Starting phenix.real_space_refine on Wed Feb 12 22:40:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lly_23436/02_2025/7lly_23436.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lly_23436/02_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_23436/02_2025/7lly_23436.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lly_23436/02_2025/7lly_23436.map" model { file = "/net/cci-nas-00/data/ceres_data/7lly_23436/02_2025/7lly_23436.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lly_23436/02_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 5.06, per 1000 atoms: 0.59 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: 2.25 Conformation dependent library (CDL) restraints added in 1.1 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: 0.93 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: 2.70 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: 0.010 Normalize map: mean=0, sd=1: 0.260 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: 0.080 Process input model: 22.350 Find NCS groups from input model: 0.100 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.140 ------------------------------------------------------------------------------- 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 : 0.997 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: 0.2348 time to fit residues: 76.7118 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 : 1.018 ------------------------------------------------------------------------------- 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 = 0.2967 r_free = 0.2967 target = 0.065639 restraints weight = 19988.117| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 3.49 r_work: 0.2784 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 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 : 1.034 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: 0.8915 (tm-30) REVERT: B 10 GLU cc_start: 0.8968 (mt-10) cc_final: 0.8637 (mt-10) REVERT: B 45 MET cc_start: 0.8904 (mmm) cc_final: 0.8036 (mpp) REVERT: B 59 TYR cc_start: 0.9350 (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: 0.9396 (OUTLIER) cc_final: 0.8692 (m-80) REVERT: G 19 LEU cc_start: 0.9170 (mp) cc_final: 0.8967 (mp) REVERT: G 20 LYS cc_start: 0.9137 (mtmm) cc_final: 0.8807 (mtmm) REVERT: N 73 ASP cc_start: 0.8204 (t0) cc_final: 0.7897 (t0) REVERT: N 95 TYR cc_start: 0.9093 (m-80) cc_final: 0.8839 (m-80) REVERT: R 202 LYS cc_start: 0.8686 (pptt) cc_final: 0.8106 (ptmt) REVERT: R 204 MET cc_start: 0.9038 (tmm) cc_final: 0.8833 (tmm) REVERT: R 221 GLN cc_start: 0.8209 (mp10) cc_final: 0.7910 (mp10) REVERT: R 257 PHE cc_start: 0.7831 (OUTLIER) cc_final: 0.7027 (m-10) REVERT: R 269 TYR cc_start: 0.9255 (m-10) cc_final: 0.9012 (m-80) REVERT: R 323 ILE cc_start: 0.9495 (mt) cc_final: 0.9286 (mm) REVERT: R 393 PHE cc_start: 0.9117 (m-10) cc_final: 0.8898 (m-10) REVERT: R 397 MET cc_start: 0.9319 (mmp) cc_final: 0.8642 (mtt) outliers start: 31 outliers final: 15 residues processed: 217 average time/residue: 0.2420 time to fit residues: 69.4350 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 : 0.905 ------------------------------------------------------------------------------- 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: 5.9990 chunk 71 optimal weight: 0.3980 chunk 14 optimal weight: 0.7980 chunk 101 optimal weight: 9.9990 chunk 93 optimal weight: 6.9990 chunk 78 optimal weight: 0.0040 chunk 53 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 overall best weight: 2.4396 ------------------------------------------------------------------------------- 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 = 0.3479 r_free = 0.3479 target = 0.093060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.064695 restraints weight = 20282.393| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 3.51 r_work: 0.2760 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8722 Z= 0.263 Angle : 0.540 10.508 11820 Z= 0.285 Chirality : 0.041 0.219 1329 Planarity : 0.003 0.046 1509 Dihedral : 4.090 58.754 1199 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.08 % Allowed : 18.22 % Favored : 78.70 % 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: -0.05 (0.26), residues: 1075 helix: 1.96 (0.26), residues: 409 sheet: -1.06 (0.33), residues: 229 loop : -1.38 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 297 HIS 0.010 0.001 HIS A 220 PHE 0.015 0.001 PHE N 108 TYR 0.018 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 222 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 195 time to evaluate : 1.083 Fit side-chains revert: symmetry clash REVERT: A 33 ASP cc_start: 0.9116 (m-30) cc_final: 0.8884 (m-30) REVERT: B 9 GLN cc_start: 0.9163 (tm-30) cc_final: 0.8889 (tm-30) REVERT: B 10 GLU cc_start: 0.9014 (mt-10) cc_final: 0.8692 (mt-10) REVERT: B 45 MET cc_start: 0.8986 (mmm) cc_final: 0.8129 (mpp) REVERT: B 59 TYR cc_start: 0.9329 (OUTLIER) cc_final: 0.8931 (m-80) REVERT: B 215 GLU cc_start: 0.8048 (mp0) cc_final: 0.7837 (mp0) REVERT: B 230 ASN cc_start: 0.9095 (m-40) cc_final: 0.8833 (m110) REVERT: B 234 PHE cc_start: 0.9405 (OUTLIER) cc_final: 0.8712 (m-80) REVERT: G 19 LEU cc_start: 0.9167 (mp) cc_final: 0.8930 (mp) REVERT: G 20 LYS cc_start: 0.9134 (mtmm) cc_final: 0.8863 (mtmm) REVERT: G 32 LYS cc_start: 0.9038 (tptp) cc_final: 0.8632 (tptp) REVERT: G 36 ASP cc_start: 0.8856 (m-30) cc_final: 0.8513 (m-30) REVERT: N 5 GLN cc_start: 0.9015 (mt0) cc_final: 0.8382 (mp10) REVERT: N 46 GLU cc_start: 0.9001 (pt0) cc_final: 0.8786 (pt0) REVERT: N 73 ASP cc_start: 0.8449 (t0) cc_final: 0.8087 (t0) REVERT: N 95 TYR cc_start: 0.9127 (m-80) cc_final: 0.8674 (m-80) REVERT: R 202 LYS cc_start: 0.8756 (pptt) cc_final: 0.8182 (ptmt) REVERT: R 204 MET cc_start: 0.9003 (tmm) cc_final: 0.8800 (tmm) REVERT: R 221 GLN cc_start: 0.8153 (mp10) cc_final: 0.7828 (mp10) REVERT: R 288 LYS cc_start: 0.9406 (tppp) cc_final: 0.9087 (tppp) REVERT: R 297 TRP cc_start: 0.8869 (m-10) cc_final: 0.8616 (m-90) REVERT: R 323 ILE cc_start: 0.9491 (mt) cc_final: 0.9243 (mm) REVERT: R 387 GLU cc_start: 0.9188 (mp0) cc_final: 0.8881 (mp0) REVERT: R 393 PHE cc_start: 0.9110 (m-10) cc_final: 0.8805 (m-10) REVERT: R 397 MET cc_start: 0.9257 (mmp) cc_final: 0.8623 (mtt) outliers start: 27 outliers final: 15 residues processed: 215 average time/residue: 0.2385 time to fit residues: 68.1943 Evaluate side-chains 207 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 190 time to evaluate : 0.930 ------------------------------------------------------------------------------- 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 234 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 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 396 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 33 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 99 optimal weight: 7.9990 chunk 41 optimal weight: 7.9990 chunk 73 optimal weight: 30.0000 chunk 17 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 66 optimal weight: 7.9990 chunk 53 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN B 340 ASN N 120 GLN R 234 GLN R 363 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.089701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.061772 restraints weight = 20374.500| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 3.43 r_work: 0.2696 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 8722 Z= 0.398 Angle : 0.593 8.406 11820 Z= 0.317 Chirality : 0.042 0.184 1329 Planarity : 0.004 0.044 1509 Dihedral : 4.023 18.351 1197 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 4.10 % Allowed : 18.45 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.03 (0.26), residues: 1075 helix: 1.95 (0.26), residues: 409 sheet: -0.92 (0.33), residues: 224 loop : -1.33 (0.28), residues: 442 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 0.022 0.001 PHE N 68 TYR 0.020 0.002 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 225 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 189 time to evaluate : 1.000 Fit side-chains revert: symmetry clash REVERT: A 33 ASP cc_start: 0.9132 (m-30) cc_final: 0.8927 (m-30) REVERT: A 346 LEU cc_start: 0.9562 (OUTLIER) cc_final: 0.9208 (mp) REVERT: A 378 ASP cc_start: 0.9169 (m-30) cc_final: 0.8501 (m-30) REVERT: B 10 GLU cc_start: 0.8998 (mt-10) cc_final: 0.8768 (mt-10) REVERT: B 42 ARG cc_start: 0.8715 (tmm-80) cc_final: 0.8351 (tmm-80) REVERT: B 59 TYR cc_start: 0.9378 (OUTLIER) cc_final: 0.8929 (m-80) REVERT: B 61 MET cc_start: 0.9146 (ptm) cc_final: 0.8926 (ptm) REVERT: B 183 