Starting phenix.real_space_refine on Sun Oct 25 01:49:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/25fq_80076/10_2026/25fq_80076.cif Found real_map, /net/cci-nas-00/data/ceres_data/25fq_80076/10_2026/25fq_80076.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/25fq_80076/10_2026/25fq_80076.cif" } default_model = "/net/cci-nas-00/data/ceres_data/25fq_80076/10_2026/25fq_80076.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/25fq_80076/10_2026/25fq_80076.map" default_real_map = "/net/cci-nas-00/data/ceres_data/25fq_80076/10_2026/25fq_80076.map" } resolution = 3.6 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= 0.002 sd= 0.028 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 50 5.16 5 C 9354 2.51 5 N 2581 2.21 5 O 2938 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14923 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 783, 6194 Classifications: {'peptide': 783} Link IDs: {'PTRANS': 29, 'TRANS': 753} Chain: "B" Number of atoms: 2776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2776 Classifications: {'peptide': 369} Link IDs: {'PTRANS': 11, 'TRANS': 357} Chain: "C" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2081 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 12, 'TRANS': 259} Chain breaks: 4 Chain: "D" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1761 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 12, 'TRANS': 205} Chain: "E" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 694 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Chain: "F" Number of atoms: 1417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1417 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 2, 'TRANS': 174} Chain breaks: 1 Time building chain proxies: 2.96, per 1000 atoms: 0.20 Number of scatterers: 14923 At special positions: 0 Unit cell: (127.84, 118.816, 151.152, 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 50 16.00 O 2938 8.00 N 2581 7.00 C 9354 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.19 Conformation dependent library (CDL) restraints added in 637.7 milliseconds 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3516 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 20 sheets defined 30.9% alpha, 23.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 38 through 44 removed outlier: 3.736A pdb=" N ALA A 42 " --> pdb=" O ALA A 38 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU A 43 " --> pdb=" O VAL A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 69 removed outlier: 4.098A pdb=" N ASN A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 117 removed outlier: 5.322A pdb=" N GLN A 112 " --> pdb=" O ASP A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 145 removed outlier: 3.705A pdb=" N ILE A 130 " --> pdb=" O ASP A 126 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA A 131 " --> pdb=" O ARG A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 196 removed outlier: 3.984A pdb=" N HIS A 196 " --> pdb=" O GLU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 232 Processing helix chain 'A' and resid 280 through 289 Processing helix chain 'A' and resid 297 through 315 removed outlier: 3.729A pdb=" N TYR A 315 " --> pdb=" O LEU A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 367 removed outlier: 3.900A pdb=" N LEU A 365 " --> pdb=" O LYS A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 393 removed outlier: 3.587A pdb=" N ASP A 383 " --> pdb=" O SER A 379 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLY A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 452 Processing helix chain 'A' and resid 542 through 553 Processing helix chain 'A' and resid 647 through 651 Processing helix chain 'A' and resid 726 through 730 Processing helix chain 'B' and resid 136 through 139 Processing helix chain 'C' and resid 29 through 34 removed outlier: 3.699A pdb=" N ARG C 33 " --> pdb=" O SER C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 44 Processing helix chain 'C' and resid 76 through 80 Processing helix chain 'C' and resid 112 through 114 No H-bonds generated for 'chain 'C' and resid 112 through 114' Processing helix chain 'C' and resid 115 through 128 removed outlier: 3.901A pdb=" N GLN C 119 " --> pdb=" O THR C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 215 removed outlier: 3.552A pdb=" N TYR C 197 " --> pdb=" O SER C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 253 Processing helix chain 'C' and resid 254 through 263 Processing helix chain 'C' and resid 327 through 343 removed outlier: 3.734A pdb=" N ALA C 336 " --> pdb=" O ASP C 332 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA C 340 " --> pdb=" O ALA C 336 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA C 341 " --> pdb=" O VAL C 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 46 removed outlier: 3.771A pdb=" N ILE D 35 " --> pdb=" O PRO D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 62 removed outlier: 3.935A pdb=" N THR D 53 " --> pdb=" O ARG D 49 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN D 54 " --> pdb=" O GLN D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 82 Processing helix chain 'D' and resid 84 through 99 removed outlier: 3.840A pdb=" N ARG D 97 " --> pdb=" O ASP D 93 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU D 98 " --> pdb=" O ARG D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 121 Processing helix chain 'D' and resid 124 through 129 removed outlier: 3.774A pdb=" N PHE D 128 " --> pdb=" O LEU D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 154 Processing helix chain 'D' and resid 159 through 189 Processing helix chain 'D' and resid 191 through 205 Processing helix chain 'D' and resid 209 through 225 Proline residue: D 216 - end of helix removed outlier: 3.595A pdb=" N MET D 225 " --> pdb=" O ALA D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 241 removed outlier: 5.091A pdb=" N LYS D 233 " --> pdb=" O ALA D 229 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N VAL D 234 " --> pdb=" O GLN D 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 45 removed outlier: 3.704A pdb=" N LYS E 45 " --> pdb=" O ASN E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 60 removed outlier: 3.576A pdb=" N VAL E 55 " --> pdb=" O THR E 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 49 removed outlier: 4.133A pdb=" N GLN F 47 " --> pdb=" O ASP F 43 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N VAL F 49 " --> pdb=" O LEU F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 55 removed outlier: 3.889A pdb=" N GLN F 55 " --> pdb=" O LEU F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 88 Processing helix chain 'F' and resid 92 through 107 Processing helix chain 'F' and resid 110 through 121 Processing helix chain 'F' and resid 124 through 149 Processing helix chain 'F' and resid 155 through 164 Processing helix chain 'F' and resid 392 through 420 removed outlier: 3.772A pdb=" N ALA F 419 " --> pdb=" O GLN F 415 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 6.260A pdb=" N HIS A 30 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N VAL A 88 " --> pdb=" O HIS A 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 100 removed outlier: 5.972A pdb=" N VAL A 163 " --> pdb=" O ILE A 94 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N SER A 96 " --> pdb=" O VAL A 163 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 181 removed outlier: 4.484A pdb=" N ILE A 177 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N VAL A 256 " --> pdb=" O ILE A 177 