Starting phenix.real_space_refine on Tue Mar 3 19:51:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lly_23436/03_2026/7lly_23436.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lly_23436/03_2026/7lly_23436.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lly_23436/03_2026/7lly_23436.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lly_23436/03_2026/7lly_23436.map" model { file = "/net/cci-nas-00/data/ceres_data/7lly_23436/03_2026/7lly_23436.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lly_23436/03_2026/7lly_23436.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 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 53 5.16 5 C 5427 2.51 5 N 1496 2.21 5 O 1573 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8549 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1660 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 6, 'TRANS': 189} Chain breaks: 3 Chain: "B" Number of atoms: 2606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2606 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "P" Number of atoms: 222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 222 Classifications: {'peptide': 26} Link IDs: {'TRANS': 25} Chain: "R" Number of atoms: 2652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2652 Classifications: {'peptide': 355} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PTRANS': 13, 'TRANS': 341} Chain breaks: 4 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 318 Unresolved non-hydrogen angles: 419 Unresolved non-hydrogen dihedrals: 287 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 5, 'TRP:plan': 6, 'ARG:plan': 7, 'GLU:plan': 5, 'TYR:plan': 3, 'ASP:plan': 6, 'PHE:plan': 4, 'ASN:plan1': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 206 Time building chain proxies: 1.82, per 1000 atoms: 0.21 Number of scatterers: 8549 At special positions: 0 Unit cell: (86.92, 170.66, 99.64, 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 53 16.00 O 1573 8.00 N 1496 7.00 C 5427 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 62 " - pdb=" SG CYS R 104 " distance=2.03 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 126 " distance=2.03 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.73 Conformation dependent library (CDL) restraints added in 351.4 milliseconds 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2080 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 11 sheets defined 41.3% alpha, 18.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 11 through 39 removed outlier: 4.320A pdb=" N GLU A 15 " --> pdb=" O ASP A 11 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 Processing helix chain 'A' and resid 266 through 278 removed outlier: 3.623A pdb=" N ASN A 278 " --> pdb=" O ASP A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.906A pdb=" N PHE A 315 " --> pdb=" O PHE A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.930A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 391 removed outlier: 3.858A pdb=" N ARG A 373 " --> pdb=" O THR A 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 25 Processing helix chain 'G' and resid 7 through 24 removed outlier: 3.652A pdb=" N GLN G 11 " --> pdb=" O ALA G 7 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.827A pdb=" N HIS G 44 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.735A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 removed outlier: 4.139A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 26 Processing helix chain 'R' and resid 36 through 53 Processing helix chain 'R' and resid 89 through 94 removed outlier: 4.041A pdb=" N SER R 94 " --> pdb=" O PRO R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 139 through 168 removed outlier: 3.649A pdb=" N VAL R 150 " --> pdb=" O ILE R 146 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY R 151 " --> pdb=" O ILE R 147 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE R 161 " --> pdb=" O SER R 157 " (cutoff:3.500A) Processing helix chain 'R' and resid 169 through 173 removed outlier: 3.597A pdb=" N HIS R 173 " --> pdb=" O ARG R 170 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 206 Processing helix chain 'R' and resid 223 through 256 removed outlier: 4.431A pdb=" N ARG R 227 " --> pdb=" O SER R 223 " (cutoff:3.500A) Processing helix chain 'R' and resid 261 through 275 Processing helix chain 'R' and resid 275 through 292 removed outlier: 3.545A pdb=" N LEU R 279 " --> pdb=" O GLY R 275 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE R 280 " --> pdb=" O VAL R 276 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL R 282 " --> pdb=" O LEU R 278 " (cutoff:3.500A) Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 302 through 337 removed outlier: 3.606A pdb=" N TRP R 306 " --> pdb=" O ASN R 302 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE R 309 " --> pdb=" O TYR R 305 " (cutoff:3.500A) Proline residue: R 312 - end of helix removed outlier: 3.663A pdb=" N ILE R 323 " --> pdb=" O VAL R 319 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ALA R 337 " --> pdb=" O SER R 333 " (cutoff:3.500A) Processing helix chain 'R' and resid 346 through 361 removed outlier: 3.565A pdb=" N THR R 355 " --> pdb=" O LYS R 351 " (cutoff:3.500A) Proline residue: R 358 - end of helix Processing helix chain 'R' and resid 362 through 368 removed outlier: 3.897A pdb=" N ALA R 368 " --> pdb=" O VAL R 365 " (cutoff:3.500A) Processing helix chain 'R' and resid 377 through 387 removed outlier: 4.004A pdb=" N PHE R 381 " --> pdb=" O GLY R 377 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR R 386 " --> pdb=" O ILE R 382 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLU R 387 " --> pdb=" O LYS R 383 " (cutoff:3.500A) Processing helix chain 'R' and resid 389 through 404 removed outlier: 3.923A pdb=" N GLY R 395 " --> pdb=" O THR R 391 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N LEU R 