Starting phenix.real_space_refine on Thu Jul 2 18:08:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k0m_36774/07_2026/8k0m_36774.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k0m_36774/07_2026/8k0m_36774.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8k0m_36774/07_2026/8k0m_36774.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k0m_36774/07_2026/8k0m_36774.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8k0m_36774/07_2026/8k0m_36774.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k0m_36774/07_2026/8k0m_36774.map" } resolution = 3.17 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.151 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: 5 Type Number sf(0) Gaussians Fe 1 7.16 5 S 50 5.16 5 C 6141 2.51 5 N 1637 2.21 5 O 1812 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9641 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 643, 5173 Classifications: {'peptide': 643} Link IDs: {'PTRANS': 33, 'TRANS': 609} Chain breaks: 2 Chain: "B" Number of atoms: 2994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2994 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 18, 'TRANS': 343} Chain: "C" Number of atoms: 1407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1407 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 6, 'TRANS': 174} Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 38 Ad-hoc single atom residues: {' FE': 1} Unusual residues: {'AKG': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.85, per 1000 atoms: 0.19 Number of scatterers: 9641 At special positions: 0 Unit cell: (95.7, 114.4, 125.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 1 26.01 S 50 16.00 O 1812 8.00 N 1637 7.00 C 6141 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 75 " - pdb=" SG CYS A 123 " distance=2.04 Simple disulfide: pdb=" SG CYS A 79 " - pdb=" SG CYS A 119 " distance=2.03 Simple disulfide: pdb=" SG CYS A 483 " - pdb=" SG CYS A 645 " distance=2.04 Simple disulfide: pdb=" SG CYS A 591 " - pdb=" SG CYS A 600 " distance=2.04 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 Links applied NAG-ASN " NAG A 801 " - " ASN A 540 " " NAG A 802 " - " ASN A 316 " " NAG B 501 " - " ASN B 87 " " NAG B 502 " - " ASN B 363 " Time building additional restraints: 0.84 Conformation dependent library (CDL) restraints added in 287.8 milliseconds 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2232 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 10 sheets defined 56.3% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 34 through 49 removed outlier: 3.662A pdb=" N LEU A 38 " --> pdb=" O THR A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 83 removed outlier: 3.590A pdb=" N ALA A 66 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE A 83 " --> pdb=" O CYS A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 125 removed outlier: 3.782A pdb=" N ALA A 103 " --> pdb=" O SER A 99 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY A 125 " --> pdb=" O ARG A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 131 removed outlier: 3.651A pdb=" N HIS A 130 " --> pdb=" O PRO A 127 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N SER A 131 " --> pdb=" O ALA A 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 127 through 131' Processing helix chain 'A' and resid 133 through 142 Processing helix chain 'A' and resid 143 through 157 removed outlier: 3.747A pdb=" N ASN A 147 " --> pdb=" O ARG A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 173 Processing helix chain 'A' and resid 176 through 189 removed outlier: 3.669A pdb=" N GLN A 180 " --> pdb=" O HIS A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 218 removed outlier: 3.621A pdb=" N PHE A 209 " --> pdb=" O HIS A 205 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG A 210 " --> pdb=" O MET A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 244 removed outlier: 3.789A pdb=" N ALA A 244 " --> pdb=" O GLU A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 281 removed outlier: 3.679A pdb=" N THR A 269 " --> pdb=" O PHE A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 315 Processing helix chain 'A' and resid 317 through 329 Processing helix chain 'A' and resid 335 through 348 Processing helix chain 'A' and resid 349 through 356 Processing helix chain 'A' and resid 359 through 384 removed outlier: 3.549A pdb=" N LEU A 371 " --> pdb=" O GLN A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 428 removed outlier: 3.539A pdb=" N GLU A 405 " --> pdb=" O LYS A 401 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS A 406 " --> pdb=" O ARG A 402 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA A 414 " --> pdb=" O GLU A 410 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL A 415 " --> pdb=" O ARG A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 493 Processing helix chain 'A' and resid 517 through 528 Processing helix chain 'A' and resid 531 through 553 removed outlier: 3.765A pdb=" N ALA A 535 " --> pdb=" O PRO A 531 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE A 553 " --> pdb=" O MET A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 699 removed outlier: 4.386A pdb=" N GLN A 689 " --> pdb=" O