HIS cc_start: 0.8463 (OUTLIER) cc_final: 0.8007 (t-90) REVERT: B 215 GLU cc_start: 0.8190 (mp0) cc_final: 0.7946 (mp0) REVERT: B 234 PHE cc_start: 0.9417 (OUTLIER) cc_final: 0.8769 (m-80) REVERT: G 20 LYS cc_start: 0.9195 (mtmm) cc_final: 0.8957 (mtmm) REVERT: G 24 ASN cc_start: 0.8940 (m-40) cc_final: 0.8720 (m-40) REVERT: G 32 LYS cc_start: 0.9014 (tptp) cc_final: 0.8666 (tptp) REVERT: G 36 ASP cc_start: 0.8940 (m-30) cc_final: 0.8592 (m-30) REVERT: G 42 GLU cc_start: 0.9022 (tp30) cc_final: 0.8792 (tm-30) REVERT: N 46 GLU cc_start: 0.8959 (pt0) cc_final: 0.8755 (pt0) REVERT: N 73 ASP cc_start: 0.8512 (t0) cc_final: 0.8167 (t0) REVERT: N 95 TYR cc_start: 0.9095 (m-80) cc_final: 0.8663 (m-80) REVERT: R 202 LYS cc_start: 0.8726 (pptt) cc_final: 0.8254 (ptmt) REVERT: R 204 MET cc_start: 0.8981 (tmm) cc_final: 0.8731 (tmm) REVERT: R 221 GLN cc_start: 0.8257 (mp10) cc_final: 0.7945 (mp10) REVERT: R 288 LYS cc_start: 0.9401 (tppp) cc_final: 0.9040 (tppp) REVERT: R 297 TRP cc_start: 0.8896 (m-10) cc_final: 0.8652 (m-90) REVERT: R 309 ILE cc_start: 0.9471 (OUTLIER) cc_final: 0.9204 (tp) REVERT: R 323 ILE cc_start: 0.9515 (mt) cc_final: 0.9260 (mm) REVERT: R 387 GLU cc_start: 0.9202 (mp0) cc_final: 0.8771 (mp0) REVERT: R 393 PHE cc_start: 0.9155 (m-10) cc_final: 0.8793 (m-10) REVERT: R 394 GLN cc_start: 0.9314 (tt0) cc_final: 0.9031 (tt0) REVERT: R 397 MET cc_start: 0.9275 (mmp) cc_final: 0.8730 (mtt) outliers start: 36 outliers final: 20 residues processed: 218 average time/residue: 0.2276 time to fit residues: 66.1648 Evaluate side-chains 206 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 181 time to evaluate : 1.027 ------------------------------------------------------------------------------- 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 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 315 VAL Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 109 ASP Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 50 optimal weight: 0.7980 chunk 84 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 62 optimal weight: 0.3980 chunk 11 optimal weight: 5.9990 chunk 95 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 13 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 120 GLN R 234 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.093674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.065998 restraints weight = 19775.954| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 3.44 r_work: 0.2794 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8722 Z= 0.148 Angle : 0.545 8.275 11820 Z= 0.280 Chirality : 0.040 0.161 1329 Planarity : 0.003 0.044 1509 Dihedral : 3.754 17.505 1197 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.42 % Allowed : 21.53 % 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: 0.29 (0.26), residues: 1075 helix: 2.11 (0.26), residues: 409 sheet: -0.64 (0.33), residues: 223 loop : -1.20 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.007 0.001 HIS A 220 PHE 0.011 0.001 PHE N 68 TYR 0.014 0.001 TYR R 145 ARG 0.005 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 234 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 204 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 ASP cc_start: 0.9025 (m-30) cc_final: 0.8806 (m-30) REVERT: A 346 LEU cc_start: 0.9536 (OUTLIER) cc_final: 0.9091 (mp) REVERT: A 378 ASP cc_start: 0.9079 (m-30) cc_final: 0.8324 (m-30) REVERT: B 9 GLN cc_start: 0.9213 (tm-30) cc_final: 0.8996 (tm-30) REVERT: B 10 GLU cc_start: 0.9016 (mt-10) cc_final: 0.8681 (mt-10) REVERT: B 42 ARG cc_start: 0.8676 (tmm-80) cc_final: 0.8261 (tmm-80) REVERT: B 45 MET cc_start: 0.8976 (mmm) cc_final: 0.8075 (mpp) REVERT: B 59 TYR cc_start: 0.9314 (OUTLIER) cc_final: 0.8939 (m-80) REVERT: B 183 HIS cc_start: 0.8078 (OUTLIER) cc_final: 0.7571 (t-90) REVERT: B 226 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.8404 (tp30) REVERT: B 230 ASN cc_start: 0.9157 (m-40) cc_final: 0.8818 (m110) REVERT: B 234 PHE cc_start: 0.9357 (OUTLIER) cc_final: 0.8612 (m-80) REVERT: G 13 ARG cc_start: 0.8927 (mtm110) cc_final: 0.8640 (mtm110) REVERT: G 20 LYS cc_start: 0.9165 (mtmm) cc_final: 0.8867 (mtmm) REVERT: G 32 LYS cc_start: 0.8898 (tptp) cc_final: 0.8413 (tptt) REVERT: G 36 ASP cc_start: 0.8891 (m-30) cc_final: 