396 " --> pdb=" O SER R 392 " (cutoff:3.500A) Processing helix chain 'R' and resid 406 through 421 removed outlier: 4.394A pdb=" N GLU R 418 " --> pdb=" O ARG R 414 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ARG R 419 " --> pdb=" O LYS R 415 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 213 removed outlier: 9.847A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 52 removed outlier: 5.305A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 62 removed outlier: 7.051A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.700A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.725A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.371A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.403A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.076A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 6 removed outlier: 3.580A pdb=" N LEU N 18 " --> pdb=" O MET N 83 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU N 20 " --> pdb=" O LEU N 81 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 11 removed outlier: 6.160A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 79 through 81 removed outlier: 3.560A pdb=" N SER R 79 " --> pdb=" O CYS R 104 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N CYS R 104 " --> pdb=" O SER R 79 " (cutoff:3.500A) 427 hydrogen bonds defined for protein. 1218 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.26 Time building geometry restraints manager: 0.96 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: 2803 1.34 - 1.46: 1775 1.46 - 1.58: 4073 1.58 - 1.70: 0 1.70 - 1.82: 71 Bond restraints: 8722 Sorted by residual: bond pdb=" C PRO R 54 " pdb=" N PRO R 55 " ideal model delta sigma weight residual 1.329 1.372 -0.043 1.18e-02 7.18e+03 1.34e+01 bond pdb=" N ARG N 118 " pdb=" CA ARG N 118 " ideal model delta sigma weight residual 1.454 1.493 -0.039 1.15e-02 7.56e+03 1.16e+01 bond pdb=" N THR N 122 " pdb=" CA THR N 122 " ideal model delta sigma weight residual 1.453 1.491 -0.038 1.31e-02 5.83e+03 8.49e+00 bond pdb=" N ASP R 59 " pdb=" CA ASP R 59 " ideal model delta sigma weight residual 1.454 1.488 -0.033 1.15e-02 7.56e+03 8.38e+00 bond pdb=" N GLN N 123 " pdb=" CA GLN N 123 " ideal model delta sigma weight residual 1.456 1.490 -0.035 1.22e-02 6.72e+03 8.01e+00 ... (remaining 8717 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.19: 11506 1.19 - 2.39: 240 2.39 - 3.58: 58 3.58 - 4.78: 12 4.78 - 5.97: 4 Bond angle restraints: 11820 Sorted by residual: angle pdb=" C PRO R 54 " pdb=" N PRO R 55 " pdb=" CA PRO R 55 " ideal model delta sigma weight residual 120.38 126.35 -5.97 1.03e+00 9.43e-01 3.36e+01 angle pdb=" CA GLN N 123 " pdb=" C GLN N 123 " pdb=" O GLN N 123 " ideal model delta sigma weight residual 121.16 117.05 4.11 1.12e+00 7.97e-01 1.35e+01 angle pdb=" CA VAL N 124 " pdb=" C VAL N 124 " pdb=" O VAL N 124 " ideal model delta sigma weight residual 120.48 116.46 4.02 1.10e+00 8.26e-01 1.34e+01 angle pdb=" CA GLN N 120 " pdb=" C GLN N 120 " pdb=" O GLN N 120 " ideal model delta sigma weight residual 122.14 117.66 4.48 1.24e+00 6.50e-01 1.31e+01 angle pdb=" CA GLY N 121 " pdb=" C GLY N 121 " pdb=" O GLY N 121 " ideal model delta sigma weight residual 122.24 117.56 4.68 1.30e+00 5.92e-01 1.29e+01 ... (remaining 11815 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 4579 17.73 - 35.47: 452 35.47 - 53.20: 107 53.20 - 70.94: 11 70.94 - 88.67: 11 Dihedral angle restraints: 5160 sinusoidal: 1951 harmonic: 3209 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual 93.00 36.63 56.37 1 1.00e+01 1.00e-02 4.28e+01 dihedral pdb=" CB GLU A 322 " pdb=" CG GLU A 322 " pdb=" CD GLU A 322 " pdb=" OE1 GLU A 322 " ideal model delta sinusoidal sigma weight residual 0.00 -84.22 84.22 1 3.00e+01 1.11e-03 9.59e+00 dihedral pdb=" CA ASP B 66 " pdb=" CB ASP B 66 " pdb=" CG ASP B 66 " pdb=" OD1 ASP B 66 " ideal model delta sinusoidal sigma weight residual -30.00 -82.86 52.86 1 2.00e+01 2.50e-03 9.51e+00 ... (remaining 5157 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1093 0.043 - 0.086: 167 0.086 - 0.129: 65 0.129 - 0.172: 1 0.172 - 0.215: 3 Chirality restraints: 1329 Sorted by residual: chirality pdb=" CA VAL N 124 " pdb=" N VAL N 124 " pdb=" C VAL N 124 " pdb=" CB VAL N 124 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA LEU R 60 " pdb=" N LEU R 60 " pdb=" C LEU R 60 " pdb=" CB LEU R 60 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.67e-01 chirality pdb=" CA GLN N 123 " pdb=" N GLN N 123 " pdb=" C GLN N 123 " pdb=" CB GLN N 123 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.56e-01 ... (remaining 1326 not shown) Planarity restraints: 1509 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL N 124 " -0.009 2.00e-02 2.50e+03 1.94e-02 3.78e+00 pdb=" C VAL N 124 " 0.034 2.00e-02 2.50e+03 pdb=" O VAL N 124 " -0.013 2.00e-02 2.50e+03 pdb=" N THR N 125 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY N 121 " 0.007 2.00e-02 2.50e+03 1.45e-02 2.09e+00 pdb=" C GLY N 121 " -0.025 2.00e-02 2.50e+03 pdb=" O GLY N 121 " 0.009 2.00e-02 2.50e+03 pdb=" N THR N 122 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL R 276 " -0.020 5.00e-02 4.00e+02 3.06e-02 1.50e+00 pdb=" N PRO R 277 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO R 277 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO R 277 " -0.017 5.00e-02 4.00e+02 ... (remaining 1506 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 82 2.57 - 3.15: 7364 3.15 - 3.73: 13225 3.73 - 4.32: 17878 4.32 - 4.90: 29803 Nonbonded interactions: 68352 Sorted by model distance: nonbonded pdb=" O GLU R 387 " pdb=" OG1 THR R 391 " model vdw 1.982 3.040 nonbonded pdb=" O HIS B 183 " pdb=" OG1 THR B 184 " model vdw 2.125 3.040 nonbonded pdb=" ND2 ASN B 230 " pdb=" OD1 ASP B 246 " model vdw 2.167 3.120 nonbonded pdb=" OD1 ASP B 163 " pdb=" OG1 THR B 165 " model vdw 2.254 3.040 nonbonded pdb=" O TYR B 145 " pdb=" N GLY B 162 " model vdw 2.296 3.120 ... (remaining 68347 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.020 Find NCS groups from input model: 0.040 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8727 Z= 0.172 Angle : 0.474 5.970 11830 Z= 0.301 Chirality : 0.038 0.215 1329 Planarity : 0.002 0.031 1509 Dihedral : 15.152 88.671 3065 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.68 % Allowed : 6.72 % Favored : 92.60 % 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: -2.48 (0.22), residues: 1075 helix: -0.80 (0.23), residues: 411 sheet: -1.74 (0.32), residues: 215 loop : -2.31 (0.24), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 96 TYR 0.006 0.001 TYR N 60 PHE 0.007 0.001 PHE R 367 TRP 0.006 0.000 TRP A 234 HIS 0.002 0.000 HIS R 363 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 8722) covalent geometry : angle 0.47316 (11820) SS BOND : bond 0.00126 ( 5) SS BOND : angle 0.81474 ( 10) hydrogen bonds : bond 0.20867 ( 427) hydrogen bonds : angle 7.64362 ( 1218) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 244 time to evaluate : 0.213 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 378 ASP cc_start: 0.8712 (m-30) cc_final: 0.8035 (m-30) REVERT: B 9 GLN cc_start: 0.9120 (tm-30) cc_final: 0.8861 (tm-30) REVERT: B 10 GLU cc_start: 0.8852 (mt-10) cc_final: 0.8535 (mt-10) REVERT: B 36 ASN cc_start: 0.9299 (p0) cc_final: 0.9026 (p0) REVERT: B 118 ASP cc_start: 0.7372 (p0) cc_final: 0.7159 (p0) REVERT: B 172 GLU cc_start: 0.7586 (mp0) cc_final: 0.7336 (mp0) REVERT: B 215 GLU cc_start: 0.7350 (mp0) cc_final: 0.6993 (mp0) REVERT: G 19 LEU cc_start: 0.9355 (mp) cc_final: 0.9073 (mp) REVERT: G 36 ASP cc_start: 0.8315 (m-30) cc_final: 0.8099 (m-30) REVERT: N 73 ASP cc_start: 0.7928 (t0) cc_final: 0.7649 (t0) REVERT: N 123 GLN cc_start: 0.7341 (tm-30) cc_final: 0.7126 (tm-30) REVERT: R 204 MET cc_start: 0.8987 (tmm) cc_final: 0.8734 (tmm) REVERT: R 221 GLN cc_start: 0.8338 (mp10) cc_final: 0.8037 (mp10) REVERT: R 277 PRO cc_start: 0.8873 (Cg_exo) cc_final: 0.8605 (Cg_endo) REVERT: R 288 LYS cc_start: 0.9198 (tppp) cc_final: 0.8892 (tppt) REVERT: R 351 LYS cc_start: 0.9094 (tmmt) cc_final: 0.8565 (pttm) REVERT: R 387 GLU cc_start: 0.8927 (mp0) cc_final: 0.8481 (mp0) outliers start: 6 outliers final: 1 residues processed: 248 average time/residue: 0.0998 time to fit residues: 33.0154 Evaluate side-chains 200 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 199 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 225 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 9.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.0770 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 overall best weight: 1.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS B 155 ASN B 259 GLN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 1 HIS P 24 GLN R 173 HIS ** R 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 410 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.096176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.068185 restraints weight = 20085.201| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 3.53 r_work: 0.2840 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8727 Z= 0.135 Angle : 0.547 10.914 11830 Z= 0.284 Chirality : 0.040 0.145 1329 Planarity : 0.004 0.048 1509 Dihedral : 3.694 57.999 1199 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.96 % Allowed : 14.69 % Favored : 82.35 % 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: -0.60 (0.25), residues: 1075 helix: 1.40 (0.26), residues: 415 sheet: -1.34 (0.33), residues: 226 loop : -1.63 (0.27), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 310 TYR 0.014 0.001 TYR R 148 PHE 0.020 0.001 PHE R 184 TRP 0.031 0.001 TRP R 297 HIS 0.008 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 8722) covalent geometry : angle 0.54712 (11820) SS BOND : bond 0.00150 ( 5) SS BOND : angle 0.62964 ( 10) hydrogen bonds : bond 0.04168 ( 427) hydrogen bonds : angle 4.81773 ( 1218) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 220 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 ASP cc_start: 0.9099 (m-30) cc_final: 0.8819 (m-30) REVERT: A 211 LYS cc_start: 0.9161 (ptpp) cc_final: 0.8924 (ptpp) REVERT: B 9 GLN cc_start: 0.9189 (tm-30) cc_final: 0.8975 (tm-30) REVERT: B 10 GLU cc_start: 0.8981 (mt-10) cc_final: 0.8693 (mt-10) REVERT: B 45 MET cc_start: 0.8947 (mmm) cc_final: 0.8081 (mpp) REVERT: B 101 MET cc_start: 0.9431 (mtp) cc_final: 0.9225 (mtp) REVERT: B 215 GLU cc_start: 0.7911 (mp0) cc_final: 0.7485 (mp0) REVERT: B 217 MET cc_start: 0.8417 (ppp) cc_final: 0.7965 (ppp) REVERT: B 226 GLU cc_start: 0.8428 (mm-30) cc_final: 0.8216 (tp30) REVERT: B 228 ASP cc_start: 0.8539 (p0) cc_final: 0.8294 (p0) REVERT: B 230 ASN cc_start: 0.8992 (m-40) cc_final: 0.8558 (m110) REVERT: B 234 PHE cc_start: 0.9351 (OUTLIER) cc_final: 0.8634 (m-80) REVERT: B 262 MET cc_start: 0.8723 (OUTLIER) cc_final: 0.8444 (tpp) REVERT: G 11 GLN cc_start: 0.8924 (tm-30) cc_final: 0.8717 (pp30) REVERT: G 19 LEU cc_start: 0.9165 (mp) cc_final: 0.8958 (mp) REVERT: G 20 LYS cc_start: 0.9135 (mtmm) cc_final: 0.8801 (mtmm) REVERT: G 29 LYS cc_start: 0.8889 (mmmt) cc_final: 0.8449 (mmmm) REVERT: N 73 ASP cc_start: 0.8178 (t0) cc_final: 0.7886 (t0) REVERT: R 139 GLU cc_start: 0.9078 (mt-10) cc_final: 0.8169 (tp30) REVERT: R 202 LYS cc_start: 0.8657 (pptt) cc_final: 0.8092 (ptmt) REVERT: R 221 GLN cc_start: 0.8161 (mp10) cc_final: 0.7898 (mp10) REVERT: R 257 PHE cc_start: 0.7677 (OUTLIER) cc_final: 0.6940 (m-10) REVERT: R 269 TYR cc_start: 0.9228 (m-10) cc_final: 0.9012 (m-80) REVERT: R 297 TRP cc_start: 0.8803 (m-10) cc_final: 0.8564 (m-90) REVERT: R 393 PHE cc_start: 0.9104 (m-10) cc_final: 0.8903 (m-10) REVERT: R 397 MET cc_start: 0.9300 (mmp) cc_final: 0.8583 (mtt) outliers start: 26 outliers final: 11 residues processed: 236 average time/residue: 