Starting phenix.real_space_refine on Fri Feb 14 01:38:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k0m_36774/02_2025/8k0m_36774.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k0m_36774/02_2025/8k0m_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8k0m_36774/02_2025/8k0m_36774.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k0m_36774/02_2025/8k0m_36774.map" model { file = "/net/cci-nas-00/data/ceres_data/8k0m_36774/02_2025/8k0m_36774.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k0m_36774/02_2025/8k0m_36774.cif" } resolution = 3.17 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= 0.003 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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, 39 Unusual residues: {' FE': 1, 'AKG': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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: 5.38, per 1000 atoms: 0.56 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: 2.62 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.00 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: 2.77 Time building geometry restraints manager: 2.89 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 2.260 nonbonded pdb=" OD1 ASP A 589 " pdb="FE FE A 803 " model vdw 2.059 2.260 nonbonded pdb=" NE2 HIS A 659 " pdb="FE FE A 803 " model vdw 2.084 2.340 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: 0.520 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.410 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 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 9876 Z= 0.220 Angle : 0.571 8.521 13352 Z= 0.300 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 (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: 0.17 (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 TRP 0.005 0.001 TRP C 137 HIS 0.005 0.001 HIS A 303 PHE 0.014 0.001 PHE C 123 TYR 0.020 0.001 TYR A 306 ARG 0.003 0.000 ARG A 554 *********************** 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 : 1.021 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: 0.3055 time to fit residues: 42.9947 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 : 1.463 ------------------------------------------------------------------------------- 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 99 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 92 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 184 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.169957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.128423 restraints weight = 10703.959| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.67 r_work: 0.2963 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.0743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9876 Z= 0.310 Angle : 0.578 7.270 13352 Z= 0.306 Chirality : 0.043 0.144 1408 Planarity : 0.005 0.063 1750 Dihedral : 5.112 58.429 1415 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.53 % Favored : 94.39 % Rotamer: Outliers : 3.25 % Allowed : 19.33 % Favored : 77.42 % 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: 0.20 (0.25), residues: 1176 helix: 1.47 (0.21), residues: 649 sheet: -0.98 (0.52), residues: 105 loop : -1.74 (0.27), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 137 HIS 0.008 0.001 HIS B 266 PHE 0.023 0.002 PHE C 153 TYR 0.017 0.002 TYR A 539 ARG 0.002 0.000 ARG A 69 *********************** 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 140 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 107 time to evaluate : 1.013 Fit side-chains REVERT: B 113 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7084 (mp) REVERT: B 173 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7641 (mp) outliers start: 33 outliers final: 22 residues processed: 134 average time/residue: 0.2848 time to fit residues: 50.5359 Evaluate side-chains 123 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 1.131 ------------------------------------------------------------------------------- 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 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 517 THR 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 119 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 330 VAL 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 13 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 94 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 chunk 80 optimal weight: 7.9990 chunk 107 optimal weight: 0.0970 chunk 93 optimal weight: 0.4980 chunk 98 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 = 0.3930 r_free = 0.3930 target = 0.175470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.130827 restraints weight = 10906.389| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.98 r_work: 0.3053 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.0996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 9876 Z= 0.155 Angle : 0.486 6.949 13352 Z= 0.258 Chirality : 0.039 0.149 1408 Planarity : 0.004 0.059 1750 Dihedral : 4.135 42.650 1407 