ARG A 685 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 41 removed outlier: 3.576A pdb=" N GLU B 40 " --> pdb=" O PRO B 37 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU B 41 " --> pdb=" O ARG B 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 37 through 41' Processing helix chain 'B' and resid 43 through 57 Processing helix chain 'B' and resid 60 through 82 Processing helix chain 'B' and resid 83 through 88 removed outlier: 4.220A pdb=" N ASN B 87 " --> pdb=" O PHE B 83 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N CYS B 88 " --> pdb=" O CYS B 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 83 through 88' Processing helix chain 'B' and resid 98 through 102 removed outlier: 3.554A pdb=" N SER B 102 " --> pdb=" O GLY B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 123 Processing helix chain 'B' and resid 124 through 125 No H-bonds generated for 'chain 'B' and resid 124 through 125' Processing helix chain 'B' and resid 126 through 130 removed outlier: 3.580A pdb=" N ARG B 130 " --> pdb=" O PRO B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 144 Processing helix chain 'B' and resid 146 through 157 removed outlier: 4.329A pdb=" N PHE B 150 " --> pdb=" O GLU B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 175 removed outlier: 3.946A pdb=" N LYS B 174 " --> pdb=" O THR B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 191 removed outlier: 3.705A pdb=" N LEU B 191 " --> pdb=" O TYR B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 219 Processing helix chain 'B' and resid 222 through 246 Proline residue: B 234 - end of helix Processing helix chain 'B' and resid 258 through 275 removed outlier: 4.234A pdb=" N ASP B 265 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N HIS B 266 " --> pdb=" O SER B 262 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N TYR B 267 " --> pdb=" O ILE B 263 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL B 268 " --> pdb=" O ALA B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 281 Processing helix chain 'B' and resid 292 through 308 Processing helix chain 'B' and resid 310 through 325 Proline residue: B 316 - end of helix Processing helix chain 'B' and resid 329 through 341 Processing helix chain 'B' and resid 341 through 346 removed outlier: 4.319A pdb=" N TRP B 345 " --> pdb=" O HIS B 341 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY B 346 " --> pdb=" O ARG B 342 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 341 through 346' Processing helix chain 'B' and resid 355 through 379 removed outlier: 4.113A pdb=" N GLU B 377 " --> pdb=" O ASP B 373 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASN B 378 " --> pdb=" O PHE B 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 82 Processing helix chain 'C' and resid 159 through 163 removed outlier: 3.528A pdb=" N LEU C 162 " --> pdb=" O THR C 159 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASP C 163 " --> pdb=" O ALA C 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 159 through 163' Processing helix chain 'C' and resid 175 through 184 removed outlier: 3.535A pdb=" N VAL C 179 " --> pdb=" O GLY C 175 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ARG C 180 " --> pdb=" O MET C 176 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS C 181 " --> pdb=" O GLU C 177 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL C 182 " --> pdb=" O VAL C 178 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU C 183 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER C 184 " --> pdb=" O ARG C 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 175 through 184' Processing sheet with id=AA1, first strand: chain 'A' and resid 458 through 461 removed outlier: 5.849A pdb=" N LEU A 459 " --> pdb=" O ASP A 475 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ASP A 475 " --> pdb=" O LEU A 459 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET A 461 " --> pdb=" O VAL A 473 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ARG A 669 " --> pdb=" O CYS A 568 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N CYS A 568 " --> pdb=" O ARG A 669 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ALA A 671 " --> pdb=" O LEU A 566 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N LEU A 566 " --> pdb=" O ALA A 671 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ALA A 673 " --> pdb=" O SER A 564 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N SER A 564 " --> pdb=" O ALA A 673 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N TRP A 675 " --> pdb=" O SER A 562 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR A 514 " --> pdb=" O CYS A 568 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR A 570 " --> pdb=" O LYS A 512 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 584 through 587 removed outlier: 5.309A pdb=" N VAL A 661 " --> pdb=" O PRO A 585 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N PHE A 627 " --> pdb=" O GLU A 640 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLU A 640 " --> pdb=" O PHE A 627 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N PHE A 629 " --> pdb=" O THR A 638 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 