = 12593.211| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.81 r_work: 0.2955 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.1117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9611 Z= 0.145 Angle : 0.516 6.902 13050 Z= 0.274 Chirality : 0.040 0.162 1444 Planarity : 0.004 0.049 1661 Dihedral : 5.408 59.020 1316 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 6.08 % Allowed : 29.98 % Favored : 63.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.26), residues: 1170 helix: 2.64 (0.24), residues: 445 sheet: 0.23 (0.35), residues: 222 loop : -1.26 (0.28), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG R 48 TYR 0.021 0.001 TYR R 148 PHE 0.014 0.001 PHE R 230 TRP 0.027 0.001 TRP R 420 HIS 0.002 0.000 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 9602) covalent geometry : angle 0.51600 (13032) SS BOND : bond 0.00173 ( 9) SS BOND : angle 0.60045 ( 18) hydrogen bonds : bond 0.04005 ( 452) hydrogen bonds : angle 3.95374 ( 1287) *********************** 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 158 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 97 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 293 LYS cc_start: 0.7468 (OUTLIER) cc_final: 0.6661 (mtpp) REVERT: A 327 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8385 (mp0) REVERT: A 380 ARG cc_start: 0.7602 (OUTLIER) cc_final: 0.6194 (tpm-80) REVERT: B 12 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8532 (pm20) REVERT: B 14 LEU cc_start: 0.7017 (OUTLIER) cc_final: 0.6721 (pt) REVERT: B 49 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.8476 (mtt-85) REVERT: B 76 ASP cc_start: 0.8668 (p0) cc_final: 0.8371 (p0) REVERT: B 134 ARG cc_start: 0.7296 (mtp85) cc_final: 0.7070 (mtp85) REVERT: B 175 GLN cc_start: 0.8396 (mm110) cc_final: 0.8103 (mm110) REVERT: B 228 ASP cc_start: 0.8627 (m-30) cc_final: 0.8349 (m-30) REVERT: G 48 ASP cc_start: 0.8198 (t0) cc_final: 0.7784 (t0) REVERT: N 83 MET cc_start: 0.6778 (ptp) cc_final: 0.5418 (ptm) REVERT: P 45 ASN cc_start: 0.6876 (OUTLIER) cc_final: 0.6394 (p0) REVERT: R 44 ARG cc_start: 0.8515 (tmm160) cc_final: 0.8219 (tmm160) REVERT: R 288 LYS cc_start: 0.8017 (OUTLIER) cc_final: 0.7786 (mptm) REVERT: R 326 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7242 (mmm160) REVERT: R 351 LYS cc_start: 0.7690 (tttm) cc_final: 0.7479 (tmtt) outliers start: 61 outliers final: 35 residues processed: 146 average time/residue: 0.4649 time to fit residues: 73.3234 Evaluate side-chains 134 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 90 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 380 ARG Chi-restraints excluded: chain B residue 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 49 ARG 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 261 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 297 TRP Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain N residue 67 ARG Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain P residue 27 ILE Chi-restraints excluded: chain P residue 45 ASN Chi-restraints excluded: chain R residue 126 CYS Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 217 LEU Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 288 LYS Chi-restraints excluded: chain R residue 326 ARG Chi-restraints excluded: chain R residue 340 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 57 optimal weight: 20.0000 chunk 69 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 68 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 111 optimal weight: 0.8980 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 263 GLN ** R 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.156809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.092527 restraints weight = 12571.431| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.80 r_work: 0.2925 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9611 Z= 0.209 Angle : 0.557 7.758 13050 Z= 0.295 Chirality : 0.042 0.161 1444 Planarity : 0.004 0.059 1661 Dihedral : 5.454 58.906 1314 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 5.78 % Allowed : 30.38 % Favored : 63.