Starting phenix.real_space_refine on Sat Jun 21 23:17:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tz1_41730/06_2025/8tz1_41730_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tz1_41730/06_2025/8tz1_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8tz1_41730/06_2025/8tz1_41730.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tz1_41730/06_2025/8tz1_41730.map" model { file = "/net/cci-nas-00/data/ceres_data/8tz1_41730/06_2025/8tz1_41730_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tz1_41730/06_2025/8tz1_41730_trim.cif" } resolution = 2.54 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'ASP:plan': 3, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 69 Chain: "A" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 153 Unusual residues: {' NA': 2, 'LBN': 4, 'RBV%rna3p': 1} Classifications: {'undetermined': 7} Modifications used: {'rna3p': 1} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 74 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Restraints were copied for chains: C, B Time building chain proxies: 21.89, per 1000 atoms: 0.88 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: 5.79 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.67 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: 9.43 Time building geometry restraints manager: 7.19 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: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 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: 0.390 Extract box with map and model: 0.880 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 61.050 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.005 0.001 TRP A 261 HIS 0.001 0.000 HIS B 288 PHE 0.011 0.001 PHE C 488 TYR 0.009 0.001 TYR C 231 ARG 0.002 0.000 ARG C 539 Details of bonding type rmsd hydrogen bonds : bond 0.17411 ( 988) hydrogen bonds : angle 5.54023 ( 2910) covalent geometry : bond 0.01147 (13002) covalent geometry : angle 0.87476 (17625) *********************** 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 : 1.990 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: 1.9144 time to fit residues: 435.8072 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 : 1.837 ------------------------------------------------------------------------------- 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 134 optimal weight: 0.8980 chunk 120 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 chunk 124 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 144 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 423 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.108574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.076034 restraints weight = 43449.799| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 1.73 r_work: 0.2742 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2616 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13002 Z= 0.121 Angle : 0.486 4.917 17625 Z= 0.255 Chirality : 0.036 0.131 2007 Planarity : 0.003 0.039 2121 Dihedral : 14.502 157.159 2071 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 1.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.60 (0.21), residues: 1593 helix: 2.93 (0.14), residues: 1338 sheet: None (None), residues: 0 loop : -0.93 (0.35), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 112 HIS 0.003 0.001 HIS A 288 PHE 0.017 0.001 PHE A 164 TYR 0.009 0.001 TYR C 231 ARG 0.002 0.000 ARG B 589 Details of bonding type rmsd hydrogen bonds : bond 0.04845 ( 988) hydrogen bonds : angle 4.02613 ( 2910) covalent geometry : bond 0.00250 (13002) covalent geometry : angle 0.48637 (17625) *********************** 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 177 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 163 time to evaluate : 1.948 Fit side-chains REVERT: A 283 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7467 (mm-30) REVERT: A 305 MET cc_start: 0.8648 (mmm) cc_final: 0.8366 (mmt) REVERT: A 421 LYS cc_start: 0.8499 (mttt) cc_final: 0.8044 (mmtt) REVERT: C 264 