Starting phenix.real_space_refine on Sun Jul 5 03:39:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tz1_41730/07_2026/8tz1_41730_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tz1_41730/07_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_41730/07_2026/8tz1_41730_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tz1_41730/07_2026/8tz1_41730_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tz1_41730/07_2026/8tz1_41730.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tz1_41730/07_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-dev-6108/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, 151 Ad-hoc single atom residues: {' NA': 2} Unusual residues: {'LBN': 4, 'RBV%rna3p': 1} Classifications: {'undetermined': 5} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain breaks: 2 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: 9.77, 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: 2.25 Conformation dependent library (CDL) restraints added in 740.7 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: 0.39 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: 5.05 Time building geometry restraints manager: 2.74 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 1.531 1.207 0.324 2.00e-02 2.50e+03 2.63e+02 bond pdb=" C2' RBV C 801 " pdb=" C3' RBV C 801 " ideal model delta sigma weight residual 1.531 1.207 0.324 2.00e-02 2.50e+03 2.62e+02 bond pdb=" C2' RBV A 801 " pdb=" C3' RBV A 801 " ideal model delta sigma weight residual 1.531 1.208 0.323 2.00e-02 2.50e+03 2.62e+02 bond pdb=" C4' RBV C 801 " pdb=" O4' RBV C 801 " ideal model delta sigma weight residual 1.431 1.270 0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" C4' RBV A 801 " pdb=" O4' RBV A 801 " ideal model delta sigma weight residual 1.431 1.270 0.161 2.00e-02 2.50e+03 6.44e+01 ... (remaining 25162 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.24: 44884 3.24 - 6.49: 215 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: 11617 35.59 - 71.19: 467 71.19 - 106.78: 15 106.78 - 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 - 0.053: 1693 0.053 - 0.106: 284 0.106 - 0.159: 12 0.159 - 0.212: 15 0.212 - 0.265: 3 Chirality restraints: 2007 Sorted by residual: chirality pdb=" C3' RBV C 801 " pdb=" C2' RBV C 801 " pdb=" C4' RBV C 801 " pdb=" O3' RBV C 801 " both_signs ideal model delta sigma weight residual False -2.71 -2.45 -0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" C3' RBV B 801 " pdb=" C2' RBV B 801 " pdb=" C4' RBV B 801 " pdb=" O3' RBV B 801 " both_signs ideal model delta sigma weight residual False -2.71 -2.45 -0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" C3' RBV A 801 " pdb=" C2' RBV A 801 " pdb=" C4' RBV A 801 " pdb=" O3' RBV A 801 " both_signs ideal model delta sigma weight residual False -2.71 -2.45 -0.26 2.00e-01 2.50e+01 1.72e+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: 0.04 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.940 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: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 27.290 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 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:6.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.330 ------------------------------------------------------------------------------- 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 0.324 13002 Z= 0.572 Angle : 0.875 16.218 17625 Z= 0.355 Chirality : 0.040 0.265 2007 Planarity : 0.002 0.033 2121 Dihedral : 16.917 177.972 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 0.01147 / 0.57 (13002) covalent geometry : angle 0.87476 / 0.35 (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 : 0.676 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: 0.8756 time to fit residues: 199.1722 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 : 0.666 ------------------------------------------------------------------------------- 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 = 0.3328 r_free = 0.3328 target = 0.108164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.075676 restraints weight = 43779.689| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 1.73 r_work: 0.2737 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2610 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 13002 Z= 0.125 Angle : 0.484 4.932 17625 Z= 0.254 Chirality : 0.037 0.137 2007 Planarity : 0.003 0.039 2121 Dihedral : 14.445 