592 through 594 removed outlier: 3.680A pdb=" N VAL A 601 " --> pdb=" O ILE A 592 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL A 599 " --> pdb=" O ASN A 594 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 623 through 624 Processing sheet with id=AA5, first strand: chain 'B' and resid 284 through 285 Processing sheet with id=AA6, first strand: chain 'B' and resid 384 through 385 Processing sheet with id=AA7, first strand: chain 'C' and resid 44 through 45 Processing sheet with id=AA8, first strand: chain 'C' and resid 55 through 56 removed outlier: 3.813A pdb=" N ILE C 52 " --> pdb=" O GLU C 55 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ILE C 61 " --> pdb=" O LEU C 173 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 55 through 56 removed outlier: 3.813A pdb=" N ILE C 52 " --> pdb=" O GLU C 55 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N TYR C 47 " --> pdb=" O CYS C 202 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N CYS C 202 " --> pdb=" O TYR C 47 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASP C 49 " --> pdb=" O ALA C 200 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 93 through 95 removed outlier: 4.971A pdb=" N GLN C 151 " --> pdb=" O ALA C 141 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N VAL C 167 " --> pdb=" O MET C 140 " (cutoff:3.500A) 500 hydrogen bonds defined for protein. 1455 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.37 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3160 1.34 - 1.47: 2417 1.47 - 1.59: 4224 1.59 - 1.72: 0 1.72 - 1.84: 75 Bond restraints: 9876 Sorted by residual: bond pdb=" C1 AKG A 804 " pdb=" O2 AKG A 804 " ideal model delta sigma weight residual 1.239 1.308 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C5 AKG A 804 " pdb=" O4 AKG A 804 " ideal model delta sigma weight residual 1.249 1.307 -0.058 2.00e-02 2.50e+03 8.33e+00 bond pdb=" C PRO A 604 " pdb=" N PRO A 605 " ideal model delta sigma weight residual 1.335 1.363 -0.029 1.19e-02 7.06e+03 5.81e+00 bond pdb=" C4 AKG A 804 " pdb=" C5 AKG A 804 " ideal model delta sigma weight residual 1.540 1.500 0.040 2.00e-02 2.50e+03 3.98e+00 bond pdb=" C5 AKG A 804 " pdb=" O3 AKG A 804 " ideal model delta sigma weight residual 1.247 1.214 0.033 2.00e-02 2.50e+03 2.72e+00 ... (remaining 9871 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 13092 1.70 - 3.41: 211 3.41 - 5.11: 38 5.11 - 6.82: 7 6.82 - 8.52: 4 Bond angle restraints: 13352 Sorted by residual: angle pdb=" CA CYS A 645 " pdb=" CB CYS A 645 " pdb=" SG CYS A 645 " ideal model delta sigma weight residual 114.40 122.92 -8.52 2.30e+00 1.89e-01 1.37e+01 angle pdb=" CA CYS A 591 " pdb=" CB CYS A 591 " pdb=" SG CYS A 591 " ideal model delta sigma weight residual 114.40 121.72 -7.32 2.30e+00 1.89e-01 1.01e+01 angle pdb=" C GLN A 644 " pdb=" N CYS A 645 " pdb=" CA CYS A 645 " ideal model delta sigma weight residual 121.42 116.93 4.49 1.43e+00 4.89e-01 9.88e+00 angle pdb=" CB MET A 347 " pdb=" CG MET A 347 " pdb=" SD MET A 347 " ideal model delta sigma weight residual 112.70 121.19 -8.49 3.00e+00 1.11e-01 8.00e+00 angle pdb=" N CYS A 645 " pdb=" CA CYS A 645 " pdb=" CB CYS A 645 " ideal model delta sigma weight residual 110.06 114.08 -4.02 1.51e+00 4.39e-01 7.10e+00 ... (remaining 13347 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 5072 17.78 - 35.56: 662 35.56 - 53.34: 198 53.34 - 71.12: 36 71.12 - 88.89: 14 Dihedral angle restraints: 5982 sinusoidal: 2503 harmonic: 3479 Sorted by residual: dihedral pdb=" CB CYS A 591 " pdb=" SG CYS A 591 " pdb=" SG CYS A 600 " pdb=" CB CYS A 600 " ideal model delta sinusoidal sigma weight residual 93.00 15.61 77.39 1 1.00e+01 1.00e-02 7.50e+01 dihedral pdb=" CA CYS A 591 " pdb=" C CYS A 591 " pdb=" N ILE A 592 " pdb=" CA ILE A 592 " ideal model delta harmonic sigma weight residual 180.00 155.25 24.75 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CA LYS A 158 " pdb=" C LYS A 158 " pdb=" N LEU A 159 " pdb=" CA LEU A 159 " ideal model delta harmonic sigma weight residual -180.00 -158.42 -21.58 0 5.00e+00 4.00e-02 1.86e+01 ... (remaining 5979 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 846 0.029 - 0.059: 388 0.059 - 0.088: 98 0.088 - 0.117: 69 0.117 - 0.146: 7 Chirality restraints: 1408 Sorted by residual: chirality pdb=" CA VAL A 599 " pdb=" N VAL A 599 " pdb=" C VAL A 599 " pdb=" CB VAL A 599 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.35e-01 chirality pdb=" C1 NAG B 502 " pdb=" ND2 ASN B 363 " pdb=" C2 NAG B 502 " pdb=" O5 NAG B 502 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 5.21e-01 chirality pdb=" CA VAL A 225 " pdb=" N VAL A 225 " pdb=" C VAL A 225 " pdb=" CB VAL A 225 " both_signs ideal model delta sigma weight residual False 2.44 2.30 0.14 2.00e-01 2.50e+01 4.94e-01 ... (remaining 1405 not shown) Planarity restraints: 1754 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 603 " -0.044 5.00e-02 4.00e+02 6.64e-02 7.06e+00 pdb=" N PRO A 604 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO A 604 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 604 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 450 " -0.035 5.00e-02 4.00e+02 5.28e-02 