Starting phenix.real_space_refine on Sat Jul 26 06:41:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lly_23436/07_2025/7lly_23436.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lly_23436/07_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_23436/07_2025/7lly_23436.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lly_23436/07_2025/7lly_23436.map" model { file = "/net/cci-nas-00/data/ceres_data/7lly_23436/07_2025/7lly_23436.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lly_23436/07_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-5711/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: 6.17, per 1000 atoms: 0.72 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: 3.06 Conformation dependent library (CDL) restraints added in 1.5 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: 0.87 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: 2.25 Time building geometry restraints manager: 3.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2803 1.34 - 1.46: 1775 1.46 - 1.58: 4073 1.58 - 1.70: 0 1.70 - 1.82: 71 Bond restraints: 8722 Sorted by residual: bond pdb=" C PRO R 54 " pdb=" N PRO R 55 " ideal model delta sigma weight residual 1.329 1.372 -0.043 1.18e-02 7.18e+03 1.34e+01 bond pdb=" N ARG N 118 " pdb=" CA ARG N 118 " ideal model delta sigma weight residual 1.454 1.493 -0.039 1.15e-02 7.56e+03 1.16e+01 bond pdb=" N THR N 122 " pdb=" CA THR N 122 " ideal model delta sigma weight residual 1.453 1.491 -0.038 1.31e-02 5.83e+03 8.49e+00 bond pdb=" N ASP R 59 " pdb=" CA ASP R 59 " ideal model delta sigma weight residual 1.454 1.488 -0.033 1.15e-02 7.56e+03 8.38e+00 bond pdb=" N GLN N 123 " pdb=" CA GLN N 123 " ideal model delta sigma weight residual 1.456 1.490 -0.035 1.22e-02 6.72e+03 8.01e+00 ... (remaining 8717 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.19: 11506 1.19 - 2.39: 240 2.39 - 3.58: 58 3.58 - 4.78: 12 4.78 - 5.97: 4 Bond angle restraints: 11820 Sorted by residual: angle pdb=" C PRO R 54 " pdb=" N PRO R 55 " pdb=" CA PRO R 55 " ideal model delta sigma weight residual 120.38 126.35 -5.97 1.03e+00 9.43e-01 3.36e+01 angle pdb=" CA GLN N 123 " pdb=" C GLN N 123 " pdb=" O GLN N 123 " ideal model delta sigma weight residual 121.16 117.05 4.11 1.12e+00 7.97e-01 1.35e+01 angle pdb=" CA VAL N 124 " pdb=" C VAL N 124 " pdb=" O VAL N 124 " ideal model delta sigma weight residual 120.48 116.46 4.02 1.10e+00 8.26e-01 1.34e+01 angle pdb=" CA GLN N 120 " pdb=" C GLN N 120 " pdb=" O GLN N 120 " ideal model delta sigma weight residual 122.14 117.66 4.48 1.24e+00 6.50e-01 1.31e+01 angle pdb=" CA GLY N 121 " pdb=" C GLY N 121 " pdb=" O GLY N 121 " ideal model delta sigma weight residual 122.24 117.56 4.68 1.30e+00 5.92e-01 1.29e+01 ... (remaining 11815 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 4579 17.73 - 35.47: 452 35.47 - 53.20: 107 53.20 - 70.94: 11 70.94 - 88.67: 11 Dihedral angle restraints: 5160 sinusoidal: 1951 harmonic: 3209 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual 93.00 36.63 56.37 1 1.00e+01 1.00e-02 4.28e+01 dihedral pdb=" CB GLU A 322 " pdb=" CG GLU A 322 " pdb=" CD GLU A 322 " pdb=" OE1 GLU A 322 " ideal model delta sinusoidal sigma weight residual 0.00 -84.22 84.22 1 3.00e+01 1.11e-03 9.59e+00 dihedral pdb=" CA ASP B 66 " pdb=" CB ASP B 66 " pdb=" CG ASP B 66 " pdb=" OD1 ASP B 66 " ideal model delta sinusoidal sigma weight residual -30.00 -82.86 52.86 1 2.00e+01 2.50e-03 9.51e+00 ... (remaining 5157 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1093 0.043 - 0.086: 167 0.086 - 0.129: 65 0.129 - 0.172: 1 0.172 - 0.215: 3 Chirality restraints: 1329 Sorted by residual: chirality pdb=" CA VAL N 124 " pdb=" N VAL N 124 " pdb=" C VAL N 124 " pdb=" CB VAL N 124 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA LEU R 60 " pdb=" N LEU R 60 " pdb=" C LEU R 60 " pdb=" CB LEU R 60 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.67e-01 chirality pdb=" CA GLN N 123 " pdb=" N GLN N 123 " pdb=" C GLN N 123 " pdb=" CB GLN N 123 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.56e-01 ... (remaining 1326 not shown) Planarity restraints: 1509 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL N 124 " -0.009 2.00e-02 2.50e+03 1.94e-02 3.78e+00 pdb=" C VAL N 124 " 0.034 2.00e-02 2.50e+03 pdb=" O VAL N 124 " -0.013 2.00e-02 2.50e+03 pdb=" N THR N 125 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY N 121 " 0.007 2.00e-02 2.50e+03 1.45e-02 2.09e+00 pdb=" C GLY N 121 " -0.025 2.00e-02 2.50e+03 pdb=" O GLY N 121 " 0.009 2.00e-02 2.50e+03 pdb=" N THR N 122 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL R 276 " -0.020 5.00e-02 4.00e+02 3.06e-02 1.50e+00 pdb=" N PRO R 277 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO R 277 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO R 277 " -0.017 5.00e-02 4.00e+02 ... (remaining 1506 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 82 2.57 - 3.15: 7364 3.15 - 3.73: 13225 3.73 - 4.32: 17878 4.32 - 4.90: 29803 Nonbonded interactions: 68352 Sorted by model distance: nonbonded pdb=" O GLU R 387 " pdb=" OG1 THR R 391 " model vdw 1.982 3.040 nonbonded pdb=" O HIS B 183 " pdb=" OG1 THR B 184 " model vdw 2.125 3.040 nonbonded pdb=" ND2 ASN B 230 " pdb=" OD1 ASP B 246 " model vdw 2.167 3.120 nonbonded pdb=" OD1 ASP B 163 " pdb=" OG1 THR B 165 " model vdw 2.254 3.040 nonbonded pdb=" O TYR B 145 " pdb=" N GLY B 162 " model vdw 2.296 3.120 ... (remaining 68347 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 24.860 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8727 Z= 0.172 Angle : 0.474 5.970 11830 Z= 0.301 Chirality : 0.038 0.215 1329 Planarity : 0.002 0.031 1509 Dihedral : 15.152 88.671 3065 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 3.05 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 Details of bonding type rmsd hydrogen bonds : bond 0.20867 ( 427) hydrogen bonds : angle 7.64362 ( 1218) SS BOND : bond 0.00126 ( 5) SS BOND : angle 0.81474 ( 10) covalent geometry : bond 0.00267 ( 8722) covalent geometry : angle 0.47316 (11820) *********************** 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 : 0.982 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: 0.2388 time to fit residues: 78.6223 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 : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 225 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 5.9990 chunk 80 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 chunk 32 optimal weight: 8.9990 chunk 50 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN B 259 GLN P 1 HIS P 24 GLN ** R 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 410 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.093672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.065648 restraints weight = 19988.119| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 3.48 r_work: 0.2786 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8727 Z= 0.194 Angle : 0.579 10.882 11830 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 Details of bonding type rmsd hydrogen bonds : bond 0.04102 ( 427) hydrogen bonds : angle 4.85246 ( 1218) SS BOND : bond 0.00153 ( 5) SS BOND : angle 0.79739 ( 10) covalent geometry : bond 0.00434 ( 8722) covalent geometry : angle 0.57919 (11820) *********************** 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 : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ASP cc_start: 0.9124 (m-30) cc_final: 0.8844 (m-30) REVERT: B 9 GLN cc_start: 0.9183 (tm-30) cc_final: 0.8914 (tm-30) REVERT: B 10 GLU cc_start: 0.8969 (mt-10) cc_final: 0.8638 (mt-10) REVERT: B 45 MET cc_start: 0.8904 (mmm) cc_final: 0.8035 (mpp) REVERT: B 59 TYR cc_start: 0.9349 (OUTLIER) cc_final: 0.8948 (m-80) REVERT: B 215 GLU cc_start: 0.7962 (mp0) cc_final: 0.7560 (mp0) REVERT: B 234 PHE cc_start: 0.9397 (OUTLIER) cc_final: 0.8693 (m-80) REVERT: G 19 LEU cc_start: 0.9173 (mp) cc_final: 0.8969 (mp) REVERT: G 20 LYS cc_start: 0.9138 (mtmm) cc_final: 0.8807 (mtmm) REVERT: N 73 ASP cc_start: 0.8206 (t0) cc_final: 0.7899 (t0) REVERT: N 95 TYR cc_start: 0.9093 (m-80) cc_final: 0.8839 (m-80) REVERT: R 202 LYS cc_start: 0.8685 (pptt) cc_final: 0.8106 (ptmt) REVERT: R 204 MET cc_start: 0.9037 (tmm) cc_final: 0.8832 (tmm) REVERT: R 221 GLN cc_start: 0.8207 (mp10) cc_final: 0.7908 (mp10) REVERT: R 257 PHE cc_start: 0.7830 (OUTLIER) cc_final: 0.7028 (m-10) REVERT: R 269 TYR cc_start: 0.9256 (m-10) cc_final: 0.9013 (m-80) REVERT: R 323 ILE cc_start: 0.9496 (mt) cc_final: 0.9287 (mm) REVERT: R 393 PHE cc_start: 0.9117 (m-10) cc_final: 0.8897 (m-10) REVERT: R 397 MET cc_start: 0.9319 (mmp) cc_final: 0.8643 (mtt) outliers start: 31 outliers final: 15 residues processed: 217 average time/residue: 0.3287 time to fit residues: 96.2634 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 : 1.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 109 ASP Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 236 CYS Chi-restraints excluded: chain R residue 246 VAL Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain R residue 257 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 86 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 71 optimal weight: 9.9990 chunk 14 optimal weight: 0.7980 chunk 101 optimal weight: 9.9990 chunk 93 optimal weight: 6.9990 chunk 78 optimal weight: 0.0040 chunk 53 optimal weight: 8.9990 chunk 60 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 overall best weight: 2.9598 ------------------------------------------------------------------------------- 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 = 0.3464 r_free = 0.3464 target = 0.092072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.063708 restraints weight = 20366.369| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 3.50 r_work: 0.2738 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 8727 Z= 0.209 Angle : 0.557 10.678 11830 Z= 0.296 Chirality : 0.041 0.231 1329 Planarity : 0.003 0.045 1509 Dihedral : 4.195 59.062 1199 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.64 % Allowed : 18.00 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.26), residues: 1075 helix: 1.92 (0.26), residues: 409 sheet: -1.11 (0.32), residues: 230 loop : -1.37 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 297 HIS 0.010 0.001 HIS A 220 PHE 0.016 0.001 PHE N 108 TYR 0.017 0.002 TYR A 318 ARG 0.005 0.000 ARG R 310 Details of bonding type rmsd hydrogen bonds : bond 