Starting phenix.real_space_refine on Wed Mar 12 23:53:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lly_23436/03_2025/7lly_23436.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lly_23436/03_2025/7lly_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_2025/7lly_23436.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lly_23436/03_2025/7lly_23436.map" model { file = "/net/cci-nas-00/data/ceres_data/7lly_23436/03_2025/7lly_23436.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lly_23436/03_2025/7lly_23436.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 3, 'TRP:plan': 6, 'ASP:plan': 6, 'PHE:plan': 4, 'GLU:plan': 5, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 206 Time building chain proxies: 5.13, per 1000 atoms: 0.60 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: 2.20 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.94 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: 2.36 Time building geometry restraints manager: 2.59 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: 0.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 22.070 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.040 ------------------------------------------------------------------------------- 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 8722 Z= 0.175 Angle : 0.473 5.970 11820 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 : 3.05 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.006 0.000 TRP A 234 HIS 0.002 0.000 HIS R 363 PHE 0.007 0.001 PHE R 367 TYR 0.006 0.001 TYR N 60 ARG 0.008 0.001 ARG B 96 *********************** 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 : 0.941 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: 0.2337 time to fit residues: 76.5100 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 : 1.009 ------------------------------------------------------------------------------- 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 89 optimal weight: 5.9990 chunk 80 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 chunk 32 optimal weight: 8.9990 chunk 50 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN B 259 GLN P 1 HIS P 24 GLN ** R 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 410 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.093672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.065648 restraints weight = 19988.119| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 3.48 r_work: 0.2786 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8722 Z= 0.287 Angle : 0.579 10.882 11820 Z= 0.304 Chirality : 0.041 0.140 1329 Planarity : 0.004 0.048 1509 Dihedral : 3.857 57.943 1199 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.53 % Allowed : 14.69 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.25), residues: 1075 helix: 1.43 (0.26), residues: 415 sheet: -1.41 (0.32), residues: 231 loop : -1.56 (0.27), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP R 297 HIS 0.008 0.001 HIS A 220 PHE 0.020 0.002 PHE R 184 TYR 0.014 0.002 TYR R 148 ARG 0.007 0.001 ARG R 310 *********************** 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 228 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 197 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ASP cc_start: 0.9124 (m-30) cc_final: 0.8844 (m-30) REVERT: B 9 GLN cc_start: 0.9183 (tm-30) cc_final: 0.8914 (tm-30) REVERT: B 10 GLU cc_start: 0.8969 (mt-10) cc_final: 0.8638 (mt-10) REVERT: B 45 MET cc_start: 0.8904 (mmm) cc_final: 0.8035 (mpp) REVERT: B 59 TYR cc_start: 0.9349 (OUTLIER) cc_final: 0.8948 (m-80) REVERT: B 215 GLU cc_start: 0.7962 (mp0) cc_final: 0.7560 (mp0) REVERT: B 234 PHE cc_start: 0.9397 (OUTLIER) cc_final: 0.8693 (m-80) REVERT: G 19 LEU cc_start: 0.9173 (mp) cc_final: 0.8969 (mp) REVERT: G 20 LYS cc_start: 0.9138 (mtmm) cc_final: 0.8807 (mtmm) REVERT: N 73 ASP cc_start: 0.8206 (t0) cc_final: 0.7899 (t0) REVERT: N 95 TYR cc_start: 0.9093 (m-80) cc_final: 0.8839 (m-80) REVERT: R 202 LYS cc_start: 0.8685 (pptt) cc_final: 0.8106 (ptmt) REVERT: R 204 MET cc_start: 0.9037 (tmm) cc_final: 0.8832 (tmm) REVERT: R 221 GLN cc_start: 0.8207 (mp10) cc_final: 0.7908 (mp10) REVERT: R 257 PHE cc_start: 0.7830 (OUTLIER) cc_final: 0.7028 (m-10) REVERT: R 269 TYR cc_start: 0.9256 (m-10) cc_final: 0.9013 (m-80) REVERT: R 323 ILE cc_start: 0.9496 (mt) cc_final: 0.9287 (mm) REVERT: R 393 PHE cc_start: 0.9117 (m-10) cc_final: 0.8897 (m-10) REVERT: R 397 MET cc_start: 0.9319 (mmp) cc_final: 0.8643 (mtt) outliers start: 31 outliers final: 15 residues