Starting phenix.real_space_refine on Sat Aug 8 02:14:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tz1_41730/08_2026/8tz1_41730_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tz1_41730/08_2026/8tz1_41730.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8tz1_41730/08_2026/8tz1_41730_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tz1_41730/08_2026/8tz1_41730_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tz1_41730/08_2026/8tz1_41730.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tz1_41730/08_2026/8tz1_41730.map" } resolution = 2.54 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.063 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: 7 Type Number sf(0) Gaussians P 12 5.49 5 S 87 5.16 5 Na 6 4.78 5 C 8436 2.51 5 N 1938 2.21 5 O 2208 1.98 5 H 12165 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24852 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 8129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 8129 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 18, 'TRANS': 514} Unresolved non-hydrogen bonds: 102 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 6, 'ASP:plan': 3, 'PHE:plan': 1, 'HIS:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 69 Chain: "A" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 153 Unusual residues: {' NA': 2, 'LBN': 4, 'RBV%rna3p': 1} Classifications: {'undetermined': 7} Modifications used: {'rna3p': 1} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 74 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Restraints were copied for chains: C, B Time building chain proxies: 9.81, per 1000 atoms: 0.39 Number of scatterers: 24852 At special positions: 0 Unit cell: (128.52, 126.36, 75.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 87 16.00 P 12 15.00 Na 6 11.00 O 2208 8.00 N 1938 7.00 C 8436 6.00 H 12165 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.58 Conformation dependent library (CDL) restraints added in 925.5 milliseconds 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2946 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 3 sheets defined 87.5% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 90 through 103 Processing helix chain 'A' and resid 103 through 130 Processing helix chain 'A' and resid 134 through 157 Processing helix chain 'A' and resid 157 through 198 Proline residue: A 167 - end of helix removed outlier: 4.562A pdb=" N PHE A 177 " --> pdb=" O ASP A 173 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N TRP A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N TRP A 181 " --> pdb=" O PHE A 177 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL A 182 " --> pdb=" O TRP A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 203 Processing helix chain 'A' and resid 203 through 223 removed outlier: 3.763A pdb=" N LEU A 207 " --> pdb=" O GLY A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 251 removed outlier: 4.553A pdb=" N VAL A 235 " --> pdb=" O TYR A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 270 Processing helix chain 'A' and resid 273 through 282 Processing helix chain 'A' and resid 284 through 287 Processing helix chain 'A' and resid 288 through 312 removed outlier: 4.148A pdb=" N LEU A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) Proline residue: A 296 - end of helix Processing helix chain 'A' and resid 312 through 330 removed outlier: 3.612A pdb=" N VAL A 324 " --> pdb=" O LYS A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 342 Processing helix chain 'A' and resid 350 through 355 removed outlier: 3.732A pdb=" N ARG A 355 " --> pdb=" O LEU A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 361 Processing helix chain 'A' and resid 362 through 375 Processing helix chain 'A' and resid 381 through 389 Processing helix chain 'A' and resid 391 through 414 removed outlier: 4.184A pdb=" N ALA A 403 " --> pdb=" O SER A 399 " (cutoff:3.500A) Proline residue: A 404 - end of helix Processing helix chain 'A' and resid 423 through 429 Processing helix chain 'A' and resid 437 through 479 removed outlier: 3.880A pdb=" N ILE A 450 " --> pdb=" O ALA A 446 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N SER A 451 " --> pdb=" O SER A 447 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU A 452 " --> pdb=" O SER A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 482 No H-bonds generated for 'chain 'A' and resid 480 through 482' Processing helix chain 'A' and resid 487 through 496 Processing helix chain 'A' and resid 496 through 503 Processing helix chain 'A' and resid 506 through 523 removed outlier: 4.073A pdb=" N PHE A 511 " --> pdb=" O TRP A 507 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N MET A 512 " --> pdb=" O GLN A 508 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS A 515 " --> pdb=" O PHE A 511 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU A 516 " --> pdb=" O MET A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 542 removed outlier: 4.035A pdb=" N ALA A 528 " --> pdb=" O ASN A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 566 Processing helix chain 'A' and resid 573 through 586 removed outlier: 4.271A pdb=" N ILE A 577 " --> pdb=" O GLY A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 619 removed outlier: 3.539A pdb=" N ALA A 595 " --> pdb=" O ARG A 591 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N MET A 598 " --> pdb=" O THR A 594 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N ARG A 599 " --> pdb=" O ALA A 595 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 