0.8075 (m-30) REVERT: G 42 GLU cc_start: 0.8991 (tp30) cc_final: 0.8741 (tm-30) REVERT: N 46 GLU cc_start: 0.8902 (pt0) cc_final: 0.8666 (pt0) REVERT: N 73 ASP cc_start: 0.8418 (t0) cc_final: 0.8084 (t0) REVERT: N 91 THR cc_start: 0.9149 (OUTLIER) cc_final: 0.8882 (t) REVERT: N 95 TYR cc_start: 0.9043 (m-80) cc_final: 0.8616 (m-80) REVERT: R 202 LYS cc_start: 0.8728 (pptt) cc_final: 0.8367 (tttt) REVERT: R 221 GLN cc_start: 0.8140 (mp10) cc_final: 0.7844 (mp10) REVERT: R 288 LYS cc_start: 0.9396 (tppp) cc_final: 0.9138 (tppt) REVERT: R 292 GLU cc_start: 0.8809 (mp0) cc_final: 0.8113 (pm20) REVERT: R 299 ARG cc_start: 0.8643 (mpt-90) cc_final: 0.8408 (mpt-90) REVERT: R 323 ILE cc_start: 0.9483 (mt) cc_final: 0.9242 (mm) REVERT: R 371 MET cc_start: 0.8877 (mmm) cc_final: 0.8647 (mmm) REVERT: R 387 GLU cc_start: 0.9093 (mp0) cc_final: 0.8580 (mp0) REVERT: R 393 PHE cc_start: 0.9118 (m-10) cc_final: 0.8742 (m-10) REVERT: R 394 GLN cc_start: 0.9284 (tt0) cc_final: 0.8845 (tt0) REVERT: R 397 MET cc_start: 0.9235 (mmp) cc_final: 0.8622 (mtt) REVERT: R 412 GLU cc_start: 0.8702 (mm-30) cc_final: 0.8419 (mm-30) outliers start: 30 outliers final: 16 residues processed: 225 average time/residue: 0.2303 time to fit residues: 68.7964 Evaluate side-chains 213 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 191 time to evaluate : 0.938 ------------------------------------------------------------------------------- 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 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 28 ILE 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 246 VAL Chi-restraints excluded: chain R residue 249 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 64 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 chunk 75 optimal weight: 50.0000 chunk 48 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 101 optimal weight: 7.9990 chunk 67 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 32 optimal weight: 9.9990 chunk 80 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN B 225 HIS ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 GLN 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 = 0.093234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.065498 restraints weight = 19617.359| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 3.43 r_work: 0.2782 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8722 Z= 0.192 Angle : 0.556 7.142 11820 Z= 0.286 Chirality : 0.040 0.193 1329 Planarity : 0.003 0.030 1509 Dihedral : 3.770 19.492 1197 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.42 % Allowed : 21.87 % Favored : 74.72 % 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: 0.36 (0.26), residues: 1075 helix: 2.11 (0.26), residues: 409 sheet: -0.56 (0.33), residues: 224 loop : -1.13 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP R 297 HIS 0.005 0.001 HIS A 220 PHE 0.012 0.001 PHE N 68 TYR 0.014 0.001 TYR A 318 ARG 0.003 0.000 ARG R 310 *********************** 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 227 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 197 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ASP cc_start: 0.9028 (m-30) cc_final: 0.8814 (m-30) REVERT: A 378 ASP cc_start: 0.9119 (m-30) cc_final: 0.8374 (m-30) REVERT: B 10 GLU cc_start: 0.9024 (mt-10) cc_final: 0.8810 (mt-10) REVERT: B 45 MET cc_start: 0.8993 (mmm) cc_final: 0.8206 (mmm) REVERT: B 59 TYR cc_start: 0.9316 (OUTLIER) cc_final: 0.8991 (m-80) REVERT: B 183 HIS cc_start: 0.8148 (OUTLIER) cc_final: 0.7691 (t-90) REVERT: B 230 ASN cc_start: 0.9118 (m-40) cc_final: 0.8778 (m110) REVERT: B 234 PHE cc_start: 0.9392 (OUTLIER) cc_final: 0.8743 (m-80) REVERT: G 20 LYS cc_start: 0.9154 (mtmm) cc_final: 0.8915 (mtmm) REVERT: G 42 GLU cc_start: 0.9043 (tp30) cc_final: 0.8758 (tm-30) REVERT: N 46 GLU cc_start: 0.8921 (pt0) cc_final: 0.8673 (pt0) REVERT: N 73 ASP cc_start: 0.8461 (t0) cc_final: 0.8123 (t0) REVERT: N 91 THR cc_start: 0.9145 (OUTLIER) cc_final: 0.8854 (t) REVERT: N 95 TYR cc_start: 0.9019 (m-80) cc_final: 0.8656 (m-80) REVERT: R 198 ASP cc_start: 0.8611 (p0) cc_final: 0.8337 (p0) REVERT: R 202 LYS cc_start: 0.8734 (pptt) cc_final: 0.8394 (tttt) REVERT: R 204 MET cc_start: 0.8920 (tmm) cc_final: 0.8648 (tmm) REVERT: R 