Starting phenix.real_space_refine on Sun Dec 29 02:31:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k0m_36774/12_2024/8k0m_36774.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k0m_36774/12_2024/8k0m_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_36774/12_2024/8k0m_36774.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k0m_36774/12_2024/8k0m_36774.map" model { file = "/net/cci-nas-00/data/ceres_data/8k0m_36774/12_2024/8k0m_36774.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k0m_36774/12_2024/8k0m_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-5532/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: 5.95, per 1000 atoms: 0.62 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: 2.65 Conformation dependent library (CDL) restraints added in 1.2 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: 1.10 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: 2.90 Time building geometry restraints manager: 2.96 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: 0.480 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: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 24.300 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.250 ------------------------------------------------------------------------------- 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 : 1.103 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: 0.3054 time to fit residues: 42.9881 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 : 1.117 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 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 : 1.063 Fit side-chains REVERT: B 113 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.7393 (mp) REVERT: B 173 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.7967 (mp) outliers start: 33 outliers final: 22 residues processed: 134 average time/residue: 0.2780 time to fit residues: 49.5611 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 : 1.163 ------------------------------------------------------------------------------- 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 59 optimal weight: 0.0170 chunk 33 optimal weight: 0.9980 chunk 89 optimal weight: 0.8980 chunk 72 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 107 optimal weight: 0.0970 chunk 115 optimal weight: 0.0470 chunk 95 optimal weight: 10.0000 chunk 106 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 86 optimal weight: 2.9990 overall best weight: 0.2914 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9876 Z= 0.134 Angle : 0.473 6.846 13352 Z= 0.251 Chirality : 0.039 0.149 1408 Planarity : 0.004 0.058 1750 Dihedral : 4.052 41.946 1407 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.08 % Favored : 95.83 % Rotamer: Outliers : 2.07 % Allowed : 21.10 % Favored : 76.82 % 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: 0.51 (0.25), residues: 1176 helix: 1.72 (0.21), residues: 645 sheet: -0.63 (0.53), residues: 103 loop : -1.62 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP C 137 HIS 0.005 0.001 HIS A 303 PHE 0.016 0.001 PHE C 153 TYR 0.013 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 132 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 1.121 Fit side-chains revert: symmetry clash REVERT: A 647 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.7552 (mtt-85) REVERT: B 173 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7868 (mp) REVERT: B 229 MET cc_start: 0.7907 (mmm) cc_final: 0.7138 (mmt) REVERT: C 98 LYS cc_start: 0.8597 (tttt) cc_final: 0.8303 (tptm) REVERT: C 122 ARG cc_start: 0.8771 (mmt180) cc_final: 0.8522 (mmt180) outliers start: 21 outliers final: 10 residues processed: 128 average time/residue: 0.2873 time to fit residues: 48.9499 Evaluate side-chains 111 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 1.205 ------------------------------------------------------------------------------- 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 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 106 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 55 optimal weight: 0.0970 chunk 11 optimal weight: 0.7980 chunk 51 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 chunk 114 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 565 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9876 Z= 0.164 Angle : 0.479 7.077 13352 Z= 0.251 Chirality : 0.039 0.146 1408 Planarity : 0.004 0.056 1750 Dihedral : 3.704 28.265 1407 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.51 % Favored : 95.41 % Rotamer: Outliers : 2.96 % Allowed : 20.41 % Favored : 76.63 % 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: 0.78 (0.25), residues: 1176 helix: 1.97 (0.21), residues: 639 sheet: -0.35 (0.54), residues: 93 loop : -1.53 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 137 HIS 0.003 0.001 HIS A 565 PHE 0.018 0.001 PHE C 153 TYR 0.015 0.001 TYR B 267 ARG 0.002 0.000 ARG A 74 *********************** 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 141 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 111 time to evaluate : 1.481 Fit side-chains revert: symmetry clash REVERT: A 484 GLN cc_start: 0.7976 (mm-40) cc_final: 0.7185 (mp10) REVERT: A 598 LEU cc_start: 0.7364 (OUTLIER) cc_final: 