processed: 217 average time/residue: 0.2259 time to fit residues: 65.1646 Evaluate side-chains 204 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 186 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 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 B residue 318 LEU Chi-restraints excluded: chain G residue 8 SER 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 189 LEU Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 236 CYS 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 257 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 86 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 71 optimal weight: 9.9990 chunk 14 optimal weight: 0.7980 chunk 101 optimal weight: 9.9990 chunk 93 optimal weight: 6.9990 chunk 78 optimal weight: 0.2980 chunk 53 optimal weight: 8.9990 chunk 60 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS B 62 HIS B 155 ASN N 5 GLN N 39 GLN N 120 GLN R 173 HIS R 234 GLN ** R 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.092046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.063877 restraints weight = 20310.730| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 3.49 r_work: 0.2740 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 8722 Z= 0.315 Angle : 0.559 10.732 11820 Z= 0.296 Chirality : 0.041 0.225 1329 Planarity : 0.003 0.046 1509 Dihedral : 4.186 59.241 1199 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.53 % Allowed : 18.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.26), residues: 1075 helix: 1.93 (0.26), residues: 409 sheet: -1.09 (0.32), residues: 229 loop : -1.39 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 234 HIS 0.011 0.001 HIS A 220 PHE 0.017 0.001 PHE N 108 TYR 0.017 0.002 TYR A 318 ARG 0.005 0.000 ARG R 310 *********************** 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 224 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 193 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ASP cc_start: 0.9132 (m-30) cc_final: 0.8903 (m-30) REVERT: B 9 GLN cc_start: 0.9174 (tm-30) cc_final: 0.8895 (tm-30) REVERT: B 10 GLU cc_start: 0.8995 (mt-10) cc_final: 0.8667 (mt-10) REVERT: B 45 MET cc_start: 0.8993 (mmm) cc_final: 0.8156 (mpp) REVERT: B 59 TYR cc_start: 0.9334 (OUTLIER) cc_final: 0.8890 (m-80) REVERT: B 172 GLU cc_start: 0.8257 (mp0) cc_final: 0.8015 (mp0) REVERT: B 234 PHE cc_start: 0.9405 (OUTLIER) cc_final: 0.8735 (m-80) REVERT: B 264 TYR cc_start: 0.9379 (m-80) cc_final: 0.9148 (m-10) REVERT: G 19 LEU cc_start: 0.9169 (mp) cc_final: 0.8944 (mp) REVERT: G 20 LYS cc_start: 0.9135 (mtmm) cc_final: 0.8862 (mtmm) REVERT: G 29 LYS cc_start: 0.8735 (tptt) cc_final: 0.8530 (tptt) REVERT: N 46 GLU cc_start: 0.8993 (pt0) cc_final: 0.8777 (pt0) REVERT: N 73 ASP cc_start: 0.8432 (t0) cc_final: 0.8040 (t0) REVERT: N 95 TYR cc_start: 0.9104 (m-80) cc_final: 0.8663 (m-80) REVERT: R 202 LYS cc_start: 0.8749 (pptt) cc_final: 0.8174 (ptmt) REVERT: R 204 MET cc_start: 0.9002 (tmm) cc_final: 0.8795 (tmm) REVERT: R 221 GLN cc_start: 0.8165 (mp10) cc_final: 0.7830 (mp10) REVERT: R 288 LYS cc_start: 0.9410 (tppp) cc_final: 0.9090 (tppp) REVERT: R 297 TRP cc_start: 0.8883 (m-10) cc_final: 0.8585 (m-90) REVERT: R 323 ILE cc_start: 0.9498 (mt) cc_final: 0.9250 (mm) REVERT: R 387 GLU cc_start: 0.9204 (mp0) cc_final: 0.8895 (mp0) REVERT: R 393 PHE cc_start: 0.9180 (m-10) cc_final: 0.8852 (m-10) REVERT: R 397 MET cc_start: 0.9259 (mmp) cc_final: 0.8635 (mtt) outliers start: 31 outliers final: 17 residues processed: 216 average time/residue: 0.2343 time to fit residues: 67.5807 Evaluate side-chains 204 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 185 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 318 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 20 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 201 LEU Chi-restraints excluded: chain R residue 236 CYS 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 396 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 33 optimal weight: 6.9990 chunk 5 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 99 optimal weight: 7.9990 chunk 41 optimal weight: 7.9990 chunk 73 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 61 optimal weight: 0.1980 chunk 59 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN N 120 GLN R 234 GLN ** R 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.093216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.065044 restraints weight = 20022.053| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 3.49 r_work: 