Starting phenix.real_space_refine on Wed Sep 17 15:04:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d66_46586/09_2025/9d66_46586.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d66_46586/09_2025/9d66_46586.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9d66_46586/09_2025/9d66_46586.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d66_46586/09_2025/9d66_46586.map" model { file = "/net/cci-nas-00/data/ceres_data/9d66_46586/09_2025/9d66_46586.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d66_46586/09_2025/9d66_46586.cif" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.141 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: 6 Type Number sf(0) Gaussians Hg 3 10.96 5 S 60 5.16 5 Na 9 4.78 5 C 6087 2.51 5 N 1479 2.21 5 O 1668 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9306 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3085 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 11, 'TRANS': 394} Chain breaks: 2 Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' HG': 1, ' NA': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 13 Unusual residues: {' HG': 1, ' NA': 3} Inner-chain residues flagged as termini: ['pdbres="ASP B 603 "'] Classifications: {'peptide': 1, 'undetermined': 4} Modifications used: {'COO': 1} Link IDs: {None: 4} Chain: "C" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 13 Unusual residues: {' HG': 1, ' NA': 3} Inner-chain residues flagged as termini: ['pdbres="ASP C 603 "'] Classifications: {'peptide': 1, 'undetermined': 4} Modifications used: {'COO': 1} Link IDs: {None: 4} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1577 SG CYS A 269 36.441 24.199 46.434 1.00 69.42 S ATOM 2858 SG CYS A 441 35.971 26.061 44.199 1.00 71.84 S Restraints were copied for chains: B, C Time building chain proxies: 2.38, per 1000 atoms: 0.26 Number of scatterers: 9306 At special positions: 0 Unit cell: (102.08, 107.88, 70.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Hg 3 79.96 S 60 16.00 Na 9 11.00 O 1668 8.00 N 1479 7.00 C 6087 6.00 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: 0.91 Conformation dependent library (CDL) restraints added in 279.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2256 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 3 sheets defined 86.7% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 18 through 42 removed outlier: 3.765A pdb=" N LEU A 22 " --> pdb=" O ASN A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.556A pdb=" N PHE A 50 " --> pdb=" O THR A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 81 removed outlier: 3.644A pdb=" N LEU A 59 " --> pdb=" O PRO A 55 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE A 66 " --> pdb=" O MET A 62 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N LEU A 68 " --> pdb=" O LYS A 64 " (cutoff:3.500A) Proline residue: A 69 - end of helix Processing helix chain 'A' and resid 84 through 117 removed outlier: 4.385A pdb=" N ILE A 90 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY A 91 " --> pdb=" O SER A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 150 removed outlier: 3.636A pdb=" N LEU A 145 " --> pdb=" O ALA A 141 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE A 146 " --> pdb=" O MET A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 158 Processing helix chain 'A' and resid 211 through 229 Processing helix chain 'A' and resid 230 through 232 No H-bonds generated for 'chain 'A' and resid 230 through 232' Processing helix chain 'A' and resid 233 through 272 removed outlier: 4.064A pdb=" N TRP A 256 " --> pdb=" O GLN A 252 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N TYR A 257 " --> pdb=" O ILE A 253 " (cutoff:3.500A) Proline residue: A 259 - end of helix removed outlier: 3.672A pdb=" N CYS A 269 " --> pdb=" O LEU A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 282 Processing helix chain 'A' and resid 282 through 299 Processing helix chain 'A' and resid 299 through 309 Processing helix chain 'A' and resid 312 through 320 removed outlier: 3.685A pdb=" N PHE A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 331 Processing helix chain 'A' and resid 336 through 347 Processing helix chain 'A' and resid 351 through 366 removed outlier: 4.612A pdb=" N PHE A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 359 " --> pdb=" O THR A 355 " (cutoff:3.500A) Proline residue: A 360 - end of helix removed outlier: 4.455A pdb=" N THR A 364 " --> pdb=" O PRO A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 385 Processing helix chain 'A' and resid 390 through 408 Processing helix chain 'A' and resid 414 through 426 removed outlier: 3.564A pdb=" N THR A 418 " --> pdb=" O ALA A 414 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL A 420 " --> pdb=" O LEU A 416 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N ILE A 421 " --> pdb=" O VAL A 417 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL A 422 " --> pdb=" O THR A 418 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL A 426 " --> pdb=" O VAL A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 438 removed outlier: 3.719A pdb=" N VAL A 433 " --> pdb=" O ALA A 430 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ILE A 437 " --> pdb=" O THR A 434 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N ALA A 438 " --> pdb=" O LEU A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 467 removed outlier: 3.588A pdb=" N ARG A 445 " --> pdb=" O CYS A 441 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE A 446 " --> pdb=" O LEU A 442 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N MET A 449 " --> pdb=" O ARG A 445 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASP A 455 " --> pdb=" O ASN A 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 42 removed outlier: 3.765A pdb=" N LEU B 22 " --> pdb=" O ASN B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 53 removed outlier: 3.557A pdb=" N PHE B 50 " --> pdb=" O THR B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 81 removed outlier: 3.644A pdb=" N LEU B 59 " --> pdb=" O PRO B 55 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE B 66 " --> pdb=" O MET B 62 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N LEU B 68 " --> pdb=" O LYS B 64 " (cutoff:3.500A) Proline residue: B 69 - end of helix Processing helix chain 'B' and resid 84 through 117 removed outlier: 4.385A pdb=" N ILE B 90 