221 GLN cc_start: 0.8302 (mp10) cc_final: 0.7963 (mp10) REVERT: R 288 LYS cc_start: 0.9387 (tppp) cc_final: 0.9051 (tptp) REVERT: R 292 GLU cc_start: 0.8810 (mp0) cc_final: 0.8442 (mp0) REVERT: R 323 ILE cc_start: 0.9487 (mt) cc_final: 0.9233 (mm) REVERT: R 387 GLU cc_start: 0.9058 (mp0) cc_final: 0.8389 (pm20) REVERT: R 393 PHE cc_start: 0.9129 (m-10) cc_final: 0.8743 (m-10) REVERT: R 394 GLN cc_start: 0.9282 (tt0) cc_final: 0.8813 (tt0) REVERT: R 397 MET cc_start: 0.9224 (mmp) cc_final: 0.8586 (mtt) REVERT: R 412 GLU cc_start: 0.8724 (mm-30) cc_final: 0.8437 (mm-30) outliers start: 30 outliers final: 17 residues processed: 220 average time/residue: 0.2257 time to fit residues: 66.3966 Evaluate side-chains 212 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 191 time to evaluate : 1.030 ------------------------------------------------------------------------------- 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 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 263 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 109 ASP Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 246 VAL Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 396 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 28 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 60 optimal weight: 8.9990 chunk 2 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 102 optimal weight: 0.3980 chunk 90 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 GLN R 180 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.093459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.065398 restraints weight = 19898.437| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 3.48 r_work: 0.2777 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8722 Z= 0.195 Angle : 0.563 6.791 11820 Z= 0.291 Chirality : 0.040 0.193 1329 Planarity : 0.003 0.031 1509 Dihedral : 3.796 17.177 1197 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.76 % Allowed : 22.55 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.41 (0.26), residues: 1075 helix: 2.17 (0.26), residues: 409 sheet: -0.52 (0.33), residues: 223 loop : -1.12 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.002 TRP R 297 HIS 0.005 0.001 HIS B 225 PHE 0.011 0.001 PHE N 108 TYR 0.012 0.001 TYR A 360 ARG 0.007 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 227 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 194 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ASP cc_start: 0.9017 (m-30) cc_final: 0.8802 (m-30) REVERT: A 378 ASP cc_start: 0.9102 (m-30) cc_final: 0.8346 (m-30) REVERT: B 59 TYR cc_start: 0.9326 (OUTLIER) cc_final: 0.8988 (m-80) REVERT: B 183 HIS cc_start: 0.8110 (OUTLIER) cc_final: 0.7643 (t-90) REVERT: B 230 ASN cc_start: 0.9007 (m-40) cc_final: 0.8530 (m110) REVERT: B 234 PHE cc_start: 0.9401 (OUTLIER) cc_final: 0.8749 (m-80) REVERT: G 13 ARG cc_start: 0.8960 (mtm110) cc_final: 0.8685 (mtm110) REVERT: G 20 LYS cc_start: 0.9157 (mtmm) cc_final: 0.8924 (mtmm) REVERT: G 42 GLU cc_start: 0.9063 (tp30) cc_final: 0.8698 (tm-30) REVERT: N 46 GLU cc_start: 0.8929 (pt0) cc_final: 0.8676 (pt0) REVERT: N 73 ASP cc_start: 0.8517 (t0) cc_final: 0.8162 (t0) REVERT: N 91 THR cc_start: 0.9156 (OUTLIER) cc_final: 0.8907 (t) REVERT: N 95 TYR cc_start: 0.8995 (m-80) cc_final: 0.8645 (m-80) REVERT: R 198 ASP cc_start: 0.8607 (OUTLIER) cc_final: 0.8319 (p0) REVERT: R 202 LYS cc_start: 0.8799 (pptt) cc_final: 0.8433 (tttt) REVERT: R 204 MET cc_start: 0.8925 (tmm) cc_final: 0.8669 (tmm) REVERT: R 221 GLN cc_start: 0.8205 (mp10) cc_final: 0.7869 (mp10) REVERT: R 288 LYS cc_start: 0.9339 (tppp) cc_final: 0.8981 (tptp) REVERT: R 292 GLU cc_start: 0.8777 (mp0) cc_final: 0.8309 (mp0) REVERT: R 323 ILE cc_start: 0.9479 (mt) cc_final: 0.9229 (mm) REVERT: R 387 GLU cc_start: 0.9040 (mp0) cc_final: 0.8510 (mp0) REVERT: R 393 PHE cc_start: 0.9138 (m-10) cc_final: 0.8747 (m-10) REVERT: R 394 GLN cc_start: 0.9283 (tt0) cc_final: 0.8788 (tt0) REVERT: R 397 MET cc_start: 0.9212 (mmp) cc_final: 0.8574 (mtt) REVERT: R 410 GLN cc_start: 0.8842 (mm-40) cc_final: 0.8291 (mt0) REVERT: R 412 GLU cc_start: 0.8707 (mm-30) cc_final: 0.8475 (mm-30) outliers start: 33 outliers final: 21 residues processed: 216 average time/residue: 0.2287 time to fit residues: 