4.45e+00 pdb=" N PRO A 451 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 451 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 451 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 146 " -0.029 5.00e-02 4.00e+02 4.35e-02 3.03e+00 pdb=" N PRO B 147 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 147 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 147 " -0.024 5.00e-02 4.00e+02 ... (remaining 1751 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 35 2.56 - 3.14: 7071 3.14 - 3.73: 13899 3.73 - 4.31: 18651 4.31 - 4.90: 33101 Nonbonded interactions: 72757 Sorted by model distance: nonbonded pdb="FE FE A 803 " pdb=" O5 AKG A 804 " model vdw 1.975 3.000 nonbonded pdb=" OD1 ASP A 589 " pdb="FE FE A 803 " model vdw 2.059 3.000 nonbonded pdb=" NE2 HIS A 659 " pdb="FE FE A 803 " model vdw 2.084 3.080 nonbonded pdb=" O PHE A 299 " pdb=" OG SER A 302 " model vdw 2.269 3.040 nonbonded pdb=" OE2 GLU B 68 " pdb=" OH TYR B 155 " model vdw 2.316 3.040 ... (remaining 72752 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 8.600 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 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 0.069 9884 Z= 0.158 Angle : 0.578 8.521 13372 Z= 0.303 Chirality : 0.040 0.146 1408 Planarity : 0.004 0.066 1750 Dihedral : 17.599 88.895 3738 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.00 % Favored : 95.83 % Rotamer: Outliers : 0.39 % Allowed : 21.79 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.25), residues: 1176 helix: 1.46 (0.21), residues: 644 sheet: -1.41 (0.52), residues: 105 loop : -1.61 (0.28), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 554 TYR 0.020 0.001 TYR A 306 PHE 0.014 0.001 PHE C 123 TRP 0.005 0.001 TRP C 137 HIS 0.005 0.001 HIS A 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.16 ( 9876) covalent geometry : angle 0.57058 / 0.30 (13352) SS BOND : bond 0.00688 / 0.41 ( 4) SS BOND : angle 3.61880 / 2.08 ( 8) hydrogen bonds : bond 0.17363 / 11.88 ( 499) hydrogen bonds : angle 5.36708 / 3.85 ( 1455) link_NAG-ASN : bond 0.00206 / 0.11 ( 4) link_NAG-ASN : angle 1.26730 / 0.71 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 104 time to evaluate : 0.365 Fit side-chains revert: symmetry clash REVERT: B 229 MET cc_start: 0.7957 (mmm) cc_final: 0.7344 (mmt) REVERT: B 331 MET cc_start: 0.8941 (tpp) cc_final: 0.8501 (tpp) outliers start: 4 outliers final: 3 residues processed: 107 average time/residue: 0.1051 time to fit residues: 14.9577 Evaluate side-chains 101 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 98 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain C residue 89 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 chunk 113 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.0020 chunk 51 optimal weight: 0.9990 chunk 117 optimal weight: 2.9990 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 184 ASN C 90 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.170254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.126710 restraints weight = 10763.143| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.94 r_work: 0.3147 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.0789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9884 Z= 0.117 Angle : 0.516 6.876 13372 Z= 0.272 Chirality : 0.039 0.149 1408 Planarity : 0.004 0.060 1750 Dihedral : 4.820 52.846 1415 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.17 % Favored : 95.75 % Rotamer: Outliers : 2.07 % Allowed : 20.22 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.25), residues: 1176 helix: 1.72 (0.21), residues: 650 sheet: -0.76 (0.53), residues: 103 loop : -1.67 (0.28), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 359 TYR 0.016 0.001 TYR A 306 PHE 0.020 0.001 PHE C 153 TRP 0.005 0.001 TRP C 137 HIS 0.005 0.001 HIS A 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.12 ( 9876) covalent geometry : angle 0.51056 / 0.27 (13352) SS BOND : bond 0.00875 / 0.50 ( 4) SS BOND : angle 2.24666 / 1.32 ( 8) hydrogen bonds : bond 0.05231 / 3.49 ( 499) hydrogen bonds : angle 3.94368 / 2.83 ( 1455) link_NAG-ASN : bond 0.00111 / 0.07 ( 4) link_NAG-ASN : angle 1.85092 / 1.04 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 110 time to evaluate : 0.253 Fit side-chains revert: symmetry clash REVERT: B 113 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.6910 (mp) REVERT: B 173 LEU cc_start: 0.7662 (OUTLIER) cc_final: 0.7374 (mp) REVERT: B 229 MET cc_start: 0.7645 (mmm) cc_final: 0.6815 (mmt) REVERT: C 98 LYS cc_start: 0.8597 (tttt) cc_final: 0.8318 (tptm) REVERT: C 122 ARG cc_start: 0.8759 (mmt180) cc_final: 0.8507 (mmt180) outliers start: 21 outliers final: 11 residues processed: 129 average time/residue: 0.1006 time to fit residues: 17.3405 Evaluate side-chains 112 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 582 ASP Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 189 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 82 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 116 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.164655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.122638 restraints weight = 