0.7089 (tt) REVERT: A 647 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.7568 (mtt-85) REVERT: B 113 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.7443 (mp) REVERT: B 173 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7880 (mp) REVERT: B 229 MET cc_start: 0.7941 (mmm) cc_final: 0.7166 (mmt) REVERT: C 98 LYS cc_start: 0.8576 (tttt) cc_final: 0.8295 (tptm) REVERT: C 122 ARG cc_start: 0.8780 (mmt180) cc_final: 0.8378 (mmt180) outliers start: 30 outliers final: 15 residues processed: 136 average time/residue: 0.3387 time to fit residues: 61.1369 Evaluate side-chains 123 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 1.091 ------------------------------------------------------------------------------- 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 415 VAL Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 565 HIS 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 64 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 173 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 2.9990 chunk 64 optimal weight: 0.0970 chunk 1 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 chunk 97 optimal weight: 0.7980 chunk 78 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 102 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9876 Z= 0.217 Angle : 0.515 8.514 13352 Z= 0.271 Chirality : 0.041 0.145 1408 Planarity : 0.004 0.057 1750 Dihedral : 3.707 22.777 1407 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.68 % Favored : 95.24 % Rotamer: Outliers : 3.25 % Allowed : 20.41 % 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 (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: 0.69 (0.25), residues: 1176 helix: 1.88 (0.21), residues: 645 sheet: -0.63 (0.51), residues: 103 loop : -1.53 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 137 HIS 0.015 0.001 HIS A 565 PHE 0.021 0.001 PHE C 153 TYR 0.014 0.001 TYR A 539 ARG 0.002 0.000 ARG A 687 *********************** 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 145 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 112 time to evaluate : 1.117 Fit side-chains REVERT: A 338 ASN cc_start: 0.9011 (OUTLIER) cc_final: 0.8661 (m-40) REVERT: A 484 GLN cc_start: 0.8023 (mm-40) cc_final: 0.7220 (mp10) REVERT: A 598 LEU cc_start: 0.7391 (OUTLIER) cc_final: 0.7122 (tt) REVERT: B 113 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.7396 (mp) REVERT: B 173 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7900 (mp) REVERT: B 229 MET cc_start: 0.7887 (mmm) cc_final: 0.7110 (mmt) REVERT: C 98 LYS cc_start: 0.8548 (tttt) cc_final: 0.8260 (tptm) outliers start: 33 outliers final: 23 residues processed: 139 average time/residue: 0.2848 time to fit residues: 52.7963 Evaluate side-chains 133 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 106 time to evaluate : 1.162 ------------------------------------------------------------------------------- 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 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 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 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 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 54 ASP 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 38 optimal weight: 4.9990 chunk 102 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 9 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 0.0980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 565 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9876 Z= 0.189 Angle : 0.504 7.409 13352 Z= 0.265 Chirality : 0.040 0.148 1408 Planarity : 0.004 0.057 1750 Dihedral : 3.652 24.585 1407 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.68 % Favored : 95.24 % Rotamer: Outliers : 3.35 % Allowed : 20.41 % Favored : 76.23 % 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: 0.81 (0.25), residues: 1176 helix: 2.00 (0.21), residues: 639 sheet: -0.60 (0.51), residues: 103 loop : -1.45 (0.28), residues: 434 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 0.020 0.001 PHE C 153 TYR 0.013 0.001 TYR A 539 ARG 0.001 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 144 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 110 time to evaluate : 1.175 Fit side-chains REVERT: A 58 MET cc_start: 0.8626 (mmt) cc_final: 0.8175 (mmt) REVERT: A 338 ASN cc_start: 0.9013 (OUTLIER) cc_final: 0.8632 (m-40) REVERT: B 113 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7379 (mp) REVERT: B 173 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7887 (mp) REVERT: B 229 MET cc_start: 0.7919 (mmm) cc_final: 0.7124 (mmt) REVERT: B 291 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7463 (pm20) REVERT: C 98 LYS cc_start: 0.8541 (tttt) cc_final: 0.8256 (tptm) outliers start: 34 outliers final: 23 residues processed: 136 average time/residue: 0.2795 time to fit residues: 50.5891 Evaluate side-chains 132 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 105 time to evaluate : 0.984 ------------------------------------------------------------------------------- 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 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 632 LEU 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 54 ASP 