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N GLN A 179 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N VAL A 258 " --> pdb=" O GLN A 179 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ASN A 181 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N ILE A 260 " --> pdb=" O ASN A 181 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N SER A 242 " --> pdb=" O ASN A 259 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N THR A 261 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ILE A 240 " --> pdb=" O THR A 261 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 267 through 274 removed outlier: 6.105A pdb=" N VAL A 335 " --> pdb=" O LEU A 268 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 349 through 355 removed outlier: 6.077A pdb=" N VAL A 412 " --> pdb=" O VAL A 349 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LYS A 351 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR A 397 " --> pdb=" O LYS A 419 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 425 through 426 removed outlier: 6.687A pdb=" N ASN A 523 " --> pdb=" O ILE A 519 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N TYR A 608 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N THR A 735 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA A 770 " --> pdb=" O GLN A 789 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 46 through 49 removed outlier: 6.897A pdb=" N SER B 389 " --> pdb=" O ALA B 47 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N SER B 49 " --> pdb=" O VAL B 387 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N VAL B 387 " --> pdb=" O SER B 49 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU B 378 " --> pdb=" O ILE B 390 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 66 through 68 removed outlier: 3.693A pdb=" N TRP B 93 " --> pdb=" O ALA B 83 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ASN B 85 " --> pdb=" O GLU B 91 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLU B 91 " --> pdb=" O ASN B 85 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 116 through 118 removed outlier: 6.451A pdb=" N VAL B 131 " --> pdb=" O GLN B 144 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLN B 144 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ALA B 133 " --> pdb=" O ALA B 142 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 156 through 158 removed outlier: 3.895A pdb=" N TRP B 183 " --> pdb=" O ALA B 173 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASN B 175 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL B 181 " --> pdb=" O ASN B 175 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 201 through 203 removed outlier: 5.642A pdb=" N LEU B 220 " --> pdb=" O MET B 226 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N MET B 226 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 252 through 254 removed outlier: 3.540A pdb=" N VAL B 252 " --> pdb=" O PHE B 259 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TRP B 279 " --> pdb=" O ALA B 269 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ASP B 271 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE B 277 " --> pdb=" O ASP B 271 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 286 through 291 removed outlier: 5.323A pdb=" N ASP B 288 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N VAL B 299 " --> pdb=" O ASP B 288 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL B 305 " --> pdb=" O GLN B 319 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N THR B 309 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N THR B 315 " --> pdb=" O THR B 309 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 331 through 333 removed outlier: 3.962A pdb=" N ALA B 358 " --> pdb=" O TRP B 348 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ASN B 350 " --> pdb=" O PHE B 356 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N PHE B 356 " --> pdb=" O ASN B 350 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 96 through 100 removed outlier: 3.615A pdb=" N LYS C 166 " --> pdb=" O ALA C 173 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLN C 133 " --> pdb=" O THR C 142 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 146 through 148 removed outlier: 4.012A pdb=" N TYR C 157 " --> pdb=" O TRP C 148 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 275 through 279 removed outlier: 4.048A pdb=" N VAL C 278 " --> pdb=" O TYR C 303 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 32 through 33 removed outlier: 3.800A pdb=" N MET E 64 " --> pdb=" O PHE E 74 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 32 through 33 removed outlier: 3.554A pdb=" N ASN E 103 " --> pdb=" O THR E 94 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 35 through 38 removed outlier: 3.728A pdb=" N ALA F 30 " --> pdb=" O VAL F 37 " (cutoff:3.500A) 702 hydrogen bonds defined for protein. 1959 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.29 Time building geometry restraints manager: 1.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5047 1.34 - 1.46: 3282 1.46 - 1.58: 6786 1.58 - 1.70: 0 1.70 - 1.82: 97 Bond restraints: 15212 Sorted by residual: bond pdb=" N VAL C 244 " pdb=" CA VAL C 244 " ideal model delta sigma weight residual 1.456 1.500 -0.044 1.11e-02 8.12e+03 1.58e+01 bond pdb=" N VAL F 89 " pdb=" CA VAL F 89 " ideal model delta sigma weight residual 1.456 1.495 -0.038 1.14e-02 7.69e+03 1.11e+01 bond pdb=" N VAL A 438 " pdb=" CA VAL A 438 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.25e-02 6.40e+03 1.10e+01 bond pdb=" N VAL F 36 " pdb=" CA VAL F 36 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.11e-02 8.12e+03 1.08e+01 bond pdb=" N ASP C 311 " pdb=" CA ASP C 311 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.21e-02 6.83e+03 1.05e+01 ... (remaining 15207 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 20213 2.46 - 4.92: 394 4.92 - 7.38: 31 7.38 - 9.83: 4 9.83 - 12.29: 4 Bond angle restraints: 20646 Sorted by residual: angle pdb=" N ASN C 312 " pdb=" CA ASN C 312 " pdb=" C ASN C 312 " ideal model delta sigma weight residual 113.43 103.32 10.11 1.26e+00 6.30e-01 6.44e+01 angle pdb=" N VAL B 257 " pdb=" CA VAL B 257 " pdb=" C VAL B 257 " ideal model delta sigma weight residual 108.58 117.68 -9.10 1.44e+00 4.82e-01 3.99e+01 angle pdb=" C VAL B 253 " pdb=" N VAL B 254 " pdb=" CA VAL B 254 " ideal model delta sigma weight residual 123.19 117.03 6.16 1.24e+00 6.50e-01 2.47e+01 angle pdb=" C ASN B 255 " pdb=" CA ASN B 255 " pdb=" CB ASN B 255 " ideal model delta sigma weight residual 116.63 111.19 5.44 1.16e+00 7.43e-01 2.20e+01 angle pdb=" N VAL E 26 " pdb=" CA VAL E 26 " pdb=" C VAL E 26 " ideal model delta sigma weight residual 113.71 109.29 4.42 9.50e-01 1.11e+00 2.17e+01 ... (remaining 20641 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 7888 17.96 - 35.92: 918 35.92 - 53.88: 201 53.88 - 71.84: 52 71.84 - 89.81: 19 Dihedral angle restraints: 9078 sinusoidal: 3575 harmonic: 5503 Sorted by residual: dihedral pdb=" CA VAL A 480 " pdb=" C VAL A 480 " pdb=" N ASP A 481 " pdb=" CA ASP A 481 " ideal model delta harmonic sigma weight residual 180.00 157.39 22.61 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA THR B 386 " pdb=" C THR B 386 " pdb=" N VAL B 387 " pdb=" CA VAL B 387 " ideal model delta harmonic sigma weight residual -180.00 -162.50 -17.50 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA ASN B 266 " pdb=" C ASN B 266 " pdb=" N LEU B 267 " pdb=" CA LEU B 267 " ideal model delta harmonic sigma weight residual 180.00 162.60 17.40 