66.4063 Evaluate side-chains 215 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 189 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 SER 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 263 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 28 ILE 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 198 ASP 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 74 optimal weight: 50.0000 chunk 69 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 104 optimal weight: 0.9980 chunk 100 optimal weight: 0.7980 chunk 47 optimal weight: 6.9990 chunk 88 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 chunk 13 optimal weight: 0.0670 chunk 83 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 overall best weight: 1.3722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.093756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.065843 restraints weight = 20136.224| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 3.49 r_work: 0.2785 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8722 Z= 0.193 Angle : 0.571 6.867 11820 Z= 0.297 Chirality : 0.041 0.195 1329 Planarity : 0.003 0.029 1509 Dihedral : 3.794 16.655 1197 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.76 % Allowed : 22.44 % Favored : 73.80 % 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: 2.11 (0.26), residues: 408 sheet: -0.50 (0.33), residues: 223 loop : -1.09 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.001 TRP R 297 HIS 0.005 0.001 HIS B 225 PHE 0.011 0.001 PHE N 108 TYR 0.016 0.001 TYR A 318 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 228 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 195 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ASP cc_start: 0.9025 (m-30) cc_final: 0.8809 (m-30) REVERT: A 346 LEU cc_start: 0.9532 (OUTLIER) cc_final: 0.9100 (mp) REVERT: A 378 ASP cc_start: 0.9095 (m-30) cc_final: 0.8336 (m-30) REVERT: B 59 TYR cc_start: 0.9291 (OUTLIER) cc_final: 0.8963 (m-80) REVERT: B 183 HIS cc_start: 0.8296 (OUTLIER) cc_final: 0.7723 (t-90) REVERT: B 230 ASN cc_start: 0.8928 (m-40) cc_final: 0.8605 (m110) REVERT: B 234 PHE cc_start: 0.9428 (OUTLIER) cc_final: 0.8732 (m-80) REVERT: G 13 ARG cc_start: 0.9036 (mtm110) cc_final: 0.8819 (mtm110) REVERT: G 20 LYS cc_start: 0.9167 (mtmm) cc_final: 0.8932 (mtmm) REVERT: G 21 MET cc_start: 0.9082 (tpp) cc_final: 0.8626 (tpp) REVERT: G 32 LYS cc_start: 0.8850 (tptp) cc_final: 0.8467 (tptt) REVERT: G 36 ASP cc_start: 0.8818 (m-30) cc_final: 0.8005 (m-30) REVERT: G 42 GLU cc_start: 0.9087 (tp30) cc_final: 0.8736 (tm-30) REVERT: N 46 GLU cc_start: 0.8907 (pt0) cc_final: 0.8658 (pt0) REVERT: N 73 ASP cc_start: 0.8510 (t0) cc_final: 0.8155 (t0) REVERT: N 83 MET cc_start: 0.8989 (mtt) cc_final: 0.8493 (mtt) REVERT: N 91 THR cc_start: 0.9188 (OUTLIER) cc_final: 0.8925 (t) REVERT: N 95 TYR cc_start: 0.9024 (m-80) cc_final: 0.8616 (m-80) REVERT: R 202 LYS cc_start: 0.8871 (pptt) cc_final: 0.8504 (tttt) REVERT: R 204 MET cc_start: 0.8911 (tmm) cc_final: 0.8634 (tmm) REVERT: R 221 GLN cc_start: 0.8189 (mp10) cc_final: 0.7859 (mp10) REVERT: R 288 LYS cc_start: 0.9306 (tppp) cc_final: 0.8970 (tptp) REVERT: R 292 GLU cc_start: 0.8795 (mp0) cc_final: 0.8339 (mp0) REVERT: R 323 ILE cc_start: 0.9494 (mt) cc_final: 0.9246 (mm) REVERT: R 387 GLU cc_start: 0.9001 (mp0) cc_final: 0.8348 (pm20) REVERT: R 393 PHE cc_start: 0.9127 (m-10) cc_final: 0.8751 (m-10) REVERT: R 394 GLN cc_start: 0.9258 (tt0) cc_final: 0.8732 (tt0) REVERT: R 397 MET cc_start: 0.9207 (mmp) cc_final: 0.8555 (mtt) REVERT: R 410 GLN cc_start: 0.8821 (mm-40) cc_final: 0.8291 (mt0) outliers start: 33 outliers final: 21 residues processed: 219 average time/residue: 0.2240 time to fit residues: 65.7901 Evaluate side-chains 217 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 191 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 352 SER 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 263 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 28 ILE 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 236 CYS Chi-restraints excluded: chain R residue 249 VAL 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: 6.9990 chunk 62 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 20 optimal weight: 0.4980 chunk 99 optimal