0.2769 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8722 Z= 0.197 Angle : 0.522 8.554 11820 Z= 0.274 Chirality : 0.040 0.178 1329 Planarity : 0.003 0.045 1509 Dihedral : 3.678 16.203 1197 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.19 % Allowed : 19.25 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.26), residues: 1075 helix: 2.07 (0.26), residues: 409 sheet: -0.88 (0.33), residues: 224 loop : -1.28 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.010 0.001 HIS A 220 PHE 0.012 0.001 PHE N 108 TYR 0.016 0.001 TYR A 318 ARG 0.004 0.000 ARG R 310 *********************** 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: 28 poor density : 196 time to evaluate : 0.953 Fit side-chains revert: symmetry clash REVERT: A 33 ASP cc_start: 0.9095 (m-30) cc_final: 0.8880 (m-30) REVERT: A 211 LYS cc_start: 0.9184 (ptpp) cc_final: 0.8972 (ptpp) REVERT: A 378 ASP cc_start: 0.9103 (m-30) cc_final: 0.8385 (m-30) REVERT: B 9 GLN cc_start: 0.9164 (tm-30) cc_final: 0.8938 (tm-30) REVERT: B 10 GLU cc_start: 0.9009 (mt-10) cc_final: 0.8685 (mt-10) REVERT: B 59 TYR cc_start: 0.9336 (OUTLIER) cc_final: 0.8976 (m-80) REVERT: B 61 MET cc_start: 0.9044 (ptm) cc_final: 0.8790 (ptm) REVERT: B 183 HIS cc_start: 0.8167 (OUTLIER) cc_final: 0.7715 (t-90) REVERT: B 230 ASN cc_start: 0.9180 (m-40) cc_final: 0.8844 (m110) REVERT: B 234 PHE cc_start: 0.9390 (OUTLIER) cc_final: 0.8690 (m-80) REVERT: B 264 TYR cc_start: 0.9456 (m-80) cc_final: 0.9128 (m-10) REVERT: G 18 GLN cc_start: 0.8685 (tp-100) cc_final: 0.8343 (tp40) REVERT: G 20 LYS cc_start: 0.9156 (mtmm) cc_final: 0.8900 (mtmm) REVERT: G 46 LYS cc_start: 0.9451 (mmmm) cc_final: 0.9121 (mtmm) REVERT: G 47 GLU cc_start: 0.8584 (mp0) cc_final: 0.8280 (mp0) REVERT: N 73 ASP cc_start: 0.8457 (t0) cc_final: 0.8139 (t0) REVERT: N 95 TYR cc_start: 0.9086 (m-80) cc_final: 0.8633 (m-80) REVERT: R 202 LYS cc_start: 0.8751 (pptt) cc_final: 0.8417 (tttt) REVERT: R 221 GLN cc_start: 0.8149 (mp10) cc_final: 0.7870 (mp10) REVERT: R 288 LYS cc_start: 0.9410 (tppp) cc_final: 0.9088 (tppp) REVERT: R 323 ILE cc_start: 0.9497 (mt) cc_final: 0.9251 (mm) REVERT: R 387 GLU cc_start: 0.9153 (mp0) cc_final: 0.8710 (mp0) REVERT: R 393 PHE cc_start: 0.9089 (m-10) cc_final: 0.8753 (m-10) REVERT: R 394 GLN cc_start: 0.9155 (tt0) cc_final: 0.8925 (tt0) REVERT: R 397 MET cc_start: 0.9261 (mmp) cc_final: 0.8687 (mtt) outliers start: 28 outliers final: 17 residues processed: 217 average time/residue: 0.2273 time to fit residues: 65.6192 Evaluate side-chains 209 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 189 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 158 VAL 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 318 LEU 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 109 ASP Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 236 CYS Chi-restraints excluded: chain R residue 246 VAL Chi-restraints excluded: chain R residue 249 VAL 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 50 optimal weight: 7.9990 chunk 84 optimal weight: 9.9990 chunk 55 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 48 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 95 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 overall best weight: 2.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 GLN ** R 363 HIS ** 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 = 0.3463 r_free = 0.3463 target = 0.091979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.063846 restraints weight = 20017.187| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 3.44 r_work: 0.2749 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 8722 Z= 0.279 Angle : 0.553 7.881 11820 Z= 0.291 Chirality : 0.041 0.187 1329 Planarity : 0.003 0.043 1509 Dihedral : 3.813 16.394 1197 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 4.10 % Allowed : 20.50 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.26), residues: 1075 helix: 2.05 (0.26), residues: 409 sheet: -0.74 (0.33), residues: 224 loop : -1.21 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP R 297 HIS 0.009 0.001 HIS A 220 PHE 0.016 0.001 PHE N 68 TYR 0.017 0.001 TYR A 318 ARG 0.003 0.000 ARG G 13 *********************** 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: 36 poor density : 196 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ASP cc_start: 0.9092 (m-30) cc_final: 0.8875 (m-30) REVERT: A 211 LYS cc_start: 0.9198 (ptpp) cc_final: 0.8971 (ptpp) REVERT: A 346 LEU cc_start: 0.9527 (OUTLIER) cc_final: 0.9145 (mp) REVERT: A 378 ASP cc_start: 0.9129 (m-30) cc_final: 0.8407 (m-30) REVERT: B 9 GLN cc_start: 0.9178 (tm-30) cc_final: 0.8940 (tm-30) REVERT: B 10 GLU cc_start: 0.9009 (mt-10) cc_final: 0.8675 (mt-10) REVERT: B 42 ARG cc_start: 0.8768 (tmm-80) cc_final: 0.8491 (tmm-80) REVERT: B 45 MET cc_start: 0.8990 (mmm) cc_final: 0.8222 (mmm) REVERT: B 59 TYR cc_start: 0.9349 (OUTLIER) cc_final: 0.8926 (m-80) REVERT: B 61 MET cc_start: 0.9085 (ptm) cc_final: 0.8828 (ptm) REVERT: B 183 HIS cc_start: 0.8247 (OUTLIER) cc_final: 0.7795 (t-90) REVERT: B 230 ASN cc_start: 0.9257 (m-40) cc_final: 0.8842 (m-40) REVERT: B 234 PHE cc_start: 0.9390 (OUTLIER) cc_final: 0.8758 (m-80) REVERT: G 20 LYS cc_start: 0.9169 (mtmm) cc_final: 0.8894 (mtmm) REVERT: G 24 ASN cc_start: 0.8891 (m-40) cc_final: 0.8649 (m-40) REVERT: G 32 LYS cc_start: 0.8895 (tptp) cc_final: 0.8393 (tptp) REVERT: G 42 GLU cc_start: 0.8982 (tm-30) cc_final: 0.8763 (tm-30) REVERT: N 73 ASP cc_start: 0.8467 (t0) cc_final: 0.8128 (t0) REVERT: N 91 THR cc_start: 0.9231 (OUTLIER) cc_final: 0.8965 (t) REVERT: N 95 TYR cc_start: 0.9066 (m-80) cc_final: 0.8617 (m-80) REVERT: R 202 LYS cc_start: 0.8725 (pptt) cc_final: 0.8372 (tttt) REVERT: R 204 MET cc_start: 0.8992 (tmm) cc_final: 0.8737 (tmm) REVERT: R 221 GLN cc_start: 0.8187 (mp10) cc_final: 0.7869 (mp10) REVERT: R 288 LYS cc_start: 0.9414 (tppp) cc_final: 0.9031 (tptp) REVERT: R 309 ILE cc_start: 0.9431 (OUTLIER) cc_final: 0.9203 (tp) REVERT: R 323 ILE cc_start: 0.9496 (mt) cc_final: 0.9252 (mm) REVERT: R 393 PHE cc_start: 0.9129 (m-10) cc_final: 0.8759 (m-10) REVERT: R 394 GLN cc_start: 0.9227 (tt0) cc_final: 0.8955 (tt0) REVERT: R 397 MET cc_start: 0.9258 (mmp) cc_final: 0.8713 (mtt) outliers start: 36 outliers final: 24 residues processed: 223 average time/residue: 0.2248 time to fit residues: 66.9960 Evaluate side-chains 223 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 193 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 117 LEU 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 262 MET Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 8 SER 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 20 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 R residue 192 LEU Chi-restraints excluded: chain R residue 236 CYS 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 309 ILE 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 64 optimal weight: 1.9990 chunk 41 optimal weight: 0.0870 chunk 75 optimal weight: 50.0000 chunk 48 optimal weight: 0.0470 chunk 0 optimal weight: 10.0000 chunk 101 optimal weight: 10.0000 chunk 67 optimal weight: 7.9990 chunk 5 optimal weight: 0.7980 chunk 32 optimal weight: 9.9990 chunk 80 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 overall best weight: 1.1860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 120 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.093742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.065581 restraints weight = 19645.373| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 3.45 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: 0.8336 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8722 Z= 0.174 Angle : 0.539 7.061 11820 Z= 0.281 Chirality : 0.040 0.181 1329 Planarity : 0.003 0.043 1509 Dihedral : 3.747 16.612 1197 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 4.21 % Allowed : 20.73 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.26), residues: 1075 helix: 2.09 (0.26), residues: 409 sheet: -0.56 (0.33), residues: 223 loop : -1.13 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.002 TRP R 297 HIS 0.007 0.001 HIS A 220 PHE 0.011 0.001 PHE N 108 TYR 0.013 0.001 TYR A 318 ARG 0.004 0.000 ARG G 13 *********************** 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 232 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 195 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 ASP cc_start: 0.9037 (m-30) cc_final: 0.8820 (m-30) REVERT: A 346 LEU cc_start: 0.9545 (OUTLIER) cc_final: 0.9127 (mp) REVERT: A 378 ASP cc_start: 0.9070 (m-30) cc_final: 0.8306 (m-30) REVERT: B 10 GLU cc_start: 0.9022 (mt-10) cc_final: 0.8694 (mt-10) REVERT: B 45 MET cc_start: 0.9004 (mmm) cc_final: 0.8222 (mmm) REVERT: B 59 TYR cc_start: 0.9289 (OUTLIER) cc_final: 0.8926 (m-80) REVERT: B 61 MET cc_start: 0.9029 (ptm) cc_final: 0.8804 (ptm) REVERT: B 183 HIS cc_start: 0.8086 (OUTLIER) cc_final: 0.7648 (t-90) REVERT: B 234 PHE cc_start: 0.9393 (OUTLIER) cc_final: 0.8718 (m-80) REVERT: B 264 TYR cc_start: 0.9483 (m-80) cc_final: 0.9238 (m-10) REVERT: G 20 LYS cc_start: 0.9168 (mtmm) cc_final: 0.8831 (mtmm) REVERT: G 24 ASN cc_start: 0.8928 (m-40) cc_final: 0.8684 (m110) REVERT: G 32 LYS cc_start: 0.8841 (tptp) cc_final: 0.8433 (tptt) REVERT: G 36 ASP cc_start: 0.8816 (m-30) cc_final: 0.8015 (m-30) REVERT: G 42 GLU cc_start: 0.9020 (tm-30) cc_final: 0.8764 (tm-30) REVERT: N 73 ASP cc_start: 0.8479 (t0) cc_final: 0.8131 (t0) REVERT: N 91 THR cc_start: 0.9152 (OUTLIER) cc_final: 0.8935 (t) REVERT: N 95 TYR cc_start: 0.9040 (m-80) cc_final: 0.8772 (m-80) REVERT: N 123 GLN cc_start: 0.7887 (tm-30) cc_final: 0.7417 (tm-30) REVERT: R 198 ASP cc_start: 0.8578 (p0) cc_final: 0.8332 (p0) REVERT: R 202 LYS cc_start: 0.8788 (pptt) cc_final: 0.8448 (tttt) REVERT: R 204 MET cc_start: 0.8942 (tmm) cc_final: 0.8668 (tmm) REVERT: R 221 GLN cc_start: 0.8147 (mp10) cc_final: 0.7829 (mp10) REVERT: R 288 LYS cc_start: 0.9366 (tppp) cc_final: 0.9013 (tptp) REVERT: R 323 ILE cc_start: 0.9484 (mt) cc_final: 0.9235 (mm) REVERT: R 387 GLU cc_start: 0.9213 (mp0) cc_final: 0.8839 (mp0) REVERT: R 393 PHE cc_start: 0.9082 (m-10) cc_final: 0.8725 (m-10) REVERT: R 394 GLN cc_start: 0.9105 (tt0) cc_final: 0.8778 (tt0) REVERT: R 397 MET cc_start: 0.9225 (mmp) cc_final: 0.8638 (mtt) outliers start: 37 outliers final: 21 residues processed: 222 average time/residue: 0.2294 time to fit residues: 68.3534 Evaluate side-chains 212 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 186 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 59 TYR 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 B residue 318 LEU Chi-restraints excluded: chain G residue 8 SER 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 64 VAL 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 R residue 192 LEU Chi-restraints excluded: chain R residue 236 CYS Chi-restraints excluded: chain R residue 246 VAL Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 254 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 28 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 60 optimal weight: 8.9990 chunk 2 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 chunk 102 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN N 120 GLN R 180 HIS ** R 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.092641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.064633 restraints weight = 19922.405| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 3.45 r_work: 0.2761 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8722 Z= 0.247 Angle : 0.563 6.861 11820 Z= 0.297 Chirality : 0.041 0.207 1329 Planarity : 0.003 0.042 1509 Dihedral : 3.852 19.590 1197 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.99 % Allowed : 22.44 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.26), residues: 1075 helix: 2.10 (0.26), residues: 409 sheet: -0.66 (0.33), residues: 231 loop : -1.04 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.083 0.002 TRP R 297 HIS 0.005 0.001 HIS A 220 PHE 0.014 0.001 PHE N 68 TYR 0.013 0.001 TYR A 318 ARG 0.004 0.000 ARG G 13 *********************** 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 220 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 185 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ASP cc_start: 0.9050 (m-30) cc_final: 0.8843 (m-30) REVERT: A 378 ASP cc_start: 0.9127 (m-30) cc_final: 0.8383 (m-30) REVERT: B 10 GLU cc_start: 0.8943 (mt-10) cc_final: 0.8720 (mt-10) REVERT: B 42 ARG cc_start: 0.8754 (tmm-80) cc_final: 0.8507 (tmm-80) REVERT: B 59 TYR cc_start: 0.9356 (OUTLIER) cc_final: 0.8945 (m-80) REVERT: B 61 MET cc_start: 0.9065 (ptm) cc_final: 0.8863 (ptm) REVERT: B 183 HIS cc_start: 0.8203 (OUTLIER) cc_final: 0.7735 (t-90) REVERT: B 234 PHE cc_start: 0.9411 (OUTLIER) cc_final: 0.8781 (m-80) REVERT: B 264 TYR cc_start: 0.9513 (m-80) cc_final: 0.9169 (m-10) REVERT: G 20 LYS cc_start: 0.9173 (mtmm) cc_final: 0.8847 (mtmm) REVERT: G 42 GLU cc_start: 0.9077 (tm-30) cc_final: 0.8793 (tm-30) REVERT: N 46 GLU cc_start: 0.8867 (pt0) cc_final: 0.8639 (pt0) REVERT: N 73 ASP cc_start: 0.8522 (t0) cc_final: 0.8164 (t0) REVERT: N 91 THR cc_start: 0.9181 (OUTLIER) cc_final: 0.8904 (t) REVERT: N 95 TYR cc_start: 0.9028 (m-80) cc_final: 0.8590 (m-80) REVERT: R 198 ASP cc_start: 0.8589 (p0) cc_final: 0.8322 (p0) REVERT: R 202 LYS cc_start: 0.8801 (pptt) cc_final: 0.8430 (tttt) REVERT: R 204 MET cc_start: 0.8938 (tmm) cc_final: 0.8640 (tmm) REVERT: R 221 GLN cc_start: 0.8278 (mp10) cc_final: 0.7940 (mp10) REVERT: R 234 GLN cc_start: 0.9480 (mm110) cc_final: 0.9120 (mm-40) REVERT: R 323 ILE cc_start: 0.9487 (mt) cc_final: 0.9230 (mm) REVERT: R 387 GLU cc_start: 0.9195 (mp0) cc_final: 0.8744 (mp0) REVERT: R 393 PHE cc_start: 0.9098 (m-10) cc_final: 0.8734 (m-10) REVERT: R 394 GLN cc_start: 0.9129 (tt0) cc_final: 0.8775 (tt0) REVERT: R 397 MET cc_start: 0.9213 (mmp) cc_final: 0.8658 (mtt) outliers start: 35 outliers final: 23 residues processed: 212 average time/residue: 0.2260 time to fit residues: 63.9462 Evaluate side-chains 215 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 188 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 71 VAL 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 B residue 318 LEU Chi-restraints excluded: chain G residue 8 SER 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 64 VAL 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 R residue 192 LEU Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 236 CYS Chi-restraints excluded: chain R residue 246 VAL Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 290 LEU 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 74 optimal weight: 50.0000 chunk 69 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 104 optimal weight: 6.9990 chunk 100 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 chunk 85 optimal weight: 0.6980 chunk 13 optimal weight: 0.2980 chunk 83 optimal weight: 8.9990 chunk 20 optimal weight: 8.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN N 120 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.094431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.066370 restraints weight = 20125.487| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 3.52 r_work: 0.2796 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8722 Z= 0.168 Angle : 0.562 7.066 11820 Z= 0.292 Chirality : 0.041 0.199 1329 Planarity : 0.003 0.043 1509 Dihedral : 3.776 17.025 1197 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.64 % Allowed : 24.03 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.26), residues: 1075 helix: 2.18 (0.26), residues: 408 sheet: -0.48 (0.33), residues: 223 loop : -1.08 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP R 297 HIS 0.005 0.001 HIS A 220 PHE 0.011 0.001 PHE N 108 TYR 0.013 0.001 TYR A 360 ARG 0.005 0.000 ARG G 13 *********************** 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 227 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 195 time to evaluate : 0.967 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: 0.9014 (m-30) cc_final: 0.8810 (m-30) REVERT: A 346 LEU cc_start: 0.9531 (OUTLIER) cc_final: 0.9081 (mp) REVERT: A 378 ASP cc_start: 0.9058 (m-30) cc_final: 0.8281 (m-30) REVERT: B 42 ARG cc_start: 0.8785 (tmm-80) cc_final: 0.8544 (tmm-80) REVERT: B 45 MET cc_start: 0.9114 (mmm) cc_final: 0.8387 (mmm) REVERT: B 59 TYR cc_start: 0.9302 (OUTLIER) cc_final: 0.8969 (m-80) REVERT: B 183 HIS cc_start: 0.8204 (OUTLIER) cc_final: 0.7629 (t-90) REVERT: B 230 ASN cc_start: 0.9023 (m-40) cc_final: 0.8616 (m110) REVERT: B 234 PHE cc_start: 0.9401 (OUTLIER) cc_final: 0.8716 (m-80) REVERT: G 20 LYS cc_start: 0.9165 (mtmm) cc_final: 0.8928 (mtmm) REVERT: G 42 GLU cc_start: 0.9075 (tm-30) cc_final: 0.8780 (tm-30) REVERT: N 73 ASP cc_start: 0.8494 (t0) cc_final: 0.8146 (t0) REVERT: N 91 THR cc_start: 0.9177 (OUTLIER) cc_final: 0.8910 (t) REVERT: N 95 TYR cc_start: 0.9012 (m-80) cc_final: 0.8640 (m-80) REVERT: R 198 ASP cc_start: 0.8528 (p0) cc_final: 0.8320 (p0) REVERT: R 202 LYS cc_start: 0.8855 (pptt) cc_final: 0.8484 (tttt) REVERT: R 204 MET cc_start: 0.8912 (tmm) cc_final: 0.8648 (tmm) REVERT: R 221 GLN cc_start: 0.8316 (mp10) cc_final: 0.8002 (mp10) REVERT: R 299 ARG cc_start: 0.8463 (mpt-90) cc_final: 0.8094 (mpt-90) REVERT: R 309 ILE cc_start: 0.9355 (OUTLIER) cc_final: 0.9104 (tp) REVERT: R 323 ILE cc_start: 0.9485 (mt) cc_final: 0.9246 (mm) REVERT: R 387 GLU cc_start: 0.9147 (mp0) cc_final: 0.8663 (mp0) REVERT: R 393 PHE cc_start: 0.9086 (m-10) cc_final: 0.8721 (m-10) REVERT: R 394 GLN cc_start: 0.9039 (tt0) cc_final: 0.8696 (tt0) REVERT: R 397 MET cc_start: 0.9204 (mmp) cc_final: 0.8555 (mtt) outliers start: 32 outliers final: 19 residues processed: 218 average time/residue: 0.2388 time to fit residues: 69.5433 Evaluate side-chains 218 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 193 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 128 THR 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 B residue 318 LEU 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 