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY B 91 " --> pdb=" O SER B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 150 removed outlier: 3.636A pdb=" N LEU B 145 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE B 146 " --> pdb=" O MET B 142 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE B 150 " --> pdb=" O ILE B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 158 Processing helix chain 'B' and resid 211 through 229 Processing helix chain 'B' and resid 230 through 232 No H-bonds generated for 'chain 'B' and resid 230 through 232' Processing helix chain 'B' and resid 233 through 272 removed outlier: 4.064A pdb=" N TRP B 256 " --> pdb=" O GLN B 252 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N TYR B 257 " --> pdb=" O ILE B 253 " (cutoff:3.500A) Proline residue: B 259 - end of helix removed outlier: 3.672A pdb=" N CYS B 269 " --> pdb=" O LEU B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 282 Processing helix chain 'B' and resid 282 through 299 Processing helix chain 'B' and resid 299 through 309 Processing helix chain 'B' and resid 312 through 320 removed outlier: 3.684A pdb=" N PHE B 316 " --> pdb=" O ASN B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 331 Processing helix chain 'B' and resid 336 through 347 Processing helix chain 'B' and resid 351 through 366 removed outlier: 4.612A pdb=" N PHE B 357 " --> pdb=" O ARG B 353 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU B 359 " --> pdb=" O THR B 355 " (cutoff:3.500A) Proline residue: B 360 - end of helix removed outlier: 4.454A pdb=" N THR B 364 " --> pdb=" O PRO B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 385 Processing helix chain 'B' and resid 390 through 408 Processing helix chain 'B' and resid 414 through 426 removed outlier: 3.565A pdb=" N THR B 418 " --> pdb=" O ALA B 414 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL B 420 " --> pdb=" O LEU B 416 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N ILE B 421 " --> pdb=" O VAL B 417 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL B 422 " --> pdb=" O THR B 418 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL B 426 " --> pdb=" O VAL B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 438 removed outlier: 3.719A pdb=" N VAL B 433 " --> pdb=" O ALA B 430 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ILE B 437 " --> pdb=" O THR B 434 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N ALA B 438 " --> pdb=" O LEU B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 467 removed outlier: 3.589A pdb=" N ARG B 445 " --> pdb=" O CYS B 441 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE B 446 " --> pdb=" O LEU B 442 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N MET B 449 " --> pdb=" O ARG B 445 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASP B 455 " --> pdb=" O ASN B 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 42 removed outlier: 3.766A pdb=" N LEU C 22 " --> pdb=" O ASN C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 53 removed outlier: 3.557A pdb=" N PHE C 50 " --> pdb=" O THR C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 81 removed outlier: 3.644A pdb=" N LEU C 59 " --> pdb=" O PRO C 55 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE C 66 " --> pdb=" O MET C 62 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LEU C 68 " --> pdb=" O LYS C 64 " (cutoff:3.500A) Proline residue: C 69 - end of helix Processing helix chain 'C' and resid 84 through 117 removed outlier: 4.385A pdb=" N ILE C 90 " --> pdb=" O VAL C 86 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY C 91 " --> pdb=" O SER C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 150 removed outlier: 3.635A pdb=" N LEU C 145 " --> pdb=" O ALA C 141 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE C 146 " --> pdb=" O MET C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 158 Processing helix chain 'C' and resid 211 through 229 Processing helix chain 'C' and resid 230 through 232 No H-bonds generated for 'chain 'C' and resid 230 through 232' Processing helix chain 'C' and resid 233 through 272 removed outlier: 4.064A pdb=" N TRP C 256 " --> pdb=" O GLN C 252 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N TYR C 257 " --> pdb=" O ILE C 253 " (cutoff:3.500A) Proline residue: C 259 - end of helix removed outlier: 3.673A pdb=" N CYS C 269 " --> pdb=" O LEU C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 282 Processing helix chain 'C' and resid 282 through 299 Processing helix chain 'C' and resid 299 through 309 Processing helix chain 'C' and resid 312 through 320 removed outlier: 3.684A pdb=" N PHE C 316 " --> pdb=" O ASN C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 331 Processing helix chain 'C' and resid 336 through 347 Processing helix chain 'C' and resid 351 through 366 removed outlier: 4.613A pdb=" N PHE C 357 " --> pdb=" O ARG C 353 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU C 359 " --> pdb=" O THR C 355 " (cutoff:3.500A) Proline residue: C 360 - end of helix removed outlier: 4.455A pdb=" N THR C 364 " --> pdb=" O PRO C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 385 Processing helix chain 'C' and resid 390 through 408 Processing helix chain 'C' and resid 414 through 426 removed outlier: 3.564A pdb=" N THR C 418 " --> pdb=" O ALA C 414 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL C 420 " --> pdb=" O LEU C 416 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ILE C 421 " --> pdb=" O VAL C 417 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL C 422 " --> pdb=" O THR C 418 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL C 426 " --> pdb=" O VAL C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 438 removed outlier: 3.720A pdb=" N VAL C 433 " --> pdb=" O ALA C 430 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ILE C 437 " --> pdb=" O THR C 434 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N ALA C 438 " --> pdb=" O LEU C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 467 removed outlier: 3.587A pdb=" N ARG C 445 " --> pdb=" O CYS C 441 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE C 446 " --> pdb=" O LEU C 442 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N MET C 449 " --> pdb=" O ARG C 445 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASP C 455 " --> pdb=" O ASN C 451 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 167 Processing sheet with id=AA2, first strand: chain 'B' and resid 160 through 167 Processing sheet with id=AA3, first strand: chain 'C' and resid 160 through 167 725 hydrogen bonds defined for protein. 