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.25), residues: 1170 helix: 2.39 (0.24), residues: 449 sheet: 0.13 (0.34), residues: 225 loop : -1.25 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG R 48 TYR 0.022 0.002 TYR R 148 PHE 0.018 0.001 PHE R 230 TRP 0.020 0.002 TRP R 420 HIS 0.002 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00502 ( 9602) covalent geometry : angle 0.55639 (13032) SS BOND : bond 0.00234 ( 9) SS BOND : angle 0.69128 ( 18) hydrogen bonds : bond 0.04467 ( 452) hydrogen bonds : angle 4.06079 ( 1287) *********************** 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 151 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 93 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 293 LYS cc_start: 0.7522 (OUTLIER) cc_final: 0.6755 (mtpp) REVERT: A 317 ARG cc_start: 0.8436 (mtm-85) cc_final: 0.8233 (mtm-85) REVERT: A 327 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8448 (mp0) REVERT: A 380 ARG cc_start: 0.7741 (OUTLIER) cc_final: 0.6268 (tpm-80) REVERT: B 14 LEU cc_start: 0.7060 (OUTLIER) cc_final: 0.6763 (pt) REVERT: B 76 ASP cc_start: 0.8672 (p0) cc_final: 0.8409 (p0) REVERT: B 134 ARG cc_start: 0.7386 (mtp85) cc_final: 0.7156 (mtp85) REVERT: B 146 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8300 (mp) REVERT: G 48 ASP cc_start: 0.8379 (t0) cc_final: 0.7966 (t0) REVERT: N 83 MET cc_start: 0.6672 (ptp) cc_final: 0.5395 (ptm) REVERT: P 45 ASN cc_start: 0.6672 (OUTLIER) cc_final: 0.6141 (p0) REVERT: R 44 ARG cc_start: 0.8575 (tmm160) cc_final: 0.8282 (tmm160) REVERT: R 288 LYS cc_start: 0.8059 (OUTLIER) cc_final: 0.7846 (mptm) REVERT: R 326 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.7433 (mmm160) outliers start: 58 outliers final: 31 residues processed: 138 average time/residue: 0.4951 time to fit residues: 73.3128 Evaluate side-chains 127 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 88 time to evaluate : 0.343 ------------------------------------------------------------------------------- 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 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 261 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 297 TRP Chi-restraints excluded: chain B residue 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 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 338 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 112 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 85 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 chunk 30 optimal weight: 0.5980 chunk 20 optimal weight: 0.4980 chunk 76 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 106 optimal weight: 0.5980 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 B 44 GLN ** R 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 263 GLN ** R 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.158499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.094470 restraints weight = 12634.134| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 2.84 r_work: 0.2951 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 9611 Z= 0.142 Angle : 0.545 8.062 13050 Z= 0.289 Chirality : 0.041 0.159 1444 Planarity : 0.004 0.069 1661 Dihedral : 5.259 59.468 1311 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 4.78 % Allowed : 31.67 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.26), residues: 1170 helix: 2.56 (0.25), residues: 445 sheet: 0.06 (0.34), residues: 230 loop : -1.29 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG R 48 TYR 0.021 0.001 TYR R 148 PHE 0.014 0.001 PHE R 230 TRP 0.025 0.001 TRP R 420 HIS 0.002 0.000 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 9602) covalent geometry : angle 0.54508 (13032) SS BOND : bond 0.00171 ( 9) SS BOND : angle 0.61676 ( 18) hydrogen bonds : bond 0.04114 ( 452) hydrogen bonds : angle 3.96677 ( 1287) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 95 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 293 LYS cc_start: 0.7450 (OUTLIER) cc_final: 0.6665 (mtpp) REVERT: A 327 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8410 (mp0) REVERT: A 380 ARG cc_start: 0.7624 (OUTLIER) cc_final: 0.6065 (tpm-80) REVERT: B 14 LEU cc_start: 0.7002 (OUTLIER) cc_final: 0.6697 (pt) REVERT: B 76 ASP cc_start: 0.8488 (p0) cc_final: 0.8249 (p0) REVERT: B 134 ARG cc_start: 0.7306 (mtp85) cc_final: 0.7068 (mtp85) REVERT: B 228 ASP cc_start: 0.8658 (m-30) cc_final: 0.8348 (m-30) REVERT: G 48 ASP cc_start: 0.8297 (t0) cc_final: 0.7909 (t0) REVERT: N 83 MET cc_start: 0.6476 (ptp) cc_final: 0.5181 (ptm) REVERT: P 45 ASN cc_start: 0.6733 (OUTLIER) cc_final: 0.6310 (p0) REVERT: R 44 ARG cc_start: 0.8522 (tmm160) cc_final: 0.8226 (tmm160) REVERT: R 48 ARG cc_start: 0.7551 (ttp80) cc_final: 0.7336 (ttp80) REVERT: R 326 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7247 (mmm160) REVERT: R 351 LYS cc_start: 0.7672 (tttm) cc_final: 0.7455 (tmtt) outliers start: 48 outliers final: 31 residues processed: 131 average time/residue: 0.4903 time to fit residues: 69.2014 Evaluate side-chains 130 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 93 time to evaluate : 0.341 ------------------------------------------------------------------------------- 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 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 234 PHE Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 297 TRP Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain P residue 45 ASN Chi-restraints excluded: chain R residue 126 CYS Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 