0.0968 time to fit residues: 30.7582 Evaluate side-chains 211 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 197 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 109 ASP Chi-restraints excluded: chain R residue 246 VAL Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain R residue 254 LEU Chi-restraints excluded: chain R residue 257 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 82 optimal weight: 2.9990 chunk 101 optimal weight: 9.9990 chunk 49 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 41 optimal weight: 0.0980 chunk 6 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN N 5 GLN N 39 GLN N 120 GLN R 182 ASN R 234 GLN ** R 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.097042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.069430 restraints weight = 19815.728| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 3.50 r_work: 0.2861 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 8727 Z= 0.107 Angle : 0.521 10.543 11830 Z= 0.270 Chirality : 0.040 0.230 1329 Planarity : 0.003 0.047 1509 Dihedral : 3.784 59.746 1199 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.62 % Allowed : 17.20 % Favored : 80.18 % 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: -0.02 (0.26), residues: 1075 helix: 1.95 (0.26), residues: 409 sheet: -1.01 (0.33), residues: 228 loop : -1.36 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 129 TYR 0.013 0.001 TYR R 148 PHE 0.014 0.001 PHE R 184 TRP 0.017 0.001 TRP R 297 HIS 0.008 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 8722) covalent geometry : angle 0.52090 (11820) SS BOND : bond 0.00158 ( 5) SS BOND : angle 0.53569 ( 10) hydrogen bonds : bond 0.03663 ( 427) hydrogen bonds : angle 4.44175 ( 1218) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 214 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ASP cc_start: 0.9065 (m-30) cc_final: 0.8819 (m-30) REVERT: A 378 ASP cc_start: 0.9051 (m-30) cc_final: 0.8338 (m-30) REVERT: B 9 GLN cc_start: 0.9209 (tm-30) cc_final: 0.8941 (tm-30) REVERT: B 10 GLU cc_start: 0.8986 (mt-10) cc_final: 0.8653 (mt-10) REVERT: B 45 MET cc_start: 0.8871 (mmm) cc_final: 0.8058 (mpp) REVERT: B 61 MET cc_start: 0.8959 (ptm) cc_final: 0.8613 (ptm) REVERT: B 215 GLU cc_start: 0.8043 (mp0) cc_final: 0.7682 (mp0) REVERT: B 226 GLU cc_start: 0.8426 (mm-30) cc_final: 0.8199 (tp30) REVERT: B 234 PHE cc_start: 0.9345 (OUTLIER) cc_final: 0.8577 (m-80) REVERT: G 19 LEU cc_start: 0.9190 (mp) cc_final: 0.8941 (mp) REVERT: G 20 LYS cc_start: 0.9106 (mtmm) cc_final: 0.8803 (mtmm) REVERT: N 5 GLN cc_start: 0.8954 (mt0) cc_final: 0.8258 (mp10) REVERT: N 73 ASP cc_start: 0.8315 (t0) cc_final: 0.7811 (t0) REVERT: N 76 LYS cc_start: 0.9395 (mtmm) cc_final: 0.9177 (mtmm) REVERT: N 95 TYR cc_start: 0.9053 (m-80) cc_final: 0.8745 (m-80) REVERT: R 173 HIS cc_start: 0.8347 (m-70) cc_final: 0.7901 (m90) REVERT: R 202 LYS cc_start: 0.8731 (pptt) cc_final: 0.8340 (ptmt) REVERT: R 204 MET cc_start: 0.8926 (tmm) cc_final: 0.8665 (tmm) REVERT: R 221 GLN cc_start: 0.8014 (mp10) cc_final: 0.7722 (mp10) REVERT: R 257 PHE cc_start: 0.7528 (OUTLIER) cc_final: 0.6868 (m-80) REVERT: R 269 TYR cc_start: 0.9248 (m-10) cc_final: 0.9007 (m-80) REVERT: R 387 GLU cc_start: 0.9246 (mp0) cc_final: 0.8932 (mp0) REVERT: R 393 PHE cc_start: 0.9119 (m-10) cc_final: 0.8852 (m-10) REVERT: R 397 MET cc_start: 0.9313 (mmp) cc_final: 0.8701 (mtt) outliers start: 23 outliers final: 16 residues processed: 227 average time/residue: 0.0951 time to fit residues: 28.9877 Evaluate side-chains 211 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 193 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 109 ASP Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 232 LEU Chi-restraints excluded: chain R residue 246 VAL Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 254 LEU Chi-restraints excluded: chain R residue 257 PHE Chi-restraints excluded: chain R residue 396 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 55 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 103 optimal weight: 10.0000 chunk 14 optimal weight: 0.9990 chunk 57 optimal weight: 0.4980 chunk 89 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 76 optimal weight: 30.0000 chunk 63 optimal weight: 0.7980 chunk 80 optimal weight: 8.9990 chunk 97 optimal weight: 2.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 HIS B 155 ASN B 230 ASN B 340 ASN N 39 GLN P 24 GLN R 234 GLN ** R 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.095989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.068027 restraints weight = 20154.767| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 3.54 r_work: 0.2837 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8727 Z= 0.120 Angle : 0.513 8.413 11830 Z= 0.266 Chirality : 0.040 0.231 1329 Planarity : 0.003 0.047 1509 Dihedral : 3.889 58.578 1199 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.42 % Allowed : 18.11 % Favored : 78.47 % 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: 0.22 (0.26), residues: 1075 helix: 2.06 (0.26), residues: 409 sheet: -0.77 (0.33), residues: 231 loop : -1.18 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 13 TYR 0.019 0.001 TYR A 318 PHE 0.011 0.001 PHE N 108 TRP 0.053 0.001 TRP R 297 HIS 0.008 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 8722) covalent geometry : angle 0.51288 (11820) SS BOND : bond 0.00190 ( 5) SS BOND : angle 0.54837 ( 10) hydrogen bonds : bond 0.03528 ( 427) hydrogen bonds : angle 4.27212 ( 1218) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 194 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ASP cc_start: 0.9052 (m-30) cc_final: 0.8827 (m-30) REVERT: A 378 ASP cc_start: 0.9080 (m-30) cc_final: 0.8356 (m-30) REVERT: B 9 GLN cc_start: 0.9186 (tm-30) cc_final: 0.8951 (tm-30) REVERT: B 10 GLU cc_start: 0.8992 (mt-10) cc_final: 0.8656 (mt-10) REVERT: B 45 MET cc_start: 