2130 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: 1.56 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1831 1.33 - 1.45: 1904 1.45 - 1.57: 5571 1.57 - 1.69: 0 1.69 - 1.81: 111 Bond restraints: 9417 Sorted by residual: bond pdb=" N VAL B 411 " pdb=" CA VAL B 411 " ideal model delta sigma weight residual 1.461 1.489 -0.029 8.70e-03 1.32e+04 1.09e+01 bond pdb=" N VAL C 411 " pdb=" CA VAL C 411 " ideal model delta sigma weight residual 1.461 1.488 -0.028 8.70e-03 1.32e+04 1.02e+01 bond pdb=" N VAL A 411 " pdb=" CA VAL A 411 " ideal model delta sigma weight residual 1.461 1.488 -0.028 8.70e-03 1.32e+04 1.00e+01 bond pdb=" N VAL A 417 " pdb=" CA VAL A 417 " ideal model delta sigma weight residual 1.461 1.497 -0.036 1.19e-02 7.06e+03 9.30e+00 bond pdb=" N VAL B 417 " pdb=" CA VAL B 417 " ideal model delta sigma weight residual 1.461 1.496 -0.036 1.19e-02 7.06e+03 9.03e+00 ... (remaining 9412 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.22: 11953 1.22 - 2.45: 680 2.45 - 3.67: 108 3.67 - 4.89: 33 4.89 - 6.11: 9 Bond angle restraints: 12783 Sorted by residual: angle pdb=" N ALA A 414 " pdb=" CA ALA A 414 " pdb=" C ALA A 414 " ideal model delta sigma weight residual 113.50 107.79 5.71 1.23e+00 6.61e-01 2.16e+01 angle pdb=" N ALA C 414 " pdb=" CA ALA C 414 " pdb=" C ALA C 414 " ideal model delta sigma weight residual 113.50 107.81 5.69 1.23e+00 6.61e-01 2.14e+01 angle pdb=" N ALA B 414 " pdb=" CA ALA B 414 " pdb=" C ALA B 414 " ideal model delta sigma weight residual 113.50 107.83 5.67 1.23e+00 6.61e-01 2.13e+01 angle pdb=" C ALA A 414 " pdb=" N GLY A 415 " pdb=" CA GLY A 415 " ideal model delta sigma weight residual 119.98 124.14 -4.16 1.11e+00 8.12e-01 1.40e+01 angle pdb=" C ALA C 414 " pdb=" N GLY C 415 " pdb=" CA GLY C 415 " ideal model delta sigma weight residual 119.98 124.12 -4.14 1.11e+00 8.12e-01 1.39e+01 ... (remaining 12778 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.18: 5183 17.18 - 34.35: 313 34.35 - 51.53: 85 51.53 - 68.70: 29 68.70 - 85.88: 12 Dihedral angle restraints: 5622 sinusoidal: 2127 harmonic: 3495 Sorted by residual: dihedral pdb=" CG ARG C 280 " pdb=" CD ARG C 280 " pdb=" NE ARG C 280 " pdb=" CZ ARG C 280 " ideal model delta sinusoidal sigma weight residual 90.00 41.36 48.64 2 1.50e+01 4.44e-03 1.20e+01 dihedral pdb=" CG ARG B 280 " pdb=" CD ARG B 280 " pdb=" NE ARG B 280 " pdb=" CZ ARG B 280 " ideal model delta sinusoidal sigma weight residual 90.00 41.39 48.61 2 1.50e+01 4.44e-03 1.20e+01 dihedral pdb=" CG ARG A 280 " pdb=" CD ARG A 280 " pdb=" NE ARG A 280 " pdb=" CZ ARG A 280 " ideal model delta sinusoidal sigma weight residual 90.00 41.48 48.52 2 1.50e+01 4.44e-03 1.20e+01 ... (remaining 5619 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1146 0.039 - 0.077: 384 0.077 - 0.116: 68 0.116 - 0.154: 25 0.154 - 0.193: 3 Chirality restraints: 1626 Sorted by residual: chirality pdb=" CA VAL B 411 " pdb=" N VAL B 411 " pdb=" C VAL B 411 " pdb=" CB VAL B 411 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 9.30e-01 chirality pdb=" CA VAL C 411 " pdb=" N VAL C 411 " pdb=" C VAL C 411 " pdb=" CB VAL C 411 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.87e-01 chirality pdb=" CA VAL A 411 " pdb=" N VAL A 411 " pdb=" C VAL A 411 " pdb=" CB VAL A 411 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.63e-01 ... (remaining 1623 not shown) Planarity restraints: 1557 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 39 " 0.149 9.50e-02 1.11e+02 6.74e-02 3.34e+00 pdb=" NE ARG B 39 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG B 39 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG B 39 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG B 39 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 39 " -0.150 9.50e-02 1.11e+02 6.75e-02 3.30e+00 pdb=" NE ARG C 39 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG C 39 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG C 39 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG C 39 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 39 " 0.148 9.50e-02 1.11e+02 6.69e-02 3.26e+00 pdb=" NE ARG A 39 " -0.013 2.00e-02 2.50e+03 pdb=" CZ ARG A 39 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A 39 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 39 " 0.001 2.00e-02 2.50e+03 ... (remaining 1554 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.62: 103 2.62 - 3.19: 9119 3.19 - 3.76: 14445 3.76 - 4.33: 21323 4.33 - 4.90: 34404 Nonbonded interactions: 79394 Sorted by model distance: nonbonded pdb=" OD1 ASP B 368 " pdb="NA NA B 601 " model vdw 2.055 2.470 nonbonded pdb=" OD1 ASP C 368 " pdb="NA NA C 601 " model vdw 2.056 2.470 nonbonded pdb=" OD1 ASP A 368 " pdb="NA NA A 603 " model vdw 2.056 2.470 nonbonded pdb=" SG CYS A 269 " pdb="HG HG A 604 " model vdw 2.078 2.880 nonbonded pdb=" SG CYS C 269 " pdb="HG HG C 605 " model vdw 2.078 2.880 ... (remaining 79389 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 17 through 470 or resid 601)) selection = (chain 'B' and (resid 17 through 470 or resid 602)) selection = (chain 'C' and (resid 17 through 470 or resid 602)) } 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: 1.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.580 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 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 : 0.004 0.036 9417 Z= 0.222 Angle : 0.684 6.115 12783 Z= 0.428 Chirality : 0.041 0.193 1626 Planarity : 0.005 0.068 1557 Dihedral : 13.815 85.876 3366 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.67 (0.22), residues: 1200 helix: -1.15 (0.15), residues: 945 sheet: 0.17 (0.68), residues: 54 loop : -0.06 (0.47), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG B 39 TYR 0.018 0.004 TYR A 98 PHE 0.018 0.002 PHE C 279 TRP 0.006 0.002 TRP C 19 HIS 0.003 0.001 HIS C 296 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 9417) covalent geometry : angle 0.68358 (12783) hydrogen bonds : bond 0.19943 ( 725) hydrogen bonds : angle 7.87612 ( 2130) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 0.333 Fit side-chains REVERT: A 149 MET cc_start: 0.8956 (mtm) cc_final: 0.8741 (mtp) REVERT: A 205 MET cc_start: 0.8290 (ptm) cc_final: 0.7919 (ptt) REVERT: A 229 MET cc_start: 0.8831 (mtm) cc_final: 0.8544 (mtm) REVERT: A 256 TRP cc_start: 0.8195 (m100) cc_final: 0.7427 (m-10) REVERT: A 272 GLU cc_start: 0.7502 (mm-30) cc_final: 0.7157 (mt-10) REVERT: A 278 ILE cc_start: 0.7780 (mt) cc_final: 0.7469 (mp) REVERT: A 280 ARG cc_start: 0.7260 (ttp80) cc_final: 0.6754 (ttm170) REVERT: A 281 LYS cc_start: 0.7194 (tttt) cc_final: 0.6412 (mmtp) REVERT: A 286 MET cc_start: 0.8152 (mtp) cc_final: 0.7786 (mtm) REVERT: A 318 MET cc_start: 0.7073 (tpt) cc_final: 0.6430 (ttp) REVERT: A 352 LYS cc_start: 0.7480 (tmtt) cc_final: 0.6913 (mttt) REVERT: A 445 ARG cc_start: 0.8356 (mtt90) cc_final: 0.8140 (mtt90) REVERT: B 205 MET cc_start: 0.8425 (ptm) cc_final: 0.8108 (ptt) REVERT: B 232 LYS cc_start: 0.8114 (ttpt) cc_final: 0.7853 (ttpt) REVERT: B 249 LYS cc_start: 0.8344 (mttt) cc_final: 0.7931 (mttm) REVERT: B 258 MET cc_start: 0.8275 (ttt) cc_final: 0.8007 (ttt) REVERT: B 260 LEU cc_start: 0.7648 (tm) cc_final: 0.7430 (tt) REVERT: B 272 GLU cc_start: 0.7384 (mm-30) cc_final: 0.7052 (mt-10) REVERT: B 278 ILE cc_start: 0.7933 (mt) cc_final: 0.7635 (OUTLIER) REVERT: B 280 ARG cc_start: 0.7193 (ttp80) cc_final: 0.6851 (ttm170) REVERT: B 281 LYS cc_start: 0.7258 (tttt) cc_final: 0.6261 (mmtp) REVERT: B 286 MET cc_start: 0.8260 (mtp) cc_final: 0.8046 (mtm) REVERT: B 304 ILE cc_start: 0.7938 (pt) cc_final: 0.7563 (mt) REVERT: B 315 ARG cc_start: 0.7620 (tpp-160) cc_final: 0.7094 (ttm110) REVERT: B 318 MET cc_start: 0.7126 (tpt) cc_final: 0.6394 (ttp) REVERT: B 352 LYS cc_start: 0.7692 (tmtt) cc_final: 0.7186 (mttt) REVERT: B 356 ARG cc_start: 0.6689 (tpm170) cc_final: 0.6255 (ptp-170) REVERT: B 357 PHE cc_start: 0.7910 (t80) cc_final: 0.7585 (t80) REVERT: C 99 PHE cc_start: 0.7550 (t80) cc_final: 0.7295 (t80) REVERT: C 232 LYS cc_start: 0.7955 (ttpt) cc_final: 0.7301 (tptm) REVERT: C 256 TRP cc_start: 0.8167 (m100) cc_final: 0.7421 (m-10) REVERT: C 258 MET cc_start: 0.8390 (ttt) cc_final: 0.7945 (ttt) REVERT: C 275 ASP cc_start: 0.6784 (m-30) cc_final: 0.6522 (t0) REVERT: C 278 ILE cc_start: 0.7815 (mt) cc_final: 0.7553 (mp) REVERT: C 280 ARG cc_start: 0.7450 (ttp80) cc_final: 0.7006 (ttm170) REVERT: C 281 LYS cc_start: 0.7405 (tttt) cc_final: 0.6640 (mmtp) REVERT: C 286 MET cc_start: 0.8136 (mtp) cc_final: 0.7737 (mtt) REVERT: C 304 ILE cc_start: 0.7831 (pt) cc_final: 0.7382 (mt) REVERT: C 318 MET cc_start: 0.7420 (tpt) cc_final: 0.6849 (ttp) REVERT: C 322 GLN cc_start: 0.8159 (tt0) cc_final: 0.7752 (tt0) REVERT: C 325 LEU cc_start: 0.7877 (mt) cc_final: 0.7649 (tp) REVERT: C 352 LYS cc_start: 0.7483 (tmtt) cc_final: 0.7028 (mttt) REVERT: C 356 ARG cc_start: 0.6348 (tpm170) cc_final: 0.6131 (ptp-170) outliers start: 0 outliers final: 1 residues processed: 207 average time/residue: 0.5664 time to fit residues: 124.6620 Evaluate side-chains 167 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 0.7980 chunk 113 optimal weight: 0.6980 chunk 53 optimal weight: 0.0570 chunk 5 optimal weight: 0.4980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 117 optimal weight: 3.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN A 252 GLN A 312 ASN A 348 ASN A 385 ASN B 211 ASN B 252 GLN C 211 ASN C 252 GLN C 312 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.185919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.150047 restraints weight = 2532.073| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 0.70 r_work: 0.3129 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9417 Z= 0.147 Angle : 0.552 7.498 12783 Z= 0.293 Chirality : 0.041 0.151 1626 Planarity : 0.004 0.036 1557 Dihedral : 4.020 13.423 1281 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 2.47 % Allowed : 10.95 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.23), residues: 1200 helix: 0.60 (0.16), residues: 954 sheet: 0.34 (0.75), residues: 54 loop : -0.07 (0.43), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 280 TYR 0.010 0.002 TYR B 373 PHE 0.027 0.002 PHE B 222 TRP 0.006 0.001 TRP B 19 HIS 0.001 0.000 HIS B 296 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 9417) covalent geometry : angle 0.55233 (12783) hydrogen bonds : bond 0.05292 ( 725) hydrogen bonds : angle 5.00562 ( 2130) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 172 time to evaluate : 0.354 Fit side-chains REVERT: A 40 GLU cc_start: 0.7147 (mt-10) cc_final: 0.6808 (mt-10) REVERT: A 117 LYS cc_start: 0.8145 (mtpp) cc_final: 0.7940 (mttm) REVERT: A 163 LYS cc_start: 0.8237 (ttmm) cc_final: 0.7427 (pttp) REVERT: A 228 LYS cc_start: 0.8195 (mptt) cc_final: 0.6866 (mtpt) REVERT: A 229 MET cc_start: 0.8829 (mtm) cc_final: 0.8475 (mtm) REVERT: A 256 TRP cc_start: 0.8539 (m100) cc_final: 0.7729 (m-10) REVERT: A 272 GLU cc_start: 0.7284 (mm-30) cc_final: 0.6746 (mt-10) REVERT: A 280 ARG cc_start: 0.7027 (ttp80) cc_final: 0.6519 (ttm170) REVERT: A 281 LYS cc_start: 0.6974 (tttt) cc_final: 0.6156 (mmtp) REVERT: A 286 MET cc_start: 0.8344 (mtp) cc_final: 0.7999 (mtm) REVERT: A 315 ARG cc_start: 0.7514 (tpp-160) cc_final: 0.7159 (ttm110) REVERT: A 318 MET cc_start: 0.7326 (tpt) cc_final: 0.6794 (ttm) REVERT: A 347 ASN cc_start: 0.8173 (OUTLIER) cc_final: 0.7819 (m110) REVERT: A 352 LYS cc_start: 0.7084 (tmtt) cc_final: 0.6687 (mttt) REVERT: A 356 ARG cc_start: 0.6607 (tpm170) cc_final: 0.6193 (ptp-110) REVERT: A 357 PHE cc_start: 0.8270 (t80) cc_final: 0.8052 (t80) REVERT: A 359 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8217 (mp) REVERT: A 368 ASP cc_start: 0.8034 (OUTLIER) cc_final: 0.7508 (m-30) REVERT: A 444 ASP cc_start: 0.7863 (t0) cc_final: 0.7636 (t0) REVERT: A 464 LYS cc_start: 0.7244 (tppp) cc_final: 0.6587 (tppt) REVERT: B 40 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6744 (mt-10) REVERT: B 205 MET cc_start: 0.8498 (ptm) cc_final: 0.8181 (ptt) REVERT: B 232 LYS cc_start: 0.7978 (ttpt) cc_final: 0.7443 (mtpt) REVERT: B 272 GLU cc_start: 0.7320 (mm-30) cc_final: 0.6838 (mt-10) REVERT: B 281 LYS cc_start: 0.6779 (tttt) cc_final: 0.5870 (mmtp) REVERT: B 304 ILE cc_start: 0.7796 (pt) cc_final: 0.7365 (mt) REVERT: B 318 MET cc_start: 0.7195 (tpt) cc_final: 0.6553 (ttp) REVERT: B 329 MET cc_start: 0.8376 (mmt) cc_final: 0.8166 (mmt) REVERT: B 352 LYS cc_start: 0.7021 (tmtt) cc_final: 0.6637 (mttt) REVERT: B 356 ARG cc_start: 0.6827 (tpm170) cc_final: 0.6321 (ptp-110) REVERT: C 232 LYS cc_start: 0.8070 (ttpt) cc_final: 0.7746 (mtmp) REVERT: C 256 TRP cc_start: 0.8528 (m100) cc_final: 0.7641 (m-10) REVERT: C 258 MET cc_start: 0.8199 (ttt) cc_final: 0.7894 (ttt) REVERT: C 280 ARG cc_start: 0.7374 (ttp80) cc_final: 0.6927 (ttm170) REVERT: C 281 LYS cc_start: 0.7178 (tttt) cc_final: 0.6422 (mmtp) REVERT: C 286 MET cc_start: 0.8286 (mtp) cc_final: 0.7941 (mtm) REVERT: C 304 ILE cc_start: 0.7521 (pt) cc_final: 0.7156 (mt) REVERT: C 318 MET cc_start: 0.7461 (tpt) cc_final: 0.6894 (ttp) REVERT: C 352 LYS cc_start: 0.7244 (tmtt) cc_final: 0.6796 (mttt) outliers start: 25 outliers final: 6 residues processed: 183 average time/residue: 0.6087 time to fit residues: 118.0591 Evaluate side-chains 173 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 163 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 368 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 113 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 115 optimal weight: 0.3980 chunk 51 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 105 optimal weight: 4.9990 chunk 116 optimal weight: 0.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 GLN A 312 ASN B 252 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.185880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.150075 restraints weight = 2538.470| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 0.67 r_work: 0.3100 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9417 Z= 0.175 Angle : 0.556 6.850 12783 Z= 0.291 Chirality : 0.042 0.140 1626 Planarity : 0.004 0.036 1557 Dihedral : 3.900 12.124 1281 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 3.35 % Allowed : 11.54 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.24), residues: 1200 helix: 0.84 (0.16), residues: 954 sheet: 0.46 (0.74), residues: 54 loop : -0.20 (0.42), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 353 TYR 0.012 0.002 TYR B 373 PHE 0.016 0.002 PHE C 240 TRP 0.004 0.001 TRP B 276 HIS 0.002 0.001 HIS B 296 Details of bonding type rmsd covalent geometry : bond 0.00432 ( 9417) covalent geometry : angle 0.55594 (12783) hydrogen bonds : bond 0.05136 ( 725) hydrogen bonds : angle 4.85763 ( 2130) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 164 time to evaluate : 0.259 Fit side-chains REVERT: A 142 MET cc_start: 0.8620 (mmm) cc_final: 0.8419 (mmp) REVERT: A 229 MET cc_start: 0.8787 (mtm) cc_final: 0.8547 (mtm) REVERT: A 256 TRP cc_start: 0.8517 (m100) cc_final: 0.7711 (m-10) REVERT: A 272 GLU cc_start: 0.7305 (mm-30) cc_final: 0.6786 (mt-10) REVERT: A 280 ARG cc_start: 0.7064 (ttp80) cc_final: 0.6567 (ttm170) REVERT: A 281 LYS cc_start: 0.7134 (tttt) cc_final: 0.6116 (mmtp) REVERT: A 286 MET cc_start: 0.8291 (mtp) cc_final: 0.8035 (mtm) REVERT: A 318 MET cc_start: 0.7236 (tpt) cc_final: 0.6794 (ttp) REVERT: A 352 LYS cc_start: 0.7115 (tmtt) cc_final: 0.6789 (mttt) REVERT: A 356 ARG cc_start: 0.6802 (tpm170) cc_final: 0.6319 (ptp-110) REVERT: A 367 MET cc_start: 0.8981 (OUTLIER) cc_final: 0.8479 (mtm) REVERT: A 368 ASP cc_start: 0.8110 (OUTLIER) cc_final: 0.7463 (m-30) REVERT: A 419 MET cc_start: 0.8460 (OUTLIER) cc_final: 0.6819 (tmm) REVERT: B 40 GLU cc_start: 0.7159 (OUTLIER) cc_final: 0.6805 (mt-10) REVERT: B 205 MET cc_start: 0.8516 (ptm) cc_final: 0.8221 (ptt) REVERT: B 232 LYS cc_start: 0.7916 (ttpt) cc_final: 0.7510 (mtpt) REVERT: B 269 CYS cc_start: 0.7166 (t) cc_final: 0.6835 (t) REVERT: B 272 GLU cc_start: 0.7218 (mm-30) cc_final: 0.6797 (mm-30) REVERT: B 280 ARG cc_start: 0.7052 (ttp80) cc_final: 0.6706 (ttm170) REVERT: B 281 LYS cc_start: 0.6925 (tttt) cc_final: 0.5910 (mmtp) REVERT: B 304 ILE cc_start: 0.7669 (pt) cc_final: 0.7396 (mt) REVERT: B 315 ARG cc_start: 0.7396 (tpp-160) cc_final: 0.7137 (ttm170) REVERT: B 318 MET cc_start: 0.7227 (tpt) cc_final: 0.6845 (ttp) REVERT: B 352 LYS cc_start: 0.7031 (tmtt) cc_final: 0.6674 (mttt) REVERT: B 356 ARG cc_start: 0.6711 (tpm170) cc_final: 0.6206 (ptp-110) REVERT: B 357 PHE cc_start: 0.8189 (t80) cc_final: 0.7922 (t80) REVERT: B 444 ASP cc_start: 0.7827 (t0) cc_final: 0.7461 (t0) REVERT: C 75 MET cc_start: 0.8376 (mmt) cc_final: 0.8033 (mmp) REVERT: C 232 LYS cc_start: 0.7999 (ttpt) cc_final: 0.7761 (mtmt) REVERT: C 256 TRP cc_start: 0.8602 (m100) cc_final: 0.7759 (m-10) REVERT: C 258 MET cc_start: 0.8266 (ttt) cc_final: 0.7978 (ttt) REVERT: C 280 ARG cc_start: 0.7388 (ttp80) cc_final: 0.6896 (ttm170) REVERT: C 281 LYS cc_start: 0.7172 (tttt) cc_final: 0.6424 (mmtp) REVERT: C 286 MET cc_start: 0.8215 (mtp) cc_final: 0.7946 (mtm) REVERT: C 304 ILE cc_start: 0.7522 (pt) cc_final: 0.7220 (mt) REVERT: C 315 ARG cc_start: 0.7630 (tpp-160) cc_final: 0.7258 (ttm170) REVERT: C 318 MET cc_start: 0.7596 (tpt) cc_final: 0.7004 (ttp) REVERT: C 352 LYS cc_start: 0.7210 (tmtt) cc_final: 0.6826 (mttt) REVERT: C 445 ARG cc_start: 0.8409 (mtt90) cc_final: 0.8091 (mmt180) outliers start: 34 outliers final: 15 residues processed: 178 average time/residue: 0.5834 time to fit residues: 110.4529 Evaluate side-chains 184 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 165 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 403 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 65 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 115 optimal weight: 1.9990 chunk 47 optimal weight: 7.9990 chunk 113 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 GLN C 312 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.184149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.147663 restraints weight = 2685.702| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 0.70 r_work: 0.3069 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 9417 Z= 0.198 Angle : 0.567 6.531 12783 Z= 0.297 Chirality : 0.043 0.156 1626 Planarity : 0.004 0.038 1557 Dihedral : 3.902 12.144 1281 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 3.94 % Allowed : 12.72 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.24), residues: 1200 helix: 0.74 (0.16), residues: 963 sheet: 1.47 (0.72), residues: 48 loop : -0.47 (0.44), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 353 TYR 0.010 0.001 TYR B 373 PHE 0.016 0.002 PHE B 264 TRP 0.004 0.001 TRP A 276 HIS 0.002 0.001 HIS B 296 Details of bonding type rmsd covalent geometry : bond 0.00502 ( 9417) covalent geometry : angle 0.56676 (12783) hydrogen bonds : bond 0.05262 ( 725) hydrogen bonds : angle 4.87441 ( 