157.834 2071 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.11 % Allowed : 8.23 % Favored : 90.66 % 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: 2.92 (0.14), residues: 1338 sheet: None (None), residues: 0 loop : -0.92 (0.35), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 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 0.00259 / 0.12 (13002) covalent geometry : angle 0.48442 / 0.25 (17625) hydrogen bonds : bond 0.05052 / 3.48 ( 988) hydrogen bonds : angle 4.03621 / 2.99 ( 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 174 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 160 time to evaluate : 0.672 Fit side-chains REVERT: A 283 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7484 (mm-30) REVERT: A 305 MET cc_start: 0.8673 (mmm) cc_final: 0.8391 (mmt) REVERT: A 421 LYS cc_start: 0.8499 (mttt) cc_final: 0.8031 (mmtt) REVERT: C 264 LYS cc_start: 0.7720 (mttt) cc_final: 0.7510 (mtmt) REVERT: C 421 LYS cc_start: 0.8539 (mttt) cc_final: 0.8002 (mmtt) REVERT: B 264 LYS cc_start: 0.7827 (mttt) cc_final: 0.7568 (mttt) REVERT: B 305 MET cc_start: 0.8665 (mmm) cc_final: 0.8280 (mmt) REVERT: B 421 LYS cc_start: 0.8547 (mttt) cc_final: 0.7973 (mmtt) REVERT: B 470 MET cc_start: 0.8218 (ttm) cc_final: 0.7876 (ttm) REVERT: B 508 GLN cc_start: 0.8225 (mt0) cc_final: 0.7734 (mm-40) REVERT: B 556 MET cc_start: 0.8058 (ttt) cc_final: 0.7807 (ttp) outliers start: 14 outliers final: 4 residues processed: 167 average time/residue: 0.8553 time to fit residues: 162.7462 Evaluate side-chains 149 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 145 time to evaluate : 0.966 ------------------------------------------------------------------------------- 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: 0.3980 chunk 85 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 114 optimal weight: 0.6980 chunk 148 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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 = 0.3266 r_free = 0.3266 target = 0.103402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.070445 restraints weight = 44449.218| |-----------------------------------------------------------------------------| r_work (start): 0.2773 rms_B_bonded: 1.74 r_work: 0.2648 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2524 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2646 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= 0.148 Angle : 0.472 4.645 17625 Z= 0.250 Chirality : 0.037 0.159 2007 Planarity : 0.003 0.043 2121 Dihedral : 13.305 158.402 2067 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.87 % Allowed : 8.79 % Favored : 90.34 % 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: 3.52 (0.21), residues: 1593 helix: 2.88 (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 0.008 0.001 TYR A 231 PHE 0.012 0.001 PHE A 488 TRP 0.007 0.001 TRP B 112 HIS 0.002 0.001 HIS A 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (13002) covalent geometry : angle 0.47241 / 0.25 (17625) hydrogen bonds : bond 0.05609 / 3.88 ( 988) hydrogen bonds : angle 3.89066 / 2.88 ( 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 166 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 155 time to evaluate : 0.610 Fit side-chains REVERT: A 283 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7735 (mm-30) REVERT: A 305 MET cc_start: 0.8744 (mmm) cc_final: 0.8439 (mmt) REVERT: A 421 LYS cc_start: 0.8554 (mttt) cc_final: 0.7990 (mmtt) REVERT: C 421 LYS cc_start: 0.8605 (mttt) cc_final: 0.7992 (mmtt) REVERT: B 264 LYS cc_start: 0.7975 (mttt) cc_final: 0.7724 (mtmt) REVERT: B 305 MET cc_start: 0.8558 (mmm) cc_final: 0.8186 (mmt) REVERT: B 421 LYS cc_start: 0.8524 (mttt) cc_final: 0.7934 (mmtt) REVERT: B 470 MET cc_start: 0.8232 (ttm) cc_final: 0.7855 (ttm) REVERT: B 508 GLN cc_start: 0.8244 (mt0) cc_final: 0.7773 (mm-40) outliers start: 11 outliers final: 1 residues processed: 160 average time/residue: 0.9244 time to fit residues: 167.5796 Evaluate side-chains 154 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 153 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 52 optimal weight: 0.6980 chunk 140 optimal weight: 4.9990 chunk 157 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.106970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.073351 restraints weight = 45647.555| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 1.92 r_work: 0.2773 