0.8997 (mmm) cc_final: 0.8178 (mpp) REVERT: B 215 GLU cc_start: 0.8043 (mp0) cc_final: 0.7731 (mp0) REVERT: B 234 PHE cc_start: 0.9382 (OUTLIER) cc_final: 0.8686 (m-80) REVERT: G 13 ARG cc_start: 0.8844 (mtm110) cc_final: 0.8616 (mtm110) REVERT: G 19 LEU cc_start: 0.9216 (mp) cc_final: 0.8955 (mp) REVERT: G 20 LYS cc_start: 0.9127 (mtmm) cc_final: 0.8858 (mtmm) REVERT: G 29 LYS cc_start: 0.9187 (mmmm) cc_final: 0.8781 (mmmm) REVERT: N 73 ASP cc_start: 0.8414 (t0) cc_final: 0.8099 (t0) REVERT: P 17 ARG cc_start: 0.8333 (tpp80) cc_final: 0.8132 (tpp80) REVERT: R 202 LYS cc_start: 0.8697 (pptt) cc_final: 0.8421 (tttt) REVERT: R 204 MET cc_start: 0.8989 (tmm) cc_final: 0.8701 (tmm) REVERT: R 221 GLN cc_start: 0.8023 (mp10) cc_final: 0.7745 (mp10) REVERT: R 257 PHE cc_start: 0.7485 (OUTLIER) cc_final: 0.6878 (m-80) REVERT: R 387 GLU cc_start: 0.9270 (mp0) cc_final: 0.8893 (mp0) REVERT: R 393 PHE cc_start: 0.9078 (m-10) cc_final: 0.8758 (m-10) REVERT: R 397 MET cc_start: 0.9250 (mmp) cc_final: 0.8687 (mtt) outliers start: 30 outliers final: 17 residues processed: 216 average time/residue: 0.0944 time to fit residues: 27.2212 Evaluate side-chains 207 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 188 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 109 ASP Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 246 VAL Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 257 PHE Chi-restraints excluded: chain R residue 396 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 72 optimal weight: 7.9990 chunk 50 optimal weight: 0.9990 chunk 40 optimal weight: 0.3980 chunk 12 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 7 optimal weight: 0.3980 chunk 59 optimal weight: 2.9990 chunk 34 optimal weight: 0.2980 chunk 49 optimal weight: 8.9990 chunk 97 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN N 120 GLN ** N 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 363 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.096998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.068971 restraints weight = 19928.267| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 3.52 r_work: 0.2856 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8727 Z= 0.106 Angle : 0.525 7.791 11830 Z= 0.270 Chirality : 0.040 0.209 1329 Planarity : 0.003 0.046 1509 Dihedral : 3.932 53.308 1199 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.53 % Allowed : 19.02 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.26), residues: 1075 helix: 2.09 (0.26), residues: 410 sheet: -0.45 (0.33), residues: 227 loop : -1.09 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 227 TYR 0.014 0.001 TYR A 318 PHE 0.009 0.001 PHE N 108 TRP 0.060 0.001 TRP R 297 HIS 0.002 0.001 HIS R 173 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 8722) covalent geometry : angle 0.52528 (11820) SS BOND : bond 0.00184 ( 5) SS BOND : angle 0.49715 ( 10) hydrogen bonds : bond 0.03400 ( 427) hydrogen bonds : angle 4.15587 ( 1218) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 201 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 ASP cc_start: 0.9009 (m-30) cc_final: 0.8775 (m-30) REVERT: A 378 ASP cc_start: 0.9044 (m-30) cc_final: 0.8292 (m-30) REVERT: B 9 GLN cc_start: 0.9181 (tm-30) cc_final: 0.8964 (tm-30) REVERT: B 10 GLU cc_start: 0.9023 (mt-10) cc_final: 0.8714 (mt-10) REVERT: B 215 GLU cc_start: 0.8059 (mp0) cc_final: 0.7827 (mp0) REVERT: B 234 PHE cc_start: 0.9364 (OUTLIER) cc_final: 0.8640 (m-80) REVERT: G 19 LEU cc_start: 0.9194 (mp) cc_final: 0.8957 (mp) REVERT: G 20 LYS cc_start: 0.9128 (mtmm) cc_final: 0.8893 (mtmm) REVERT: G 32 LYS cc_start: 0.8815 (tptp) cc_final: 0.8360 (tptt) REVERT: N 73 ASP cc_start: 0.8468 (t0) cc_final: 0.8157 (t0) REVERT: N 89 GLU cc_start: 0.8693 (pm20) cc_final: 0.8492 (pm20) REVERT: N 91 THR cc_start: 0.9249 (OUTLIER) cc_final: 0.8993 (t) REVERT: N 95 TYR cc_start: 0.8952 (m-80) cc_final: 0.8612 (m-80) REVERT: R 173 HIS cc_start: 0.8288 (m-70) cc_final: 0.7834 (m90) REVERT: R 202 LYS cc_start: 0.8732 (pptt) cc_final: 0.8473 (tttt) REVERT: R 204 MET cc_start: 0.8964 (tmm) cc_final: 0.8698 (tmm) REVERT: R 221 GLN cc_start: 0.8115 (mp10) cc_final: 0.7833 (mp10) REVERT: R 257 PHE cc_start: 0.7417 (OUTLIER) cc_final: 0.7059 (m-80) REVERT: R 393 PHE cc_start: 0.9078 (m-10) cc_final: 0.8753 (m-10) REVERT: R 394 GLN cc_start: 0.9098 (tt0) cc_final: 0.8829 (tt0) REVERT: R 397 MET cc_start: 0.9241 (mmp) cc_final: 0.8656 (mtt) outliers start: 31 outliers final: 19 residues processed: 222 average time/residue: 0.0969 time to fit residues: 28.7819 Evaluate side-chains 212 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 190 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 109 ASP Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 246 VAL Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 254 LEU Chi-restraints excluded: chain R residue 257 PHE Chi-restraints excluded: chain R residue 396 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 54 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 53 optimal weight: 8.9990 chunk 48 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 GLN ** N 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 180 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.093152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.064913 restraints weight = 20004.892| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 3.47 r_work: 0.2770 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8727 Z= 0.193 Angle : 0.571 7.180 11830 Z= 0.300 Chirality : 0.041 0.206 1329 Planarity : 0.003 0.043 1509 Dihedral : 3.755 15.587 1197 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 4.10 % Allowed : 20.05 % Favored : 75.85 % 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: 0.43 (0.26), residues: 1075 helix: 2.05 (0.26), residues: 412 sheet: -0.43 (0.34), residues: 229 loop : -1.03 