103 Processing helix chain 'C' and resid 103 through 130 Processing helix chain 'C' and resid 134 through 157 Processing helix chain 'C' and resid 157 through 198 Proline residue: C 167 - end of helix removed outlier: 4.563A pdb=" N PHE C 177 " --> pdb=" O ASP C 173 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N TRP C 178 " --> pdb=" O SER C 174 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N TRP C 181 " --> pdb=" O PHE C 177 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL C 182 " --> pdb=" O TRP C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 203 Processing helix chain 'C' and resid 203 through 223 removed outlier: 3.763A pdb=" N LEU C 207 " --> pdb=" O GLY C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 251 removed outlier: 4.553A pdb=" N VAL C 235 " --> pdb=" O TYR C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 270 Processing helix chain 'C' and resid 273 through 282 Processing helix chain 'C' and resid 284 through 287 Processing helix chain 'C' and resid 288 through 312 removed outlier: 4.148A pdb=" N LEU C 295 " --> pdb=" O ALA C 291 " (cutoff:3.500A) Proline residue: C 296 - end of helix Processing helix chain 'C' and resid 312 through 330 removed outlier: 3.612A pdb=" N VAL C 324 " --> pdb=" O LYS C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 342 Processing helix chain 'C' and resid 350 through 355 removed outlier: 3.731A pdb=" N ARG C 355 " --> pdb=" O LEU C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 361 Processing helix chain 'C' and resid 362 through 375 Processing helix chain 'C' and resid 381 through 389 Processing helix chain 'C' and resid 391 through 414 removed outlier: 4.185A pdb=" N ALA C 403 " --> pdb=" O SER C 399 " (cutoff:3.500A) Proline residue: C 404 - end of helix Processing helix chain 'C' and resid 423 through 429 Processing helix chain 'C' and resid 437 through 479 removed outlier: 3.880A pdb=" N ILE C 450 " --> pdb=" O ALA C 446 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N SER C 451 " --> pdb=" O SER C 447 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU C 452 " --> pdb=" O SER C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 482 No H-bonds generated for 'chain 'C' and resid 480 through 482' Processing helix chain 'C' and resid 487 through 496 Processing helix chain 'C' and resid 496 through 503 Processing helix chain 'C' and resid 506 through 523 removed outlier: 4.073A pdb=" N PHE C 511 " --> pdb=" O TRP C 507 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N MET C 512 " --> pdb=" O GLN C 508 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS C 515 " --> pdb=" O PHE C 511 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU C 516 " --> pdb=" O MET C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 542 removed outlier: 4.034A pdb=" N ALA C 528 " --> pdb=" O ASN C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 566 Processing helix chain 'C' and resid 573 through 586 removed outlier: 4.271A pdb=" N ILE C 577 " --> pdb=" O GLY C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 619 removed outlier: 3.540A pdb=" N ALA C 595 " --> pdb=" O ARG C 591 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N MET C 598 " --> pdb=" O THR C 594 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N ARG C 599 " --> pdb=" O ALA C 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 103 Processing helix chain 'B' and resid 103 through 130 Processing helix chain 'B' and resid 134 through 157 Processing helix chain 'B' and resid 157 through 198 Proline residue: B 167 - end of helix removed outlier: 4.562A pdb=" N PHE B 177 " --> pdb=" O ASP B 173 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N TRP B 178 " --> pdb=" O SER B 174 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N TRP B 181 " --> pdb=" O PHE B 177 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL B 182 " --> pdb=" O TRP B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 203 Processing helix chain 'B' and resid 203 through 223 removed outlier: 3.763A pdb=" N LEU B 207 " --> pdb=" O GLY B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 251 removed outlier: 4.553A pdb=" N VAL B 235 " --> pdb=" O TYR B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 270 Processing helix chain 'B' and resid 273 through 282 Processing helix chain 'B' and resid 284 through 287 Processing helix chain 'B' and resid 288 through 312 removed outlier: 4.149A pdb=" N LEU B 295 " --> pdb=" O ALA B 291 " (cutoff:3.500A) Proline residue: B 296 - end of helix Processing helix chain 'B' and resid 312 through 330 removed outlier: 3.611A pdb=" N VAL B 324 " --> pdb=" O LYS B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 342 Processing helix chain 'B' and resid 350 through 355 removed outlier: 3.731A pdb=" N ARG B 355 " --> pdb=" O LEU B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 361 Processing helix chain 'B' and resid 362 through 375 Processing helix chain 'B' and resid 381 through 389 Processing helix chain 'B' and resid 391 through 414 removed outlier: 4.184A pdb=" N ALA B 403 " --> pdb=" O SER B 399 " (cutoff:3.500A) Proline residue: B 404 - end of helix Processing helix chain 'B' and resid 423 through 429 Processing helix chain 'B' and resid 437 through 479 removed outlier: 3.880A pdb=" N ILE B 450 " --> pdb=" O ALA B 446 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N SER B 451 " --> pdb=" O SER B 447 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU B 452 " --> pdb=" O SER B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 482 No H-bonds generated for 'chain 'B' and resid 480 through 482' Processing helix chain 'B' and resid 487 through 496 Processing helix chain 'B' and resid 496 through 503 Processing helix chain 'B' and resid 506 through 523 removed outlier: 4.073A pdb=" N PHE B 511 " --> pdb=" O TRP B 507 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N MET B 512 " --> pdb=" O GLN B 508 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS B 515 " --> pdb=" O PHE B 511 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU B 516 " --> pdb=" O MET B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 542 removed outlier: 4.034A pdb=" N ALA B 528 " --> pdb=" O ASN B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 566 Processing helix chain 'B' and resid 573 through 586 removed outlier: 4.271A pdb=" N ILE B 577 " --> pdb=" O GLY B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 619 removed outlier: 3.539A pdb=" N ALA B 595 " --> pdb=" O ARG B 591 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N MET B 598 " --> pdb=" O THR B 594 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N ARG B 599 " --> pdb=" O ALA B 595 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 546 through 547 Processing sheet with id=AA2, first strand: chain 'C' and resid 546 through 547 Processing sheet with id=AA3, first strand: chain 'B' and resid 546 through 547 988 hydrogen bonds defined for protein. 2910 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: 6.41 Time building geometry restraints manager: 3.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 12147 1.03 - 1.23: 48 1.23 - 1.42: 5424 1.42 - 1.61: 7365 1.61 - 1.81: 183 Bond restraints: 25167 Sorted by residual: bond pdb=" C2' RBV B 801 " pdb=" C3' RBV B 801 " ideal model delta sigma weight residual 1.523 1.207 0.316 1.50e-02 4.44e+03 4.44e+02 bond pdb=" C2' RBV C 801 " pdb=" C3' RBV C 801 " ideal model delta sigma weight residual 1.523 1.207 0.316 1.50e-02 4.44e+03 4.44e+02 bond pdb=" C2' RBV A 801 " pdb=" C3' RBV A 801 " ideal model delta sigma weight residual 1.523 1.208 0.315 1.50e-02 4.44e+03 4.42e+02 bond pdb=" C4' RBV C 801 " pdb=" O4' RBV C 801 " ideal model delta sigma weight residual 1.451 1.270 0.181 1.50e-02 4.44e+03 1.45e+02 bond pdb=" C4' RBV A 801 " pdb=" O4' RBV A 801 " ideal model delta sigma weight residual 1.451 1.270 0.181 1.50e-02 4.44e+03 1.45e+02 ... (remaining 25162 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.24: 44887 3.24 - 6.49: 212 6.49 - 9.73: 24 9.73 - 12.97: 12 12.97 - 16.22: 12 Bond angle restraints: 45147 Sorted by residual: angle pdb=" O1 LBN B 805 " pdb=" P1 LBN B 805 " pdb=" O2 LBN B 805 " ideal model delta sigma weight residual 93.45 109.67 -16.22 3.00e+00 1.11e-01 2.92e+01 angle pdb=" O1 LBN A 805 " pdb=" P1 LBN A 805 " pdb=" O2 LBN A 805 " ideal model delta sigma weight residual 93.45 109.65 -16.20 3.00e+00 1.11e-01 2.92e+01 angle pdb=" O1 LBN C 805 " pdb=" P1 LBN C 805 " pdb=" O2 LBN C 805 " ideal model delta sigma weight residual 93.45 109.63 -16.18 3.00e+00 1.11e-01 2.91e+01 angle pdb=" O1 LBN B 807 " pdb=" P1 LBN B 807 " pdb=" O2 LBN B 807 " ideal model delta sigma weight residual 93.45 109.59 -16.14 3.00e+00 1.11e-01 2.89e+01 angle pdb=" O1 LBN B 804 " pdb=" P1 LBN B 804 " pdb=" O2 LBN B 804 " ideal model delta sigma weight residual 93.45 109.58 -16.13 3.00e+00 1.11e-01 2.89e+01 ... (remaining 45142 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.59: 11629 35.59 - 71.19: 458 71.19 - 106.78: 12 106.78 - 142.38: 3 142.38 - 177.97: 9 Dihedral angle restraints: 12111 sinusoidal: 6381 harmonic: 5730 Sorted by residual: dihedral pdb=" O5 LBN B 804 " pdb=" C2 LBN B 804 " pdb=" C3 LBN B 804 " pdb=" O7 LBN B 804 " ideal model delta sinusoidal sigma weight residual 62.67 -115.30 177.97 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O5 LBN C 804 " pdb=" C2 LBN C 804 " pdb=" C3 LBN C 804 " pdb=" O7 LBN C 804 " ideal model delta sinusoidal sigma weight residual 62.67 -115.29 177.96 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O5 LBN A 804 " pdb=" C2 LBN A 804 " pdb=" C3 LBN A 804 " pdb=" O7 LBN A 804 " ideal model delta sinusoidal sigma weight residual 62.67 -115.27 177.94 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 12108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1879 0.072 - 0.144: 116 0.144 - 0.215: 9 0.215 - 0.287: 0 0.287 - 0.359: 3 Chirality restraints: 2007 Sorted by residual: chirality pdb=" C2' RBV C 801 " pdb=" C1' RBV C 801 " pdb=" C3' RBV C 801 " pdb=" O2' RBV C 801 " both_signs ideal model delta sigma weight residual False -2.75 -2.39 -0.36 2.00e-01 2.50e+01 3.22e+00 chirality pdb=" C2' RBV B 801 " pdb=" C1' RBV B 801 " pdb=" C3' RBV B 801 " pdb=" O2' RBV B 801 " both_signs ideal model delta sigma weight residual False -2.75 -2.40 -0.36 2.00e-01 2.50e+01 3.18e+00 chirality pdb=" C2' RBV A 801 " pdb=" C1' RBV A 801 " pdb=" C3' RBV A 801 " pdb=" O2' RBV A 801 " both_signs ideal model delta sigma weight residual False -2.75 -2.40 -0.36 2.00e-01 2.50e+01 3.16e+00 ... (remaining 2004 not shown) Planarity restraints: 3663 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 524 " 0.037 2.00e-02 2.50e+03 3.98e-02 2.37e+01 pdb=" CG ASN A 524 " -0.001 2.00e-02 2.50e+03 pdb=" OD1 ASN A 524 " -0.037 2.00e-02 2.50e+03 pdb=" ND2 ASN A 524 " -0.000 2.00e-02 2.50e+03 pdb="HD21 ASN A 524 " 0.059 2.00e-02 2.50e+03 pdb="HD22 ASN A 524 " -0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 524 " -0.037 2.00e-02 2.50e+03 3.95e-02 2.34e+01 pdb=" CG ASN C 524 " 0.002 2.00e-02 2.50e+03 pdb=" OD1 ASN C 524 " 0.036 2.00e-02 2.50e+03 pdb=" ND2 ASN C 524 " 0.000 2.00e-02 2.50e+03 pdb="HD21 ASN C 524 " -0.058 2.00e-02 2.50e+03 pdb="HD22 ASN C 524 " 0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 524 " 0.037 2.00e-02 2.50e+03 3.94e-02 2.33e+01 pdb=" CG ASN B 524 " -0.002 2.00e-02 2.50e+03 pdb=" OD1 ASN B 524 " -0.036 2.00e-02 2.50e+03 pdb=" ND2 ASN B 524 " -0.000 2.00e-02 2.50e+03 pdb="HD21 ASN B 524 " 0.058 2.00e-02 2.50e+03 pdb="HD22 ASN B 524 " -0.057 2.00e-02 2.50e+03 ... (remaining 3660 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 1889 2.24 - 2.83: 53663 2.83 - 3.42: 63306 3.42 - 4.01: 87638 4.01 - 4.60: 138251 Nonbonded interactions: 344747 Sorted by model distance: nonbonded pdb=" O ALA C 446 " pdb=" HG SER C 449 " model vdw 1.648 2.450 nonbonded pdb=" O ALA A 446 " pdb=" HG SER A 449 " model vdw 1.648 2.450 nonbonded pdb=" O ALA B 446 " pdb=" HG SER B 449 " model vdw 1.649 2.450 nonbonded pdb=" OE1 GLN B 315 " pdb=" H GLN B 315 " model vdw 1.659 2.450 nonbonded pdb=" OE1 GLN A 315 " pdb=" H GLN A 315 " model vdw 1.659 2.450 ... (remaining 344742 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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: 1.410 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: 0.110 Extract box with map and model: 0.250 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 31.240 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 42.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 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 : 0.011 0.316 13002 Z= 0.650 Angle : 0.876 16.218 17625 Z= 0.374 Chirality : 0.040 0.359 2007 Planarity : 0.002 0.033 2121 Dihedral : 16.716 177.972 4617 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 1.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 0.48 % Allowed : 3.56 % Favored : 95.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.54 (0.21), residues: 1593 helix: 2.87 (0.14), residues: 1338 sheet: None (None), residues: 0 loop : -0.75 (0.37), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 539 TYR 0.009 0.001 TYR C 231 PHE 0.011 0.001 PHE C 488 TRP 0.005 0.001 TRP A 261 HIS 0.001 0.000 HIS B 288 Details of bonding type rmsd/Z covalent geometry : bond 0.01144 / 0.65 (13002) covalent geometry : angle 0.87610 / 0.37 (17625) hydrogen bonds : bond 0.17411 / 12.04 ( 988) hydrogen bonds : angle 5.54023 / 4.15 ( 2910) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Evaluate side-chains 202 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 196 time to evaluate : 0.661 Fit side-chains REVERT: A 305 MET cc_start: 0.7963 (mmm) cc_final: 0.7629 (mmt) REVERT: A 421 LYS cc_start: 0.8396 (mttt) cc_final: 0.8189 (mmtt) REVERT: C 421 LYS cc_start: 0.8359 (mttt) cc_final: 0.8134 (mmtt) REVERT: C 555 SER cc_start: 0.7935 (m) cc_final: 0.7709 (p) REVERT: B 305 MET cc_start: 0.7888 (mmm) cc_final: 0.7471 (mmt) REVERT: B 421 LYS cc_start: 0.8374 (mttt) cc_final: 0.8130 (mmtt) REVERT: B 508 GLN cc_start: 0.7876 (mt0) cc_final: 0.7445 (mm-40) outliers start: 6 outliers final: 3 residues processed: 202 average time/residue: 0.7716 time to fit residues: 175.7857 Evaluate side-chains 143 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 140 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain B residue 171 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.107772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.075224 restraints weight = 43774.015| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 1.74 r_work: 0.2727 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2601 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13002 Z= 0.125 Angle : 0.485 4.959 17625 Z= 0.255 Chirality : 0.037 0.123 2007 Planarity : 0.003 0.039 2121 Dihedral : 16.450 157.580 2071 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 1.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.11 % Allowed : 8.16 % Favored : 90.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.58 (0.21), residues: 1593 helix: 2.93 (0.14), residues: 1338 sheet: None (None), residues: 0 loop : -0.93 (0.35), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG B 557 TYR 0.009 0.001 TYR C 231 PHE 0.016 0.001 PHE A 164 TRP 0.008 0.001 TRP B 112 HIS 0.002 0.001 HIS C 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (13002) covalent geometry : angle 0.48458 / 0.26 (17625) hydrogen bonds : bond 0.05025 / 3.46 ( 988) hydrogen bonds : angle 4.01942 / 2.98 ( 2910) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Evaluate side-chains 173 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 159 time to evaluate : 0.497 Fit side-chains REVERT: A 283 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7476 (mm-30) REVERT: A 305 MET cc_start: 0.8671 (mmm) cc_final: 0.8389 (mmt) REVERT: A 421 LYS cc_start: 0.8494 (mttt) cc_final: 0.8026 (mmtt) REVERT: C 264 LYS cc_start: 0.7715 (mttt) cc_final: 0.7505 (mtmt) REVERT: C 421 LYS cc_start: 0.8533 (mttt) cc_final: 0.7995 (mmtt) REVERT: B 169 GLN cc_start: 0.7674 (tm-30) cc_final: 0.7465 (tm-30) REVERT: B 264 LYS cc_start: 0.7858 (mttt) cc_final: 0.7635 (mtmt) REVERT: B 305 MET cc_start: 0.8665 (mmm) cc_final: 0.8281 (mmt) REVERT: B 421 LYS cc_start: 0.8546 (mttt) cc_final: 0.7969 (mmtt) REVERT: B 470 MET cc_start: 0.8212 (ttm) cc_final: 0.7871 (ttm) REVERT: B 508 GLN cc_start: 0.8226 (mt0) cc_final: 0.7731 (mm-40) REVERT: B 556 MET cc_start: 0.8036 (ttt) cc_final: 0.7786 (ttp) outliers start: 14 outliers final: 4 residues processed: 166 average time/residue: 0.7334 time to fit residues: 139.0127 Evaluate side-chains 150 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 146 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 132 HIS Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain B residue 132 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 132 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 96 optimal weight: 0.7980 chunk 136 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.102547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.069663 restraints weight = 44637.537| |-----------------------------------------------------------------------------| r_work (start): 0.2757 rms_B_bonded: 1.74 r_work: 0.2630 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2508 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13002 Z= 0.151 Angle : 0.478 4.750 17625 Z= 0.255 Chirality : 0.037 0.136 2007 Planarity : 0.003 0.043 2121 Dihedral : 15.457 159.182 2067 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.87 % Allowed : 8.63 % Favored : 90.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.50 (0.21), residues: 1593 helix: 2.87 (0.14), residues: 1341 sheet: None (None), residues: 0 loop : -1.00 (0.33), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 557 TYR 0.009 0.001 TYR C 385 PHE 0.013 0.001 PHE A 488 TRP 0.007 0.001 TRP B 112 HIS 0.002 0.001 HIS B 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (13002) covalent geometry : angle 0.47778 / 0.25 (17625) hydrogen bonds : bond 0.05795 / 4.01 ( 988) hydrogen bonds : angle 3.90353 / 2.89 ( 2910) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Evaluate side-chains 165 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 154 time to evaluate : 0.659 Fit side-chains REVERT: A 283 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7782 (mm-30) REVERT: A 305 MET cc_start: 0.8745 (mmm) cc_final: 0.8436 (mmt) REVERT: A 421 LYS cc_start: 0.8557 (mttt) cc_final: 0.7990 (mmtt) REVERT: C 421 LYS cc_start: 0.8607 (mttt) cc_final: 0.7984 (mmtt) REVERT: B 169 GLN cc_start: 0.7575 (tm-30) cc_final: 0.7308 (tm-30) REVERT: B 264 LYS cc_start: 0.7980 (mttt) cc_final: 0.7723 (mtmt) REVERT: B 305 MET cc_start: 0.8552 (mmm) cc_final: 0.8192 (mmt) REVERT: B 421 LYS cc_start: 0.8524 (mttt) cc_final: 0.7926 (mmtt) REVERT: B 470 MET cc_start: 0.8245 (ttm) cc_final: 0.7868 (ttm) REVERT: B 508 GLN cc_start: 0.8249 (mt0) cc_final: 0.7779 (mm-40) outliers start: 11 outliers final: 2 residues processed: 159 average time/residue: 0.8539 time to fit residues: 153.7442 Evaluate side-chains 151 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 149 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain C residue 189 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 35 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 chunk 157 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 94 optimal weight: 2.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.104865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.071271 restraints weight = 45900.154| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 1.91 r_work: 0.2709 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2599 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13002 Z= 0.146 Angle : 0.465 4.646 17625 Z= 0.249 Chirality : 0.036 0.128 2007 Planarity : 0.003 0.044 2121 Dihedral : 14.896 157.447 2067 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.11 % Allowed : 9.66 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.44 (0.21), residues: 1593 helix: 2.84 (0.14), residues: 1341 sheet: None (None), residues: 0 loop : -1.10 (0.32), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 557 TYR 0.007 0.001 TYR C 360 PHE 0.018 0.001 PHE A 164 TRP 0.007 0.001 TRP A 112 HIS 0.003 0.001 HIS A 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (13002) covalent geometry : angle 0.46534 / 0.25 (17625) hydrogen bonds : bond 0.05300 / 3.66 ( 988) hydrogen bonds : angle 3.84644 / 2.84 ( 2910) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Evaluate side-chains 172 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 158 time to evaluate : 0.635 Fit side-chains REVERT: A 283 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7853 (mm-30) REVERT: A 305 MET cc_start: 0.8242 (mmm) cc_final: 0.7939 (mmt) REVERT: A 421 LYS cc_start: 0.8309 (mttt) cc_final: 0.7720 (mmtt) REVERT: C 421 LYS cc_start: 0.8401 (mttt) cc_final: 0.7716 (mmtt) REVERT: B 169 GLN cc_start: 0.7434 (tm-30) cc_final: 0.7205 (tm-30) REVERT: B 264 LYS cc_start: 0.7555 (mttt) cc_final: 0.7266 (mtmt) REVERT: B 267 GLN cc_start: 0.7848 (tt0) cc_final: 0.7620 (mt0) REVERT: B 305 MET cc_start: 0.8112 (mmm) cc_final: 0.7743 (mmt) REVERT: B 421 LYS cc_start: 0.8379 (mttt) cc_final: 0.7684 (mmtt) REVERT: B 470 MET cc_start: 0.7766 (ttm) cc_final: 0.7401 (ttm) REVERT: B 503 MET cc_start: 0.8458 (OUTLIER) cc_final: 0.8216 (mtm) REVERT: B 508 GLN cc_start: 0.8027 (mt0) cc_final: 0.7498 (mm-40) outliers start: 14 outliers final: 4 residues processed: 162 average time/residue: 0.8011 time to fit residues: 146.7169 Evaluate side-chains 157 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 152 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 556 MET Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 566 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 132 optimal weight: 0.0040 chunk 39 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 113 optimal weight: 