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13002 Z= 0.119 Angle : 0.444 4.584 17625 Z= 0.235 Chirality : 0.035 0.123 2007 Planarity : 0.003 0.041 2121 Dihedral : 12.183 155.176 2067 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.87 % Allowed : 9.98 % Favored : 89.15 % 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: 3.65 (0.21), residues: 1593 helix: 2.98 (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 0.001 0.000 ARG A 557 TYR 0.007 0.001 TYR C 231 PHE 0.017 0.001 PHE A 164 TRP 0.008 0.001 TRP B 112 HIS 0.002 0.001 HIS A 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (13002) covalent geometry : angle 0.44368 / 0.23 (17625) hydrogen bonds : bond 0.04714 / 3.26 ( 988) hydrogen bonds : angle 3.75310 / 2.77 ( 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 176 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 165 time to evaluate : 0.690 Fit side-chains REVERT: A 283 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7831 (mm-30) REVERT: A 305 MET cc_start: 0.8240 (mmm) cc_final: 0.7936 (mmt) REVERT: A 421 LYS cc_start: 0.8344 (mttt) cc_final: 0.7757 (mmtt) REVERT: C 421 LYS cc_start: 0.8422 (mttt) cc_final: 0.7741 (mmtt) REVERT: B 264 LYS cc_start: 0.7566 (mttt) cc_final: 0.7250 (mtmt) REVERT: B 267 GLN cc_start: 0.7894 (tt0) cc_final: 0.7650 (mt0) REVERT: B 305 MET cc_start: 0.8129 (mmm) cc_final: 0.7750 (mmt) REVERT: B 421 LYS cc_start: 0.8368 (mttt) cc_final: 0.7676 (mmtt) REVERT: B 470 MET cc_start: 0.7773 (ttm) cc_final: 0.7401 (ttm) REVERT: B 508 GLN cc_start: 0.8033 (mt0) cc_final: 0.7572 (mm-40) outliers start: 11 outliers final: 5 residues processed: 168 average time/residue: 0.9003 time to fit residues: 171.6514 Evaluate side-chains 160 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 155 time to evaluate : 0.682 ------------------------------------------------------------------------------- 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 189 LEU Chi-restraints excluded: chain C residue 260 ASP 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: 0.0570 chunk 39 optimal weight: 0.3980 chunk 92 optimal weight: 0.0570 chunk 28 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 120 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 113 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 overall best weight: 0.4216 ------------------------------------------------------------------------------- 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 = 0.3378 r_free = 0.3378 target = 0.110596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.077178 restraints weight = 45432.999| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 1.92 r_work: 0.2833 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 13002 Z= 0.092 Angle : 0.409 4.835 17625 Z= 0.215 Chirality : 0.034 0.121 2007 Planarity : 0.003 0.038 2121 Dihedral : 11.038 150.130 2067 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.55 % Allowed : 10.53 % Favored : 88.92 % 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: 4.02 (0.21), residues: 1593 helix: 3.24 (0.14), residues: 1344 sheet: None (None), residues: 0 loop : -0.99 (0.33), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 355 TYR 0.006 0.001 TYR A 157 PHE 0.020 0.001 PHE C 164 TRP 0.008 0.001 TRP A 112 HIS 0.002 0.000 HIS A 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00189 / 0.09 (13002) covalent geometry : angle 0.40896 / 0.21 (17625) hydrogen bonds : bond 0.03729 / 2.58 ( 988) hydrogen bonds : angle 3.52410 / 2.61 ( 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 171 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 164 time to evaluate : 0.751 Fit side-chains REVERT: A 283 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7812 (mm-30) REVERT: A 305 MET cc_start: 0.8283 (mmm) cc_final: 0.7971 (mmt) REVERT: A 421 LYS cc_start: 0.8323 (mttt) cc_final: 0.7734 (mmtt) REVERT: C 421 LYS cc_start: 0.8415 (mttt) cc_final: 0.7739 (mmtt) REVERT: B 264 LYS cc_start: 0.7425 (mttt) cc_final: 0.7205 (mtmt) REVERT: B 267 GLN cc_start: 0.7871 (tt0) cc_final: 0.7621 (mt0) REVERT: B 305 MET cc_start: 0.8047 (mmm) cc_final: 0.7636 (mmt) REVERT: B 421 LYS cc_start: 0.8395 (mttt) cc_final: 0.7683 (mmtt) REVERT: B 470 MET cc_start: 0.7789 (ttm) cc_final: 0.7419 (ttm) REVERT: B 508 GLN cc_start: 0.7957 (mt0) cc_final: 0.7552 (mm-40) outliers start: 7 outliers final: 1 residues processed: 166 average time/residue: 0.9447 time to fit residues: 177.6983 Evaluate