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 9075 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1746 0.053 - 0.107: 399 0.107 - 0.160: 95 0.160 - 0.214: 28 0.214 - 0.267: 7 Chirality restraints: 2275 Sorted by residual: chirality pdb=" CG LEU A 66 " pdb=" CB LEU A 66 " pdb=" CD1 LEU A 66 " pdb=" CD2 LEU A 66 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" CG LEU C 181 " pdb=" CB LEU C 181 " pdb=" CD1 LEU C 181 " pdb=" CD2 LEU C 181 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CB VAL C 244 " pdb=" CA VAL C 244 " pdb=" CG1 VAL C 244 " pdb=" CG2 VAL C 244 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.24 2.00e-01 2.50e+01 1.49e+00 ... (remaining 2272 not shown) Planarity restraints: 2722 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 404 " -0.401 9.50e-02 1.11e+02 1.80e-01 1.98e+01 pdb=" NE ARG F 404 " 0.025 2.00e-02 2.50e+03 pdb=" CZ ARG F 404 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG F 404 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG F 404 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 129 " -0.397 9.50e-02 1.11e+02 1.78e-01 1.95e+01 pdb=" NE ARG F 129 " 0.025 2.00e-02 2.50e+03 pdb=" CZ ARG F 129 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG F 129 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG F 129 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 314 " 0.019 2.00e-02 2.50e+03 3.84e-02 1.47e+01 pdb=" C SER C 314 " -0.066 2.00e-02 2.50e+03 pdb=" O SER C 314 " 0.024 2.00e-02 2.50e+03 pdb=" N SER C 315 " 0.023 2.00e-02 2.50e+03 ... (remaining 2719 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 4066 2.80 - 3.33: 15094 3.33 - 3.85: 25178 3.85 - 4.38: 28517 4.38 - 4.90: 48028 Nonbonded interactions: 120883 Sorted by model distance: nonbonded pdb=" N ASN C 180 " pdb=" OD1 ASN C 180 " model vdw 2.277 3.120 nonbonded pdb=" O VAL C 244 " pdb=" O SER C 314 " model vdw 2.394 3.040 nonbonded pdb=" O PRO A 157 " pdb=" N ASP C 309 " model vdw 2.432 3.120 nonbonded pdb=" O LYS C 211 " pdb=" OG1 THR C 214 " model vdw 2.486 3.040 nonbonded pdb=" O LEU F 118 " pdb=" N LEU F 123 " model vdw 2.500 3.120 ... (remaining 120878 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.270 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: 0.000 Extract box with map and model: 0.300 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.530 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 15212 Z= 0.351 Angle : 0.771 12.293 20646 Z= 0.490 Chirality : 0.053 0.267 2275 Planarity : 0.008 0.180 2722 Dihedral : 16.393 89.805 5562 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 3.61 % Allowed : 20.78 % Favored : 75.61 % 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 are not related in a simple way. whole: -0.31 (0.19), residues: 1886 helix: 1.31 (0.23), residues: 503 sheet: -0.30 (0.24), residues: 505 loop : -1.01 (0.21), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 134 TYR 0.024 0.001 TYR D 107 PHE 0.027 0.001 PHE A 586 TRP 0.009 0.001 TRP A 745 HIS 0.006 0.001 HIS F 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00578 / 0.35 (15212) covalent geometry : angle 0.77069 / 0.49 (20646) hydrogen bonds : bond 0.12484 / 8.57 ( 700) hydrogen bonds : angle 6.31839 / 4.44 ( 1959) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 213 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.8222 (pmm) cc_final: 0.7740 (pmm) REVERT: A 61 ASN cc_start: 0.9768 (m-40) cc_final: 0.9134 (m-40) REVERT: A 120 ARG cc_start: 0.8900 (ptp90) cc_final: 0.8688 (ptp90) REVERT: A 161 ASN cc_start: 0.7816 (t0) cc_final: 0.7591 (t0) REVERT: A 218 LYS cc_start: 0.9214 (mtpt) cc_final: 0.8973 (ttmm) REVERT: A 247 LEU cc_start: 0.9518 (tp) cc_final: 0.9181 (mm) REVERT: A 383 ASP cc_start: 0.9151 (t70) cc_final: 0.8841 (p0) REVERT: A 401 ASP cc_start: 0.8161 (t70) cc_final: 0.7780 (p0) REVERT: A 804 PHE cc_start: 0.8512 (OUTLIER) cc_final: 0.7973 (t80) REVERT: B 72 VAL cc_start: 0.9624 (t) cc_final: 0.9361 (p) REVERT: B 278 MET cc_start: 0.9098 (ptp) cc_final: 0.8620 (pmm) REVERT: C 155 GLU cc_start: 0.8183 (tp30) cc_final: 0.7755 (tp30) REVERT: C 201 MET cc_start: 0.9347 (tmm) cc_final: 0.8848 (tmm) REVERT: C 316 LEU cc_start: 0.5725 (OUTLIER) cc_final: 0.5419 (pp) REVERT: E 66 ASP cc_start: 0.7996 (t0) cc_final: 0.7425 (t0) outliers start: 58 outliers final: 45 residues processed: 263 average time/residue: 0.1238 time to fit residues: 47.4738 Evaluate side-chains 186 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 139 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 677 HIS Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 804 PHE Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 180 ASN Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain D residue 178 GLU Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 42 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149] chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 30.0000 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 0.8980 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 170 GLN B 225 GLN ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 GLN ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 68 HIS ** 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 = 0.3716 r_free = 0.3716 target = 0.077356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.052008 restraints weight = 62839.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.053905 restraints weight = 31101.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.055086 restraints weight = 20852.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.055788 restraints weight = 16633.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.056181 restraints weight = 14657.516| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15212 Z= 0.169 Angle : 0.612 10.551 20646 Z= 0.318 Chirality : 0.045 0.262 2275 Planarity : 0.004 0.044 2722 Dihedral : 6.578 57.666 2160 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 5.04 % Allowed : 20.91 % Favored : 74.05 % 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 are not related in a simple way. whole: -0.12 (0.20), residues: 1886 helix: 1.53 (0.22), residues: 512 sheet: -0.21 (0.24), residues: 496 loop : -0.93 (0.21), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 212 TYR 0.028 0.002 TYR F 125 PHE 0.021 0.001 PHE C 342 TRP 0.013 0.001 TRP C 117 HIS 0.006 0.001 HIS F 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.17 (15212) covalent geometry : angle 0.61177 / 0.32 (20646) hydrogen bonds : bond 0.03909 / 2.62 ( 700) hydrogen bonds : angle 5.20340 / 3.65 ( 1959) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 156 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.8188 (pmm) cc_final: 0.7901 (pmm) REVERT: A 109 MET cc_start: 0.7501 (ppp) cc_final: 0.6828 (pmm) REVERT: A 170 GLN cc_start: 0.7564 (OUTLIER) cc_final: 0.7209 (tm-30) REVERT: A 804 PHE cc_start: 0.8160 (OUTLIER) cc_final: 0.7845 (t80) REVERT: B 32 MET cc_start: 0.7322 (mpp) cc_final: 0.7043 (mmp) REVERT: B 197 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.7632 (mp0) REVERT: B 295 ARG cc_start: 0.8384 (OUTLIER) cc_final: 0.8005 (mtp180) REVERT: B 298 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.8000 (pp) REVERT: C 56 MET cc_start: 0.8048 (OUTLIER) cc_final: 0.7617 (tmm) REVERT: C 201 MET cc_start: 0.9111 (tmm) cc_final: 0.8347 (ppp) REVERT: D 109 MET cc_start: 0.8378 (mtm) cc_final: 0.8070 (mtm) REVERT: D 187 GLU cc_start: 0.8253 (tm-30) cc_final: 0.7956 (tm-30) REVERT: F 46 MET cc_start: 0.9135 (mmm) cc_final: 0.8735 (mmm) REVERT: F 70 ILE cc_start: 0.9441 (mm) cc_final: 0.9214 (mm) REVERT: F 71 MET cc_start: 0.9531 (ptp) cc_final: 0.9018 (ptt) REVERT: F 80 ILE cc_start: 0.9735 (mm) cc_final: 0.9531 (mt) REVERT: F 128 TYR cc_start: 0.9557 (t80) cc_final: 0.9046 (m-80) outliers start: 81 outliers final: 48 residues processed: 226 average time/residue: 0.1065 time to fit residues: 37.0772 Evaluate side-chains 179 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 125 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 170 GLN Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 677 HIS Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 804 PHE Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 295 ARG Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 134 ARG Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 42 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: [52, 181, 30, 156, 2, 121, 118, 67, 101, 104, 111] chunk 52 optimal weight: 1.9990 chunk 181 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 156 optimal weight: 0.8980 chunk 2 optimal weight: 20.0000 chunk 121 optimal weight: 10.0000 chunk 118 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 101 optimal weight: 9.9990 chunk 104 optimal weight: 9.9990 chunk 111 optimal weight: 20.0000 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 51 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.075909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.050667 restraints weight = 63403.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.052481 restraints weight = 31933.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.053609 restraints weight = 21698.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.054287 restraints weight = 17447.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.054683 restraints weight = 15441.764| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15212 Z= 0.188 Angle : 0.598 11.687 20646 Z= 0.312 Chirality : 0.045 0.281 2275 Planarity : 0.004 0.045 2722 Dihedral : 5.922 58.966 2132 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 5.29 % Allowed : 21.53 % Favored : 73.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.20), residues: 1886 helix: 1.56 (0.22), residues: 513 sheet: -0.14 (0.24), residues: 504 loop : -1.09 (0.21), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 64 TYR 0.016 0.002 TYR C 161 PHE 0.024 0.001 PHE A 586 TRP 0.008 0.001 TRP D 191 HIS 0.007 0.001 HIS C 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.19 (15212) covalent geometry : angle 0.59794 / 0.31 (20646) hydrogen bonds : bond 0.03902 / 2.63 ( 700) hydrogen bonds : angle 5.11184 / 3.58 ( 1959) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 132 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.8272 (pmm) cc_final: 0.8032 (pmm) REVERT: A 111 LYS cc_start: 0.9555 (mmmt) cc_final: 0.9238 (mmtm) REVERT: A 804 PHE cc_start: 0.8165 (OUTLIER) cc_final: 0.7899 (t80) REVERT: B 32 MET cc_start: 0.7309 (mpp) cc_final: 0.7036 (mmm) REVERT: B 197 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.7527 (mp0) REVERT: B 295 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.8034 (mtp180) REVERT: B 298 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8328 (pp) REVERT: C 157 TYR cc_start: 0.8354 (m-80) cc_final: 0.8111 (m-80) REVERT: C 161 TYR cc_start: 0.6984 (m-80) cc_final: 0.6646 (m-80) REVERT: C 201 MET cc_start: 0.9107 (tmm) cc_final: 0.8265 (ppp) REVERT: C 228 MET cc_start: 0.8388 (mmt) cc_final: 0.8059 (mmm) REVERT: D 58 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8829 (tt) REVERT: D 178 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8010 (mp0) REVERT: D 187 GLU cc_start: 0.8244 (tm-30) cc_final: 0.7903 (tm-30) REVERT: E 37 TYR cc_start: 0.7701 (OUTLIER) cc_final: 0.7298 (p90) REVERT: F 46 MET cc_start: 0.9089 (mmm) cc_final: 0.8697 (mmm) REVERT: F 128 TYR cc_start: 0.9564 (t80) cc_final: 0.9103 (m-80) outliers start: 85 outliers final: 59 residues processed: 205 average time/residue: 0.1059 time to fit residues: 33.2584 Evaluate side-chains 193 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 127 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 677 HIS Chi-restraints excluded: chain A residue 686 TYR Chi-restraints excluded: chain A residue 690 CYS Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 804 PHE Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 295 ARG Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 134 ARG Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 302 ASP Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 178 GLU Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain E residue 37 TYR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 42 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: [9, 74, 88, 166, 91, 59, 152, 20, 93, 111, 133] chunk 9 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 166 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 152 optimal weight: 7.9990 chunk 20 optimal weight: 0.9990 chunk 93 optimal weight: 9.9990 chunk 111 optimal weight: 20.0000 chunk 133 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 51 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.075353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.049917 restraints weight = 62764.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.051757 restraints weight = 30981.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.052900 restraints weight = 20862.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.053582 restraints weight = 16699.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.053960 restraints weight = 14784.522| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 15212 Z= 0.168 Angle : 0.602 13.439 20646 Z= 0.309 Chirality : 0.044 0.316 2275 Planarity : 0.004 0.045 2722 Dihedral : 5.692 58.252 2126 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 5.91 % Allowed : 21.84 % Favored : 72.25 % 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 are not related in a simple way. whole: -0.19 (0.20), residues: 1886 helix: 1.50 (0.22), residues: 516 sheet: -0.12 (0.24), residues: 503 loop : -1.12 (0.21), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 76 TYR 0.015 0.001 TYR D 184 PHE 0.023 0.001 PHE A 586 TRP 0.007 0.001 TRP B 348 HIS 0.006 0.001 HIS C 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.17 (15212) covalent geometry : angle 0.60199 / 0.31 (20646) hydrogen bonds : bond 0.03658 / 2.45 ( 700) hydrogen bonds : angle 5.01736 / 3.52 ( 1959) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 135 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.8263 (pmm) cc_final: 0.8028 (pmm) REVERT: A 72 PHE cc_start: 0.9355 (m-80) cc_final: 0.9083 (t80) REVERT: A 109 MET cc_start: 0.7711 (ppp) cc_final: 0.7045 (pmm) REVERT: A 115 GLU cc_start: 0.9166 (mm-30) cc_final: 0.8770 (mm-30) REVERT: A 120 ARG cc_start: 0.6770 (ptp90) cc_final: 0.6530 (ptp90) REVERT: A 641 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8993 (pp) REVERT: A 804 PHE cc_start: 0.8243 (OUTLIER) cc_final: 0.7995 (t80) REVERT: B 197 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.7999 (mp0) REVERT: B 295 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.8087 (mtp180) REVERT: B 298 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8342 (pp) REVERT: C 56 MET cc_start: 0.8165 (OUTLIER) cc_final: 0.7704 (tmm) REVERT: C 157 TYR cc_start: 0.8513 (m-80) cc_final: 0.8188 (m-80) REVERT: C 163 ILE cc_start: 0.9587 (mm) cc_final: 0.9234 (tp) REVERT: C 201 MET cc_start: 0.9182 (tmm) cc_final: 0.8892 (tmm) REVERT: C 273 GLN cc_start: 0.8710 (mt0) cc_final: 0.8361 (tp-100) REVERT: D 58 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8809 (tt) REVERT: D 178 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.8083 (mp0) REVERT: E 37 TYR cc_start: 0.7688 (OUTLIER) cc_final: 0.7138 (p90) REVERT: F 27 LYS cc_start: 0.9518 (tppt) cc_final: 0.9163 (tppt) REVERT: F 46 MET cc_start: 0.9133 (mmm) cc_final: 0.8785 (mmm) REVERT: F 71 MET cc_start: 0.9349 (ptt) cc_final: 0.9109 (ptp) REVERT: F 87 MET cc_start: 0.9507 (tpp) cc_final: 0.9272 (tmm) REVERT: F 128 TYR cc_start: 0.9593 (t80) cc_final: 0.9144 (m-80) outliers start: 95 outliers final: 65 residues processed: 215 average time/residue: 0.1080 time to fit residues: 35.5372 Evaluate side-chains 198 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 124 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 677 HIS Chi-restraints excluded: chain A residue 686 TYR Chi-restraints excluded: chain A residue 690 CYS Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 804 PHE Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 295 ARG Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 134 ARG Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 178 GLU Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain E residue 37 TYR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 42 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: [174, 162, 117, 34, 130, 137, 2, 128, 86, 79, 181] chunk 174 optimal weight: 7.9990 chunk 162 optimal weight: 0.8980 chunk 117 optimal weight: 0.0670 chunk 34 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 137 optimal weight: 7.9990 chunk 2 optimal weight: 30.0000 chunk 128 optimal weight: 10.0000 chunk 86 optimal weight: 6.9990 chunk 79 optimal weight: 7.9990 chunk 181 optimal weight: 5.9990 overall best weight: 2.7924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 51 HIS ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.076325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.050334 restraints weight = 63608.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.052148 restraints weight = 32329.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.053274 restraints weight = 22158.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.053952 restraints weight = 17971.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.054248 restraints weight = 16014.106| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15212 Z= 0.161 Angle : 0.598 12.327 20646 Z= 0.308 Chirality : 0.044 0.339 2275 Planarity : 0.004 0.044 2722 Dihedral : 5.620 58.099 2126 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 5.79 % Allowed : 22.28 % Favored : 71.94 % 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 are not related in a simple way. whole: -0.12 (0.20), residues: 1886 helix: 1.62 (0.22), residues: 517 sheet: -0.11 (0.24), residues: 502 loop : -1.10 (0.21), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 67 TYR 0.016 0.001 TYR C 161 PHE 0.024 0.001 PHE A 586 TRP 0.007 0.001 TRP B 348 HIS 0.007 0.001 HIS C 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 (15212) covalent geometry : angle 0.59819 / 0.31 (20646) hydrogen bonds : bond 0.03541 / 2.38 ( 700) hydrogen bonds : angle 4.94195 / 3.47 ( 1959) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 129 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLU cc_start: 0.9145 (mm-30) cc_final: 0.8631 (mm-30) REVERT: A 120 ARG cc_start: 0.7048 (ptp90) cc_final: 0.6583 (ptp90) REVERT: A 133 ILE cc_start: 0.9066 (mm) cc_final: 0.8860 (mm) REVERT: A 641 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.8966 (pp) REVERT: A 804 PHE cc_start: 0.8255 (OUTLIER) cc_final: 0.8029 (t80) REVERT: B 197 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.8257 (mm-30) REVERT: B 295 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.8065 (mtp180) REVERT: B 298 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8414 (pp) REVERT: C 56 MET cc_start: 0.8041 (OUTLIER) cc_final: 0.7590 (tmm) REVERT: C 157 TYR cc_start: 0.8489 (m-80) cc_final: 0.8095 (m-80) REVERT: C 201 MET cc_start: 0.9119 (tmm) cc_final: 0.8518 (ppp) REVERT: C 228 MET cc_start: 0.8552 (mmt) cc_final: 0.8259 (mmm) REVERT: C 273 GLN cc_start: 0.8694 (mt0) cc_final: 0.8336 (tp40) REVERT: D 178 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7909 (mp0) REVERT: D 187 GLU cc_start: 0.8225 (tm-30) cc_final: 0.7898 (tm-30) REVERT: F 27 LYS cc_start: 0.9476 (tppt) cc_final: 0.9200 (tppt) REVERT: F 46 MET cc_start: 0.9198 (mmm) cc_final: 0.8888 (mmm) REVERT: F 83 MET cc_start: 0.9324 (tpt) cc_final: 0.8964 (tpt) REVERT: F 128 TYR cc_start: 0.9593 (t80) cc_final: 0.9151 (m-80) outliers start: 93 outliers final: 72 residues processed: 207 average time/residue: 0.1010 time to fit residues: 32.7758 Evaluate side-chains 203 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 124 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 494 PHE Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 677 HIS Chi-restraints excluded: chain A residue 686 TYR Chi-restraints excluded: chain A residue 690 CYS Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 804 PHE Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 295 ARG Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 134 ARG Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 302 ASP Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 178 GLU Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 228 ASN Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 91 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: [119, 34, 74, 122, 141, 116, 125, 70, 166, 130, 30] chunk 119 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 122 optimal weight: 50.0000 chunk 141 optimal weight: 20.0000 chunk 116 optimal weight: 8.9990 chunk 125 optimal weight: 50.0000 chunk 70 optimal weight: 5.9990 chunk 166 optimal weight: 7.9990 chunk 130 optimal weight: 0.6980 chunk 30 optimal weight: 6.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 51 HIS ** C 162 GLN ** 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 = 0.3668 r_free = 0.3668 target = 0.076247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.050311 restraints weight = 63341.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.052154 restraints weight = 31313.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.053330 restraints weight = 21235.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.054020 restraints weight = 17097.