LYS cc_start: 0.7716 (mttt) cc_final: 0.7506 (mtmt) REVERT: C 421 LYS cc_start: 0.8537 (mttt) cc_final: 0.8015 (mmtt) REVERT: B 169 GLN cc_start: 0.7627 (tm-30) cc_final: 0.7424 (tm-30) REVERT: B 264 LYS cc_start: 0.7856 (mttt) cc_final: 0.7635 (mtmt) REVERT: B 305 MET cc_start: 0.8654 (mmm) cc_final: 0.8272 (mmt) REVERT: B 421 LYS cc_start: 0.8548 (mttt) cc_final: 0.7981 (mmtt) REVERT: B 470 MET cc_start: 0.8209 (ttm) cc_final: 0.7870 (ttm) REVERT: B 508 GLN cc_start: 0.8231 (mt0) cc_final: 0.7738 (mm-40) REVERT: B 556 MET cc_start: 0.8027 (ttt) cc_final: 0.7775 (ttp) outliers start: 14 outliers final: 4 residues processed: 170 average time/residue: 1.8080 time to fit residues: 349.6148 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 : 1.746 ------------------------------------------------------------------------------- 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 23 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 154 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.102785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.068976 restraints weight = 46118.587| |-----------------------------------------------------------------------------| r_work (start): 0.2812 rms_B_bonded: 1.91 r_work: 0.2688 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2579 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13002 Z= 0.211 Angle : 0.530 5.596 17625 Z= 0.283 Chirality : 0.039 0.134 2007 Planarity : 0.004 0.048 2121 Dihedral : 14.370 161.509 2067 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.11 % Allowed : 8.63 % Favored : 90.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.18 (0.21), residues: 1593 helix: 2.64 (0.14), residues: 1341 sheet: None (None), residues: 0 loop : -1.04 (0.33), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 112 HIS 0.003 0.001 HIS A 288 PHE 0.015 0.001 PHE C 413 TYR 0.011 0.002 TYR C 385 ARG 0.002 0.000 ARG B 557 Details of bonding type rmsd hydrogen bonds : bond 0.06658 ( 988) hydrogen bonds : angle 4.06132 ( 2910) covalent geometry : bond 0.00504 (13002) covalent geometry : angle 0.52987 (17625) *********************** 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 168 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 154 time to evaluate : 2.552 Fit side-chains REVERT: A 283 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7824 (mm-30) REVERT: A 305 MET cc_start: 0.8395 (mmm) cc_final: 0.8064 (mmt) REVERT: A 421 LYS cc_start: 0.8323 (mttt) cc_final: 0.7743 (mmtt) REVERT: C 421 LYS cc_start: 0.8450 (mttt) cc_final: 0.7763 (mmtt) REVERT: B 169 GLN cc_start: 0.7489 (tm-30) cc_final: 0.7265 (tm-30) REVERT: B 264 LYS cc_start: 0.7605 (mttt) cc_final: 0.7344 (mtmt) REVERT: B 305 MET cc_start: 0.8138 (mmm) cc_final: 0.7752 (mmt) REVERT: B 421 LYS cc_start: 0.8409 (mttt) cc_final: 0.7732 (mmtt) REVERT: B 470 MET cc_start: 0.7854 (ttm) cc_final: 0.7472 (ttm) REVERT: B 503 MET cc_start: 0.8563 (OUTLIER) cc_final: 0.8338 (mtm) REVERT: B 506 ASP cc_start: 0.7631 (p0) cc_final: 0.7412 (p0) REVERT: B 508 GLN cc_start: 0.8019 (mt0) cc_final: 0.7415 (mm-40) REVERT: B 556 MET cc_start: 0.8059 (ttt) cc_final: 0.7815 (ttp) outliers start: 14 outliers final: 2 residues processed: 159 average time/residue: 2.5698 time to fit residues: 461.3504 Evaluate side-chains 152 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 149 time to evaluate : 2.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 566 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 117 optimal weight: 0.9980 chunk 121 optimal weight: 1.9990 chunk 138 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 141 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.105488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.071784 restraints weight = 46016.987| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 1.92 r_work: 0.2730 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2619 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.2993 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= 0.124 Angle : 0.455 4.854 17625 Z= 0.242 Chirality : 0.036 0.125 2007 Planarity : 0.003 0.043 2121 Dihedral : 12.915 157.939 2067 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.79 % Allowed : 9.82 % Favored : 89.