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.42 % Favored : 95.49 % Rotamer: Outliers : 2.27 % Allowed : 21.30 % 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 (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 (0.25), residues: 1176 helix: 1.64 (0.21), residues: 651 sheet: -0.64 (0.53), residues: 103 loop : -1.68 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 137 HIS 0.005 0.001 HIS A 303 PHE 0.018 0.001 PHE C 153 TYR 0.012 0.001 TYR A 306 ARG 0.001 0.000 ARG B 121 *********************** 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: 23 poor density : 112 time to evaluate : 1.146 Fit side-chains revert: symmetry clash REVERT: A 647 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.7236 (mtt-85) REVERT: B 173 LEU cc_start: 0.7635 (OUTLIER) cc_final: 0.7325 (mp) REVERT: B 229 MET cc_start: 0.7605 (mmm) cc_final: 0.6715 (mmt) REVERT: C 122 ARG cc_start: 0.8691 (mmt180) cc_final: 0.8468 (mmt180) outliers start: 23 outliers final: 11 residues processed: 131 average time/residue: 0.2825 time to fit residues: 48.9567 Evaluate side-chains 113 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 1.045 ------------------------------------------------------------------------------- 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 453 LEU 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 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 357 GLU Chi-restraints excluded: chain C residue 44 VAL 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 24 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 39 optimal weight: 9.9990 chunk 12 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 chunk 67 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 = 0.3751 r_free = 0.3751 target = 0.161027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.121627 restraints weight = 10981.065| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.96 r_work: 0.3014 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 9876 Z= 0.305 Angle : 0.556 7.219 13352 Z= 0.293 Chirality : 0.043 0.146 1408 Planarity : 0.004 0.060 1750 Dihedral : 4.051 29.764 1407 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.19 % Favored : 94.73 % Rotamer: Outliers : 4.04 % Allowed : 20.02 % Favored : 75.94 % 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: 0.42 (0.25), residues: 1176 helix: 1.62 (0.21), residues: 650 sheet: -0.68 (0.52), residues: 103 loop : -1.65 (0.28), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 85 HIS 0.004 0.001 HIS A 303 PHE 0.025 0.002 PHE C 153 TYR 0.017 0.002 TYR A 539 ARG 0.002 0.000 ARG A 143 *********************** 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 147 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 106 time to evaluate : 1.050 Fit side-chains REVERT: A 598 LEU cc_start: 0.7456 (OUTLIER) cc_final: 0.7180 (tt) REVERT: A 647 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.7548 (mtt-85) REVERT: B 113 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.7467 (mp) REVERT: B 229 MET cc_start: 0.7932 (mmm) cc_final: 0.7502 (mmt) REVERT: C 122 ARG cc_start: 0.8769 (mmt180) cc_final: 0.8516 (mmt180) outliers start: 41 outliers final: 29 residues processed: 140 average time/residue: 0.2818 time to fit residues: 52.5021 Evaluate side-chains 132 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 100 time to evaluate : 1.061 ------------------------------------------------------------------------------- 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 415 VAL Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 517 THR 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 598 LEU Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 632 LEU 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 244 LEU 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 B residue 366 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 3 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 70 optimal weight: 9.9990 chunk 7 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3762 r_free = 0.3762 target = 0.162480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.121999 restraints weight = 10969.556| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.60 r_work: 0.2998 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.1154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9876 Z= 0.182 Angle : 0.506 7.864 13352 Z= 0.268 Chirality : 0.040 0.157 1408 Planarity : 0.004 0.058 1750 Dihedral : 3.788 25.872 1407 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.42 % Favored : 95.49 % Rotamer: Outliers : 3.35 % Allowed : 20.51 % 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 (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: 0.63 (0.25), residues: 1176 helix: 1.82 (0.21), residues: 645 sheet: -0.65 (0.52), residues: 105 loop : -1.56 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 137 HIS 0.004 0.000 HIS A 303 PHE 0.019 0.001 PHE C 153 TYR 0.013 0.001 TYR A 539 ARG 0.002 0.000 ARG A 141 *********************** 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 