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.054371 restraints weight = 15197.593| |-----------------------------------------------------------------------------| r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15212 Z= 0.143 Angle : 0.603 13.585 20646 Z= 0.308 Chirality : 0.044 0.348 2275 Planarity : 0.003 0.044 2722 Dihedral : 5.465 58.615 2125 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 5.91 % Allowed : 22.78 % Favored : 71.31 % 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 are not related in a simple way. whole: -0.11 (0.20), residues: 1886 helix: 1.63 (0.22), residues: 517 sheet: -0.09 (0.24), residues: 503 loop : -1.10 (0.21), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 67 TYR 0.015 0.001 TYR D 184 PHE 0.023 0.001 PHE A 586 TRP 0.008 0.001 TRP B 228 HIS 0.007 0.001 HIS C 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (15212) covalent geometry : angle 0.60258 / 0.31 (20646) hydrogen bonds : bond 0.03485 / 2.34 ( 700) hydrogen bonds : angle 4.87935 / 3.43 ( 1959) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 130 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 MET cc_start: 0.7786 (ppp) cc_final: 0.7104 (pmm) REVERT: A 115 GLU cc_start: 0.9197 (mm-30) cc_final: 0.8690 (mm-30) REVERT: A 120 ARG cc_start: 0.7074 (ptp90) cc_final: 0.6631 (ptp90) REVERT: A 133 ILE cc_start: 0.9120 (mm) cc_final: 0.8890 (mm) REVERT: A 428 PHE cc_start: 0.8155 (OUTLIER) cc_final: 0.7712 (m-80) REVERT: A 641 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8926 (pp) REVERT: A 804 PHE cc_start: 0.8277 (OUTLIER) cc_final: 0.8059 (t80) REVERT: B 197 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8203 (mm-30) REVERT: B 295 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.8072 (mtp180) REVERT: B 298 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8364 (pp) REVERT: C 56 MET cc_start: 0.7971 (OUTLIER) cc_final: 0.7523 (tmm) REVERT: C 157 TYR cc_start: 0.8465 (m-80) cc_final: 0.8067 (m-80) REVERT: C 201 MET cc_start: 0.9150 (tmm) cc_final: 0.8584 (ppp) REVERT: C 228 MET cc_start: 0.8546 (mmt) cc_final: 0.8224 (mmm) REVERT: C 273 GLN cc_start: 0.8687 (mt0) cc_final: 0.8312 (tp40) REVERT: C 303 TYR cc_start: 0.8688 (m-80) cc_final: 0.8363 (m-80) REVERT: D 178 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8080 (mp0) REVERT: D 201 MET cc_start: 0.8279 (tpp) cc_final: 0.8058 (tpp) REVERT: E 37 TYR cc_start: 0.7572 (OUTLIER) cc_final: 0.7083 (p90) REVERT: F 27 LYS cc_start: 0.9469 (tppt) cc_final: 0.9170 (tppt) REVERT: F 46 MET cc_start: 0.9222 (mmm) cc_final: 0.8959 (mmm) REVERT: F 114 MET cc_start: 0.8981 (mmp) cc_final: 0.8753 (mmp) REVERT: F 128 TYR cc_start: 0.9600 (t80) cc_final: 0.9174 (m-80) outliers start: 95 outliers final: 67 residues processed: 210 average time/residue: 0.1049 time to fit residues: 34.2387 Evaluate side-chains 200 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 124 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 677 HIS Chi-restraints excluded: chain A residue 686 TYR Chi-restraints excluded: chain A residue 690 CYS Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 804 PHE Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 197 GLU Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 295 ARG Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 134 ARG Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 302 ASP Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 178 GLU Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 228 ASN Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain E residue 37 TYR Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 91 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: [59, 70, 72, 65, 38, 125, 19, 127, 153, 103, 50] chunk 59 optimal weight: 6.9990 chunk 70 optimal weight: 0.6980 chunk 72 optimal weight: 7.9990 chunk 65 optimal weight: 5.9990 chunk 38 optimal weight: 0.0050 chunk 125 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 chunk 127 optimal weight: 0.0980 chunk 153 optimal weight: 0.9980 chunk 103 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 overall best weight: 0.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 51 HIS ** C 162 GLN ** 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 = 0.3689 r_free = 0.3689 target = 0.075877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.050809 restraints weight = 61984.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.052696 restraints weight = 30262.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.053861 restraints weight = 20270.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.054569 restraints weight = 16174.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.054995 restraints weight = 14271.066| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.3904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15212 Z= 0.104 Angle : 0.595 13.367 20646 Z= 0.301 Chirality : 0.044 0.355 2275 Planarity : 0.003 0.043 2722 Dihedral : 5.153 58.737 2122 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 4.60 % Allowed : 24.39 % Favored : 71.00 % 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 are not related in a simple way. whole: -0.05 (0.20), residues: 1886 helix: 1.68 (0.23), residues: 517 sheet: -0.08 (0.24), residues: 488 loop : -1.04 (0.21), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 734 TYR 0.018 0.001 TYR D 107 PHE 0.015 0.001 PHE A 586 TRP 0.010 0.001 TRP B 228 HIS 0.007 0.001 HIS C 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (15212) covalent geometry : angle 0.59465 / 0.30 (20646) hydrogen bonds : bond 0.03246 / 2.17 ( 700) hydrogen bonds : angle 4.72235 / 3.32 ( 1959) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 131 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 MET cc_start: 0.7778 (ppp) cc_final: 0.7124 (pmm) REVERT: A 115 GLU cc_start: 0.9220 (mm-30) cc_final: 0.8564 (mm-30) REVERT: A 120 ARG cc_start: 0.7126 (ptp90) cc_final: 0.6517 (ptp90) REVERT: A 233 ARG cc_start: 0.8881 (OUTLIER) cc_final: 0.8550 (tpp80) REVERT: A 641 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8807 (pp) REVERT: A 804 PHE cc_start: 0.8291 (OUTLIER) cc_final: 0.8073 (t80) REVERT: B 295 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.8164 (mtp180) REVERT: B 298 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8197 (pp) REVERT: C 56 MET cc_start: 0.7878 (OUTLIER) cc_final: 0.7340 (tmm) REVERT: C 157 TYR cc_start: 0.8494 (m-80) cc_final: 0.8079 (m-80) REVERT: C 201 MET cc_start: 0.9104 (tmm) cc_final: 0.8549 (ppp) REVERT: C 228 MET cc_start: 0.8477 (mmt) cc_final: 0.8258 (mmt) REVERT: C 273 GLN cc_start: 0.8654 (mt0) cc_final: 0.8288 (tp40) REVERT: C 303 TYR cc_start: 0.8736 (m-80) cc_final: 0.8400 (m-80) REVERT: D 178 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.8027 (mp0) REVERT: D 187 GLU cc_start: 0.8320 (tm-30) cc_final: 0.8089 (tm-30) REVERT: F 27 LYS cc_start: 0.9465 (tppt) cc_final: 0.9141 (tppt) REVERT: F 46 MET cc_start: 0.9180 (mmm) cc_final: 0.8954 (mmm) REVERT: F 71 MET cc_start: 0.9328 (ptt) cc_final: 0.9066 (ptp) REVERT: F 128 TYR cc_start: 0.9602 (t80) cc_final: 0.9188 (m-80) outliers start: 74 outliers final: 57 residues processed: 191 average time/residue: 0.1055 time to fit residues: 30.8347 Evaluate side-chains 193 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 129 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 233 ARG Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 677 HIS Chi-restraints excluded: chain A residue 686 TYR Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 804 PHE Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 295 ARG Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 134 ARG Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 302 ASP Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain D residue 178 GLU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 151 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: [154, 103, 177, 79, 28, 66, 171, 3, 158, 84, 20] chunk 154 optimal weight: 9.9990 chunk 103 optimal weight: 8.9990 chunk 177 optimal weight: 10.0000 chunk 79 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 171 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 158 optimal weight: 0.8980 chunk 84 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 51 HIS ** C 162 GLN ** 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 = 0.3659 r_free = 0.3659 target = 0.074530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.049268 restraints weight = 62504.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.051071 restraints weight = 30845.