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 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 32 optimal weight: 9.9990 chunk 62 optimal weight: 0.3980 chunk 40 optimal weight: 8.9990 chunk 45 optimal weight: 1.9990 chunk 85 optimal weight: 9.9990 chunk 56 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 chunk 99 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 120 GLN ** R 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.092396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.064301 restraints weight = 19989.364| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 3.48 r_work: 0.2748 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8722 Z= 0.275 Angle : 0.597 7.891 11820 Z= 0.315 Chirality : 0.042 0.211 1329 Planarity : 0.003 0.042 1509 Dihedral : 3.907 17.643 1197 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.19 % Allowed : 24.03 % Favored : 72.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.26), residues: 1075 helix: 2.06 (0.26), residues: 408 sheet: -0.57 (0.33), residues: 230 loop : -1.00 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP R 297 HIS 0.008 0.001 HIS A 220 PHE 0.012 0.001 PHE N 108 TYR 0.023 0.002 TYR A 318 ARG 0.007 0.000 ARG G 13 *********************** 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: 28 poor density : 194 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ASP cc_start: 0.9085 (m-30) cc_final: 0.8884 (m-30) REVERT: A 343 ASP cc_start: 0.8932 (m-30) cc_final: 0.8719 (p0) REVERT: A 346 LEU cc_start: 0.9543 (OUTLIER) cc_final: 0.9168 (mp) REVERT: A 378 ASP cc_start: 0.9115 (m-30) cc_final: 0.8361 (m-30) REVERT: B 45 MET cc_start: 0.9074 (mmm) cc_final: 0.8310 (mmm) REVERT: B 59 TYR cc_start: 0.9310 (OUTLIER) cc_final: 0.8968 (m-80) REVERT: B 66 ASP cc_start: 0.8781 (OUTLIER) cc_final: 0.8364 (p0) REVERT: B 183 HIS cc_start: 0.8335 (OUTLIER) cc_final: 0.7826 (t-90) REVERT: B 230 ASN cc_start: 0.9114 (m-40) cc_final: 0.8851 (m-40) REVERT: B 234 PHE cc_start: 0.9429 (OUTLIER) cc_final: 0.8819 (m-80) REVERT: G 20 LYS cc_start: 0.9181 (mtmm) cc_final: 0.8922 (mtmm) REVERT: G 32 LYS cc_start: 0.8877 (tptp) cc_final: 0.8502 (tptt) REVERT: G 42 GLU cc_start: 0.9007 (tm-30) cc_final: 0.8719 (tm-30) REVERT: N 73 ASP cc_start: 0.8529 (t0) cc_final: 0.8167 (t0) REVERT: N 91 THR cc_start: 0.9265 (OUTLIER) cc_final: 0.9013 (t) REVERT: N 95 TYR cc_start: 0.9044 (m-80) cc_final: 0.8685 (m-80) REVERT: R 139 GLU cc_start: 0.8980 (mt-10) cc_final: 0.8094 (tp30) REVERT: R 202 LYS cc_start: 0.8878 (pptt) cc_final: 0.8515 (tttt) REVERT: R 204 MET cc_start: 0.8940 (tmm) cc_final: 0.8579 (tmm) REVERT: R 221 GLN cc_start: 0.8326 (mp10) cc_final: 0.7972 (mp10) REVERT: R 234 GLN cc_start: 0.9413 (mm110) cc_final: 0.9012 (mm-40) REVERT: R 299 ARG cc_start: 0.8411 (mpt-90) cc_final: 0.8165 (mpt-90) REVERT: R 308 ILE cc_start: 0.9586 (tt) cc_final: 0.9363 (pt) REVERT: R 323 ILE cc_start: 0.9467 (mt) cc_final: 0.9215 (mm) REVERT: R 387 GLU cc_start: 0.9156 (mp0) cc_final: 0.8657 (mp0) REVERT: R 393 PHE cc_start: 0.9104 (m-10) cc_final: 0.8735 (m-10) REVERT: R 394 GLN cc_start: 0.9121 (tt0) cc_final: 0.8766 (tt0) REVERT: R 397 MET cc_start: 0.9219 (mmp) cc_final: 0.8624 (mtt) REVERT: R 412 GLU cc_start: 0.8668 (mm-30) cc_final: 0.8334 (mm-30) outliers start: 28 outliers final: 19 residues processed: 217 average time/residue: 0.2363 time to fit residues: 68.4273 Evaluate side-chains 213 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 188 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 128 THR 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 B residue 318 LEU 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 R residue 192 LEU Chi-restraints excluded: chain R residue 249 VAL 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 41 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 88 optimal weight: 7.9990 chunk 101 optimal weight: 10.0000 chunk 98 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 96 optimal weight: 0.7980 chunk 62 optimal weight: 6.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 363 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.092586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.065042 restraints weight = 19921.806| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 3.41 r_work: 0.2770 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8722 Z= 0.223 Angle : 0.613 8.556 11820 Z= 0.321 Chirality : 0.042 0.221 1329 Planarity : 0.003 0.034 1509 Dihedral : 3.940 17.858 1197 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.73 % Allowed : 24.83 % Favored : 72.