2130) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 162 time to evaluate : 0.333 Fit side-chains REVERT: A 60 MET cc_start: 0.8581 (mmm) cc_final: 0.8267 (mmm) REVERT: A 229 MET cc_start: 0.8859 (mtm) cc_final: 0.8641 (mtm) REVERT: A 231 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7621 (tm-30) REVERT: A 256 TRP cc_start: 0.8520 (m100) cc_final: 0.7718 (m-10) REVERT: A 272 GLU cc_start: 0.7397 (mm-30) cc_final: 0.6874 (mt-10) REVERT: A 280 ARG cc_start: 0.7091 (ttp80) cc_final: 0.6598 (ttm170) REVERT: A 281 LYS cc_start: 0.7175 (tttt) cc_final: 0.6106 (mmtp) REVERT: A 286 MET cc_start: 0.8284 (mtp) cc_final: 0.8007 (mtm) REVERT: A 318 MET cc_start: 0.7291 (tpt) cc_final: 0.6909 (ttp) REVERT: A 347 ASN cc_start: 0.8410 (OUTLIER) cc_final: 0.8144 (m110) REVERT: A 352 LYS cc_start: 0.6984 (tmtt) cc_final: 0.6755 (mttt) REVERT: A 356 ARG cc_start: 0.6871 (tpm170) cc_final: 0.6299 (ptp-110) REVERT: A 359 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8346 (mp) REVERT: A 368 ASP cc_start: 0.8193 (OUTLIER) cc_final: 0.7450 (m-30) REVERT: A 419 MET cc_start: 0.8496 (OUTLIER) cc_final: 0.6866 (tmm) REVERT: A 444 ASP cc_start: 0.7836 (t0) cc_final: 0.7626 (t0) REVERT: B 205 MET cc_start: 0.8565 (ptm) cc_final: 0.8277 (ptt) REVERT: B 231 GLU cc_start: 0.7999 (tp30) cc_final: 0.7726 (tm-30) REVERT: B 232 LYS cc_start: 0.7953 (ttpt) cc_final: 0.7577 (mtpt) REVERT: B 269 CYS cc_start: 0.7364 (t) cc_final: 0.6970 (t) REVERT: B 272 GLU cc_start: 0.7265 (mm-30) cc_final: 0.6820 (mm-30) REVERT: B 280 ARG cc_start: 0.7261 (ttp80) cc_final: 0.6803 (ttm170) REVERT: B 281 LYS cc_start: 0.7002 (tttt) cc_final: 0.5933 (mmtp) REVERT: B 304 ILE cc_start: 0.7806 (pt) cc_final: 0.7554 (mt) REVERT: B 315 ARG cc_start: 0.7456 (tpp-160) cc_final: 0.7245 (ttm170) REVERT: B 318 MET cc_start: 0.7276 (tpt) cc_final: 0.7008 (ttp) REVERT: B 347 ASN cc_start: 0.8485 (OUTLIER) cc_final: 0.8192 (m110) REVERT: B 352 LYS cc_start: 0.7030 (tmtt) cc_final: 0.6535 (mttt) REVERT: B 353 ARG cc_start: 0.7978 (mtm-85) cc_final: 0.7752 (mpp80) REVERT: B 356 ARG cc_start: 0.6783 (tpm170) cc_final: 0.6341 (ptt90) REVERT: B 419 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.8042 (tpp) REVERT: B 445 ARG cc_start: 0.8399 (mtt90) cc_final: 0.8093 (mmt180) REVERT: C 40 GLU cc_start: 0.7340 (mt-10) cc_final: 0.6934 (mp0) REVERT: C 232 LYS cc_start: 0.7951 (ttpt) cc_final: 0.7708 (mtmt) REVERT: C 256 TRP cc_start: 0.8621 (m100) cc_final: 0.7774 (m-10) REVERT: C 258 MET cc_start: 0.8278 (OUTLIER) cc_final: 0.7947 (ttt) REVERT: C 280 ARG cc_start: 0.7368 (ttp80) cc_final: 0.6918 (ttm170) REVERT: C 281 LYS cc_start: 0.7226 (tttt) cc_final: 0.6305 (mmmm) REVERT: C 286 MET cc_start: 0.8214 (mtp) cc_final: 0.7928 (mtm) REVERT: C 304 ILE cc_start: 0.7522 (pt) cc_final: 0.7203 (mt) REVERT: C 307 ILE cc_start: 0.7567 (OUTLIER) cc_final: 0.7327 (mt) REVERT: C 315 ARG cc_start: 0.7622 (tpp-160) cc_final: 0.7288 (ttm170) REVERT: C 318 MET cc_start: 0.7760 (tpt) cc_final: 0.7311 (ttp) REVERT: C 352 LYS cc_start: 0.7198 (tmtt) cc_final: 0.6853 (mttt) REVERT: C 445 ARG cc_start: 0.8405 (mtt90) cc_final: 0.8143 (mmt180) outliers start: 40 outliers final: 19 residues processed: 178 average time/residue: 0.5613 time to fit residues: 106.3674 Evaluate side-chains 184 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 156 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 347 ASN Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 258 MET Chi-restraints excluded: chain C residue 269 CYS Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 347 ASN Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 403 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 32 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 117 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.186422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.150318 restraints weight = 2733.495| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 0.69 r_work: 0.3100 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9417 Z= 0.145 Angle : 0.506 5.494 12783 Z= 0.265 Chirality : 0.040 0.140 1626 Planarity : 0.004 0.037 1557 Dihedral : 3.708 11.807 1281 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 3.55 % Allowed : 13.51 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.24), residues: 1200 helix: 1.02 (0.17), residues: 948 sheet: 1.72 (0.74), residues: 48 loop : -0.43 (0.41), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 353 TYR 0.012 0.001 TYR B 373 PHE 0.013 0.002 PHE B 222 TRP 0.004 0.001 TRP A 276 HIS 0.001 0.001 HIS B 296 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 9417) covalent geometry : angle 0.50557 (12783) hydrogen bonds : bond 0.04650 ( 725) hydrogen bonds : angle 4.71931 ( 2130) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 162 time to evaluate : 0.243 Fit side-chains REVERT: A 256 TRP cc_start: 0.8520 (m100) cc_final: 0.7712 (m-10) REVERT: A 272 GLU cc_start: 0.7404 (mm-30) cc_final: 0.6839 (mt-10) REVERT: A 280 ARG cc_start: 0.7263 (ttp80) cc_final: 0.6818 (ttm170) REVERT: A 281 LYS cc_start: 0.7195 (tttt) cc_final: 0.6169 (mmtp) REVERT: A 286 MET cc_start: 0.8276 (mtp) cc_final: 0.8032 (mtm) REVERT: A 318 MET cc_start: 0.7228 (tpt) cc_final: 0.6879 (ttp) REVERT: A 356 ARG cc_start: 0.6789 (tpm170) cc_final: 0.6310 (ptp-110) REVERT: A 357 PHE cc_start: 0.8332 (t80) cc_final: 0.8088 (t80) REVERT: A 359 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8197 (mp) REVERT: A 368 ASP cc_start: 0.8084 (OUTLIER) cc_final: 0.7419 (m-30) REVERT: A 419 MET cc_start: 0.8457 (OUTLIER) cc_final: 0.6883 (tmm) REVERT: B 40 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.7124 (mt-10) REVERT: B 205 MET cc_start: 0.8556 (ptm) cc_final: 0.8258 (ptt) REVERT: B 232 LYS cc_start: 0.7815 (ttpt) cc_final: 0.7448 (mtpt) REVERT: B 269 CYS cc_start: 0.7410 (t) cc_final: 0.6971 (t) REVERT: B 281 LYS cc_start: 0.7087 (tttt) cc_final: 0.5959 (mmtp) REVERT: B 307 ILE cc_start: 0.7559 (OUTLIER) cc_final: 0.7279 (OUTLIER) REVERT: B 318 MET cc_start: 0.7294 (tpt) cc_final: 0.7079 (ttp) REVERT: B 352 LYS cc_start: 0.6972 (tmtt) cc_final: 0.6723 (mttt) REVERT: B 356 ARG cc_start: 0.6788 (tpm170) cc_final: 0.6251 (ptp-110) REVERT: B 419 MET cc_start: 0.8355 (OUTLIER) cc_final: 0.7984 (tpp) REVERT: B 444 ASP cc_start: 0.7660 (t0) cc_final: 0.7360 (t0) REVERT: C 40 GLU cc_start: 0.7356 (mt-10) cc_final: 