0.04050 ( 427) hydrogen bonds : angle 4.60225 ( 1218) SS BOND : bond 0.00205 ( 5) SS BOND : angle 0.87920 ( 10) covalent geometry : bond 0.00466 ( 8722) covalent geometry : angle 0.55629 (11820) *********************** 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 225 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 193 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 ASP cc_start: 0.9130 (m-30) cc_final: 0.8900 (m-30) REVERT: B 9 GLN cc_start: 0.9171 (tm-30) cc_final: 0.8893 (tm-30) REVERT: B 10 GLU cc_start: 0.8994 (mt-10) cc_final: 0.8666 (mt-10) REVERT: B 45 MET cc_start: 0.8992 (mmm) cc_final: 0.8153 (mpp) REVERT: B 59 TYR cc_start: 0.9337 (OUTLIER) cc_final: 0.8896 (m-80) REVERT: B 172 GLU cc_start: 0.8262 (mp0) cc_final: 0.8017 (mp0) REVERT: B 234 PHE cc_start: 0.9410 (OUTLIER) cc_final: 0.8765 (m-80) REVERT: G 19 LEU cc_start: 0.9171 (mp) cc_final: 0.8943 (mp) REVERT: G 20 LYS cc_start: 0.9137 (mtmm) cc_final: 0.8868 (mtmm) REVERT: N 46 GLU cc_start: 0.8995 (pt0) cc_final: 0.8781 (pt0) REVERT: N 73 ASP cc_start: 0.8456 (t0) cc_final: 0.8079 (t0) REVERT: N 95 TYR cc_start: 0.9104 (m-80) cc_final: 0.8660 (m-80) REVERT: R 202 LYS cc_start: 0.8749 (pptt) cc_final: 0.8173 (ptmt) REVERT: R 204 MET cc_start: 0.9015 (tmm) cc_final: 0.8810 (tmm) REVERT: R 221 GLN cc_start: 0.8165 (mp10) cc_final: 0.7832 (mp10) REVERT: R 288 LYS cc_start: 0.9413 (tppp) cc_final: 0.9100 (tppp) REVERT: R 297 TRP cc_start: 0.8887 (m-10) cc_final: 0.8587 (m-90) REVERT: R 309 ILE cc_start: 0.9464 (OUTLIER) cc_final: 0.9186 (tp) REVERT: R 323 ILE cc_start: 0.9506 (mt) cc_final: 0.9244 (mm) REVERT: R 387 GLU cc_start: 0.9210 (mp0) cc_final: 0.8897 (mp0) REVERT: R 393 PHE cc_start: 0.9180 (m-10) cc_final: 0.8844 (m-10) REVERT: R 397 MET cc_start: 0.9262 (mmp) cc_final: 0.8640 (mtt) outliers start: 32 outliers final: 17 residues processed: 217 average time/residue: 0.2449 time to fit residues: 71.1196 Evaluate side-chains 207 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 187 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 109 ASP Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 236 CYS Chi-restraints excluded: chain R residue 246 VAL Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 253 THR Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain R residue 396 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 33 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 99 optimal weight: 6.9990 chunk 41 optimal weight: 7.9990 chunk 73 optimal weight: 8.9990 chunk 17 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN N 120 GLN R 234 GLN R 363 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.091262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.063188 restraints weight = 20189.129| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 3.44 r_work: 0.2728 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 8727 Z= 0.211 Angle : 0.560 8.492 11830 Z= 0.296 Chirality : 0.041 0.174 1329 Planarity : 0.003 0.045 1509 Dihedral : 3.853 17.134 1197 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.42 % Allowed : 19.59 % Favored : 76.99 % 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: 0.06 (0.26), residues: 1075 helix: 2.01 (0.26), residues: 409 sheet: -0.94 (0.33), residues: 224 loop : -1.31 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 234 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 0.004 0.000 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.03870 ( 427) hydrogen bonds : angle 4.48819 ( 1218) SS BOND : bond 0.00245 ( 5) SS BOND : angle 0.78000 ( 10) covalent geometry : bond 0.00470 ( 8722) covalent geometry : angle 0.55958 (11820) *********************** 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 226 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 196 time to evaluate : 1.406 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 ASP cc_start: 0.9112 (m-30) cc_final: 0.8903 (m-30) REVERT: A 346 LEU cc_start: 0.9546 (OUTLIER) cc_final: 0.9165 (mp) REVERT: A 378 ASP cc_start: 0.9147 (m-30) cc_final: 0.8440 (m-30) REVERT: B 10 GLU cc_start: 0.9011 (mt-10) cc_final: 0.8786 (mt-10) REVERT: B 42 ARG cc_start: 0.8781 (tmm-80) cc_final: 0.8504 (tmm-80) REVERT: B 59 TYR cc_start: 0.9380 (OUTLIER) cc_final: 0.8977 (m-80) REVERT: B 183 HIS cc_start: 0.8366 (OUTLIER) cc_final: 0.7909 (t-90) REVERT: B 234 PHE cc_start: 0.9404 (OUTLIER) cc_final: 0.8745 (m-80) REVERT: G 20 LYS cc_start: 0.9169 (mtmm) cc_final: 0.8938 (mtmm) REVERT: G 24 ASN cc_start: 0.8884 (m-40) cc_final: 0.8620 (m-40) REVERT: G 32 LYS cc_start: 0.8939 (tptp) cc_final: 0.8439 (tptp) REVERT: N 73 ASP cc_start: 0.8494 (t0) cc_final: 0.8161 (t0) REVERT: N 95 TYR cc_start: 0.9102 (m-80) cc_final: 0.8640 (m-80) REVERT: R 202 LYS cc_start: 0.8726 (pptt) cc_final: 0.8260 (ptmt) REVERT: R 221 GLN cc_start: 0.8193 (mp10) cc_final: 0.7905 (mp10) REVERT: R 288 LYS cc_start: 0.9419 (tppp) cc_final: 0.9068 (tppp) REVERT: R 297 TRP cc_start: 0.8873 (m-10) cc_final: 0.8648 (m-90) REVERT: R 323 ILE cc_start: 0.9503 (mt) cc_final: 0.9244 (mm) REVERT: R 387 GLU cc_start: 0.9185 (mp0) cc_final: 0.8740 (mp0) REVERT: R 393 PHE cc_start: 0.9139 (m-10) cc_final: 0.8779 (m-10) REVERT: R 394 