10930.191| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.85 r_work: 0.2938 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.0898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9884 Z= 0.174 Angle : 0.557 11.552 13372 Z= 0.293 Chirality : 0.042 0.152 1408 Planarity : 0.004 0.059 1750 Dihedral : 4.263 42.538 1407 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.10 % Favored : 94.81 % Rotamer: Outliers : 2.96 % Allowed : 19.72 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.25), residues: 1176 helix: 1.63 (0.21), residues: 650 sheet: -0.74 (0.52), residues: 103 loop : -1.67 (0.28), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 471 TYR 0.016 0.001 TYR A 539 PHE 0.021 0.002 PHE C 153 TRP 0.005 0.001 TRP C 137 HIS 0.006 0.001 HIS B 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.17 ( 9876) covalent geometry : angle 0.54290 / 0.29 (13352) SS BOND : bond 0.00592 / 0.35 ( 4) SS BOND : angle 4.63126 / 2.83 ( 8) hydrogen bonds : bond 0.06196 / 4.13 ( 499) hydrogen bonds : angle 3.96061 / 2.86 ( 1455) link_NAG-ASN : bond 0.00090 / 0.05 ( 4) link_NAG-ASN : angle 1.81885 / 1.04 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 105 time to evaluate : 0.257 Fit side-chains REVERT: B 113 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7011 (mp) REVERT: B 173 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7634 (mp) REVERT: C 122 ARG cc_start: 0.8755 (mmt180) cc_final: 0.8427 (mmt180) outliers start: 30 outliers final: 20 residues processed: 131 average time/residue: 0.0968 time to fit residues: 17.0739 Evaluate side-chains 122 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 565 HIS Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 582 ASP Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 189 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 93 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 83 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 74 optimal weight: 7.9990 chunk 92 optimal weight: 0.0870 chunk 49 optimal weight: 0.0270 chunk 70 optimal weight: 0.0050 chunk 100 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.3630 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 127 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.166411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.126674 restraints weight = 11111.932| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.57 r_work: 0.3021 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9884 Z= 0.100 Angle : 0.477 8.723 13372 Z= 0.251 Chirality : 0.039 0.146 1408 Planarity : 0.004 0.057 1750 Dihedral : 3.790 29.588 1407 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.25 % Favored : 95.66 % Rotamer: Outliers : 2.66 % Allowed : 20.61 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.25), residues: 1176 helix: 1.97 (0.21), residues: 638 sheet: -0.54 (0.53), residues: 103 loop : -1.50 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 669 TYR 0.017 0.001 TYR A 306 PHE 0.017 0.001 PHE C 153 TRP 0.005 0.001 TRP C 137 HIS 0.004 0.000 HIS A 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.10 ( 9876) covalent geometry : angle 0.46574 / 0.25 (13352) SS BOND : bond 0.00386 / 0.22 ( 4) SS BOND : angle 3.97146 / 2.37 ( 8) hydrogen bonds : bond 0.04074 / 2.69 ( 499) hydrogen bonds : angle 3.63607 / 2.63 ( 1455) link_NAG-ASN : bond 0.00164 / 0.10 ( 4) link_NAG-ASN : angle 1.44300 / 0.81 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 110 time to evaluate : 0.338 Fit side-chains revert: symmetry clash REVERT: A 598 LEU cc_start: 0.7415 (OUTLIER) cc_final: 0.7170 (tt) REVERT: A 647 ARG cc_start: 0.7950 (OUTLIER) cc_final: 0.7312 (mtt-85) REVERT: B 173 LEU cc_start: 0.7799 (OUTLIER) cc_final: 0.7495 (mp) REVERT: B 229 MET cc_start: 0.7756 (mmm) cc_final: 0.6910 (mmt) REVERT: B 278 GLU cc_start: 0.8154 (tp30) cc_final: 0.7505 (tt0) REVERT: C 98 LYS cc_start: 0.8500 (tttt) cc_final: 0.8183 (tptm) outliers start: 27 outliers final: 15 residues processed: 134 average time/residue: 0.1004 time to fit residues: 18.2357 Evaluate side-chains 118 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 565 HIS Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 582 ASP Chi-restraints excluded: chain A residue 591 CYS Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 647 ARG Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 189 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 117 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 chunk 55 optimal weight: 0.0870 chunk 33 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 113 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 6 optimal weight: 20.0000 chunk 37 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.166303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.126082 restraints weight = 11040.640| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.62 r_work: 0.3029 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9884 Z= 0.112 Angle : 0.500 7.805 13372 Z= 0.261 Chirality : 0.040 0.146 1408 Planarity : 0.004 0.056 1750 Dihedral : 3.572 22.039 1407 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.25 % Favored : 95.66 % Rotamer: Outliers : 3.16 % Allowed : 20.41 