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.052225 restraints weight = 20750.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.052901 restraints weight = 16607.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.053309 restraints weight = 14672.616| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.4100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15212 Z= 0.175 Angle : 0.622 14.537 20646 Z= 0.317 Chirality : 0.044 0.359 2275 Planarity : 0.004 0.043 2722 Dihedral : 5.242 58.544 2117 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 4.73 % Allowed : 24.77 % Favored : 70.50 % 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 are not related in a simple way. whole: -0.09 (0.20), residues: 1886 helix: 1.64 (0.23), residues: 517 sheet: -0.08 (0.24), residues: 502 loop : -1.09 (0.21), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 734 TYR 0.015 0.001 TYR D 107 PHE 0.026 0.001 PHE A 586 TRP 0.017 0.001 TRP F 413 HIS 0.006 0.001 HIS C 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.18 (15212) covalent geometry : angle 0.62167 / 0.32 (20646) hydrogen bonds : bond 0.03539 / 2.37 ( 700) hydrogen bonds : angle 4.85686 / 3.42 ( 1959) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 125 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 MET cc_start: 0.7822 (ppp) cc_final: 0.7202 (pmm) REVERT: A 115 GLU cc_start: 0.9187 (mm-30) cc_final: 0.8496 (mm-30) REVERT: A 120 ARG cc_start: 0.7199 (ptp90) cc_final: 0.6589 (ptp90) REVERT: A 192 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8471 (tm-30) REVERT: A 233 ARG cc_start: 0.8904 (OUTLIER) cc_final: 0.8543 (tpp80) REVERT: A 428 PHE cc_start: 0.8138 (OUTLIER) cc_final: 0.7683 (m-80) REVERT: A 804 PHE cc_start: 0.8342 (OUTLIER) cc_final: 0.8115 (t80) REVERT: B 32 MET cc_start: 0.7672 (mmp) cc_final: 0.7461 (mmp) REVERT: B 295 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.8181 (mtp180) REVERT: B 298 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8368 (pp) REVERT: C 56 MET cc_start: 0.7859 (OUTLIER) cc_final: 0.7449 (tmm) REVERT: C 201 MET cc_start: 0.9190 (tmm) cc_final: 0.8601 (ppp) REVERT: C 273 GLN cc_start: 0.8694 (mt0) cc_final: 0.8350 (tt0) REVERT: C 303 TYR cc_start: 0.8784 (m-80) cc_final: 0.8429 (m-80) REVERT: D 178 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8133 (mp0) REVERT: D 187 GLU cc_start: 0.8253 (tm-30) cc_final: 0.7994 (tm-30) REVERT: D 201 MET cc_start: 0.8392 (tpp) cc_final: 0.8183 (tpp) REVERT: F 46 MET cc_start: 0.9108 (mmm) cc_final: 0.8884 (mmm) REVERT: F 71 MET cc_start: 0.9332 (ptt) cc_final: 0.9077 (ptp) REVERT: F 114 MET cc_start: 0.9078 (mmp) cc_final: 0.8756 (mmm) REVERT: F 128 TYR cc_start: 0.9603 (t80) cc_final: 0.9197 (m-80) outliers start: 76 outliers final: 61 residues processed: 189 average time/residue: 0.1079 time to fit residues: 31.3109 Evaluate side-chains 191 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 122 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 233 ARG Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 677 HIS Chi-restraints excluded: chain A residue 686 TYR Chi-restraints excluded: chain A residue 690 CYS Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 804 PHE Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 295 ARG Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 134 ARG Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 302 ASP Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain D residue 178 GLU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 228 ASN Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 91 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: [93, 183, 147, 113, 12, 95, 119, 91, 118, 110, 177] chunk 93 optimal weight: 9.9990 chunk 183 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 113 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 chunk 95 optimal weight: 7.9990 chunk 119 optimal weight: 0.0050 chunk 91 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 110 optimal weight: 10.0000 chunk 177 optimal weight: 9.9990 overall best weight: 1.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 51 HIS ** C 162 GLN ** 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 = 0.3679 r_free = 0.3679 target = 0.075262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.050265 restraints weight = 62561.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.052128 restraints weight = 30280.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.053341 restraints weight = 20191.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.054027 restraints weight = 16041.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.054457 restraints weight = 14160.065| |-----------------------------------------------------------------------------| r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.4217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15212 Z= 0.124 Angle : 0.650 15.762 20646 Z= 0.329 Chirality : 0.044 0.369 2275 Planarity : 0.003 0.043 2722 Dihedral : 5.133 58.456 2117 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 4.60 % Allowed : 25.02 % Favored : 70.38 % 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 are not related in a simple way. whole: -0.08 (0.20), residues: 1886 helix: 1.57 (0.23), residues: 517 sheet: -0.03 (0.24), residues: 493 loop : -1.05 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 734 TYR 0.027 0.001 TYR D 107 PHE 0.018 0.001 PHE A 586 TRP 0.014 0.001 TRP F 413 HIS 0.006 0.001 HIS C 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (15212) covalent geometry : angle 0.65045 / 0.33 (20646) hydrogen bonds : bond 0.03424 / 2.28 ( 700) hydrogen bonds : angle 4.79908 / 3.37 ( 1959) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 129 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 MET cc_start: 0.7829 (ppp) cc_final: 0.7218 (pmm) REVERT: A 115 GLU cc_start: 0.9182 (mm-30) cc_final: 0.8482 (mm-30) REVERT: A 120 ARG cc_start: 0.7229 (ptp90) cc_final: 0.6619 (ptp90) REVERT: A 192 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8460 (tm-30) REVERT: A 233 ARG cc_start: 0.8884 (OUTLIER) cc_final: 0.8555 (tpp80) REVERT: A 641 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8824 (pp) REVERT: B 295 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.8181 (mtp180) REVERT: B 298 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8294 (pp) REVERT: C 56 MET cc_start: 0.7806 (OUTLIER) cc_final: 0.7262 (tmm) REVERT: C 201 MET cc_start: 0.9109 (tmm) cc_final: 0.8563 (ppp) REVERT: C 228 MET cc_start: 0.8391 (mmt) cc_final: 0.8101 (tpp) REVERT: C 273 GLN cc_start: 0.8634 (mt0) cc_final: 0.8274 (tp40) REVERT: C 303 TYR cc_start: 0.8842 (m-80) cc_final: 0.8474 (m-80) REVERT: D 111 MET cc_start: 0.8733 (OUTLIER) cc_final: 0.7890 (mpp) REVERT: D 178 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.8124 (mp0) REVERT: D 187 GLU cc_start: 0.8267 (tm-30) cc_final: 0.8003 (tm-30) REVERT: D 218 MET cc_start: 0.8148 (mtt) cc_final: 0.7926 (mtt) REVERT: F 46 MET cc_start: 0.9131 (mmm) cc_final: 0.8906 (mmm) REVERT: F 128 TYR cc_start: 0.9596 (t80) cc_final: 0.9183 (m-80) REVERT: F 136 MET cc_start: 0.9199 (ptt) cc_final: 0.8954 (ptt) outliers start: 74 outliers final: 58 residues processed: 190 average time/residue: 0.1106 time to fit residues: 31.9670 Evaluate side-chains 191 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 125 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 192 GLU Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 233 ARG Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 677 HIS Chi-restraints excluded: chain A residue 686 TYR Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 295 ARG Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 56 MET Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 144 ASP Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 302 ASP Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain D residue 111 MET Chi-restraints excluded: chain D residue 178 GLU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 151 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: [106, 178, 155, 179, 133, 131, 103, 45, 77, 25, 132] chunk 106 optimal weight: 3.9990 chunk 178 optimal weight: 40.0000 chunk 155 optimal weight: 1.9990 chunk 179 optimal weight: 9.9990 chunk 133 optimal weight: 5.9990 chunk 131 optimal weight: 5.9990 chunk 103 optimal weight: 9.9990 chunk 45 optimal weight: 0.8980 chunk 77 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 132 optimal weight: 8.