GLN cc_start: 0.9295 (tt0) cc_final: 0.8997 (tt0) REVERT: R 397 MET cc_start: 0.9269 (mmp) cc_final: 0.8715 (mtt) outliers start: 30 outliers final: 19 residues processed: 219 average time/residue: 0.3296 time to fit residues: 97.8007 Evaluate side-chains 208 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 185 time to evaluate : 1.141 ------------------------------------------------------------------------------- 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 179 THR Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 109 ASP Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 236 CYS Chi-restraints excluded: chain R residue 246 VAL Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 253 THR 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: 5.9990 chunk 84 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 95 optimal weight: 0.7980 chunk 49 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 = 0.3474 r_free = 0.3474 target = 0.092659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.064689 restraints weight = 19860.003| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 3.45 r_work: 0.2764 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8727 Z= 0.134 Angle : 0.543 7.698 11830 Z= 0.283 Chirality : 0.040 0.173 1329 Planarity : 0.003 0.044 1509 Dihedral : 3.788 16.894 1197 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.76 % Allowed : 21.30 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.24 (0.26), residues: 1075 helix: 2.09 (0.26), residues: 409 sheet: -0.76 (0.33), residues: 225 loop : -1.20 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.008 0.001 HIS A 220 PHE 0.012 0.001 PHE N 108 TYR 0.016 0.001 TYR A 318 ARG 0.008 0.000 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.03594 ( 427) hydrogen bonds : angle 4.33191 ( 1218) SS BOND : bond 0.00264 ( 5) SS BOND : angle 0.70154 ( 10) covalent geometry : bond 0.00301 ( 8722) covalent geometry : angle 0.54286 (11820) *********************** 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 233 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 200 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ASP cc_start: 0.9059 (m-30) cc_final: 0.8840 (m-30) REVERT: A 211 LYS cc_start: 0.9200 (ptpp) cc_final: 0.8974 (ptpp) REVERT: A 346 LEU cc_start: 0.9542 (OUTLIER) cc_final: 0.9136 (mp) REVERT: A 378 ASP cc_start: 0.9089 (m-30) cc_final: 0.8348 (m-30) REVERT: B 9 GLN cc_start: 0.9193 (tm-30) cc_final: 0.8965 (tm-30) REVERT: B 10 GLU cc_start: 0.9016 (mt-10) cc_final: 0.8687 (mt-10) REVERT: B 45 MET cc_start: 0.8986 (mmm) cc_final: 0.8261 (mmm) REVERT: B 59 TYR cc_start: 0.9338 (OUTLIER) cc_final: 0.8918 (m-80) REVERT: B 61 MET cc_start: 0.9048 (ptm) cc_final: 0.8798 (ptm) REVERT: B 183 HIS cc_start: 0.8205 (OUTLIER) cc_final: 0.7756 (t-90) REVERT: B 230 ASN cc_start: 0.9191 (m-40) cc_final: 0.8813 (m-40) REVERT: B 234 PHE cc_start: 0.9382 (OUTLIER) cc_final: 0.8717 (m-80) REVERT: G 20 LYS cc_start: 0.9171 (mtmm) cc_final: 0.8876 (mtmm) REVERT: G 42 GLU cc_start: 0.8970 (tm-30) cc_final: 0.8453 (tm-30) REVERT: G 46 LYS cc_start: 0.9422 (mmmm) cc_final: 0.9105 (mtmm) REVERT: N 73 ASP cc_start: 0.8463 (t0) cc_final: 0.8134 (t0) REVERT: N 91 THR cc_start: 0.9150 (OUTLIER) cc_final: 0.8880 (t) REVERT: N 95 TYR cc_start: 0.9079 (m-80) cc_final: 0.8718 (m-80) REVERT: R 202 LYS cc_start: 0.8734 (pptt) cc_final: 0.8378 (tttt) REVERT: R 204 MET cc_start: 0.8926 (tmm) cc_final: 0.8650 (tmm) REVERT: R 221 GLN cc_start: 0.8233 (mp10) cc_final: 0.7897 (mp10) REVERT: R 288 LYS cc_start: 0.9390 (tppp) cc_final: 0.9122 (tppt) REVERT: R 292 GLU cc_start: 0.8820 (mp0) cc_final: 0.8084 (pm20) REVERT: R 299 ARG cc_start: 0.8622 (mpt-90) cc_final: 0.8374 (mpt-90) REVERT: R 323 ILE cc_start: 0.9499 (mt) cc_final: 0.9257 (mm) REVERT: R 387 GLU cc_start: 0.9119 (mp0) cc_final: 0.8615 (mp0) REVERT: R 393 PHE cc_start: 0.9130 (m-10) cc_final: 0.8757 (m-10) REVERT: R 394 GLN cc_start: 0.9305 (tt0) cc_final: 0.8865 (tt0) REVERT: R 397 MET cc_start: 0.9249 (mmp) cc_final: 0.8682 (mtt) REVERT: R 412 GLU cc_start: 0.8704 (mm-30) cc_final: 0.8417 (mm-30) outliers start: 33 outliers final: 21 residues processed: 225 average time/residue: 0.2210 time to fit residues: 66.9624 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 : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 109 ASP Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 236 CYS Chi-restraints excluded: chain R residue 246 VAL Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 396 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 64 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 75 optimal weight: 40.0000 chunk 48 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 101 optimal weight: 8.9990 chunk 67 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 32 optimal weight: 9.9990 chunk 80 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 120 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.090708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.062786 restraints weight = 19806.462| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 3.40 r_work: 0.2721 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 8727 Z= 0.210 