217 LEU Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 326 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 95 optimal weight: 0.9990 chunk 57 optimal weight: 20.0000 chunk 23 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 3 optimal weight: 0.0270 chunk 9 optimal weight: 0.1980 chunk 12 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 chunk 53 optimal weight: 5.9990 chunk 60 optimal weight: 0.0030 overall best weight: 0.2848 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN R 82 ASN R 320 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.160593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.097450 restraints weight = 12570.181| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.83 r_work: 0.2999 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9611 Z= 0.107 Angle : 0.522 8.634 13050 Z= 0.275 Chirality : 0.039 0.157 1444 Planarity : 0.004 0.064 1661 Dihedral : 5.149 59.156 1311 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 3.09 % Allowed : 33.27 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.97 (0.26), residues: 1170 helix: 2.86 (0.25), residues: 440 sheet: 0.16 (0.34), residues: 228 loop : -1.22 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG R 48 TYR 0.021 0.001 TYR R 148 PHE 0.009 0.001 PHE R 230 TRP 0.027 0.001 TRP R 420 HIS 0.002 0.000 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 9602) covalent geometry : angle 0.52183 (13032) SS BOND : bond 0.00144 ( 9) SS BOND : angle 0.52027 ( 18) hydrogen bonds : bond 0.03651 ( 452) hydrogen bonds : angle 3.85889 ( 1287) ********************** 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 131 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 100 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 ARG cc_start: 0.7575 (OUTLIER) cc_final: 0.6179 (tpm-80) REVERT: B 14 LEU cc_start: 0.6963 (OUTLIER) cc_final: 0.6701 (pt) REVERT: B 134 ARG cc_start: 0.7298 (mtp85) cc_final: 0.7073 (mtp85) REVERT: B 228 ASP cc_start: 0.8542 (m-30) cc_final: 0.8239 (m-30) REVERT: G 48 ASP cc_start: 0.8245 (t0) cc_final: 0.7858 (t0) REVERT: N 83 MET cc_start: 0.6500 (ptp) cc_final: 0.5176 (ptm) REVERT: P 45 ASN cc_start: 0.6692 (m110) cc_final: 0.6284 (p0) REVERT: R 44 ARG cc_start: 0.8521 (tmm160) cc_final: 0.8227 (tmm160) REVERT: R 326 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7206 (mmm160) REVERT: R 351 LYS cc_start: 0.7650 (tttm) cc_final: 0.7446 (tmtt) outliers start: 31 outliers final: 23 residues processed: 125 average time/residue: 0.5020 time to fit residues: 67.8779 Evaluate side-chains 120 residues out of total 1027 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 94 time to evaluate : 0.356 ------------------------------------------------------------------------------- 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 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 97 SER Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 234 PHE 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 G residue 54 VAL Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain R residue 126 CYS Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 217 LEU Chi-restraints excluded: chain R residue 224 LEU Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 326 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 32 optimal weight: 0.6980 chunk 40 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 94 optimal weight: 0.5980 chunk 74 optimal weight: 0.9980 chunk 100 optimal weight: 0.4980 chunk 59 optimal weight: 0.3980 chunk 82 optimal weight: 0.0770 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN ** R 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.159940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.096707 restraints weight = 12506.386| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.81 r_work: 0.2989 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 9611 Z= 0.122 Angle : 0.545 8.155 13050 Z= 0.288 Chirality : 0.040 0.155 1444 Planarity : 0.004 0.056 1661 Dihedral : 5.121 58.640 1311 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 2.99 % Allowed : 33.57 % Favored : 63.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.26), residues: 1170 helix: 2.83 (0.25), residues: 439 sheet: 0.17 (0.34), residues: 228 loop : -1.20 (0.28), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG R 48 TYR 0.020 0.001 TYR R 148 PHE 0.011 0.001 PHE R 230 TRP 0.028 0.001 TRP R 420 HIS 0.002 0.000 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 9602) covalent geometry : angle 0.54483 (13032) SS BOND : bond 0.00145 ( 9) SS BOND : angle 0.52982 ( 18) hydrogen bonds : bond 0.03731 ( 452) hydrogen bonds : angle 3.82564 ( 1287) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3352.28 seconds wall clock time: 57 minutes 49.75 seconds (3469.75 seconds total)