weight: 7.9990 chunk 87 optimal weight: 7.9990 chunk 27 optimal weight: 0.8980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS B 225 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.094254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.066317 restraints weight = 19885.212| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 3.49 r_work: 0.2792 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8722 Z= 0.189 Angle : 0.591 8.308 11820 Z= 0.305 Chirality : 0.041 0.205 1329 Planarity : 0.003 0.028 1509 Dihedral : 3.790 16.014 1197 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.30 % Allowed : 23.12 % 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: 0.45 (0.26), residues: 1075 helix: 2.15 (0.26), residues: 407 sheet: -0.45 (0.33), residues: 223 loop : -1.06 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP R 297 HIS 0.004 0.001 HIS R 173 PHE 0.010 0.001 PHE N 108 TYR 0.016 0.001 TYR A 318 ARG 0.006 0.000 ARG B 129 *********************** 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 224 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 195 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ASP cc_start: 0.9015 (m-30) cc_final: 0.8802 (m-30) REVERT: A 343 ASP cc_start: 0.8919 (m-30) cc_final: 0.8716 (p0) REVERT: A 346 LEU cc_start: 0.9527 (OUTLIER) cc_final: 0.9110 (mp) REVERT: A 378 ASP cc_start: 0.9092 (m-30) cc_final: 0.8327 (m-30) REVERT: B 59 TYR cc_start: 0.9265 (OUTLIER) cc_final: 0.8992 (m-80) REVERT: B 66 ASP cc_start: 0.8762 (OUTLIER) cc_final: 0.8361 (p0) REVERT: B 183 HIS cc_start: 0.8237 (OUTLIER) cc_final: 0.7663 (t-90) REVERT: B 230 ASN cc_start: 0.8821 (m-40) cc_final: 0.8617 (m110) REVERT: B 234 PHE cc_start: 0.9434 (OUTLIER) cc_final: 0.8785 (m-80) REVERT: G 13 ARG cc_start: 0.9019 (mtm110) cc_final: 0.8789 (mtm110) REVERT: G 20 LYS cc_start: 0.9169 (mtmm) cc_final: 0.8946 (mtmm) REVERT: G 21 MET cc_start: 0.9080 (tpp) cc_final: 0.8624 (tpp) REVERT: G 42 GLU cc_start: 0.9064 (tp30) cc_final: 0.8683 (tm-30) REVERT: N 73 ASP cc_start: 0.8529 (t0) cc_final: 0.8172 (t0) REVERT: N 83 MET cc_start: 0.8972 (mtt) cc_final: 0.8476 (mtt) REVERT: N 91 THR cc_start: 0.9258 (OUTLIER) cc_final: 0.8998 (t) REVERT: N 95 TYR cc_start: 0.8995 (m-80) cc_final: 0.8564 (m-80) REVERT: R 202 LYS cc_start: 0.8881 (pptt) cc_final: 0.8534 (tttt) REVERT: R 204 MET cc_start: 0.8893 (tmm) cc_final: 0.8627 (tmm) REVERT: R 221 GLN cc_start: 0.8223 (mp10) cc_final: 0.7896 (mp10) REVERT: R 234 GLN cc_start: 0.9393 (mm110) cc_final: 0.9059 (mm-40) REVERT: R 257 PHE cc_start: 0.7869 (OUTLIER) cc_final: 0.7459 (m-80) REVERT: R 323 ILE cc_start: 0.9479 (mt) cc_final: 0.9231 (mm) REVERT: R 387 GLU cc_start: 0.8980 (mp0) cc_final: 0.8334 (pm20) REVERT: R 393 PHE cc_start: 0.9129 (m-10) cc_final: 0.8744 (m-10) REVERT: R 394 GLN cc_start: 0.9249 (tt0) cc_final: 0.8741 (tt0) REVERT: R 397 MET cc_start: 0.9194 (mmp) cc_final: 0.8582 (mtt) REVERT: R 410 GLN cc_start: 0.8656 (mm-40) cc_final: 0.8091 (mt0) outliers start: 29 outliers final: 21 residues processed: 216 average time/residue: 0.2270 time to fit residues: 65.8139 Evaluate side-chains 216 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 188 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 352 SER 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 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 263 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 28 ILE 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 236 CYS Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 257 PHE Chi-restraints excluded: chain R residue 396 LEU Rotamers are restrained with sigma=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: 0.9980 chunk 52 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 88 optimal weight: 6.9990 chunk 101 optimal weight: 6.9990 chunk 98 optimal weight: 0.3980 chunk 50 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.093740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.066204 restraints weight = 19836.026| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 3.45 r_work: 0.2797 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8722 Z= 0.189 Angle : 0.601 8.382 11820 Z= 0.310 Chirality : 0.041 0.203 1329 Planarity : 0.003 0.033 1509 Dihedral : 