146 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 112 time to evaluate : 1.063 Fit side-chains REVERT: A 338 ASN cc_start: 0.8936 (OUTLIER) cc_final: 0.8508 (m-40) REVERT: A 598 LEU cc_start: 0.7405 (OUTLIER) cc_final: 0.7156 (tt) REVERT: A 647 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.7333 (mtt-85) REVERT: B 113 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7164 (mp) REVERT: B 229 MET cc_start: 0.7745 (mmm) cc_final: 0.6922 (mmt) REVERT: C 98 LYS cc_start: 0.8500 (tttt) cc_final: 0.8220 (tptm) outliers start: 34 outliers final: 22 residues processed: 139 average time/residue: 0.2880 time to fit residues: 52.8191 Evaluate side-chains 131 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 105 time to evaluate : 1.157 ------------------------------------------------------------------------------- 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 136 MET 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 565 HIS Chi-restraints excluded: chain A residue 572 ILE Chi-restraints excluded: chain A residue 582 ASP Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 632 LEU 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 173 LEU Chi-restraints excluded: chain B residue 178 ASP Chi-restraints excluded: chain B residue 243 CYS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 64 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 112 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 117 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 overall best weight: 1.5984 ------------------------------------------------------------------------------- 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 = 0.3763 r_free = 0.3763 target = 0.162153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.124047 restraints weight = 10983.282| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.38 r_work: 0.2940 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9876 Z= 0.278 Angle : 0.555 8.608 13352 Z= 0.292 Chirality : 0.042 0.169 1408 Planarity : 0.004 0.059 1750 Dihedral : 3.882 28.697 1407 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.44 % Favored : 94.47 % Rotamer: Outliers : 3.35 % Allowed : 21.01 % Favored : 75.64 % 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: 0.55 (0.25), residues: 1176 helix: 1.76 (0.21), residues: 644 sheet: -0.71 (0.51), residues: 105 loop : -1.58 (0.28), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 137 HIS 0.004 0.001 HIS A 303 PHE 0.023 0.002 PHE C 153 TYR 0.017 0.001 TYR A 539 ARG 0.002 0.000 ARG A 141 *********************** 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 136 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 102 time to evaluate : 0.967 Fit side-chains REVERT: B 113 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7209 (mp) REVERT: B 229 MET cc_start: 0.7795 (mmm) cc_final: 0.7279 (mmt) REVERT: B 291 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7432 (pm20) REVERT: B 379 ILE cc_start: 0.8690 (OUTLIER) cc_final: 0.8436 (mt) REVERT: C 98 LYS cc_start: 0.8583 (tttt) cc_final: 0.8282 (tptm) REVERT: C 122 ARG cc_start: 0.8851 (mmt180) cc_final: 0.8558 (mmt180) outliers start: 34 outliers final: 24 residues processed: 129 average time/residue: 0.2900 time to fit residues: 49.5841 Evaluate side-chains 125 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 98 time to evaluate : 1.071 ------------------------------------------------------------------------------- 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 136 MET 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 415 VAL 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 611 ASP Chi-restraints excluded: chain A residue 632 LEU 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 243 CYS 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 B residue 379 ILE Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 187 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 58 optimal weight: 0.0770 chunk 37 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 105 optimal weight: 0.2980 chunk 100 optimal weight: 0.0970 chunk 0 optimal weight: 3.9990 chunk 104 optimal weight: 0.6980 chunk 77 optimal weight: 7.9990 chunk 36 optimal weight: 0.9980 chunk 102 optimal weight: 0.6980 chunk 16 optimal weight: 7.9990 overall best weight: 0.3536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 491 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 = 0.166861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.127818 restraints weight = 10993.324| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.53 r_work: 0.3046 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9876 Z= 0.134 Angle : 0.485 8.479 13352 Z= 0.253 Chirality : 0.039 0.149 1408 Planarity : 0.004 0.059 1750 Dihedral : 3.592 26.159 1407 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.86 % Allowed : 21.50 % Favored : 75.64 % 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: 0.89 (0.25), residues: 1176 helix: 2.04 (0.21), residues: 638 