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.26), residues: 1075 helix: 2.00 (0.26), residues: 410 sheet: -0.53 (0.33), residues: 229 loop : -0.97 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP R 297 HIS 0.009 0.001 HIS A 220 PHE 0.012 0.001 PHE N 108 TYR 0.017 0.001 TYR A 318 ARG 0.009 0.000 ARG G 13 ********************** 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 216 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 192 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ASP cc_start: 0.9055 (m-30) cc_final: 0.8854 (m-30) REVERT: A 343 ASP cc_start: 0.8943 (m-30) cc_final: 0.8732 (p0) REVERT: A 346 LEU cc_start: 0.9566 (OUTLIER) cc_final: 0.9142 (mp) REVERT: A 378 ASP cc_start: 0.9032 (m-30) cc_final: 0.8272 (m-30) REVERT: B 45 MET cc_start: 0.9078 (mmm) cc_final: 0.8365 (mmm) REVERT: B 59 TYR cc_start: 0.9307 (OUTLIER) cc_final: 0.8991 (m-80) REVERT: B 61 MET cc_start: 0.9071 (ptm) cc_final: 0.8841 (ptm) REVERT: B 183 HIS cc_start: 0.8297 (OUTLIER) cc_final: 0.7717 (t-90) REVERT: B 226 GLU cc_start: 0.8355 (tp30) cc_final: 0.7905 (tp30) REVERT: B 230 ASN cc_start: 0.9055 (m-40) cc_final: 0.8800 (m110) REVERT: B 234 PHE cc_start: 0.9457 (OUTLIER) cc_final: 0.8812 (m-80) REVERT: B 292 PHE cc_start: 0.9047 (m-80) cc_final: 0.8787 (m-80) REVERT: G 18 GLN cc_start: 0.8720 (tp-100) cc_final: 0.8357 (tp40) REVERT: G 20 LYS cc_start: 0.9198 (mtmm) cc_final: 0.8942 (mtmm) REVERT: G 21 MET cc_start: 0.9100 (tpp) cc_final: 0.8614 (tpp) REVERT: G 42 GLU cc_start: 0.9045 (tm-30) cc_final: 0.8756 (tm-30) REVERT: N 73 ASP cc_start: 0.8508 (t0) cc_final: 0.8167 (t0) REVERT: N 91 THR cc_start: 0.9287 (OUTLIER) cc_final: 0.9022 (t) REVERT: N 95 TYR cc_start: 0.9022 (m-80) cc_final: 0.8670 (m-80) REVERT: R 139 GLU cc_start: 0.8955 (mt-10) cc_final: 0.8085 (tp30) REVERT: R 202 LYS cc_start: 0.8865 (pptt) cc_final: 0.8509 (tttt) REVERT: R 204 MET cc_start: 0.8956 (tmm) cc_final: 0.8590 (tmm) REVERT: R 221 GLN cc_start: 0.8370 (mp10) cc_final: 0.7990 (mp10) REVERT: R 234 GLN cc_start: 0.9407 (mm110) cc_final: 0.9063 (mm-40) REVERT: R 299 ARG cc_start: 0.8473 (mpt-90) cc_final: 0.8233 (mpt-90) REVERT: R 308 ILE cc_start: 0.9593 (tt) cc_final: 0.9373 (pt) REVERT: R 323 ILE cc_start: 0.9476 (mt) cc_final: 0.9221 (mm) REVERT: R 387 GLU cc_start: 0.9168 (mp0) cc_final: 0.8658 (mp0) REVERT: R 393 PHE cc_start: 0.9100 (m-10) cc_final: 0.8734 (m-10) REVERT: R 394 GLN cc_start: 0.9077 (tt0) cc_final: 0.8639 (tt0) REVERT: R 397 MET cc_start: 0.9202 (mmp) cc_final: 0.8584 (mtt) REVERT: R 410 GLN cc_start: 0.8807 (mm-40) cc_final: 0.8128 (mt0) outliers start: 24 outliers final: 18 residues processed: 211 average time/residue: 0.2150 time to fit residues: 60.8679 Evaluate side-chains 209 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 186 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 128 THR 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 B residue 318 LEU 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 R residue 192 LEU Chi-restraints excluded: chain R residue 249 VAL 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 94 optimal weight: 10.0000 chunk 64 optimal weight: 0.9980 chunk 20 optimal weight: 6.9990 chunk 48 optimal weight: 0.8980 chunk 11 optimal weight: 0.0270 chunk 12 optimal weight: 0.1980 chunk 28 optimal weight: 0.0020 chunk 81 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 overall best weight: 0.4246 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS R 363 HIS R 394 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.095710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.067731 restraints weight = 20068.456| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 3.51 r_work: 0.2838 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8722 Z= 0.161 Angle : 0.600 8.610 11820 Z= 0.309 Chirality : 0.041 0.219 1329 Planarity : 0.003 0.038 1509 Dihedral : 3.739 15.571 1197 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.96 % Allowed : 24.60 % Favored : 72.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.26), residues: 1075 helix: 2.01 (0.26), residues: 410 sheet: -0.29 (0.34), residues: 223 loop : -0.98 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP R 297 HIS 0.006 0.001 HIS A 220 PHE 0.010 0.001 PHE N 27 TYR 0.014 0.001 TYR A 360 ARG 0.010 0.000 ARG G 13 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4539.69 seconds wall clock time: 79 minutes 24.89 seconds (4764.89 seconds total)