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.25), residues: 1176 helix: 2.08 (0.21), residues: 639 sheet: -0.50 (0.53), residues: 103 loop : -1.47 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 647 TYR 0.014 0.001 TYR B 267 PHE 0.018 0.001 PHE C 153 TRP 0.006 0.001 TRP C 137 HIS 0.003 0.001 HIS A 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 ( 9876) covalent geometry : angle 0.49009 / 0.26 (13352) SS BOND : bond 0.00602 / 0.35 ( 4) SS BOND : angle 3.73824 / 2.24 ( 8) hydrogen bonds : bond 0.04501 / 2.97 ( 499) hydrogen bonds : angle 3.63026 / 2.63 ( 1455) link_NAG-ASN : bond 0.00147 / 0.09 ( 4) link_NAG-ASN : angle 1.43833 / 0.82 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 112 time to evaluate : 0.363 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.8168 (mmt) cc_final: 0.7717 (mmt) REVERT: A 338 ASN cc_start: 0.8836 (OUTLIER) cc_final: 0.8421 (m-40) REVERT: A 598 LEU cc_start: 0.7396 (OUTLIER) cc_final: 0.7137 (tt) REVERT: B 113 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7125 (mp) REVERT: B 173 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7575 (mp) REVERT: B 229 MET cc_start: 0.7777 (mmm) cc_final: 0.6894 (mmt) REVERT: C 98 LYS cc_start: 0.8533 (tttt) cc_final: 0.8234 (tptm) outliers start: 32 outliers final: 20 residues processed: 137 average time/residue: 0.1082 time to fit residues: 20.0263 Evaluate side-chains 126 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 582 ASP Chi-restraints excluded: chain A residue 591 CYS Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 329 LYS Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 189 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 1 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 95 optimal weight: 9.9990 chunk 55 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.162452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.124455 restraints weight = 10975.790| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.41 r_work: 0.2977 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9884 Z= 0.189 Angle : 0.568 8.372 13372 Z= 0.297 Chirality : 0.043 0.172 1408 Planarity : 0.004 0.058 1750 Dihedral : 3.807 27.926 1407 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.10 % Favored : 94.81 % Rotamer: Outliers : 3.55 % Allowed : 20.02 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.25), residues: 1176 helix: 1.79 (0.21), residues: 651 sheet: -0.71 (0.51), residues: 107 loop : -1.53 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 687 TYR 0.018 0.001 TYR A 539 PHE 0.026 0.002 PHE C 153 TRP 0.005 0.001 TRP C 137 HIS 0.004 0.001 HIS A 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.19 ( 9876) covalent geometry : angle 0.55932 / 0.29 (13352) SS BOND : bond 0.00625 / 0.34 ( 4) SS BOND : angle 3.59887 / 2.15 ( 8) hydrogen bonds : bond 0.06220 / 4.13 ( 499) hydrogen bonds : angle 3.83414 / 2.78 ( 1455) link_NAG-ASN : bond 0.00131 / 0.07 ( 4) link_NAG-ASN : angle 1.75268 / 0.99 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 109 time to evaluate : 0.316 Fit side-chains REVERT: A 338 ASN cc_start: 0.9050 (OUTLIER) cc_final: 0.8661 (m-40) REVERT: A 647 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7422 (mtt-85) REVERT: B 113 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7253 (mp) REVERT: B 229 MET cc_start: 0.7827 (mmm) cc_final: 0.7324 (mmt) REVERT: B 291 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7434 (pm20) outliers start: 36 outliers final: 25 residues processed: 139 average time/residue: 0.1088 time to fit residues: 19.9188 Evaluate side-chains 131 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 102 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 565 HIS Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 582 ASP Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 647 ARG Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 329 LYS Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 333 GLN Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 189 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 8 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 26 optimal weight: 0.0170 chunk 95 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 97 optimal weight: 0.4980 chunk 103 optimal weight: 0.0980 chunk 100 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 overall best weight: 0.6820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.166846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.129008 restraints weight = 10891.558| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.35 r_work: 0.3045 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9884 Z= 0.113 Angle : 0.508 7.907 13372 Z= 0.265 Chirality : 0.040 0.148 1408 Planarity : 0.004 0.056 1750 Dihedral : 3.621 25.745 1407 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.25 % Favored : 95.66 % Rotamer: Outliers : 2.86 % Allowed : 20.81 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.25), residues: 1176 helix: 1.98 (0.21), residues: 645 sheet: -0.49 (0.53), residues: 103 loop : -1.45 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 141 TYR 0.016 0.001 TYR A 306 PHE 0.018 0.001 PHE C 153 TRP 0.006 0.001 TRP C 