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 13 TYR 0.016 0.002 TYR A 318 PHE 0.016 0.001 PHE N 68 TRP 0.039 0.001 TRP R 297 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00433 ( 8722) covalent geometry : angle 0.57112 (11820) SS BOND : bond 0.00206 ( 5) SS BOND : angle 0.79087 ( 10) hydrogen bonds : bond 0.03674 ( 427) hydrogen bonds : angle 4.29174 ( 1218) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 188 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 ASP cc_start: 0.9054 (m-30) cc_final: 0.8838 (m-30) REVERT: A 378 ASP cc_start: 0.9136 (m-30) cc_final: 0.8374 (m-30) REVERT: B 10 GLU cc_start: 0.9009 (mt-10) cc_final: 0.8739 (mp0) REVERT: B 45 MET cc_start: 0.8992 (mmm) cc_final: 0.8173 (mmm) REVERT: B 61 MET cc_start: 0.9059 (ptm) cc_final: 0.8815 (ptm) REVERT: B 183 HIS cc_start: 0.8176 (OUTLIER) cc_final: 0.7710 (t-90) REVERT: B 215 GLU cc_start: 0.8108 (mp0) cc_final: 0.7905 (mp0) REVERT: B 234 PHE cc_start: 0.9447 (OUTLIER) cc_final: 0.8847 (m-80) REVERT: G 20 LYS cc_start: 0.9170 (mtmm) cc_final: 0.8893 (mtmm) REVERT: N 73 ASP cc_start: 0.8565 (t0) cc_final: 0.8222 (t0) REVERT: N 91 THR cc_start: 0.9359 (OUTLIER) cc_final: 0.9135 (t) REVERT: N 95 TYR cc_start: 0.9026 (m-80) cc_final: 0.8539 (m-80) REVERT: R 198 ASP cc_start: 0.8495 (p0) cc_final: 0.8271 (p0) REVERT: R 202 LYS cc_start: 0.8789 (pptt) cc_final: 0.8501 (tttt) REVERT: R 221 GLN cc_start: 0.7991 (mp10) cc_final: 0.7692 (mp10) REVERT: R 257 PHE cc_start: 0.7625 (OUTLIER) cc_final: 0.7316 (m-80) REVERT: R 371 MET cc_start: 0.9019 (mmp) cc_final: 0.8730 (mmp) REVERT: R 387 GLU cc_start: 0.9306 (mp0) cc_final: 0.9010 (mp0) REVERT: R 393 PHE cc_start: 0.9136 (m-10) cc_final: 0.8765 (m-10) REVERT: R 397 MET cc_start: 0.9298 (mmp) cc_final: 0.8694 (mtt) outliers start: 36 outliers final: 20 residues processed: 214 average time/residue: 0.0922 time to fit residues: 26.5756 Evaluate side-chains 207 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 183 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 109 ASP Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 246 VAL Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 257 PHE Chi-restraints excluded: chain R residue 386 THR Chi-restraints excluded: chain R residue 396 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 18 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 80 optimal weight: 6.9990 chunk 98 optimal weight: 0.6980 chunk 95 optimal weight: 10.0000 chunk 41 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS N 39 GLN ** N 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.094474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.066292 restraints weight = 20150.314| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 3.53 r_work: 0.2798 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8727 Z= 0.136 Angle : 0.557 6.790 11830 Z= 0.290 Chirality : 0.040 0.194 1329 Planarity : 0.003 0.043 1509 Dihedral : 3.730 18.098 1197 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.19 % Allowed : 21.64 % Favored : 75.17 % 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: 0.51 (0.26), residues: 1075 helix: 2.06 (0.26), residues: 410 sheet: -0.30 (0.34), residues: 227 loop : -0.96 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 13 TYR 0.017 0.002 TYR B 264 PHE 0.011 0.001 PHE N 108 TRP 0.031 0.001 TRP R 297 HIS 0.002 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 8722) covalent geometry : angle 0.55723 (11820) SS BOND : bond 0.00195 ( 5) SS BOND : angle 0.71349 ( 10) hydrogen bonds : bond 0.03538 ( 427) hydrogen bonds : angle 4.20041 ( 1218) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 199 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ASP cc_start: 0.9051 (m-30) cc_final: 0.8843 (m-30) REVERT: A 378 ASP cc_start: 0.9102 (m-30) cc_final: 0.8323 (m-30) REVERT: B 10 GLU cc_start: 0.8927 (mt-10) cc_final: 0.8711 (mt-10) REVERT: B 45 MET cc_start: 0.9001 (mmm) cc_final: 0.8156 (mmm) REVERT: B 61 MET cc_start: 0.9017 (ptm) cc_final: 0.8803 (ptm) REVERT: B 183 HIS cc_start: 0.8303 (OUTLIER) cc_final: 0.7749 (t-90) REVERT: B 234 PHE cc_start: 0.9411 (OUTLIER) cc_final: 0.8734 (m-80) REVERT: G 20 LYS cc_start: 0.9159 (mtmm) cc_final: 0.8924 (mtmm) REVERT: N 73 ASP cc_start: 0.8499 (t0) cc_final: 0.8160 (t0) REVERT: N 91 THR cc_start: 0.9311 (OUTLIER) cc_final: 0.9061 (t) REVERT: N 95 TYR cc_start: 0.8994 (m-80) cc_final: 0.8596 (m-80) REVERT: R 198 ASP cc_start: 0.8488 (p0) cc_final: 0.8249 (p0) REVERT: R 202 LYS cc_start: 0.8826 (pptt) cc_final: 0.8546 (tttt) REVERT: R 204 MET cc_start: 0.9019 (tmm) cc_final: 0.8641 (tmm) REVERT: R 221 GLN cc_start: 0.7988 (mp10) cc_final: 0.7675 (mp10) REVERT: R 257 PHE cc_start: 0.7591 (OUTLIER) cc_final: 0.7156 (m-80) REVERT: R 294 GLU cc_start: 0.8868 (pm20) cc_final: 0.8430 (pm20) REVERT: R 297 TRP cc_start: 0.8993 (m-10) cc_final: 0.8732 (m-90) REVERT: R 299 ARG cc_start: 0.8547 (mpt-90) cc_final: 0.8275 (mpt-90) REVERT: R 371 MET cc_start: 0.9064 (mmp) cc_final: 0.8779 (mmp) REVERT: R 387 GLU cc_start: 0.9212 (mp0) cc_final: 0.8646 (mp0) REVERT: R 393 PHE cc_start: 0.9155 (m-10) cc_final: 0.8772 (m-10) REVERT: R 394 GLN cc_start: 0.9284 (tt0) cc_final: 0.8915 (tt0) REVERT: R 397 MET cc_start: 0.9280 (mmp) cc_final: 0.8644 (mtt) REVERT: R 410 GLN cc_start: 0.8844 (mm110) cc_final: 0.8432 (mt0) outliers start: 28 outliers final: 21 residues processed: 220 average time/residue: 0.0959 time to fit residues: 28.2017 Evaluate side-chains 208 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 183 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 109 ASP Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 257 PHE Chi-restraints excluded: chain R residue 396 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 52 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 chunk 28 optimal weight: 0.0570 chunk 82 optimal weight: 