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.41 (0.21), residues: 1593 helix: 2.81 (0.14), residues: 1341 sheet: None (None), residues: 0 loop : -1.08 (0.33), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 323 HIS 0.002 0.001 HIS B 288 PHE 0.017 0.001 PHE A 164 TYR 0.007 0.001 TYR C 231 ARG 0.002 0.000 ARG A 557 Details of bonding type rmsd hydrogen bonds : bond 0.05026 ( 988) hydrogen bonds : angle 3.85991 ( 2910) covalent geometry : bond 0.00270 (13002) covalent geometry : angle 0.45534 (17625) *********************** 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 164 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 154 time to evaluate : 1.902 Fit side-chains REVERT: A 283 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7872 (mm-30) REVERT: A 305 MET cc_start: 0.8274 (mmm) cc_final: 0.7951 (mmt) REVERT: A 421 LYS cc_start: 0.8349 (mttt) cc_final: 0.7770 (mmtt) REVERT: C 421 LYS cc_start: 0.8434 (mttt) cc_final: 0.7755 (mmtt) REVERT: B 169 GLN cc_start: 0.7466 (tm-30) cc_final: 0.7235 (tm-30) REVERT: B 264 LYS cc_start: 0.7588 (mttt) cc_final: 0.7283 (mtmt) REVERT: B 267 GLN cc_start: 0.7871 (tt0) cc_final: 0.7632 (mt0) REVERT: B 305 MET cc_start: 0.8167 (mmm) cc_final: 0.7781 (mmt) REVERT: B 421 LYS cc_start: 0.8386 (mttt) cc_final: 0.7698 (mmtt) REVERT: B 470 MET cc_start: 0.7765 (ttm) cc_final: 0.7393 (ttm) REVERT: B 508 GLN cc_start: 0.8052 (mt0) cc_final: 0.7526 (mm-40) REVERT: B 556 MET cc_start: 0.7849 (ttt) cc_final: 0.7600 (ttp) outliers start: 10 outliers final: 2 residues processed: 157 average time/residue: 1.9410 time to fit residues: 344.4823 Evaluate side-chains 151 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 149 time to evaluate : 1.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 556 MET Chi-restraints excluded: chain C residue 620 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 68 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 54 optimal weight: 20.0000 chunk 8 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.103554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.069807 restraints weight = 46242.477| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 1.90 r_work: 0.2700 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2592 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.3178 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= 0.168 Angle : 0.483 5.245 17625 Z= 0.259 Chirality : 0.037 0.127 2007 Planarity : 0.004 0.047 2121 Dihedral : 12.968 159.023 2067 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.95 % Allowed : 10.37 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.28 (0.21), residues: 1593 helix: 2.74 (0.14), residues: 1341 sheet: None (None), residues: 0 loop : -1.21 (0.32), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 112 HIS 0.003 0.001 HIS C 288 PHE 0.019 0.001 PHE C 164 TYR 0.008 0.001 TYR C 360 ARG 0.002 0.000 ARG A 557 Details of bonding type rmsd hydrogen bonds : bond 0.05719 ( 988) hydrogen bonds : angle 3.90285 ( 2910) covalent geometry : bond 0.00395 (13002) covalent geometry : angle 0.48285 (17625) *********************** 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 161 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 149 time to evaluate : 1.994 Fit side-chains REVERT: A 283 GLU cc_start: 0.8232 (mm-30) cc_final: 0.7893 (mm-30) REVERT: A 305 MET cc_start: 0.8241 (mmm) cc_final: 0.7910 (mmt) REVERT: A 421 LYS cc_start: 0.8247 (mttt) cc_final: 0.7683 (mmtt) REVERT: C 421 LYS cc_start: 0.8360 (mttt) cc_final: 0.7723 (mmtt) REVERT: C 503 MET cc_start: 0.8257 (OUTLIER) cc_final: 0.8028 (mtp) REVERT: B 108 ARG cc_start: 0.5762 (ttm-80) cc_final: 0.5539 (ttt-90) REVERT: B 169 GLN cc_start: 0.7404 (tm-30) cc_final: 0.7163 (tm-30) REVERT: B 264 LYS cc_start: 0.7578 (mttt) cc_final: 0.7289 (mtmt) REVERT: B 305 MET cc_start: 0.8176 (mmm) cc_final: 0.7795 (mmt) REVERT: B 421 LYS cc_start: 0.8368 (mttt) cc_final: 0.7662 (mmtt) REVERT: B 470 MET cc_start: 0.7739 (ttm) cc_final: 0.7370 (ttm) REVERT: B 508 GLN cc_start: 0.7994 (mt0) cc_final: 0.7499 (mm-40) REVERT: B 556 MET cc_start: 0.7875 (ttt) cc_final: 0.7642 (ttp) outliers start: 12 outliers final: 4 residues processed: 155 average time/residue: 1.9694 time to fit residues: 344.0417 Evaluate side-chains 153 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 148 time to evaluate : 1.