Angle : 0.582 7.094 11830 Z= 0.306 Chirality : 0.042 0.187 1329 Planarity : 0.003 0.030 1509 Dihedral : 3.976 21.415 1197 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 4.67 % Allowed : 20.62 % 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: 0.25 (0.26), residues: 1075 helix: 2.07 (0.26), residues: 409 sheet: -0.66 (0.33), residues: 224 loop : -1.21 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP R 297 HIS 0.009 0.001 HIS A 220 PHE 0.014 0.001 PHE N 108 TYR 0.014 0.002 TYR A 318 ARG 0.005 0.000 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.03757 ( 427) hydrogen bonds : angle 4.40443 ( 1218) SS BOND : bond 0.00217 ( 5) SS BOND : angle 0.92714 ( 10) covalent geometry : bond 0.00474 ( 8722) covalent geometry : angle 0.58208 (11820) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2150 Ramachandran restraints generated. 1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 191 time to evaluate : 1.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ASP cc_start: 0.9071 (m-30) cc_final: 0.8868 (m-30) REVERT: A 346 LEU cc_start: 0.9545 (OUTLIER) cc_final: 0.9162 (mp) REVERT: A 378 ASP cc_start: 0.9148 (m-30) cc_final: 0.8433 (m-30) REVERT: B 10 GLU cc_start: 0.9010 (mt-10) cc_final: 0.8790 (mt-10) REVERT: B 59 TYR cc_start: 0.9359 (OUTLIER) cc_final: 0.8927 (m-80) REVERT: B 61 MET cc_start: 0.9094 (ptm) cc_final: 0.8862 (ptm) REVERT: B 183 HIS cc_start: 0.8341 (OUTLIER) cc_final: 0.7887 (t-90) REVERT: B 215 GLU cc_start: 0.8140 (mp0) cc_final: 0.7877 (mp0) REVERT: B 226 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8527 (tp30) REVERT: B 230 ASN cc_start: 0.9300 (m-40) cc_final: 0.8910 (m-40) REVERT: B 234 PHE cc_start: 0.9439 (OUTLIER) cc_final: 0.8777 (m-80) REVERT: G 20 LYS cc_start: 0.9188 (mtmm) cc_final: 0.8914 (mtmm) REVERT: G 32 LYS cc_start: 0.8922 (tptp) cc_final: 0.8686 (tptp) REVERT: G 36 ASP cc_start: 0.8876 (m-30) cc_final: 0.8591 (m-30) REVERT: G 42 GLU cc_start: 0.9089 (tm-30) cc_final: 0.8835 (tm-30) REVERT: N 73 ASP cc_start: 0.8517 (t0) cc_final: 0.8166 (t0) REVERT: N 91 THR cc_start: 0.9259 (OUTLIER) cc_final: 0.8985 (t) REVERT: N 95 TYR cc_start: 0.9055 (m-80) cc_final: 0.8565 (m-80) REVERT: R 171 HIS cc_start: 0.7944 (p-80) cc_final: 0.7549 (p-80) REVERT: R 202 LYS cc_start: 0.8771 (pptt) cc_final: 0.8383 (tttt) REVERT: R 204 MET cc_start: 0.8976 (tmm) cc_final: 0.8682 (tmm) REVERT: R 221 GLN cc_start: 0.8343 (mp10) cc_final: 0.8000 (mp10) REVERT: R 309 ILE cc_start: 0.9438 (OUTLIER) cc_final: 0.9236 (tp) REVERT: R 323 ILE cc_start: 0.9503 (mt) cc_final: 0.9252 (mm) REVERT: R 387 GLU cc_start: 0.9130 (mp0) cc_final: 0.8459 (pm20) REVERT: R 393 PHE cc_start: 0.9151 (m-10) cc_final: 0.8757 (m-10) REVERT: R 394 GLN cc_start: 0.9333 (tt0) cc_final: 0.8902 (tt0) REVERT: R 397 MET cc_start: 0.9255 (mmp) cc_final: 0.8706 (mtt) REVERT: R 412 GLU cc_start: 0.8753 (mm-30) cc_final: 0.7960 (mm-30) outliers start: 41 outliers final: 23 residues processed: 222 average time/residue: 0.2604 time to fit residues: 79.5860 Evaluate side-chains 216 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 186 time to evaluate : 1.211 ------------------------------------------------------------------------------- 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 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 B residue 315 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 109 ASP Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 236 CYS Chi-restraints excluded: chain R residue 246 VAL Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 309 ILE 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: 3.9990 chunk 42 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 chunk 16 optimal weight: 0.1980 chunk 49 optimal weight: 9.9990 chunk 102 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 120 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.093042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.065233 restraints weight = 19819.965| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 3.43 r_work: 0.2777 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8727 Z= 0.123 Angle : 0.557 8.204 11830 Z= 0.289 Chirality : 0.040 0.182 1329 Planarity : 0.003 0.031 1509 Dihedral : 3.823 17.872 1197 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.87 % Allowed : 22.55 % 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: 0.40 (0.26), residues: 1075 helix: 2.21 (0.26), residues: 406 sheet: -0.54 (0.33), residues: 224 loop : -1.15 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP R 297 HIS 0.007 0.001 HIS A 220 PHE 0.011 0.001 PHE N 108 TYR 0.014 0.001 TYR A 318 ARG 0.006 0.000 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.03490 ( 427) hydrogen bonds : angle 4.21838 ( 1218) SS BOND : bond 0.00204 ( 5) SS BOND : angle 0.66003 ( 10) covalent geometry : bond 0.00274 ( 8722) covalent geometry : angle 0.55680 (11820) *********************** 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 230 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 196 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ASP cc_start: 0.9028 (m-30) cc_final: 0.8823 (m-30) REVERT: A 346 LEU cc_start: 0.9537 (OUTLIER) cc_final: 0.9110 (mp) REVERT: A 378 ASP cc_start: 0.9072 (m-30) cc_final: 0.8307 (m-30) REVERT: B 45 MET cc_start: 0.9108 (mmm) cc_final: 0.8344 (mmm) REVERT: B 59 TYR cc_start: 0.9305 (OUTLIER) cc_final: 0.8922 (m-80) REVERT: B 183 HIS cc_start: 0.8144 (OUTLIER) cc_final: 0.7622 (t-90) REVERT: B 215 GLU cc_start: 0.8192 (mp0) cc_final: 0.7942 (mp0) REVERT: B 230 ASN cc_start: 0.9163 (m-40) cc_final: 0.8848 (m110) REVERT: B 234 PHE cc_start: 0.9395 (OUTLIER) cc_final: 0.8717 (m-80) REVERT: G 20 LYS cc_start: 0.9168 (mtmm) cc_final: 0.8901 (mtmm) REVERT: G 21 MET cc_start: 0.9083 (tpp) cc_final: 0.8625 (tpp) REVERT: G 42 GLU cc_start: 0.9138 (tm-30) cc_final: 0.8864 (tm-30) REVERT: N 73 ASP cc_start: 0.8464 (t0) cc_final: 0.8122 (t0) REVERT: N 91 THR cc_start: 0.9178 (OUTLIER) cc_final: 0.8926 (t) REVERT: N 95 TYR cc_start: 0.9038 (m-80) cc_final: 0.8650 (m-80) REVERT: R 202 LYS cc_start: 0.8862 (pptt) cc_final: 0.8483 (tttt) REVERT: R 204 MET cc_start: 0.8947 (tmm) cc_final: 0.8651 (tmm) REVERT: R 221 GLN cc_start: 0.8191 (mp10) cc_final: 0.7856 (mp10) REVERT: R 297 TRP cc_start: 0.8830 (m-10) cc_final: 0.8595 (m-90) REVERT: R 299 ARG cc_start: 0.8569 (mpt-90) cc_final: 0.8252 (mpt-90) REVERT: R 323 ILE cc_start: 0.9482 (mt) cc_final: 0.9232 (mm) REVERT: R 387 GLU cc_start: 0.9078 (mp0) cc_final: 0.8402 (pm20) REVERT: R 393 PHE cc_start: 0.9131 (m-10) cc_final: 0.8737 (m-10) REVERT: R 394 GLN cc_start: 0.9270 (tt0) cc_final: 0.8822 (tt0) REVERT: R 397 MET cc_start: 0.9228 (mmp) cc_final: 0.8581 (mtt) REVERT: R 410 GLN cc_start: 0.8816 (mm-40) cc_final: 0.8282 (mt0) REVERT: R 412 GLU cc_start: 0.8761 (mm-30) cc_final: 0.8309 (mm-30) outliers start: 34 outliers final: 20 residues processed: 222 average time/residue: 0.2912 time to fit residues: 86.7096 Evaluate side-chains 215 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 190 time to evaluate : 1.643 ------------------------------------------------------------------------------- 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 128 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 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 189 LEU 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 254 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 74 optimal weight: 0.0770 chunk 69 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 47 optimal weight: 6.9990 chunk 88 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 83 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 overall best weight: 0.7738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.093929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.066526 restraints weight = 20024.435| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 3.45 r_work: 0.2808 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8727 Z= 0.111 Angle : 0.568 9.127 11830 Z= 0.293 Chirality : 0.040 0.203 1329 Planarity : 0.003 0.037 1509 Dihedral : 3.749 17.108 1197 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.42 % Allowed : 23.23 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.15 (0.26), residues: 406 sheet: -0.48 (0.33), residues: 223 loop : -1.14 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP R 297 HIS 0.004 0.001 HIS A 220 PHE 0.010 0.001 PHE N 108 TYR 0.015 0.001 TYR A 318 ARG 0.008 0.000 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.03405 ( 427) hydrogen bonds : angle 4.09495 ( 1218) SS BOND : bond 0.00199 ( 5) SS BOND : angle 0.54404 ( 10) covalent geometry : bond 0.00248 ( 8722) covalent geometry : angle 0.56850 (11820) *********************** 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 231 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 201 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ASP cc_start: 0.9021 (m-30) cc_final: 0.8799 (m-30) REVERT: A 346 LEU cc_start: 0.9551 (OUTLIER) cc_final: 0.9100 (mp) REVERT: A 378 ASP cc_start: 0.9056 (m-30) cc_final: 0.8276 (m-30) REVERT: B 45 MET cc_start: 0.9074 (mmm) cc_final: 0.8350 (mmm) REVERT: B 59 TYR cc_start: 0.9284 (OUTLIER) cc_final: 0.8972 (m-80) REVERT: B 183 HIS cc_start: 0.8088 (OUTLIER) cc_final: 0.7565 (t-90) REVERT: B 215 GLU cc_start: 0.8246 (mp0) cc_final: 0.8017 (mp0) REVERT: B 228 ASP cc_start: 0.8626 (p0) cc_final: 0.8403 (p0) REVERT: B 230 ASN cc_start: 0.8927 (m-40) cc_final: 0.8440 (m110) REVERT: B 234 PHE cc_start: 0.9406 (OUTLIER) cc_final: 0.8698 (m-80) REVERT: G 20 LYS cc_start: 0.9169 (mtmm) cc_final: 0.8937 (mtmm) REVERT: G 21 MET cc_start: 0.9069 (tpp) cc_final: 0.8603 (tpp) REVERT: G 32 LYS cc_start: 0.8863 (tptp) cc_final: 0.8506 (tptt) REVERT: G 42 GLU cc_start: 0.9073 (tm-30) cc_final: 0.8791 (tm-30) REVERT: N 73 ASP cc_start: 0.8476 (t0) cc_final: 0.8138 (t0) REVERT: N 91 THR cc_start: 0.9187 (OUTLIER) cc_final: 0.8919 (t) REVERT: N 95 TYR cc_start: 0.9034 (m-80) cc_final: 0.8604 (m-80) REVERT: R 202 LYS cc_start: 0.8889 (pptt) cc_final: 0.8487 (tttt) REVERT: R 204 MET cc_start: 0.8940 (tmm) cc_final: 0.8658 (tmm) REVERT: R 221 GLN cc_start: 0.8191 (mp10) cc_final: 0.7860 (mp10) REVERT: R 297 TRP cc_start: 0.8785 (m-10) cc_final: 0.8525 (m-90) REVERT: R 299 ARG cc_start: 0.8553 (mpt-90) cc_final: 0.8268 (mpt-90) REVERT: R 323 ILE cc_start: 0.9504 (mt) cc_final: 0.9254 (mm) REVERT: R 387 GLU cc_start: 0.9019 (mp0) cc_final: 0.8350 (pm20) REVERT: R 393 PHE cc_start: 0.9102 (m-10) cc_final: 0.8729 (m-10) REVERT: R 394 GLN cc_start: 0.9211 (tt0) cc_final: 0.8705 (tt0) REVERT: R 397 MET cc_start: 0.9197 (mmp) cc_final: 0.8549 (mtt) REVERT: R 410 GLN cc_start: 0.8730 (mm-40) cc_final: 0.8194 (mt0) outliers start: 30 outliers final: 22 residues processed: 221 average time/residue: 0.2823 time to fit residues: 84.2571 Evaluate side-chains 217 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 190 time to evaluate : 1.