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 51 HIS ** C 162 GLN ** 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 = 0.3648 r_free = 0.3648 target = 0.074045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.048798 restraints weight = 62519.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.050604 restraints weight = 30969.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.051729 restraints weight = 20910.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.052395 restraints weight = 16787.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.052719 restraints weight = 14851.174| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.4420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15212 Z= 0.194 Angle : 0.687 14.667 20646 Z= 0.351 Chirality : 0.045 0.361 2275 Planarity : 0.004 0.044 2722 Dihedral : 5.220 58.841 2114 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 4.60 % Allowed : 25.02 % Favored : 70.38 % 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 are not related in a simple way. whole: -0.17 (0.20), residues: 1886 helix: 1.48 (0.23), residues: 517 sheet: -0.06 (0.24), residues: 499 loop : -1.11 (0.21), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 76 TYR 0.026 0.002 TYR D 107 PHE 0.028 0.001 PHE A 804 TRP 0.016 0.001 TRP A 739 HIS 0.006 0.001 HIS C 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.19 (15212) covalent geometry : angle 0.68734 / 0.35 (20646) hydrogen bonds : bond 0.03652 / 2.42 ( 700) hydrogen bonds : angle 4.94945 / 3.48 ( 1959) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3772 Ramachandran restraints generated. 1886 Oldfield, 0 Emsley, 1886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 125 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 MET cc_start: 0.7914 (ppp) cc_final: 0.7314 (pmm) REVERT: A 115 GLU cc_start: 0.9175 (mm-30) cc_final: 0.8460 (mm-30) REVERT: A 120 ARG cc_start: 0.7246 (ptp90) cc_final: 0.6598 (ptp90) REVERT: A 428 PHE cc_start: 0.8106 (OUTLIER) cc_final: 0.7645 (m-80) REVERT: A 641 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8888 (pp) REVERT: A 741 MET cc_start: 0.7803 (mtp) cc_final: 0.7582 (mtm) REVERT: B 295 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.8198 (mtp180) REVERT: B 298 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8445 (pp) REVERT: C 56 MET cc_start: 0.7826 (ppp) cc_final: 0.7477 (tmm) REVERT: C 201 MET cc_start: 0.9203 (tmm) cc_final: 0.8605 (ppp) REVERT: C 228 MET cc_start: 0.8408 (mmt) cc_final: 0.8122 (tpp) REVERT: C 264 MET cc_start: 0.9109 (mmp) cc_final: 0.8896 (mmp) REVERT: C 273 GLN cc_start: 0.8701 (mt0) cc_final: 0.8478 (mm-40) REVERT: C 303 TYR cc_start: 0.8890 (m-80) cc_final: 0.8546 (m-80) REVERT: D 111 MET cc_start: 0.8786 (OUTLIER) cc_final: 0.7963 (mpp) REVERT: D 178 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8056 (mp0) REVERT: D 187 GLU cc_start: 0.8250 (tm-30) cc_final: 0.7977 (tm-30) REVERT: F 27 LYS cc_start: 0.9450 (mmtm) cc_final: 0.9176 (tppt) REVERT: F 46 MET cc_start: 0.9196 (mmm) cc_final: 0.8969 (mmm) REVERT: F 114 MET cc_start: 0.8702 (mmm) cc_final: 0.8483 (mmm) REVERT: F 128 TYR cc_start: 0.9620 (t80) cc_final: 0.9199 (m-80) outliers start: 74 outliers final: 64 residues processed: 189 average time/residue: 0.1101 time to fit residues: 32.2987 Evaluate side-chains 189 residues out of total 1607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 119 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 233 ARG Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 532 VAL Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 677 HIS Chi-restraints excluded: chain A residue 686 TYR Chi-restraints excluded: chain A residue 690 CYS Chi-restraints excluded: chain A residue 711 MET Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 735 THR Chi-restraints excluded: chain A residue 743 THR Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 63 LEU Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 295 ARG Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 230 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 302 ASP Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain D residue 111 MET Chi-restraints excluded: chain D residue 178 GLU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 205 TYR Chi-restraints excluded: chain D residue 228 ASN Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 151 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: [125, 43, 80, 6, 64, 134, 60, 48, 15, 143, 91] chunk 125 optimal weight: 9.9990 chunk 43 optimal weight: 3.9990 chunk 80 optimal weight: 0.6980 chunk 6 optimal weight: 7.9990 chunk 64 optimal weight: 0.9990 chunk 134 optimal weight: 20.0000 chunk 60 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 15 optimal weight: 8.9990 chunk 143 optimal weight: 10.0000 chunk 91 optimal weight: 9.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 61 ASN ** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** 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 = 0.3628 r_free = 0.3628 target = 0.073141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.047894 restraints weight = 62655.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.049641 restraints weight = 31765.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.050735 restraints weight = 21716.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.051380 restraints weight = 17543.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.051762 restraints weight = 15596.311| |-----------------------------------------------------------------------------| r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.4655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 15212 Z= 0.237 Angle : 0.708 14.859 20646 Z= 0.364 Chirality : 0.046 0.332 2275 Planarity : 0.004 0.050 2722 Dihedral : 5.447 58.290 2114 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 4.54 % Allowed : 25.33 % Favored : 70.13 % 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 are not related in a simple way. whole: -0.32 (0.20), residues: 1886 helix: 1.32 (0.23), residues: 515 sheet: -0.16 (0.24), residues: 500 loop : -1.16 (0.21), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 134 TYR 0.027 0.002 TYR D 107 PHE 0.030 0.002 PHE A 586 TRP 0.017 0.002 TRP A 739 HIS 0.010 0.001 HIS F 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.24 (15212) covalent geometry : angle 0.70783 / 0.36 (20646) hydrogen bonds : bond 0.03904 / 2.63 ( 700) hydrogen bonds : angle 5.06161 / 3.56 ( 1959) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3033.99 seconds wall clock time: 52 minutes 58.37 seconds (3178.37 seconds total)