7.9990 chunk 20 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 overall best weight: 0.8794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.107034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.073456 restraints weight = 45680.150| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 1.92 r_work: 0.2759 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2649 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13002 Z= 0.110 Angle : 0.431 4.876 17625 Z= 0.230 Chirality : 0.035 0.128 2007 Planarity : 0.003 0.040 2121 Dihedral : 14.193 154.051 2067 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.63 % Allowed : 10.61 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.75 (0.21), residues: 1593 helix: 3.06 (0.14), residues: 1341 sheet: None (None), residues: 0 loop : -1.07 (0.33), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 108 TYR 0.006 0.001 TYR C 231 PHE 0.020 0.001 PHE C 164 TRP 0.009 0.001 TRP B 112 HIS 0.002 0.000 HIS B 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (13002) covalent geometry : angle 0.43065 / 0.23 (17625) hydrogen bonds : bond 0.04455 / 3.08 ( 988) hydrogen bonds : angle 3.67638 / 2.72 ( 2910) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Evaluate side-chains 172 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 164 time to evaluate : 0.494 Fit side-chains REVERT: A 283 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7896 (mm-30) REVERT: A 305 MET cc_start: 0.8239 (mmm) cc_final: 0.7915 (mmt) REVERT: A 421 LYS cc_start: 0.8331 (mttt) cc_final: 0.7747 (mmtt) REVERT: A 556 MET cc_start: 0.7913 (OUTLIER) cc_final: 0.7702 (mtp) REVERT: C 421 LYS cc_start: 0.8392 (mttt) cc_final: 0.7741 (mmtt) REVERT: B 169 GLN cc_start: 0.7430 (tm-30) cc_final: 0.7168 (tm-30) REVERT: B 264 LYS cc_start: 0.7581 (mttt) cc_final: 0.7350 (mtmt) REVERT: B 267 GLN cc_start: 0.7897 (tt0) cc_final: 0.7652 (mt0) REVERT: B 305 MET cc_start: 0.8109 (mmm) cc_final: 0.7748 (mmt) REVERT: B 421 LYS cc_start: 0.8383 (mttt) cc_final: 0.7690 (mmtt) REVERT: B 470 MET cc_start: 0.7777 (ttm) cc_final: 0.7433 (ttm) REVERT: B 508 GLN cc_start: 0.7993 (mt0) cc_final: 0.7544 (mm-40) outliers start: 8 outliers final: 0 residues processed: 167 average time/residue: 0.7598 time to fit residues: 143.8472 Evaluate side-chains 159 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 158 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 556 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 143 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 25 optimal weight: 0.0030 chunk 19 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 79 optimal weight: 0.1980 overall best weight: 1.2396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.105743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.072368 restraints weight = 45715.935| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 1.88 r_work: 0.2740 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2632 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13002 Z= 0.130 Angle : 0.449 4.903 17625 Z= 0.240 Chirality : 0.036 0.122 2007 Planarity : 0.003 0.042 2121 Dihedral : 14.265 155.554 2067 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.87 % Allowed : 11.08 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.66 (0.21), residues: 1593 helix: 3.01 (0.14), residues: 1341 sheet: None (None), residues: 0 loop : -1.20 (0.32), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 557 TYR 0.006 0.001 TYR A 310 PHE 0.017 0.001 PHE A 164 TRP 0.008 0.001 TRP B 112 HIS 0.003 0.001 HIS B 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (13002) covalent geometry : angle 0.44938 / 0.24 (17625) hydrogen bonds : bond 0.04914 / 3.39 ( 988) hydrogen bonds : angle 3.72652 / 2.76 ( 2910) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Evaluate side-chains 163 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 152 time to evaluate : 0.500 Fit side-chains REVERT: A 283 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7877 (mm-30) REVERT: A 305 MET cc_start: 0.8252 (mmm) cc_final: 0.7929 (mmt) REVERT: A 421 LYS cc_start: 0.8328 (mttt) cc_final: 0.7748 (mmtt) REVERT: C 421 LYS cc_start: 0.8402 (mttt) cc_final: 0.7759 (mmtt) REVERT: B 169 GLN cc_start: 0.7453 (tm-30) cc_final: 0.7218 (tm-30) REVERT: B 264 LYS cc_start: 0.7608 (mttt) cc_final: 0.7361 (mtmt) REVERT: B 267 GLN cc_start: 0.7914 (tt0) cc_final: 0.7664 (mt0) REVERT: B 305 MET cc_start: 0.8199 (mmm) cc_final: 0.7819 (mmt) REVERT: B 421 LYS cc_start: 0.8364 (mttt) cc_final: 0.7666 (mmtt) REVERT: B 470 MET cc_start: 0.7806 (ttm) cc_final: 0.7463 (ttm) REVERT: B 503 MET cc_start: 0.8434 (OUTLIER) cc_final: 0.8204 (mtm) REVERT: B 508 GLN cc_start: 0.7994 (mt0) cc_final: 0.7546 (mm-40) outliers start: 11 outliers final: 3 residues processed: 154 average time/residue: 0.8357 time to fit residues: 144.9602 Evaluate side-chains 155 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 151 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 556 MET Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain B residue 503 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 3 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 77 optimal weight: 0.0980 chunk 24 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 2 optimal weight: 6.