137 HIS 0.004 0.000 HIS A 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 ( 9876) covalent geometry : angle 0.49870 / 0.26 (13352) SS BOND : bond 0.00505 / 0.28 ( 4) SS BOND : angle 3.66507 / 2.17 ( 8) hydrogen bonds : bond 0.04635 / 3.06 ( 499) hydrogen bonds : angle 3.64855 / 2.64 ( 1455) link_NAG-ASN : bond 0.00148 / 0.09 ( 4) link_NAG-ASN : angle 1.47945 / 0.85 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 107 time to evaluate : 0.361 Fit side-chains REVERT: A 58 MET cc_start: 0.8510 (mmt) cc_final: 0.7784 (mmt) REVERT: A 338 ASN cc_start: 0.8939 (OUTLIER) cc_final: 0.8517 (m-40) REVERT: A 647 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7589 (mtt-85) REVERT: B 113 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7363 (mp) REVERT: B 229 MET cc_start: 0.7927 (mmm) cc_final: 0.7151 (mmt) REVERT: B 278 GLU cc_start: 0.8495 (tp30) cc_final: 0.7923 (tt0) outliers start: 29 outliers final: 22 residues processed: 130 average time/residue: 0.1128 time to fit residues: 19.2781 Evaluate side-chains 126 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 101 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 565 HIS Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 582 ASP Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 647 ARG Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 329 LYS Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 333 GLN Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 189 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 97 optimal weight: 0.6980 chunk 108 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 102 optimal weight: 0.0270 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.166469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.128038 restraints weight = 10912.193| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.43 r_work: 0.3035 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9884 Z= 0.111 Angle : 0.508 7.841 13372 Z= 0.263 Chirality : 0.039 0.149 1408 Planarity : 0.004 0.057 1750 Dihedral : 3.547 26.680 1407 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.68 % Favored : 95.24 % Rotamer: Outliers : 2.86 % Allowed : 20.81 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.25), residues: 1176 helix: 2.03 (0.21), residues: 645 sheet: -0.44 (0.53), residues: 103 loop : -1.41 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 141 TYR 0.018 0.001 TYR B 187 PHE 0.018 0.001 PHE C 153 TRP 0.005 0.001 TRP C 137 HIS 0.004 0.000 HIS A 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 ( 9876) covalent geometry : angle 0.49889 / 0.26 (13352) SS BOND : bond 0.00690 / 0.44 ( 4) SS BOND : angle 3.66910 / 2.16 ( 8) hydrogen bonds : bond 0.04534 / 2.99 ( 499) hydrogen bonds : angle 3.61239 / 2.61 ( 1455) link_NAG-ASN : bond 0.00146 / 0.09 ( 4) link_NAG-ASN : angle 1.44611 / 0.82 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 104 time to evaluate : 0.253 Fit side-chains REVERT: A 58 MET cc_start: 0.8413 (mmt) cc_final: 0.7772 (mmt) REVERT: A 338 ASN cc_start: 0.8825 (OUTLIER) cc_final: 0.8409 (m-40) REVERT: B 113 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7257 (mp) REVERT: B 229 MET cc_start: 0.7850 (mmm) cc_final: 0.7016 (mmt) REVERT: B 278 GLU cc_start: 0.8361 (tp30) cc_final: 0.7773 (tt0) REVERT: B 291 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7420 (pm20) REVERT: C 98 LYS cc_start: 0.8527 (tttt) cc_final: 0.8223 (tptm) outliers start: 29 outliers final: 21 residues processed: 129 average time/residue: 0.0900 time to fit residues: 15.4768 Evaluate side-chains 127 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 103 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 79 CYS Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 565 HIS Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 582 ASP Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 329 LYS Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 333 GLN Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 189 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 52 optimal weight: 0.5980 chunk 84 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 75 optimal weight: 0.0870 chunk 116 optimal weight: 5.9990 chunk 19 optimal weight: 0.0060 chunk 40 optimal weight: 9.9990 chunk 67 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 102 optimal weight: 0.9990 overall best weight: 0.5174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 127 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.166753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.127769 restraints weight = 10906.084| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.51 r_work: 0.3034 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9884 Z= 0.103 Angle : 0.497 8.532 13372 Z= 0.257 Chirality : 0.039 0.149 1408 Planarity : 0.004 0.057 1750 Dihedral : 3.466 26.021 1407 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.59 % Favored : 95.32 % Rotamer: Outliers : 2.56 % Allowed : 21.30 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.25), residues: 1176 helix: 2.11 (0.21), residues: 645 sheet: -0.45 (0.52), residues: 103 loop : -1.44 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 447 TYR 