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 556 MET Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain C residue 503 MET Chi-restraints excluded: chain C residue 620 ASN Chi-restraints excluded: chain B residue 566 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 5 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 113 optimal weight: 7.9990 chunk 8 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.103581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.069788 restraints weight = 46115.820| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 1.92 r_work: 0.2697 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2588 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.3304 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= 0.162 Angle : 0.475 5.028 17625 Z= 0.255 Chirality : 0.037 0.126 2007 Planarity : 0.004 0.046 2121 Dihedral : 12.695 159.203 2067 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.79 % Allowed : 10.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.30 (0.21), residues: 1593 helix: 2.75 (0.14), residues: 1341 sheet: None (None), residues: 0 loop : -1.21 (0.33), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 112 HIS 0.003 0.001 HIS B 288 PHE 0.019 0.001 PHE A 164 TYR 0.007 0.001 TYR A 310 ARG 0.002 0.000 ARG A 557 Details of bonding type rmsd hydrogen bonds : bond 0.05514 ( 988) hydrogen bonds : angle 3.87255 ( 2910) covalent geometry : bond 0.00379 (13002) covalent geometry : angle 0.47542 (17625) *********************** 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 162 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 152 time to evaluate : 4.035 Fit side-chains REVERT: A 283 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7887 (mm-30) REVERT: A 305 MET cc_start: 0.8339 (mmm) cc_final: 0.8008 (mmt) REVERT: A 421 LYS cc_start: 0.8240 (mttt) cc_final: 0.7659 (mmtt) REVERT: C 421 LYS cc_start: 0.8312 (mttt) cc_final: 0.7645 (mmtt) REVERT: C 503 MET cc_start: 0.8209 (OUTLIER) cc_final: 0.7987 (mtp) REVERT: B 169 GLN cc_start: 0.7415 (tm-30) cc_final: 0.7155 (tm-30) REVERT: B 264 LYS cc_start: 0.7600 (mttt) cc_final: 0.7275 (mtmt) REVERT: B 267 GLN cc_start: 0.7890 (tt0) cc_final: 0.7681 (mt0) REVERT: B 305 MET cc_start: 0.8180 (mmm) cc_final: 0.7790 (mmt) REVERT: B 421 LYS cc_start: 0.8336 (mttt) cc_final: 0.7619 (mmtt) REVERT: B 470 MET cc_start: 0.7748 (ttm) cc_final: 0.7393 (ttm) REVERT: B 503 MET cc_start: 0.8528 (OUTLIER) cc_final: 0.8309 (mtm) REVERT: B 508 GLN cc_start: 0.7987 (mt0) cc_final: 0.7533 (mm-40) REVERT: B 556 MET cc_start: 0.7876 (ttt) cc_final: 0.7653 (ttp) outliers start: 10 outliers final: 4 residues processed: 154 average time/residue: 3.0895 time to fit residues: 543.1547 Evaluate side-chains 153 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 147 time to evaluate : 3.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 556 MET Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain C residue 503 MET Chi-restraints excluded: chain C residue 620 ASN 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 6 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 26 optimal weight: 0.0040 chunk 64 optimal weight: 0.9980 overall best weight: 1.