sheet: -0.49 (0.52), residues: 103 loop : -1.42 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 137 HIS 0.004 0.000 HIS A 303 PHE 0.014 0.001 PHE C 153 TYR 0.012 0.001 TYR A 306 ARG 0.002 0.000 ARG A 141 *********************** 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 140 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 111 time to evaluate : 1.056 Fit side-chains REVERT: A 325 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.7787 (mttt) REVERT: A 338 ASN cc_start: 0.8890 (OUTLIER) cc_final: 0.8480 (m-40) REVERT: B 113 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7215 (mp) REVERT: B 229 MET cc_start: 0.7749 (mmm) cc_final: 0.6963 (mmt) REVERT: B 278 GLU cc_start: 0.8294 (tp30) cc_final: 0.7740 (tt0) REVERT: C 98 LYS cc_start: 0.8472 (tttt) cc_final: 0.8204 (tptm) outliers start: 29 outliers final: 18 residues processed: 133 average time/residue: 0.2870 time to fit residues: 50.4946 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 : 1.212 ------------------------------------------------------------------------------- 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 136 MET Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 325 LYS Chi-restraints excluded: chain A residue 338 ASN 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 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 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 54 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 17 optimal weight: 0.0270 chunk 84 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 52 optimal weight: 0.1980 chunk 30 optimal weight: 3.9990 chunk 53 optimal weight: 0.0060 chunk 1 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 overall best weight: 0.4256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.168098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.128895 restraints weight = 11073.435| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.60 r_work: 0.3026 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 9876 Z= 0.147 Angle : 0.487 7.711 13352 Z= 0.254 Chirality : 0.039 0.148 1408 Planarity : 0.004 0.058 1750 Dihedral : 3.486 26.000 1407 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.76 % Allowed : 21.70 % Favored : 75.54 % 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: 0.98 (0.25), residues: 1176 helix: 2.14 (0.21), residues: 638 sheet: -0.57 (0.52), residues: 105 loop : -1.37 (0.28), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 137 HIS 0.004 0.000 HIS A 303 PHE 0.014 0.001 PHE C 153 TYR 0.019 0.001 TYR B 187 ARG 0.002 0.000 ARG B 183 *********************** 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 136 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 108 time to evaluate : 1.015 Fit side-chains revert: symmetry clash REVERT: A 325 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7660 (mttt) REVERT: A 338 ASN cc_start: 0.8818 (OUTLIER) cc_final: 0.8405 (m-40) REVERT: A 512 LYS cc_start: 0.8051 (OUTLIER) cc_final: 0.7779 (mtpp) REVERT: B 113 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7109 (mp) REVERT: B 291 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7329 (pm20) REVERT: C 97 ILE cc_start: 0.8308 (mt) cc_final: 0.8107 (mt) REVERT: C 98 LYS cc_start: 0.8532 (tttt) cc_final: 0.8331 (tptm) outliers start: 28 outliers final: 19 residues processed: 132 average time/residue: 0.2806 time to fit residues: 49.1771 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 : 0.998 ------------------------------------------------------------------------------- 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 136 MET Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 325 LYS Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 512 LYS Chi-restraints excluded: chain A residue 555 LEU 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 243 CYS 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 54 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 74 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 6 optimal weight: 20.0000 chunk 5 optimal weight: 0.5980 chunk 114 optimal weight: 0.0670 chunk 45 optimal weight: 0.8980 overall best weight: 1.1122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.163934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.123833 restraints weight = 10921.728| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.69 r_work: 0.3032 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9876 Z= 0.212 Angle : 0.529 9.183 13352 Z= 0.274 Chirality : 0.041 0.159 1408 Planarity : 0.004 0.058 1750 Dihedral : 3.625 27.017 1407 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.19 % Favored : 94.73 % Rotamer: Outliers : 3.06 % Allowed : 21.20 % Favored : 75.74 % 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: 0.88 (0.25), residues: 1176 helix: 2.06 (0.21), residues: 645 sheet: -0.66 (0.51), residues: 105 loop : -1.47 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 137 HIS 0.004 0.001 HIS A 303 PHE 0.021 0.001 PHE C 153 TYR 0.015 0.001 TYR A 306 ARG 