0.018 0.001 TYR A 306 PHE 0.016 0.001 PHE C 153 TRP 0.005 0.000 TRP C 137 HIS 0.003 0.000 HIS A 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 ( 9876) covalent geometry : angle 0.48729 / 0.25 (13352) SS BOND : bond 0.00428 / 0.23 ( 4) SS BOND : angle 3.61692 / 2.12 ( 8) hydrogen bonds : bond 0.04160 / 2.74 ( 499) hydrogen bonds : angle 3.54331 / 2.56 ( 1455) link_NAG-ASN : bond 0.00166 / 0.10 ( 4) link_NAG-ASN : angle 1.35946 / 0.77 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 108 time to evaluate : 0.310 Fit side-chains revert: symmetry clash REVERT: A 338 ASN cc_start: 0.8818 (OUTLIER) cc_final: 0.8415 (m-40) REVERT: B 113 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7054 (mp) REVERT: B 229 MET cc_start: 0.7726 (mmm) cc_final: 0.6831 (mmt) REVERT: B 278 GLU cc_start: 0.8200 (tp30) cc_final: 0.7642 (tt0) REVERT: B 291 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7355 (pm20) REVERT: C 98 LYS cc_start: 0.8454 (tttt) cc_final: 0.8151 (tptm) outliers start: 26 outliers final: 18 residues processed: 130 average time/residue: 0.0988 time to fit residues: 17.3899 Evaluate side-chains 125 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 582 ASP Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 329 LYS Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 333 GLN Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 189 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 0.4980 chunk 90 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 6 optimal weight: 20.0000 chunk 1 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.165339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.125270 restraints weight = 10870.388| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.62 r_work: 0.3000 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9884 Z= 0.122 Angle : 0.519 9.444 13372 Z= 0.270 Chirality : 0.040 0.211 1408 Planarity : 0.004 0.058 1750 Dihedral : 3.545 33.007 1407 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.17 % Allowed : 21.79 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.25), residues: 1176 helix: 2.09 (0.21), residues: 645 sheet: -0.51 (0.52), residues: 103 loop : -1.43 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 121 TYR 0.016 0.001 TYR A 306 PHE 0.019 0.001 PHE C 153 TRP 0.005 0.001 TRP C 137 HIS 0.003 0.001 HIS A 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 9876) covalent geometry : angle 0.51043 / 0.27 (13352) SS BOND : bond 0.00767 / 0.44 ( 4) SS BOND : angle 3.59066 / 2.06 ( 8) hydrogen bonds : bond 0.04847 / 3.21 ( 499) hydrogen bonds : angle 3.60345 / 2.60 ( 1455) link_NAG-ASN : bond 0.00140 / 0.08 ( 4) link_NAG-ASN : angle 1.40256 / 0.79 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2352 Ramachandran restraints generated. 1176 Oldfield, 0 Emsley, 1176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 0.344 Fit side-chains REVERT: A 338 ASN cc_start: 0.8800 (OUTLIER) cc_final: 0.8390 (m-40) REVERT: B 113 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7101 (mp) REVERT: B 229 MET cc_start: 0.7818 (mmm) cc_final: 0.6952 (mmt) REVERT: B 291 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7366 (pm20) REVERT: C 98 LYS cc_start: 0.8477 (tttt) cc_final: 0.8170 (tptm) outliers start: 22 outliers final: 18 residues processed: 122 average time/residue: 0.1257 time to fit residues: 20.4430 Evaluate side-chains 123 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 582 ASP Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 696 MET Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 329 LYS Chi-restraints excluded: chain B residue 330 VAL Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 189 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 33 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 90 optimal weight: 0.0970 chunk 51 optimal weight: 0.9990 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.165717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.125607 restraints weight = 10883.329| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.64 r_work: 0.3034 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9884 Z= 0.115 Angle : 0.515 9.116 13372 Z= 0.267 Chirality : 0.040 0.223 1408 Planarity : 0.004 0.057 1750 Dihedral : 3.561 38.062 1407 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.68 % Favored : 95.24 % Rotamer: Outliers : 2.27 % Allowed : 21.79 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.25), residues: 1176 helix: 2.10 (0.21), residues: 645 sheet: -0.51 (0.52), residues: 103 loop : -1.43 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 183 TYR 0.016 0.001 TYR A 306 PHE 0.018 0.001 PHE C 153 TRP 0.006 0.001 TRP C 137 HIS 0.004 0.001 HIS A 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 ( 9876) covalent geometry : angle 0.50648 / 0.26 (13352) SS BOND : bond 0.00548 / 0.32 ( 4) SS BOND : angle 3.44209 / 2.02 ( 8) hydrogen bonds : bond 0.04637 / 3.07 ( 499) hydrogen bonds : angle 3.60830 / 2.61 ( 1455) link_NAG-ASN : bond 0.00152 / 0.09 ( 4) link_NAG-ASN : angle 1.39793 / 0.79 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2151.80 seconds wall clock time: 37 minutes 26.50 seconds (2246.50 seconds total)