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.104577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.070919 restraints weight = 45927.386| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 1.90 r_work: 0.2719 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2611 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.3388 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= 0.138 Angle : 0.457 5.218 17625 Z= 0.244 Chirality : 0.036 0.123 2007 Planarity : 0.003 0.044 2121 Dihedral : 12.337 159.248 2067 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.71 % Allowed : 11.32 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.45 (0.21), residues: 1593 helix: 2.87 (0.14), residues: 1341 sheet: None (None), residues: 0 loop : -1.25 (0.33), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 112 HIS 0.003 0.001 HIS B 288 PHE 0.020 0.001 PHE C 164 TYR 0.007 0.001 TYR C 494 ARG 0.002 0.000 ARG A 557 Details of bonding type rmsd hydrogen bonds : bond 0.05102 ( 988) hydrogen bonds : angle 3.79605 ( 2910) covalent geometry : bond 0.00316 (13002) covalent geometry : angle 0.45658 (17625) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Evaluate side-chains 160 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 151 time to evaluate : 1.817 Fit side-chains REVERT: A 283 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7893 (mm-30) REVERT: A 305 MET cc_start: 0.8315 (mmm) cc_final: 0.7980 (mmt) REVERT: A 421 LYS cc_start: 0.8213 (mttt) cc_final: 0.7637 (mmtt) REVERT: C 421 LYS cc_start: 0.8297 (mttt) cc_final: 0.7643 (mmtt) REVERT: C 503 MET cc_start: 0.8150 (OUTLIER) cc_final: 0.7900 (mtp) REVERT: B 169 GLN cc_start: 0.7395 (tm-30) cc_final: 0.7148 (tm-30) REVERT: B 264 LYS cc_start: 0.7592 (mttt) cc_final: 0.7347 (mtmt) REVERT: B 267 GLN cc_start: 0.7878 (tt0) cc_final: 0.7622 (mt0) REVERT: B 305 MET cc_start: 0.8187 (mmm) cc_final: 0.7797 (mmt) REVERT: B 421 LYS cc_start: 0.8311 (mttt) cc_final: 0.7615 (mmtt) REVERT: B 470 MET cc_start: 0.7776 (ttm) cc_final: 0.7420 (ttm) REVERT: B 508 GLN cc_start: 0.7961 (mt0) cc_final: 0.7543 (mm-40) REVERT: B 556 MET cc_start: 0.7860 (ttt) cc_final: 0.7645 (ttp) outliers start: 9 outliers final: 4 residues processed: 154 average time/residue: 2.4097 time to fit residues: 420.7557 Evaluate side-chains 153 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 148 time to evaluate : 3.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 556 MET Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain C residue 503 MET Chi-restraints excluded: chain C residue 620 ASN Chi-restraints excluded: chain B residue 566 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 55 optimal weight: 8.9990 chunk 65 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.103937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.070230 restraints weight = 46076.708| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 1.90 r_work: 0.2707 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2598 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13002 Z= 0.154 Angle : 0.469 5.244 17625 Z= 0.251 Chirality : 0.037 0.140 2007 Planarity : 0.004 0.045 2121 Dihedral : 12.379 160.734 2067 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.55 % Allowed : 11.48 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.37 (0.21), residues: 1593 helix: 2.82 (0.14), residues: 1341 sheet: None (None), residues: 0 loop : -1.29 (0.33), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 112 HIS 0.003 0.001 HIS B 288 PHE 0.020 0.001 PHE A 164 TYR 0.007 0.001 TYR C 494 ARG 0.002 0.000 ARG A 108 Details of bonding type rmsd hydrogen bonds : bond 0.05370 ( 988) hydrogen bonds : angle 3.82997 ( 2910) covalent geometry : bond 0.00358 (13002) covalent geometry : angle 0.46862 (17625) *********************** 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: 7 poor density : 148 time to evaluate : 1.749 Fit side-chains REVERT: A 283 GLU cc_start: 0.8204 (mm-30) cc_final: 0.7910 (mm-30) REVERT: A 305 MET cc_start: 0.8317 (mmm) cc_final: 0.7984 (mmt) REVERT: A 421 LYS cc_start: 0.8214 (mttt) cc_final: 0.7633 (mmtt) REVERT: C 421 LYS cc_start: 0.8296 (mttt) cc_final: 0.7642 (mmtt) REVERT: C 503 MET cc_start: 