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 318 LEU 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 20 LEU Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 109 ASP Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 254 LEU Chi-restraints excluded: chain R residue 396 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 32 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 56 optimal weight: 20.0000 chunk 51 optimal weight: 0.9990 chunk 20 optimal weight: 0.0980 chunk 99 optimal weight: 6.9990 chunk 87 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.092623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.065236 restraints weight = 19855.708| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 3.41 r_work: 0.2775 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8727 Z= 0.150 Angle : 0.583 8.828 11830 Z= 0.303 Chirality : 0.041 0.205 1329 Planarity : 0.003 0.046 1509 Dihedral : 3.813 17.101 1197 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.19 % Allowed : 23.69 % 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: 0.43 (0.26), residues: 1075 helix: 2.16 (0.26), residues: 406 sheet: -0.47 (0.33), residues: 224 loop : -1.08 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP R 297 HIS 0.004 0.001 HIS A 220 PHE 0.015 0.001 PHE B 292 TYR 0.020 0.001 TYR A 318 ARG 0.008 0.000 ARG B 129 Details of bonding type rmsd hydrogen bonds : bond 0.03452 ( 427) hydrogen bonds : angle 4.12778 ( 1218) SS BOND : bond 0.00203 ( 5) SS BOND : angle 0.67493 ( 10) covalent geometry : bond 0.00340 ( 8722) covalent geometry : angle 0.58318 (11820) *********************** 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 217 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 189 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 346 LEU cc_start: 0.9555 (OUTLIER) cc_final: 0.9132 (mp) REVERT: A 378 ASP cc_start: 0.9100 (m-30) cc_final: 0.8347 (m-30) REVERT: B 45 MET cc_start: 0.9076 (mmm) cc_final: 0.8327 (mmm) REVERT: B 59 TYR cc_start: 0.9267 (OUTLIER) cc_final: 0.8954 (m-80) REVERT: B 61 MET cc_start: 0.9082 (ptm) cc_final: 0.8830 (ptm) REVERT: B 66 ASP cc_start: 0.8684 (OUTLIER) cc_final: 0.8273 (p0) REVERT: B 183 HIS cc_start: 0.8372 (OUTLIER) cc_final: 0.7799 (t-90) REVERT: B 215 GLU cc_start: 0.8223 (mp0) cc_final: 0.7959 (mp0) REVERT: B 226 GLU cc_start: 0.8422 (tp30) cc_final: 0.7979 (tp30) REVERT: B 234 PHE cc_start: 0.9450 (OUTLIER) cc_final: 0.8855 (m-80) REVERT: G 18 GLN cc_start: 0.8705 (tp-100) cc_final: 0.8335 (tp40) REVERT: G 20 LYS cc_start: 0.9185 (mtmm) cc_final: 0.8926 (mtmm) REVERT: G 21 MET cc_start: 0.9093 (tpp) cc_final: 0.8593 (tpp) REVERT: G 42 GLU cc_start: 0.9021 (tm-30) cc_final: 0.8740 (tm-30) REVERT: N 73 ASP cc_start: 0.8517 (t0) cc_final: 0.8166 (t0) REVERT: N 91 THR cc_start: 0.9285 (OUTLIER) cc_final: 0.9026 (t) REVERT: N 95 TYR cc_start: 0.9047 (m-80) cc_final: 0.8815 (m-80) REVERT: R 202 LYS cc_start: 0.8851 (pptt) cc_final: 0.8482 (tttt) REVERT: R 204 MET cc_start: 0.8934 (tmm) cc_final: 0.8591 (tmm) REVERT: R 221 GLN cc_start: 0.8320 (mp10) cc_final: 0.7956 (mp10) REVERT: R 234 GLN cc_start: 0.9508 (mm110) cc_final: 0.9038 (mm-40) REVERT: R 288 LYS cc_start: 0.9334 (tppp) cc_final: 0.9129 (tppp) REVERT: R 297 TRP cc_start: 0.8819 (m-10) cc_final: 0.8575 (m-90) REVERT: R 299 ARG cc_start: 0.8596 (mpt-90) cc_final: 0.8289 (mpt-90) REVERT: R 323 ILE cc_start: 0.9507 (mt) cc_final: 0.9258 (mm) REVERT: R 387 GLU cc_start: 0.9021 (mp0) cc_final: 0.8464 (mp0) REVERT: R 393 PHE cc_start: 0.9115 (m-10) cc_final: 0.8741 (m-10) REVERT: R 394 GLN cc_start: 0.9236 (tt0) cc_final: 0.8746 (tt0) REVERT: R 397 MET cc_start: 0.9205 (mmp) cc_final: 0.8609 (mtt) REVERT: R 410 GLN cc_start: 0.8723 (mm-40) cc_final: 0.8195 (mt0) outliers start: 28 outliers final: 20 residues processed: 211 average time/residue: 0.3366 time to fit residues: 96.5504 Evaluate side-chains 210 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 184 time to evaluate : 1.154 ------------------------------------------------------------------------------- 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 66 ASP Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 109 ASP Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 254 LEU Chi-restraints excluded: chain R residue 396 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 41 optimal weight: 7.9990 chunk 17 optimal weight: 6.9990 chunk 19 optimal weight: 0.4980 chunk 52 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- 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 = 0.3467 r_free = 0.3467 target = 0.092047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.064370 restraints weight = 19994.085| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 3.42 r_work: 0.2759 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8727 Z= 0.164 Angle : 0.606 8.721 11830 Z= 0.315 Chirality : 0.041 0.207 1329 Planarity : 0.003 0.045 1509 Dihedral : 3.875 17.916 1197 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.42 % Allowed : 23.80 % Favored : 72.