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 110 optimal weight: 0.9980 chunk 12 optimal weight: 0.4980 chunk 65 optimal weight: 0.9980 chunk 83 optimal weight: 10.0000 chunk 64 optimal weight: 0.0000 chunk 96 optimal weight: 10.0000 chunk 63 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 565 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.1365 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= 0.162 Angle : 0.493 7.683 13352 Z= 0.258 Chirality : 0.040 0.149 1408 Planarity : 0.004 0.056 1750 Dihedral : 3.601 25.700 1407 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.51 % Favored : 95.41 % 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 (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: 0.90 (0.25), residues: 1176 helix: 2.06 (0.21), residues: 639 sheet: -0.49 (0.52), residues: 103 loop : -1.42 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 137 HIS 0.006 0.001 HIS A 565 PHE 0.019 0.001 PHE C 153 TYR 0.015 0.001 TYR A 306 ARG 0.001 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 137 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 108 time to evaluate : 1.049 Fit side-chains REVERT: A 338 ASN cc_start: 0.8976 (OUTLIER) cc_final: 0.8602 (m-40) REVERT: A 647 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7612 (mtt-85) REVERT: B 113 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7371 (mp) REVERT: B 173 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7873 (mp) REVERT: B 229 MET cc_start: 0.7971 (mmm) cc_final: 0.7155 (mmt) REVERT: B 278 GLU cc_start: 0.8254 (tp30) cc_final: 0.7693 (tt0) REVERT: B 291 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7456 (pm20) REVERT: C 98 LYS cc_start: 0.8521 (tttt) cc_final: 0.8240 (tptm) outliers start: 29 outliers final: 22 residues processed: 133 average time/residue: 0.2887 time to fit residues: 50.5953 Evaluate side-chains 131 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 104 time to evaluate : 1.115 ------------------------------------------------------------------------------- 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 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 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 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 54 ASP 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 70 optimal weight: 0.0010 chunk 45 optimal weight: 0.7980 chunk 67 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 77 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 GLN A 565 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 9876 Z= 0.163 Angle : 0.499 7.882 13352 Z= 0.259 Chirality : 0.039 0.149 1408 Planarity : 0.004 0.056 1750 Dihedral : 3.554 25.574 1407 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.68 % Favored : 95.24 % Rotamer: Outliers : 3.35 % Allowed : 20.61 % Favored : 76.04 % 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: 0.95 (0.25), residues: 1176 helix: 2.10 (0.21), residues: 639 sheet: -0.49 (0.51), residues: 103 loop : -1.39 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 137 HIS 0.004 0.000 HIS A 303 PHE 0.018 0.001 PHE C 153 TYR 0.014 0.001 TYR A 306 ARG 0.001 0.000 ARG A 569 *********************** 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 138 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 104 time to evaluate : 1.149 Fit side-chains REVERT: A 58 MET cc_start: 0.8605 (mmt) cc_final: 0.8210 (mmt) REVERT: A 338 ASN cc_start: 0.8972 (OUTLIER) cc_final: 0.8601 (m-40) REVERT: A 647 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7651 (mtt-85) REVERT: B 113 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7373 (mp) REVERT: B 173 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7865 (mp) REVERT: B 229 MET cc_start: 0.7968 (mmm) cc_final: 0.7168 (mmt) REVERT: B 278 GLU cc_start: 0.8231 (tp30) cc_final: 0.7673 (tt0) REVERT: B 291 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7463 (pm20) REVERT: C 98 LYS cc_start: 0.8526 (tttt) cc_final: 0.8260 (tptm) outliers start: 34 outliers final: 24 residues processed: 132 average time/residue: 0.2683 time to fit residues: 47.8226 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 : 1.167 ------------------------------------------------------------------------------- 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 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 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 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 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 108 optimal weight: 0.5980 chunk 99 optimal weight: 0.0060 chunk 105 optimal weight: 0.0770 chunk 63 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 83 optimal weight: 10.0000 chunk 32 optimal weight: 0.8980 chunk 95 optimal weight: 8.9990 chunk 100 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 112 optimal weight: 0.9980 overall best weight: 0.4754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 565 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 9876 Z= 0.148 Angle : 0.491 8.132 13352 Z= 0.255 Chirality : 0.039 0.149 1408 Planarity : 0.004 0.056 1750 Dihedral : 3.489 25.668 1407 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.76 % Favored : 95.15 % Rotamer: Outliers : 2.86 % Allowed : 21.30 % Favored : 75.84 % 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: 1.02 (0.25), residues: 1176 helix: 2.16 (0.21), residues: 638 sheet: -0.49 (0.51), residues: 103 loop : -1.36 (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 0.017 0.001 PHE C 153 TYR 0.018 0.001 TYR B 187 ARG 0.002 0.000 ARG A 569 *********************** 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 135 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 106 time to evaluate : 1.140 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.8562 (mmt) cc_final: 0.8177 (mmt) REVERT: A 338 ASN cc_start: 0.8963 (OUTLIER) cc_final: 0.8624 (m-40) REVERT: A 484 GLN cc_start: 0.8010 (mm-40) cc_final: 0.7187 (mp10) REVERT: B 113 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7398 (mp) REVERT: B 173 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7881 (mp) REVERT: B 229 MET cc_start: 0.7926 (mmm) cc_final: 0.7120 (mmt) REVERT: B 278 GLU cc_start: 0.8212 (tp30) cc_final: 0.7662 (tt0) REVERT: B 291 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7430 (pm20) REVERT: C 98 LYS cc_start: 0.8494 (tttt) cc_final: 0.8271 (tptm) outliers start: 29 outliers final: 23 residues processed: 131 average time/residue: 0.2656 time to fit residues: 47.5538 Evaluate side-chains 131 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 104 time to evaluate : 1.124 ------------------------------------------------------------------------------- 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 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 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 54 ASP 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 68 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 117 optimal weight: 0.9990 chunk 108 optimal weight: 0.4980 chunk 93 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 74 optimal weight: 7.9990 chunk 99 optimal weight: 0.0770 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 565 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.1524 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= 0.168 Angle : 0.509 10.828 13352 Z= 0.265 Chirality : 0.040 0.216 1408 Planarity : 0.004 0.056 1750 Dihedral : 3.533 31.290 1407 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.93 % Favored : 94.98 % Rotamer: Outliers : 2.96 % Allowed : 21.60 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 2.12 (0.21), residues: 645 sheet: -0.51 (0.50), residues: 103 loop : -1.42 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 137 HIS 0.003 0.000 HIS A 303 PHE 0.018 0.001 PHE C 153 TYR 0.015 0.001 TYR A 306 ARG 0.002 0.000 ARG A 121 ********************** 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 136 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 106 time to evaluate : 1.128 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.8566 (mmt) cc_final: 0.8120 (mmt) REVERT: A 338 ASN cc_start: 0.8967 (OUTLIER) cc_final: 0.8622 (m-40) REVERT: A 484 GLN cc_start: 0.8057 (mm-40) cc_final: 0.7250 (mp10) REVERT: B 113 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.7403 (mp) REVERT: B 173 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7903 (mp) REVERT: B 229 MET cc_start: 0.7928 (mmm) cc_final: 0.7128 (mmt) REVERT: B 291 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7422 (pm20) REVERT: C 98 LYS cc_start: 0.8463 (tttt) cc_final: 0.8258 (tptm) outliers start: 30 outliers final: 25 residues processed: 132 average time/residue: 0.2595 time to fit residues: 46.2831 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 : 1.201 ------------------------------------------------------------------------------- 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 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 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 244 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 42 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 54 ASP 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 28 optimal weight: 0.3980 chunk 86 optimal weight: 5.9990 chunk 13 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 39 optimal weight: 8.9990 chunk 96 optimal weight: 6.9990 chunk 11 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 565 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.165415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.125118 restraints weight = 10888.930| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.68 r_work: 0.3059 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9876 Z= 0.193 Angle : 0.517 10.237 13352 Z= 0.268 Chirality : 0.040 0.215 1408 Planarity : 0.004 0.056 1750 Dihedral : 3.593 36.395 1407 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.85 % Favored : 95.07 % Rotamer: Outliers : 3.16 % Allowed : 21.40 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.97 (0.25), residues: 1176 helix: 2.11 (0.21), residues: 645 sheet: -0.52 (0.51), residues: 103 loop : -1.41 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 137 HIS 0.003 0.001 HIS A 303 PHE 0.020 0.001 PHE C 153 TYR 0.014 0.001 TYR A 539 ARG 0.001 0.000 ARG B 183 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2121.29 seconds wall clock time: 39 minutes 34.30 seconds (2374.30 seconds total)