0.8210 (OUTLIER) cc_final: 0.7969 (mtp) REVERT: B 169 GLN cc_start: 0.7350 (tm-30) cc_final: 0.7095 (tm-30) REVERT: B 264 LYS cc_start: 0.7600 (mttt) cc_final: 0.7352 (mtmt) REVERT: B 267 GLN cc_start: 0.7888 (tt0) cc_final: 0.7632 (mt0) REVERT: B 305 MET cc_start: 0.8176 (mmm) cc_final: 0.7784 (mmt) REVERT: B 421 LYS cc_start: 0.8379 (mttt) cc_final: 0.7709 (mmtt) REVERT: B 470 MET cc_start: 0.7756 (ttm) cc_final: 0.7402 (ttm) REVERT: B 503 MET cc_start: 0.8478 (OUTLIER) cc_final: 0.8265 (mtm) REVERT: B 508 GLN cc_start: 0.7970 (mt0) cc_final: 0.7555 (mm-40) REVERT: B 556 MET cc_start: 0.7908 (ttt) cc_final: 0.7694 (ttp) outliers start: 7 outliers final: 4 residues processed: 150 average time/residue: 2.0191 time to fit residues: 340.0570 Evaluate side-chains 151 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 145 time to evaluate : 1.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 556 MET Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain C residue 503 MET Chi-restraints excluded: chain C residue 620 ASN Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 566 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 109 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 55 optimal weight: 8.9990 chunk 93 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 111 optimal weight: 0.4980 chunk 73 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 70 optimal weight: 0.4980 chunk 44 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.106205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.072412 restraints weight = 45563.901| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 1.91 r_work: 0.2744 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2635 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13002 Z= 0.114 Angle : 0.435 5.229 17625 Z= 0.231 Chirality : 0.035 0.122 2007 Planarity : 0.003 0.042 2121 Dihedral : 11.785 158.614 2067 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.32 % Allowed : 11.64 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.69 (0.22), residues: 1593 helix: 3.03 (0.14), residues: 1341 sheet: None (None), residues: 0 loop : -1.15 (0.34), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 112 HIS 0.002 0.000 HIS B 288 PHE 0.020 0.001 PHE C 164 TYR 0.008 0.001 TYR B 157 ARG 0.001 0.000 ARG A 557 Details of bonding type rmsd hydrogen bonds : bond 0.04495 ( 988) hydrogen bonds : angle 3.68805 ( 2910) covalent geometry : bond 0.00250 (13002) covalent geometry : angle 0.43463 (17625) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Residue MET 92 is missing expected H atoms. Skipping. Residue MET 96 is missing expected H atoms. Skipping. Residue SER 97 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue TYR 109 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 421 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 610 is missing expected H atoms. Skipping. Evaluate side-chains 156 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 152 time to evaluate : 1.873 Fit side-chains REVERT: A 283 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7876 (mm-30) REVERT: A 305 MET cc_start: 0.8261 (mmm) cc_final: 0.7926 (mmt) REVERT: A 421 LYS cc_start: 0.8203 (mttt) cc_final: 0.7625 (mmtt) REVERT: C 421 LYS cc_start: 0.8279 (mttt) cc_final: 0.7620 (mmtt) REVERT: B 169 GLN cc_start: 0.7452 (tm-30) cc_final: 0.7180 (tm-30) REVERT: B 264 LYS cc_start: 0.7458 (mttt) cc_final: 0.7207 (mtmt) REVERT: B 267 GLN cc_start: 0.7845 (tt0) cc_final: 0.7584 (mt0) REVERT: B 305 MET cc_start: 0.8136 (mmm) cc_final: 0.7749 (mmt) REVERT: B 421 LYS cc_start: 0.8378 (mttt) cc_final: 0.7700 (mmtt) REVERT: B 470 MET cc_start: 0.7770 (ttm) cc_final: 0.7391 (ttm) REVERT: B 508 GLN cc_start: 0.7930 (mt0) cc_final: 0.7520 (mm-40) outliers start: 4 outliers final: 2 residues processed: 154 average time/residue: 1.9096 time to fit residues: 330.4500 Evaluate side-chains 150 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 148 time to evaluate : 1.