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.26), residues: 1075 helix: 2.16 (0.26), residues: 406 sheet: -0.48 (0.33), residues: 224 loop : -1.04 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP R 297 HIS 0.003 0.001 HIS A 362 PHE 0.015 0.001 PHE N 68 TYR 0.018 0.001 TYR A 318 ARG 0.009 0.000 ARG G 13 Details of bonding type rmsd hydrogen bonds : bond 0.03515 ( 427) hydrogen bonds : angle 4.16198 ( 1218) SS BOND : bond 0.00201 ( 5) SS BOND : angle 0.72424 ( 10) covalent geometry : bond 0.00374 ( 8722) covalent geometry : angle 0.60570 (11820) ********************** 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 217 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 187 time to evaluate : 2.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 346 LEU cc_start: 0.9563 (OUTLIER) cc_final: 0.9138 (mp) REVERT: A 378 ASP cc_start: 0.9052 (m-30) cc_final: 0.8301 (m-30) REVERT: B 45 MET cc_start: 0.9089 (mmm) cc_final: 0.8352 (mmm) REVERT: B 59 TYR cc_start: 0.9322 (OUTLIER) cc_final: 0.8949 (m-80) REVERT: B 66 ASP cc_start: 0.8720 (OUTLIER) cc_final: 0.8300 (p0) REVERT: B 183 HIS cc_start: 0.8350 (OUTLIER) cc_final: 0.7768 (t-90) REVERT: B 215 GLU cc_start: 0.8197 (mp0) cc_final: 0.7842 (mp0) REVERT: B 226 GLU cc_start: 0.8511 (tp30) cc_final: 0.8173 (tp30) REVERT: B 234 PHE cc_start: 0.9459 (OUTLIER) cc_final: 0.8867 (m-80) REVERT: G 18 GLN cc_start: 0.8708 (tp-100) cc_final: 0.8348 (tp40) REVERT: G 20 LYS cc_start: 0.9196 (mtmm) cc_final: 0.8944 (mtmm) REVERT: G 21 MET cc_start: 0.9111 (tpp) cc_final: 0.8617 (tpp) REVERT: G 32 LYS cc_start: 0.8846 (tptp) cc_final: 0.8641 (tptp) REVERT: G 42 GLU cc_start: 0.9054 (tm-30) cc_final: 0.8773 (tm-30) REVERT: N 73 ASP cc_start: 0.8528 (t0) cc_final: 0.8170 (t0) REVERT: N 91 THR cc_start: 0.9296 (OUTLIER) cc_final: 0.9030 (t) REVERT: N 95 TYR cc_start: 0.9029 (m-80) cc_final: 0.8816 (m-80) REVERT: R 202 LYS cc_start: 0.8880 (pptt) cc_final: 0.8534 (tttt) REVERT: R 204 MET cc_start: 0.8941 (tmm) cc_final: 0.8535 (tmm) REVERT: R 221 GLN cc_start: 0.8351 (mp10) cc_final: 0.7978 (mp10) REVERT: R 234 GLN cc_start: 0.9503 (mm110) cc_final: 0.9037 (mm-40) REVERT: R 288 LYS cc_start: 0.9340 (tppp) cc_final: 0.9128 (tppp) REVERT: R 297 TRP cc_start: 0.8826 (m-10) cc_final: 0.8506 (m-90) REVERT: R 299 ARG cc_start: 0.8587 (mpt-90) cc_final: 0.8202 (mpt-90) REVERT: R 323 ILE cc_start: 0.9509 (mt) cc_final: 0.9261 (mm) REVERT: R 387 GLU cc_start: 0.9043 (mp0) cc_final: 0.8484 (mp0) REVERT: R 393 PHE cc_start: 0.9138 (m-10) cc_final: 0.8754 (m-10) REVERT: R 394 GLN cc_start: 0.9266 (tt0) cc_final: 0.8789 (tt0) REVERT: R 397 MET cc_start: 0.9204 (mmp) cc_final: 0.8607 (mtt) REVERT: R 410 GLN cc_start: 0.8705 (mm-40) cc_final: 0.8197 (mt0) outliers start: 30 outliers final: 22 residues processed: 210 average time/residue: 0.3735 time to fit residues: 105.3558 Evaluate side-chains 214 residues out of total 955 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 186 time to evaluate : 1.071 ------------------------------------------------------------------------------- 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 66 ASP Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 318 LEU 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 20 LEU Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 109 ASP Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 189 LEU Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 254 LEU Chi-restraints excluded: chain R residue 396 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 94 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 chunk 28 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.093457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.066003 restraints weight = 20084.994| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 3.48 r_work: 0.2794 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8727 Z= 0.124 Angle : 0.588 8.815 11830 Z= 0.303 Chirality : 0.041 0.201 1329 Planarity : 0.003 0.044 1509 Dihedral : 3.794 16.915 1197 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % 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: 0.48 (0.26), residues: 1075 helix: 2.16 (0.26), residues: 406 sheet: -0.39 (0.34), residues: 223 loop : -1.04 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP R 297 HIS 0.003 0.001 HIS A 362 PHE 0.012 0.001 PHE N 68 TYR 0.017 0.001 TYR A 318 ARG 0.010 0.000 ARG G 13 Details of bonding type rmsd hydrogen bonds : bond 0.03381 ( 427) hydrogen bonds : angle 4.09066 ( 1218) SS BOND : bond 0.00210 ( 5) SS BOND : angle 0.58254 ( 10) covalent geometry : bond 0.00279 ( 8722) covalent geometry : angle 0.58795 (11820) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5901.22 seconds wall clock time: 110 minutes 31.81 seconds (6631.81 seconds total)