3.788 15.703 1197 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.64 % Allowed : 23.23 % Favored : 73.12 % 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: 0.49 (0.26), residues: 1075 helix: 2.15 (0.26), residues: 406 sheet: -0.37 (0.34), residues: 223 loop : -1.03 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP R 297 HIS 0.007 0.001 HIS R 171 PHE 0.011 0.001 PHE N 108 TYR 0.018 0.001 TYR A 318 ARG 0.008 0.000 ARG B 129 ********************** 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 224 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 192 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ASP cc_start: 0.8982 (m-30) cc_final: 0.8764 (m-30) REVERT: A 343 ASP cc_start: 0.8927 (m-30) cc_final: 0.8717 (p0) REVERT: A 346 LEU cc_start: 0.9537 (OUTLIER) cc_final: 0.9095 (mp) REVERT: A 378 ASP cc_start: 0.9074 (m-30) cc_final: 0.8306 (m-30) REVERT: B 59 TYR cc_start: 0.9298 (OUTLIER) cc_final: 0.8992 (m-80) REVERT: B 66 ASP cc_start: 0.8729 (OUTLIER) cc_final: 0.8334 (p0) REVERT: B 183 HIS cc_start: 0.8244 (OUTLIER) cc_final: 0.7681 (t-90) REVERT: B 230 ASN cc_start: 0.8790 (m-40) cc_final: 0.8519 (m110) REVERT: B 234 PHE cc_start: 0.9452 (OUTLIER) cc_final: 0.8789 (m-80) REVERT: G 13 ARG cc_start: 0.9011 (mtm110) cc_final: 0.8777 (mtm110) REVERT: G 20 LYS cc_start: 0.9180 (mtmm) cc_final: 0.8955 (mtmm) REVERT: G 21 MET cc_start: 0.9071 (tpp) cc_final: 0.8600 (tpp) REVERT: G 42 GLU cc_start: 0.9089 (tp30) cc_final: 0.8742 (tm-30) REVERT: N 73 ASP cc_start: 0.8519 (t0) cc_final: 0.8176 (t0) REVERT: N 83 MET cc_start: 0.8970 (mtt) cc_final: 0.8460 (mtt) REVERT: N 91 THR cc_start: 0.9229 (OUTLIER) cc_final: 0.8955 (t) REVERT: N 95 TYR cc_start: 0.9028 (m-80) cc_final: 0.8827 (m-80) REVERT: R 202 LYS cc_start: 0.8891 (pptt) cc_final: 0.8525 (tttt) REVERT: R 204 MET cc_start: 0.8918 (tmm) cc_final: 0.8585 (tmm) REVERT: R 221 GLN cc_start: 0.8241 (mp10) cc_final: 0.7870 (mp10) REVERT: R 234 GLN cc_start: 0.9384 (mm110) cc_final: 0.9066 (mm-40) REVERT: R 288 LYS cc_start: 0.9317 (tppp) cc_final: 0.9108 (tppp) REVERT: R 299 ARG cc_start: 0.8364 (mpt-90) cc_final: 0.8138 (mmt-90) REVERT: R 323 ILE cc_start: 0.9492 (mt) cc_final: 0.9241 (mm) REVERT: R 387 GLU cc_start: 0.8966 (mp0) cc_final: 0.8444 (mp0) REVERT: R 393 PHE cc_start: 0.9130 (m-10) cc_final: 0.8735 (m-10) REVERT: R 394 GLN cc_start: 0.9214 (tt0) cc_final: 0.8703 (tt0) REVERT: R 397 MET cc_start: 0.9188 (mmp) cc_final: 0.8587 (mtt) REVERT: R 410 GLN cc_start: 0.8615 (mm-40) cc_final: 0.8067 (mt0) outliers start: 32 outliers final: 22 residues processed: 216 average time/residue: 0.2153 time to fit residues: 62.1197 Evaluate side-chains 218 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 190 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 352 SER 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 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 263 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 28 ILE 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 236 CYS 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: 7.9990 chunk 64 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 11 optimal weight: 0.0170 chunk 12 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 overall best weight: 2.6024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.091689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.063995 restraints weight = 20156.054| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 3.43 r_work: 0.2748 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8722 Z= 0.288 Angle : 0.633 8.945 11820 Z= 0.330 Chirality : 0.042 0.213 1329 Planarity : 0.003 0.038 1509 Dihedral : 3.995 20.934 1197 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.64 % Allowed : 23.69 % Favored : 72.67 % 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: 0.46 (0.26), residues: 1075 helix: 2.10 (0.26), residues: 406 sheet: -0.42 (0.34), residues: 224 loop : -1.00 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.099 0.002 TRP R 297 HIS 0.003 0.001 HIS A 362 PHE 0.028 0.001 PHE R 169 TYR 0.019 0.002 TYR A 318 ARG 0.006 0.000 ARG B 129 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4386.61 seconds wall clock time: 78 minutes 33.65 seconds (4713.65 seconds total)