0.002 0.000 ARG A 687 *********************** 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: 31 poor density : 103 time to evaluate : 1.027 Fit side-chains REVERT: A 325 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.8004 (mttt) REVERT: A 338 ASN cc_start: 0.9046 (OUTLIER) cc_final: 0.8641 (m-40) REVERT: B 113 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7319 (mp) REVERT: B 291 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7430 (pm20) outliers start: 31 outliers final: 25 residues processed: 127 average time/residue: 0.2681 time to fit residues: 45.3992 Evaluate side-chains 130 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 101 time to evaluate : 1.011 ------------------------------------------------------------------------------- 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 136 MET Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 176 HIS Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 325 LYS Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 361 SER 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 243 CYS 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 B residue 380 MET Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 54 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 16 optimal weight: 7.9990 chunk 57 optimal weight: 0.6980 chunk 103 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 54 optimal weight: 0.0670 chunk 81 optimal weight: 1.9990 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.165679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.126198 restraints weight = 11008.901| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.61 r_work: 0.3020 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 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 : 0.003 0.040 9876 Z= 0.165 Angle : 0.504 8.376 13352 Z= 0.261 Chirality : 0.040 0.150 1408 Planarity : 0.004 0.058 1750 Dihedral : 3.547 25.833 1407 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.68 % Favored : 95.24 % Rotamer: Outliers : 2.86 % Allowed : 21.70 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.25), residues: 1176 helix: 2.13 (0.21), residues: 644 sheet: -0.55 (0.52), residues: 103 loop : -1.39 (0.28), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 137 HIS 0.004 0.000 HIS A 303 PHE 0.017 0.001 PHE C 153 TYR 0.021 0.001 TYR A 306 ARG 0.001 0.000 ARG B 183 ********************** 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 130 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 101 time to evaluate : 1.070 Fit side-chains REVERT: A 325 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.7966 (mttt) REVERT: A 338 ASN cc_start: 0.8855 (OUTLIER) cc_final: 0.8434 (m-40) REVERT: B 113 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7083 (mp) outliers start: 29 outliers final: 24 residues processed: 126 average time/residue: 0.2691 time to fit residues: 45.6597 Evaluate side-chains 127 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 100 time to evaluate : 1.044 ------------------------------------------------------------------------------- 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 136 MET Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 176 HIS Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain A residue 325 LYS Chi-restraints excluded: chain A residue 338 ASN Chi-restraints excluded: chain A residue 361 SER 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 243 CYS 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 42 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 54 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 116 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 102 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 105 optimal weight: 0.0040 chunk 113 optimal weight: 0.7980 chunk 58 optimal weight: 0.0470 chunk 30 optimal weight: 0.9990 chunk 85 optimal weight: 0.5980 chunk 111 optimal weight: 3.9990 overall best weight: 0.4090 ------------------------------------------------------------------------------- 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 = 0.3806 r_free = 0.3806 target = 0.166477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.127561 restraints weight = 10936.173| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.56 r_work: 0.3033 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9876 Z= 0.139 Angle : 0.491 8.279 13352 Z= 0.254 Chirality : 0.039 0.149 1408 Planarity : 0.004 0.058 1750 Dihedral : 3.428 25.594 1407 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.86 % Allowed : 21.70 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.25), residues: 1176 helix: 2.24 (0.21), residues: 638 sheet: -0.55 (0.52), residues: 103 loop : -1.29 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP C 137 HIS 0.004 0.000 HIS A 303 PHE 0.015 0.001 PHE C 153 TYR 0.020 0.001 TYR A 306 ARG 0.002 0.000 ARG B 183 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4890.39 seconds wall clock time: 87 minutes 13.54 seconds (5233.54 seconds total)