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.105914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.072162 restraints weight = 45155.725| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 1.90 r_work: 0.2740 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2631 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13002 Z= 0.123 Angle : 0.439 4.948 17625 Z= 0.236 Chirality : 0.035 0.124 2007 Planarity : 0.003 0.041 2121 Dihedral : 14.142 154.729 2067 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.79 % Allowed : 11.01 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.73 (0.21), residues: 1593 helix: 3.07 (0.14), residues: 1341 sheet: None (None), residues: 0 loop : -1.24 (0.32), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 557 TYR 0.006 0.001 TYR C 494 PHE 0.020 0.001 PHE C 164 TRP 0.010 0.001 TRP A 112 HIS 0.002 0.001 HIS B 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (13002) covalent geometry : angle 0.43943 / 0.24 (17625) hydrogen bonds : bond 0.04698 / 3.25 ( 988) hydrogen bonds : angle 3.67975 / 2.72 ( 2910) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Evaluate side-chains 160 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 150 time to evaluate : 0.581 Fit side-chains REVERT: A 283 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7864 (mm-30) REVERT: A 305 MET cc_start: 0.8199 (mmm) cc_final: 0.7874 (mmt) REVERT: A 421 LYS cc_start: 0.8305 (mttt) cc_final: 0.7724 (mmtt) REVERT: C 421 LYS cc_start: 0.8364 (mttt) cc_final: 0.7708 (mmtt) REVERT: B 169 GLN cc_start: 0.7483 (tm-30) cc_final: 0.7197 (tm-30) REVERT: B 264 LYS cc_start: 0.7557 (mttt) cc_final: 0.7309 (mtmt) REVERT: B 267 GLN cc_start: 0.7865 (tt0) cc_final: 0.7610 (mt0) REVERT: B 305 MET cc_start: 0.8174 (mmm) cc_final: 0.7792 (mmt) REVERT: B 421 LYS cc_start: 0.8350 (mttt) cc_final: 0.7642 (mmtt) REVERT: B 470 MET cc_start: 0.7756 (ttm) cc_final: 0.7389 (ttm) REVERT: B 508 GLN cc_start: 0.7957 (mt0) cc_final: 0.7520 (mm-40) outliers start: 10 outliers final: 3 residues processed: 154 average time/residue: 0.8526 time to fit residues: 148.3175 Evaluate side-chains 153 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 150 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 556 MET Chi-restraints excluded: chain C residue 260 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 69 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 151 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 80 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.104059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.070278 restraints weight = 45690.875| |-----------------------------------------------------------------------------| r_work (start): 0.2829 rms_B_bonded: 1.90 r_work: 0.2705 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2596 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13002 Z= 0.160 Angle : 0.472 4.980 17625 Z= 0.253 Chirality : 0.037 0.150 2007 Planarity : 0.004 0.043 2121 Dihedral : 14.374 157.975 2067 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.63 % Allowed : 11.24 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.53 (0.21), residues: 1593 helix: 2.93 (0.14), residues: 1341 sheet: None (None), residues: 0 loop : -1.28 (0.32), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 108 TYR 0.007 0.001 TYR A 310 PHE 0.013 0.001 PHE B 279 TRP 0.009 0.001 TRP B 112 HIS 0.003 0.001 HIS B 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 (13002) covalent geometry : angle 0.47165 / 0.25 (17625) hydrogen bonds : bond 0.05393 / 3.72 ( 988) hydrogen bonds : angle 3.79087 / 2.81 ( 2910) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Evaluate side-chains 162 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 154 time to evaluate : 0.566 Fit side-chains REVERT: A 283 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7897 (mm-30) REVERT: A 305 MET cc_start: 0.8211 (mmm) cc_final: 0.7876 (mmt) REVERT: A 421 LYS cc_start: 0.8271 (mttt) cc_final: 0.7715 (mmtt) REVERT: C 421 LYS cc_start: 0.8298 (mttt) cc_final: 0.7653 (mmtt) REVERT: B 169 GLN cc_start: 0.7432 (tm-30) cc_final: 0.7134 (tm-30) REVERT: B 264 LYS cc_start: 0.7564 (mttt) cc_final: 0.7320 (mtmt) REVERT: B 267 GLN cc_start: 0.7863 (tt0) cc_final: 0.7613 (mt0) REVERT: B 305 MET cc_start: 0.8179 (mmm) cc_final: 0.7771 (mmt) REVERT: B 421 LYS cc_start: 0.8378 (mttt) cc_final: 0.7699 (mmtt) REVERT: B 470 MET cc_start: 0.7748 (ttm) cc_final: 0.7396 (ttm) REVERT: B 508 GLN cc_start: 0.7966 (mt0) cc_final: 0.7475 (mm-40) outliers start: 8 outliers final: 3 residues processed: 159 average time/residue: 0.8746 time to fit residues: 157.2768 Evaluate side-chains 156 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 153 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 556 MET Chi-restraints excluded: chain C residue 260 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 117 optimal weight: 0.8980 chunk 114 optimal weight: 0.9990 chunk 155 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 138 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 72 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.106619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.072843 restraints weight = 45579.082| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 1.91 r_work: 0.2751 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2642 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13002 Z= 0.110 Angle : 0.434 4.912 17625 Z= 0.232 Chirality : 0.035 0.123 2007 Planarity : 0.003 0.041 2121 Dihedral : 13.938 155.718 2067 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.24 % Allowed : 11.48 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.81 (0.22), residues: 1593 helix: 3.11 (0.14), residues: 1341 sheet: None (None), residues: 0 loop : -1.12 (0.34), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 557 TYR 0.005 0.001 TYR C 519 PHE 0.021 0.001 PHE C 164 TRP 0.010 0.001 TRP A 112 HIS 0.002 0.000 HIS B 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (13002) covalent geometry : angle 0.43363 / 0.23 (17625) hydrogen bonds : bond 0.04381 / 3.03 ( 988) hydrogen bonds : angle 3.64958 / 2.71 ( 2910) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Evaluate side-chains 156 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 153 time to evaluate : 0.703 Fit side-chains REVERT: A 283 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7883 (mm-30) REVERT: A 305 MET cc_start: 0.8238 (mmm) cc_final: 0.7896 (mmt) REVERT: A 421 LYS cc_start: 0.8266 (mttt) cc_final: 0.7675 (mmtt) REVERT: A 556 MET cc_start: 0.7903 (OUTLIER) cc_final: 0.7693 (mtp) REVERT: C 421 LYS cc_start: 0.8350 (mttt) cc_final: 0.7717 (mmtt) REVERT: B 169 GLN cc_start: 0.7456 (tm-30) cc_final: 0.7170 (tm-30) REVERT: B 264 LYS cc_start: 0.7538 (mttt) cc_final: 0.7291 (mtmt) REVERT: B 267 GLN cc_start: 0.7836 (tt0) cc_final: 0.7588 (mt0) REVERT: B 305 MET cc_start: 0.8148 (mmm) cc_final: 0.7766 (mmt) REVERT: B 421 LYS cc_start: 0.8403 (mttt) cc_final: 0.7704 (mmtt) REVERT: B 470 MET cc_start: 0.7783 (ttm) cc_final: 0.7410 (ttm) REVERT: B 508 GLN cc_start: 0.7897 (mt0) cc_final: 0.7480 (mm-40) outliers start: 3 outliers final: 2 residues processed: 154 average time/residue: 0.9485 time to fit residues: 164.7219 Evaluate side-chains 155 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 152 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 556 MET Chi-restraints excluded: chain C residue 260 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 55 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 126 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.103294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.069462 restraints weight = 45713.913| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 1.90 r_work: 0.2698 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2590 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13002 Z= 0.178 Angle : 0.489 5.269 17625 Z= 0.264 Chirality : 0.038 0.120 2007 Planarity : 0.004 0.044 2121 Dihedral : 14.477 160.159 2067 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.24 % Allowed : 11.72 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.45 (0.21), residues: 1593 helix: 2.86 (0.14), residues: 1341 sheet: None (None), residues: 0 loop : -1.16 (0.34), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 557 TYR 0.008 0.001 TYR A 310 PHE 0.024 0.001 PHE B 164 TRP 0.010 0.001 TRP B 112 HIS 0.004 0.001 HIS C 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.18 (13002) covalent geometry : angle 0.48947 / 0.26 (17625) hydrogen bonds : bond 0.05730 / 3.95 ( 988) hydrogen bonds : angle 3.84559 / 2.85 ( 2910) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Evaluate side-chains 153 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 150 time to evaluate : 0.671 Fit side-chains REVERT: A 283 GLU cc_start: 0.8242 (mm-30) cc_final: 0.7917 (mm-30) REVERT: A 305 MET cc_start: 0.8319 (mmm) cc_final: 0.7973 (mmt) REVERT: A 421 LYS cc_start: 0.8237 (mttt) cc_final: 0.7644 (mmtt) REVERT: C 421 LYS cc_start: 0.8300 (mttt) cc_final: 0.7634 (mmtt) REVERT: B 169 GLN cc_start: 0.7406 (tm-30) cc_final: 0.7090 (tm-30) REVERT: B 264 LYS cc_start: 0.7623 (mttt) cc_final: 0.7383 (mtmt) REVERT: B 305 MET cc_start: 0.8209 (mmm) cc_final: 0.7857 (mmt) REVERT: B 421 LYS cc_start: 0.8386 (mttt) cc_final: 0.7712 (mmtt) REVERT: B 470 MET cc_start: 0.7816 (ttm) cc_final: 0.7472 (ttm) REVERT: B 508 GLN cc_start: 0.7985 (mt0) cc_final: 0.7532 (mm-40) outliers start: 3 outliers final: 3 residues processed: 152 average time/residue: 0.9280 time to fit residues: 159.2273 Evaluate side-chains 152 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 149 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain C residue 506 ASP Chi-restraints excluded: chain B residue 566 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 103 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 130 optimal weight: 1.9990 chunk 113 optimal weight: 0.4980 chunk 111 optimal weight: 0.8980 chunk 150 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 94 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.106404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.072672 restraints weight = 45604.074| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 1.91 r_work: 0.2764 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13002 Z= 0.106 Angle : 0.436 5.202 17625 Z= 0.233 Chirality : 0.035 0.122 2007 Planarity : 0.003 0.041 2121 Dihedral : 13.888 157.097 2067 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.16 % Allowed : 11.56 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.79 (0.22), residues: 1593 helix: 3.09 (0.14), residues: 1341 sheet: None (None), residues: 0 loop : -1.05 (0.35), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 355 TYR 0.005 0.001 TYR C 231 PHE 0.020 0.001 PHE C 164 TRP 0.010 0.001 TRP A 112 HIS 0.002 0.000 HIS B 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.11 (13002) covalent geometry : angle 0.43630 / 0.23 (17625) hydrogen bonds : bond 0.04388 / 3.04 ( 988) hydrogen bonds : angle 3.67137 / 2.73 ( 2910) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7193.65 seconds wall clock time: 122 minutes 14.24 seconds (7334.24 seconds total)