8.9990 chunk 32 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 36 optimal weight: 0.4980 chunk 64 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 overall best weight: 1.9102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 234 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.093973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.065829 restraints weight = 19919.925| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 3.48 r_work: 0.2788 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8727 Z= 0.156 Angle : 0.588 7.003 11830 Z= 0.304 Chirality : 0.041 0.210 1329 Planarity : 0.003 0.042 1509 Dihedral : 3.761 16.748 1197 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.53 % Allowed : 21.98 % Favored : 74.49 % 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: 0.51 (0.26), residues: 1075 helix: 2.07 (0.26), residues: 410 sheet: -0.36 (0.33), residues: 229 loop : -0.95 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 13 TYR 0.014 0.002 TYR A 318 PHE 0.012 0.001 PHE N 108 TRP 0.029 0.001 TRP R 297 HIS 0.002 0.001 HIS R 173 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 8722) covalent geometry : angle 0.58749 (11820) SS BOND : bond 0.00173 ( 5) SS BOND : angle 0.80900 ( 10) hydrogen bonds : bond 0.03555 ( 427) hydrogen bonds : angle 4.18674 ( 1218) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 186 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ASP cc_start: 0.9049 (m-30) cc_final: 0.8849 (m-30) REVERT: A 378 ASP cc_start: 0.9125 (m-30) cc_final: 0.8348 (m-30) REVERT: B 42 ARG cc_start: 0.8724 (tmm-80) cc_final: 0.8264 (tmm-80) REVERT: B 45 MET cc_start: 0.9014 (mmm) cc_final: 0.8177 (mmm) REVERT: B 183 HIS cc_start: 0.8317 (OUTLIER) cc_final: 0.7746 (t-90) REVERT: B 215 GLU cc_start: 0.8069 (mp0) cc_final: 0.7860 (mp0) REVERT: B 234 PHE cc_start: 0.9416 (OUTLIER) cc_final: 0.8781 (m-80) REVERT: G 20 LYS cc_start: 0.9161 (mtmm) cc_final: 0.8928 (mtmm) REVERT: G 42 GLU cc_start: 0.8946 (tp30) cc_final: 0.8650 (tm-30) REVERT: N 73 ASP cc_start: 0.8516 (t0) cc_final: 0.8166 (t0) REVERT: N 91 THR cc_start: 0.9319 (OUTLIER) cc_final: 0.9028 (t) REVERT: N 95 TYR cc_start: 0.8984 (m-80) cc_final: 0.8631 (m-80) REVERT: R 202 LYS cc_start: 0.8835 (pptt) cc_final: 0.8552 (tttt) REVERT: R 204 MET cc_start: 0.8980 (tmm) cc_final: 0.8600 (tmm) REVERT: R 221 GLN cc_start: 0.8032 (mp10) cc_final: 0.7694 (mp10) REVERT: R 234 GLN cc_start: 0.9431 (mm110) cc_final: 0.9123 (mm-40) REVERT: R 257 PHE cc_start: 0.7685 (OUTLIER) cc_final: 0.7230 (m-80) REVERT: R 297 TRP cc_start: 0.8953 (m-10) cc_final: 0.8663 (m-90) REVERT: R 309 ILE cc_start: 0.9379 (OUTLIER) cc_final: 0.9132 (tp) REVERT: R 371 MET cc_start: 0.9090 (mmp) cc_final: 0.8801 (mmp) REVERT: R 387 GLU cc_start: 0.9234 (mp0) cc_final: 0.8670 (mp0) REVERT: R 393 PHE cc_start: 0.9163 (m-10) cc_final: 0.8781 (m-10) REVERT: R 397 MET cc_start: 0.9282 (mmp) cc_final: 0.8672 (mtt) REVERT: R 410 GLN cc_start: 0.8823 (mm110) cc_final: 0.8391 (mt0) outliers start: 31 outliers final: 22 residues processed: 210 average time/residue: 0.0974 time to fit residues: 27.3799 Evaluate side-chains 214 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 187 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 109 ASP Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 257 PHE Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain R residue 396 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 35 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 45 optimal weight: 7.9990 chunk 34 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 57 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.093077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.064777 restraints weight = 19995.578| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 3.49 r_work: 0.2768 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8727 Z= 0.169 Angle : 0.607 8.517 11830 Z= 0.315 Chirality : 0.041 0.194 1329 Planarity : 0.003 0.042 1509 Dihedral : 3.813 17.473 1197 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.42 % Allowed : 22.67 % Favored : 73.92 % 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: 0.43 (0.26), residues: 1075 helix: 1.94 (0.26), residues: 410 sheet: -0.38 (0.33), residues: 229 loop : -0.92 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 13 TYR 0.016 0.001 TYR A 318 PHE 0.012 0.001 PHE N 68 TRP 0.027 0.001 TRP R 297 HIS 0.003 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 8722) covalent geometry : angle 0.60667 (11820) SS BOND : bond 0.00172 ( 5) SS BOND : angle 0.84193 ( 10) hydrogen bonds : bond 0.03642 ( 427) hydrogen bonds : angle 4.23396 ( 1218) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 192 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ASP cc_start: 0.9104 (m-30) cc_final: 0.8902 (m-30) REVERT: A 352 SER cc_start: 0.8723 (t) cc_final: 0.8448 (p) REVERT: A 378 ASP cc_start: 0.9123 (m-30) cc_final: 0.8358 (m-30) REVERT: A 392 GLU cc_start: 0.9190 (mt-10) cc_final: 0.8954 (mp0) REVERT: B 45 MET cc_start: 0.9017 (mmm) cc_final: 0.8176 (mmm) REVERT: B 183 HIS cc_start: 0.8366 (OUTLIER) cc_final: 0.7777 (t-90) REVERT: B 215 GLU cc_start: 0.8041 (mp0) cc_final: 0.7840 (mp0) REVERT: B 234 PHE cc_start: 0.9416 (OUTLIER) cc_final: 0.8778 (m-80) REVERT: G 20 LYS cc_start: 0.9176 (mtmm) cc_final: 0.8950 (mtmm) REVERT: G 42 GLU cc_start: 0.8993 (tp30) cc_final: 0.8668 (tm-30) REVERT: N 73 ASP cc_start: 0.8519 (t0) cc_final: 0.8164 (t0) REVERT: N 91 THR cc_start: 0.9358 (OUTLIER) cc_final: 0.9126 (t) REVERT: N 95 TYR cc_start: 0.8986 (m-80) cc_final: 0.8621 (m-80) REVERT: R 139 GLU cc_start: 0.8987 (mt-10) cc_final: 0.8058 (tp30) REVERT: R 202 LYS cc_start: 0.8893 (pptt) cc_final: 0.8578 (tttt) REVERT: R 204 MET cc_start: 0.8979 (tmm) cc_final: 0.8573 (tmm) REVERT: R 221 GLN cc_start: 0.8164 (mp10) cc_final: 0.7838 (mp10) REVERT: R 257 PHE cc_start: 0.7745 (OUTLIER) cc_final: 0.7244 (m-80) REVERT: R 309 ILE cc_start: 0.9378 (OUTLIER) cc_final: 0.9167 (tp) REVERT: R 371 MET cc_start: 0.9089 (mmp) cc_final: 0.8784 (mmp) REVERT: R 393 PHE cc_start: 0.9167 (m-10) cc_final: 0.8800 (m-10) REVERT: R 397 MET cc_start: 0.9270 (mmp) cc_final: 0.8634 (mtt) REVERT: R 410 GLN cc_start: 0.8828 (mm110) cc_final: 0.8359 (mt0) outliers start: 30 outliers final: 21 residues processed: 215 average time/residue: 0.0932 time to fit residues: 27.0061 Evaluate side-chains 213 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 187 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 109 ASP Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 257 PHE Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain R residue 396 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 79 optimal weight: 50.0000 chunk 31 optimal weight: 4.9990 chunk 82 optimal weight: 7.9990 chunk 61 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 29 optimal weight: 0.3980 chunk 13 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS N 120 GLN R 234 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.095063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.067162 restraints weight = 19898.525| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 3.51 r_work: 0.2818 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8727 Z= 0.120 Angle : 0.608 8.155 11830 Z= 0.313 Chirality : 0.041 0.191 1329 Planarity : 0.003 0.043 1509 Dihedral : 3.701 15.731 1197 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.19 % Allowed : 23.23 % Favored : 73.58 % 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: 0.51 (0.26), residues: 1075 helix: 1.97 (0.26), residues: 409 sheet: -0.21 (0.34), residues: 227 loop : -0.92 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 13 TYR 0.014 0.001 TYR A 318 PHE 0.010 0.001 PHE N 108 TRP 0.027 0.001 TRP R 297 HIS 0.003 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 8722) covalent geometry : angle 0.60805 (11820) SS BOND : bond 0.00171 ( 5) SS BOND : angle 0.60143 ( 10) hydrogen bonds : bond 0.03459 ( 427) hydrogen bonds : angle 4.12753 ( 1218) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 197 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ASP cc_start: 0.9058 (m-30) cc_final: 0.8515 (m-30) REVERT: A 378 ASP cc_start: 0.9075 (m-30) cc_final: 0.8289 (m-30) REVERT: A 392 GLU cc_start: 0.9182 (mt-10) cc_final: 0.8977 (mp0) REVERT: B 45 MET cc_start: 0.9034 (mmm) cc_final: 0.8206 (mmm) REVERT: B 61 MET cc_start: 0.9034 (ptm) cc_final: 0.8820 (ptm) REVERT: B 183 HIS cc_start: 0.8160 (OUTLIER) cc_final: 0.7593 (t-90) REVERT: B 234 PHE cc_start: 0.9403 (OUTLIER) cc_final: 0.8724 (m-80) REVERT: B 262 MET cc_start: 0.8717 (ttm) cc_final: 0.8492 (mmm) REVERT: G 18 GLN cc_start: 0.8684 (tp-100) cc_final: 0.8397 (tp40) REVERT: G 20 LYS cc_start: 0.9169 (mtmm) cc_final: 0.8940 (mtmm) REVERT: G 42 GLU cc_start: 0.8960 (tp30) cc_final: 0.8641 (tm-30) REVERT: N 73 ASP cc_start: 0.8499 (t0) cc_final: 0.8157 (t0) REVERT: N 91 THR cc_start: 0.9358 (OUTLIER) cc_final: 0.9108 (t) REVERT: N 95 TYR cc_start: 0.8955 (m-80) cc_final: 0.8669 (m-80) REVERT: R 139 GLU cc_start: 0.8978 (mt-10) cc_final: 0.8080 (tp30) REVERT: R 202 LYS cc_start: 0.8834 (pptt) cc_final: 0.8566 (tttt) REVERT: R 204 MET cc_start: 0.8905 (tmm) cc_final: 0.8542 (tmm) REVERT: R 221 GLN cc_start: 0.8195 (mp10) cc_final: 0.7838 (mp10) REVERT: R 257 PHE cc_start: 0.7664 (OUTLIER) cc_final: 0.7221 (m-80) REVERT: R 371 MET cc_start: 0.9100 (mmp) cc_final: 0.8799 (mmp) REVERT: R 387 GLU cc_start: 0.9224 (mp0) cc_final: 0.8912 (mp0) REVERT: R 393 PHE cc_start: 0.9157 (m-10) cc_final: 0.8791 (m-10) REVERT: R 397 MET cc_start: 0.9200 (mmp) cc_final: 0.8574 (mtt) REVERT: R 410 GLN cc_start: 0.8803 (mm110) cc_final: 0.8326 (mt0) outliers start: 28 outliers final: 22 residues processed: 218 average time/residue: 0.0970 time to fit residues: 28.3179 Evaluate side-chains 213 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 187 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 109 ASP Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 254 LEU Chi-restraints excluded: chain R residue 257 PHE Chi-restraints excluded: chain R residue 396 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 62 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 56 optimal weight: 30.0000 chunk 2 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 76 optimal weight: 0.0980 chunk 33 optimal weight: 0.2980 chunk 23 optimal weight: 0.7980 chunk 4 optimal weight: 5.9990 chunk 9 optimal weight: 0.0060 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS N 120 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.097018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.069239 restraints weight = 19999.292| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 3.51 r_work: 0.2859 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8727 Z= 0.113 Angle : 0.613 8.134 11830 Z= 0.312 Chirality : 0.040 0.196 1329 Planarity : 0.003 0.043 1509 Dihedral : 3.584 14.968 1197 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.08 % Allowed : 23.23 % Favored : 73.69 % 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: 0.53 (0.26), residues: 1075 helix: 1.94 (0.26), residues: 411 sheet: -0.07 (0.34), residues: 217 loop : -0.93 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 13 TYR 0.014 0.001 TYR A 318 PHE 0.010 0.001 PHE N 68 TRP 0.025 0.001 TRP R 297 HIS 0.004 0.001 HIS R 173 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 8722) covalent geometry : angle 0.61323 (11820) SS BOND : bond 0.00202 ( 5) SS BOND : angle 0.45786 ( 10) hydrogen bonds : bond 0.03301 ( 427) hydrogen bonds : angle 4.00125 ( 1218) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2116.88 seconds wall clock time: 36 minutes 56.87 seconds (2216.87 seconds total)