side-chains 156 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 155 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 189 LEU 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: 0.6980 chunk 19 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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 = 0.3296 r_free = 0.3296 target = 0.104553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.070878 restraints weight = 45637.927| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 1.91 r_work: 0.2716 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2606 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13002 Z= 0.163 Angle : 0.475 5.035 17625 Z= 0.254 Chirality : 0.037 0.120 2007 Planarity : 0.004 0.043 2121 Dihedral : 12.064 156.266 2067 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.87 % Allowed : 11.01 % 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: 3.64 (0.21), residues: 1593 helix: 2.99 (0.14), residues: 1341 sheet: None (None), residues: 0 loop : -1.16 (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 385 PHE 0.016 0.001 PHE A 164 TRP 0.007 0.001 TRP A 112 HIS 0.003 0.001 HIS C 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 (13002) covalent geometry : angle 0.47525 / 0.25 (17625) hydrogen bonds : bond 0.05450 / 3.76 ( 988) hydrogen bonds : angle 3.78576 / 2.80 ( 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 164 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 153 time to evaluate : 0.685 Fit side-chains REVERT: A 283 GLU cc_start: 0.8247 (mm-30) cc_final: 0.7945 (mm-30) REVERT: A 305 MET cc_start: 0.8246 (mmm) cc_final: 0.7926 (mmt) REVERT: A 421 LYS cc_start: 0.8301 (mttt) cc_final: 0.7722 (mmtt) REVERT: C 421 LYS cc_start: 0.8392 (mttt) cc_final: 0.7667 (mmtt) REVERT: B 264 LYS cc_start: 0.7594 (mttt) cc_final: 0.7306 (mtmt) REVERT: B 305 MET cc_start: 0.8119 (mmm) cc_final: 0.7734 (mmt) REVERT: B 421 LYS cc_start: 0.8356 (mttt) cc_final: 0.7655 (mmtt) REVERT: B 470 MET cc_start: 0.7760 (ttm) cc_final: 0.7389 (ttm) REVERT: B 503 MET cc_start: 0.8403 (OUTLIER) cc_final: 0.8168 (mtm) REVERT: B 508 GLN cc_start: 0.7996 (mt0) cc_final: 0.7481 (mm-40) outliers start: 11 outliers final: 3 residues processed: 157 average time/residue: 0.9390 time to fit residues: 166.8896 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 : 0.699 ------------------------------------------------------------------------------- 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 503 MET Chi-restraints excluded: chain B residue 566 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 3 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 146 optimal weight: 0.0980 chunk 101 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 79 optimal weight: 0.0370 chunk 2 optimal weight: 3.9990 overall best weight: 0.4858 ------------------------------------------------------------------------------- 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 = 0.3351 r_free = 0.3351 target = 0.108608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.075070 restraints weight = 45053.312| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 1.90 r_work: 0.2789 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13002 Z= 0.097 Angle : 0.422 4.936 17625 Z= 0.223 Chirality : 0.035 0.122 2007 Planarity : 0.003 0.039 2121 Dihedral : 11.144 151.431 2067 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.16 % Allowed : 11.48 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.96 (0.21), residues: 1593 helix: 3.21 (0.14), residues: 1344 sheet: None (None), residues: 0 loop : -1.10 (0.33), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 108 TYR 0.006 0.001 TYR A 157 PHE 0.018 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 0.00201 / 0.10 (13002) covalent geometry : angle 0.42181 / 0.22 (17625) hydrogen bonds : bond 0.03926 / 2.72 ( 988) hydrogen bonds : angle 3.57337 / 2.65 ( 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 155 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 153 time to evaluate : 0.690 Fit side-chains REVERT: A 283 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7875 (mm-30) REVERT: A 305 MET cc_start: 0.8264 (mmm) cc_final: 0.7946 (mmt) REVERT: A 421 LYS cc_start: 0.8307 (mttt) cc_final: 0.7727 (mmtt) REVERT: C 421 LYS cc_start: 0.8381 (mttt) cc_final: 0.7711 (mmtt) REVERT: B 264 LYS cc_start: 0.7480 (mttt) cc_final: 0.7230 (mtmt) REVERT: B 267 GLN cc_start: 0.7886 (tt0) cc_final: 0.7623 (mt0) REVERT: B 305 MET cc_start: 0.8128 (mmm) cc_final: 0.7741 (mmt) REVERT: B 421 LYS cc_start: 0.8351 (mttt) cc_final: 0.7645 (mmtt) REVERT: B 470 MET cc_start: 0.7774 (ttm) cc_final: 0.7397 (ttm) REVERT: B 508 GLN cc_start: 0.7913 (mt0) cc_final: 0.7522 (mm-40) outliers start: 2 outliers final: 0 residues processed: 153 average time/residue: 0.9420 time to fit residues: 162.5538 Evaluate side-chains 153 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 69 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 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: 2.9990 chunk 137 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 7 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 = 0.3321 r_free = 0.3321 target = 0.106394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.073075 restraints weight = 45578.505| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 1.87 r_work: 0.2751 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2642 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.3449 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= 0.131 Angle : 0.451 4.971 17625 Z= 0.239 Chirality : 0.036 0.136 2007 Planarity : 0.003 0.041 2121 Dihedral : 11.486 154.315 2067 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.32 % Allowed : 11.32 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.85 (0.21), residues: 1593 helix: 3.14 (0.14), residues: 1341 sheet: None (None), residues: 0 loop : -1.12 (0.33), 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 0.012 0.001 PHE B 279 TRP 0.010 0.001 TRP A 112 HIS 0.003 0.001 HIS B 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (13002) covalent geometry : angle 0.45079 / 0.24 (17625) hydrogen bonds : bond 0.04796 / 3.31 ( 988) hydrogen bonds : angle 3.67505 / 2.72 ( 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 155 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 151 time to evaluate : 0.725 Fit side-chains REVERT: A 283 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7912 (mm-30) REVERT: A 305 MET cc_start: 0.8239 (mmm) cc_final: 0.7916 (mmt) REVERT: A 421 LYS cc_start: 0.8275 (mttt) cc_final: 0.7671 (mmtt) REVERT: C 421 LYS cc_start: 0.8366 (mttt) cc_final: 0.7732 (mmtt) REVERT: B 264 LYS cc_start: 0.7597 (mttt) cc_final: 0.7363 (mtmt) REVERT: B 305 MET cc_start: 0.8179 (mmm) cc_final: 0.7799 (mmt) REVERT: B 421 LYS cc_start: 0.8342 (mttt) cc_final: 0.7640 (mmtt) REVERT: B 470 MET cc_start: 0.7781 (ttm) cc_final: 0.7411 (ttm) REVERT: B 508 GLN cc_start: 0.7948 (mt0) cc_final: 0.7528 (mm-40) outliers start: 4 outliers final: 0 residues processed: 153 average time/residue: 0.9642 time to fit residues: 166.4043 Evaluate side-chains 149 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 117 optimal weight: 0.6980 chunk 114 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 138 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 33 optimal weight: 0.0670 chunk 72 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 overall best weight: 1.1524 ------------------------------------------------------------------------------- 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 = 0.106498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.072667 restraints weight = 45543.948| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 1.91 r_work: 0.2750 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2641 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13002 Z= 0.125 Angle : 0.446 4.959 17625 Z= 0.237 Chirality : 0.036 0.124 2007 Planarity : 0.003 0.041 2121 Dihedral : 11.364 154.624 2067 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.08 % Allowed : 11.48 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.85 (0.21), residues: 1593 helix: 3.13 (0.14), residues: 1341 sheet: None (None), residues: 0 loop : -1.08 (0.34), 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 157 PHE 0.020 0.001 PHE C 164 TRP 0.010 0.001 TRP A 112 HIS 0.003 0.001 HIS A 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (13002) covalent geometry : angle 0.44558 / 0.24 (17625) hydrogen bonds : bond 0.04622 / 3.19 ( 988) hydrogen bonds : angle 3.66045 / 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 152 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 151 time to evaluate : 0.630 Fit side-chains REVERT: A 283 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7906 (mm-30) REVERT: A 305 MET cc_start: 0.8211 (mmm) cc_final: 0.7883 (mmt) REVERT: A 421 LYS cc_start: 0.8253 (mttt) cc_final: 0.7661 (mmtt) REVERT: C 421 LYS cc_start: 0.8353 (mttt) cc_final: 0.7697 (mmtt) REVERT: B 264 LYS cc_start: 0.7578 (mttt) cc_final: 0.7342 (mtmt) REVERT: B 305 MET cc_start: 0.8149 (mmm) cc_final: 0.7758 (mmt) REVERT: B 421 LYS cc_start: 0.8394 (mttt) cc_final: 0.7696 (mmtt) REVERT: B 470 MET cc_start: 0.7760 (ttm) cc_final: 0.7389 (ttm) REVERT: B 508 GLN cc_start: 0.7935 (mt0) cc_final: 0.7524 (mm-40) outliers start: 1 outliers final: 0 residues processed: 152 average time/residue: 0.9267 time to fit residues: 158.9657 Evaluate side-chains 151 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 55 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 144 optimal weight: 0.8980 chunk 86 optimal weight: 0.7980 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: 0.7980 chunk 47 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.106451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.072619 restraints weight = 45388.155| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 1.91 r_work: 0.2746 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2637 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13002 Z= 0.123 Angle : 0.445 5.205 17625 Z= 0.237 Chirality : 0.036 0.121 2007 Planarity : 0.003 0.041 2121 Dihedral : 11.305 155.069 2067 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.16 % Allowed : 11.64 % 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: 3.87 (0.21), residues: 1593 helix: 3.15 (0.14), residues: 1341 sheet: None (None), residues: 0 loop : -1.04 (0.34), 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 0.024 0.001 PHE B 164 TRP 0.010 0.001 TRP A 112 HIS 0.003 0.001 HIS A 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (13002) covalent geometry : angle 0.44497 / 0.24 (17625) hydrogen bonds : bond 0.04618 / 3.19 ( 988) hydrogen bonds : angle 3.65035 / 2.71 ( 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 152 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 150 time to evaluate : 0.690 Fit side-chains REVERT: A 283 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7921 (mm-30) REVERT: A 305 MET cc_start: 0.8224 (mmm) cc_final: 0.7899 (mmt) REVERT: A 421 LYS cc_start: 0.8254 (mttt) cc_final: 0.7662 (mmtt) REVERT: C 421 LYS cc_start: 0.8349 (mttt) cc_final: 0.7693 (mmtt) REVERT: B 264 LYS cc_start: 0.7588 (mttt) cc_final: 0.7350 (mtmt) REVERT: B 305 MET cc_start: 0.8161 (mmm) cc_final: 0.7770 (mmt) REVERT: B 421 LYS cc_start: 0.8370 (mttt) cc_final: 0.7693 (mmtt) REVERT: B 470 MET cc_start: 0.7767 (ttm) cc_final: 0.7399 (ttm) REVERT: B 508 GLN cc_start: 0.7918 (mt0) cc_final: 0.7517 (mm-40) outliers start: 2 outliers final: 1 residues processed: 150 average time/residue: 0.9232 time to fit residues: 156.1407 Evaluate side-chains 151 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 150 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 556 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 103 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 130 optimal weight: 0.6980 chunk 113 optimal weight: 0.5980 chunk 111 optimal weight: 0.7980 chunk 150 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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 = 0.3307 r_free = 0.3307 target = 0.105327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.071581 restraints weight = 45655.529| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 1.90 r_work: 0.2729 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2620 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13002 Z= 0.141 Angle : 0.460 5.130 17625 Z= 0.245 Chirality : 0.036 0.122 2007 Planarity : 0.003 0.042 2121 Dihedral : 11.461 156.760 2067 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.08 % Allowed : 11.80 % 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: 3.76 (0.21), residues: 1593 helix: 3.07 (0.14), residues: 1341 sheet: None (None), residues: 0 loop : -1.06 (0.34), 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 494 PHE 0.021 0.001 PHE C 164 TRP 0.010 0.001 TRP A 112 HIS 0.003 0.001 HIS A 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (13002) covalent geometry : angle 0.45990 / 0.24 (17625) hydrogen bonds : bond 0.05008 / 3.46 ( 988) hydrogen bonds : angle 3.71270 / 2.75 ( 2910) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7837.43 seconds wall clock time: 133 minutes 32.59 seconds (8012.59 seconds total)