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain B residue 566 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 142 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 1 optimal weight: 9.9990 chunk 27 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.104058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.070271 restraints weight = 45938.034| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 1.90 r_work: 0.2704 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2595 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.3566 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= 0.155 Angle : 0.473 5.287 17625 Z= 0.252 Chirality : 0.037 0.121 2007 Planarity : 0.004 0.044 2121 Dihedral : 12.232 160.451 2067 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.16 % Allowed : 12.19 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.50 (0.21), residues: 1593 helix: 2.89 (0.14), residues: 1341 sheet: None (None), residues: 0 loop : -1.12 (0.35), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 112 HIS 0.003 0.001 HIS B 288 PHE 0.023 0.001 PHE B 164 TYR 0.007 0.001 TYR C 494 ARG 0.001 0.000 ARG C 557 Details of bonding type rmsd hydrogen bonds : bond 0.05350 ( 988) hydrogen bonds : angle 3.80014 ( 2910) covalent geometry : bond 0.00362 (13002) covalent geometry : angle 0.47288 (17625) ********************** 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 149 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 147 time to evaluate : 2.000 Fit side-chains REVERT: A 283 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7898 (mm-30) REVERT: A 305 MET cc_start: 0.8292 (mmm) cc_final: 0.7957 (mmt) REVERT: A 421 LYS cc_start: 0.8163 (mttt) cc_final: 0.7568 (mmtt) REVERT: C 421 LYS cc_start: 0.8273 (mttt) cc_final: 0.7611 (mmtt) REVERT: B 169 GLN cc_start: 0.7380 (tm-30) cc_final: 0.7069 (tm-30) REVERT: B 264 LYS cc_start: 0.7586 (mttt) cc_final: 0.7335 (mtmt) REVERT: B 267 GLN cc_start: 0.7885 (tt0) cc_final: 0.7618 (mt0) REVERT: B 305 MET cc_start: 0.8151 (mmm) cc_final: 0.7763 (mmt) REVERT: B 421 LYS cc_start: 0.8338 (mttt) cc_final: 0.7696 (mmtt) REVERT: B 470 MET cc_start: 0.7753 (ttm) cc_final: 0.7384 (ttm) REVERT: B 508 GLN cc_start: 0.7965 (mt0) cc_final: 0.7545 (mm-40) outliers start: 2 outliers final: 2 residues processed: 148 average time/residue: 2.0158 time to fit residues: 334.7123 Evaluate side-chains 149 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 147 time to evaluate : 1.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain B residue 566 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 5 optimal weight: 2.9990 chunk 109 optimal weight: 0.0060 chunk 93 optimal weight: 0.4980 chunk 56 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 overall best weight: 1.3002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.105044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.071326 restraints weight = 45705.253| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 1.88 r_work: 0.2728 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2620 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.3590 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= 0.134 Angle : 0.454 5.260 17625 Z= 0.242 Chirality : 0.036 0.122 2007 Planarity : 0.003 0.043 2121 Dihedral : 11.935 159.479 2067 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.16 % Allowed : 12.27 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.60 (0.21), residues: 1593 helix: 2.96 (0.14), residues: 1341 sheet: None (None), residues: 0 loop : -1.08 (0.35), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 112 HIS 0.003 0.001 HIS A 288 PHE 0.021 0.001 PHE A 164 TYR 0.009 0.001 TYR B 157 ARG 0.002 0.000 ARG A 557 Details of bonding type rmsd hydrogen bonds : bond 0.04919 ( 988) hydrogen bonds : angle 3.74329 ( 2910) covalent geometry : bond 0.00306 (13002) covalent geometry : angle 0.45419 (17625) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17107.47 seconds wall clock time: 299 minutes 6.12 seconds (17946.12 seconds total)