0.6987 (mp0) REVERT: C 232 LYS cc_start: 0.7825 (ttpt) cc_final: 0.7577 (mtmt) REVERT: C 256 TRP cc_start: 0.8590 (m100) cc_final: 0.7737 (m-10) REVERT: C 258 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.7921 (ttt) REVERT: C 280 ARG cc_start: 0.7438 (ttp80) cc_final: 0.7042 (ttm170) REVERT: C 281 LYS cc_start: 0.7232 (tttt) cc_final: 0.6324 (mmmm) REVERT: C 286 MET cc_start: 0.8228 (mtp) cc_final: 0.7939 (mtm) REVERT: C 307 ILE cc_start: 0.7640 (OUTLIER) cc_final: 0.7403 (mt) REVERT: C 315 ARG cc_start: 0.7572 (tpp-160) cc_final: 0.7272 (ttm170) REVERT: C 318 MET cc_start: 0.7550 (tpt) cc_final: 0.7150 (ttp) REVERT: C 352 LYS cc_start: 0.7176 (tmtt) cc_final: 0.6859 (mttt) REVERT: C 353 ARG cc_start: 0.7781 (mpp80) cc_final: 0.7569 (mpp80) REVERT: C 419 MET cc_start: 0.8672 (OUTLIER) cc_final: 0.7237 (tmm) REVERT: C 445 ARG cc_start: 0.8327 (mtt90) cc_final: 0.8098 (mmt180) outliers start: 36 outliers final: 14 residues processed: 179 average time/residue: 0.4954 time to fit residues: 95.1970 Evaluate side-chains 179 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 157 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain C residue 258 MET Chi-restraints excluded: chain C residue 269 CYS Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 419 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 0.5980 chunk 99 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 54 optimal weight: 0.3980 chunk 95 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN C 312 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.186954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.151142 restraints weight = 2677.197| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 0.68 r_work: 0.3113 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9417 Z= 0.138 Angle : 0.500 5.183 12783 Z= 0.262 Chirality : 0.040 0.179 1626 Planarity : 0.004 0.036 1557 Dihedral : 3.624 11.473 1281 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 3.75 % Allowed : 14.40 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.32 (0.24), residues: 1200 helix: 1.16 (0.17), residues: 948 sheet: 1.84 (0.74), residues: 48 loop : -0.38 (0.41), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 353 TYR 0.009 0.001 TYR B 373 PHE 0.012 0.001 PHE C 240 TRP 0.004 0.001 TRP A 276 HIS 0.001 0.000 HIS B 296 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 9417) covalent geometry : angle 0.49987 (12783) hydrogen bonds : bond 0.04509 ( 725) hydrogen bonds : angle 4.67901 ( 2130) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 158 time to evaluate : 0.307 Fit side-chains REVERT: A 256 TRP cc_start: 0.8505 (m100) cc_final: 0.7703 (m-10) REVERT: A 272 GLU cc_start: 0.7406 (mm-30) cc_final: 0.6843 (mt-10) REVERT: A 280 ARG cc_start: 0.7277 (ttp80) cc_final: 0.6835 (ttm170) REVERT: A 281 LYS cc_start: 0.7219 (tttt) cc_final: 0.6199 (mmtp) REVERT: A 286 MET cc_start: 0.8308 (mtp) cc_final: 0.8054 (mtm) REVERT: A 307 ILE cc_start: 0.7574 (OUTLIER) cc_final: 0.7312 (mt) REVERT: A 318 MET cc_start: 0.7185 (tpt) cc_final: 0.6828 (ttp) REVERT: A 347 ASN cc_start: 0.8396 (OUTLIER) cc_final: 0.8123 (m110) REVERT: A 356 ARG cc_start: 0.6710 (tpm170) cc_final: 0.6205 (ptp-110) REVERT: A 357 PHE cc_start: 0.8267 (t80) cc_final: 0.8021 (t80) REVERT: A 359 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8175 (mp) REVERT: A 368 ASP cc_start: 0.8056 (OUTLIER) cc_final: 0.7423 (m-30) REVERT: B 40 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.7281 (mt-10) REVERT: B 42 SER cc_start: 0.8499 (t) cc_final: 0.8229 (m) REVERT: B 99 PHE cc_start: 0.8005 (t80) cc_final: 0.7642 (t80) REVERT: B 205 MET cc_start: 0.8531 (ptm) cc_final: 0.8233 (ptt) REVERT: B 232 LYS cc_start: 0.7750 (ttpt) cc_final: 0.7397 (mtpt) REVERT: B 269 CYS cc_start: 0.7267 (t) cc_final: 0.6786 (t) REVERT: B 281 LYS cc_start: 0.6986 (tttt) cc_final: 0.5865 (mmtp) REVERT: B 307 ILE cc_start: 0.7553 (OUTLIER) cc_final: 0.7298 (OUTLIER) REVERT: B 352 LYS cc_start: 0.6949 (tmtt) cc_final: 0.6722 (mttt) REVERT: B 356 ARG cc_start: 0.6817 (tpm170) cc_final: 0.6264 (ptp-110) REVERT: B 357 PHE cc_start: 0.8126 (t80) cc_final: 0.7884 (t80) REVERT: B 419 MET cc_start: 0.8343 (OUTLIER) cc_final: 0.7994 (tpp) REVERT: B 444 ASP cc_start: 0.7710 (t0) cc_final: 0.7466 (t0) REVERT: C 40 GLU cc_start: 0.7239 (mt-10) cc_final: 0.6917 (mp0) REVERT: C 92 LEU cc_start: 0.7295 (OUTLIER) cc_final: 0.6800 (mm) REVERT: C 232 LYS cc_start: 0.7773 (ttpt) cc_final: 0.7529 (mtmt) REVERT: C 256 TRP cc_start: 0.8579 (m100) cc_final: 0.7722 (m-10) REVERT: C 258 MET cc_start: 0.8295 (OUTLIER) cc_final: 0.7946 (ttt) REVERT: C 280 ARG cc_start: 0.7421 (ttp80) cc_final: 0.7024 (ttm170) REVERT: C 281 LYS cc_start: 0.7235 (tttt) cc_final: 0.6316 (mmmm) REVERT: C 286 MET cc_start: 0.8228 (mtp) cc_final: 0.7956 (mtm) REVERT: C 307 ILE cc_start: 0.7590 (OUTLIER) cc_final: 0.7377 (mt) REVERT: C 315 ARG cc_start: 0.7614 (tpp-160) cc_final: 0.7131 (ttm170) REVERT: C 318 MET cc_start: 0.7402 (tpt) cc_final: 0.7047 (ptt) REVERT: C 352 LYS cc_start: 0.7172 (tmtt) cc_final: 0.6869 (mttt) REVERT: C 419 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.7151 (tmm) REVERT: C 445 ARG cc_start: 0.8341 (mtt90) cc_final: 0.8115 (mmt180) outliers start: 38 outliers final: 16 residues processed: 175 average time/residue: 0.5128 time to fit residues: 96.2031 Evaluate side-chains 180 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 154 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 258 MET Chi-restraints excluded: chain C residue 269 CYS Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 419 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 106 optimal weight: 0.0670 chunk 110 optimal weight: 7.9990 chunk 94 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 99 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 241 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.178677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.138458 restraints weight = 2751.059| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 0.82 r_work: 0.3104 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9417 Z= 0.126 Angle : 0.486 5.687 12783 Z= 0.255 Chirality : 0.039 0.178 1626 Planarity : 0.004 0.036 1557 Dihedral : 3.538 11.446 1281 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 3.35 % Allowed : 15.38 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.52 (0.24), residues: 1200 helix: 1.29 (0.17), residues: 948 sheet: 1.92 (0.75), residues: 48 loop : -0.29 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 353 TYR 0.009 0.001 TYR B 373 PHE 0.011 0.001 PHE B 222 TRP 0.004 0.001 TRP A 19 HIS 0.001 0.000 HIS C 296 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 9417) covalent geometry : angle 0.48647 (12783) hydrogen bonds : bond 0.04295 ( 725) hydrogen bonds : angle 4.63104 ( 2130) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 157 time to evaluate : 0.359 Fit side-chains REVERT: A 256 TRP cc_start: 0.8459 (m100) cc_final: 0.7593 (m-10) REVERT: A 272 GLU cc_start: 0.7387 (mm-30) cc_final: 0.6811 (mt-10) REVERT: A 280 ARG cc_start: 0.7241 (ttp80) cc_final: 0.6744 (ttm170) REVERT: A 281 LYS cc_start: 0.7121 (tttt) cc_final: 0.6046 (mmtp) REVERT: A 286 MET cc_start: 0.8282 (mtp) cc_final: 0.8019 (mtm) REVERT: A 307 ILE cc_start: 0.7451 (OUTLIER) cc_final: 0.7168 (mt) REVERT: A 318 MET cc_start: 0.7146 (tpt) cc_final: 0.6737 (ttp) REVERT: A 347 ASN cc_start: 0.8310 (OUTLIER) cc_final: 0.7980 (m110) REVERT: A 356 ARG cc_start: 0.6695 (tpm170) cc_final: 0.6058 (ptp-110) REVERT: A 357 PHE cc_start: 0.8153 (t80) cc_final: 0.7915 (t80) REVERT: A 368 ASP cc_start: 0.8044 (OUTLIER) cc_final: 0.7463 (m-30) REVERT: B 40 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.6933 (mt-10) REVERT: B 42 SER cc_start: 0.8478 (t) cc_final: 0.8203 (m) REVERT: B 99 PHE cc_start: 0.7897 (t80) cc_final: 0.7485 (t80) REVERT: B 142 MET cc_start: 0.8240 (mmm) cc_final: 0.7776 (tpp) REVERT: B 205 MET cc_start: 0.8576 (ptm) cc_final: 0.8256 (ptt) REVERT: B 241 ASN cc_start: 0.7778 (OUTLIER) cc_final: 0.7387 (m110) REVERT: B 269 CYS cc_start: 0.7191 (t) cc_final: 0.6717 (t) REVERT: B 281 LYS cc_start: 0.6885 (tttt) cc_final: 0.5722 (mmtp) REVERT: B 307 ILE cc_start: 0.7414 (OUTLIER) cc_final: 0.7169 (OUTLIER) REVERT: B 352 LYS cc_start: 0.6859 (tmtt) cc_final: 0.6589 (mttt) REVERT: B 353 ARG cc_start: 0.8023 (mtm-85) cc_final: 0.7815 (mpp80) REVERT: B 356 ARG cc_start: 0.6780 (tpm170) cc_final: 0.6148 (ptp-110) REVERT: B 357 PHE cc_start: 0.8036 (t80) cc_final: 0.7780 (t80) REVERT: B 419 MET cc_start: 0.8261 (OUTLIER) cc_final: 0.7901 (tpp) REVERT: C 40 GLU cc_start: 0.7245 (mt-10) cc_final: 0.6860 (mp0) REVERT: C 42 SER cc_start: 0.8550 (t) cc_final: 0.8342 (t) REVERT: C 92 LEU cc_start: 0.7235 (OUTLIER) cc_final: 0.6786 (mm) REVERT: C 232 LYS cc_start: 0.7699 (ttpt) cc_final: 0.7413 (mtmt) REVERT: C 256 TRP cc_start: 0.8535 (m100) cc_final: 0.7615 (m-10) REVERT: C 258 MET cc_start: 0.8270 (OUTLIER) cc_final: 0.7902 (ttt) REVERT: C 280 ARG cc_start: 0.7390 (ttp80) cc_final: 0.6971 (ttm170) REVERT: C 281 LYS cc_start: 0.7151 (tttt) cc_final: 0.6212 (mmmm) REVERT: C 286 MET cc_start: 0.8145 (mtp) cc_final: 0.7852 (mtm) REVERT: C 307 ILE cc_start: 0.7515 (OUTLIER) cc_final: 0.7277 (mt) REVERT: C 315 ARG cc_start: 0.7529 (tpp-160) cc_final: 0.7019 (ttm170) REVERT: C 318 MET cc_start: 0.7319 (tpt) cc_final: 0.6907 (ptt) REVERT: C 352 LYS cc_start: 0.7076 (tmtt) cc_final: 0.6747 (mttt) REVERT: C 445 ARG cc_start: 0.8248 (mtt90) cc_final: 0.8014 (mmt180) outliers start: 34 outliers final: 14 residues processed: 174 average time/residue: 0.5009 time to fit residues: 93.4597 Evaluate side-chains 175 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 152 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 241 ASN Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 258 MET Chi-restraints excluded: chain C residue 269 CYS Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 403 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 8 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 82 optimal weight: 0.7980 chunk 46 optimal weight: 0.4980 chunk 79 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 17 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4027 r_free = 0.4027 target = 0.182657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.142926 restraints weight = 2705.612| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 0.81 r_work: 0.3108 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9417 Z= 0.128 Angle : 0.491 5.954 12783 Z= 0.258 Chirality : 0.040 0.210 1626 Planarity : 0.004 0.035 1557 Dihedral : 3.499 11.411 1281 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 3.16 % Allowed : 16.27 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.59 (0.24), residues: 1200 helix: 1.34 (0.17), residues: 948 sheet: 1.96 (0.76), residues: 48 loop : -0.27 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 353 TYR 0.008 0.001 TYR A 285 PHE 0.014 0.001 PHE B 240 TRP 0.003 0.001 TRP A 19 HIS 0.001 0.000 HIS C 296 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 9417) covalent geometry : angle 0.49070 (12783) hydrogen bonds : bond 0.04291 ( 725) hydrogen bonds : angle 4.62873 ( 2130) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 154 time to evaluate : 0.319 Fit side-chains REVERT: A 92 LEU cc_start: 0.6794 (OUTLIER) cc_final: 0.6348 (mm) REVERT: A 256 TRP cc_start: 0.8476 (m100) cc_final: 0.7636 (m-10) REVERT: A 272 GLU cc_start: 0.7399 (mm-30) cc_final: 0.6830 (mt-10) REVERT: A 280 ARG cc_start: 0.7267 (ttp80) cc_final: 0.6766 (ttm170) REVERT: A 281 LYS cc_start: 0.7160 (tttt) cc_final: 0.6076 (mmtp) REVERT: A 286 MET cc_start: 0.8322 (mtp) cc_final: 0.8101 (mtm) REVERT: A 307 ILE cc_start: 0.7486 (OUTLIER) cc_final: 0.7204 (mt) REVERT: A 318 MET cc_start: 0.7194 (tpt) cc_final: 0.6825 (ttp) REVERT: A 347 ASN cc_start: 0.8278 (OUTLIER) cc_final: 0.8003 (m110) REVERT: A 356 ARG cc_start: 0.6724 (tpm170) cc_final: 0.6103 (ptp-110) REVERT: A 357 PHE cc_start: 0.8171 (t80) cc_final: 0.7934 (t80) REVERT: A 359 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8165 (mp) REVERT: A 368 ASP cc_start: 0.8074 (OUTLIER) cc_final: 0.7499 (m-30) REVERT: B 40 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.6965 (mt-10) REVERT: B 42 SER cc_start: 0.8469 (t) cc_final: 0.8201 (m) REVERT: B 99 PHE cc_start: 0.7944 (t80) cc_final: 0.7557 (t80) REVERT: B 142 MET cc_start: 0.8239 (mmm) cc_final: 0.7889 (mmm) REVERT: B 205 MET cc_start: 0.8587 (ptm) cc_final: 0.8270 (ptt) REVERT: B 269 CYS cc_start: 0.7461 (t) cc_final: 0.7038 (t) REVERT: B 272 GLU cc_start: 0.7157 (mm-30) cc_final: 0.6803 (mm-30) REVERT: B 281 LYS cc_start: 0.6928 (tttt) cc_final: 0.5759 (mmtp) REVERT: B 307 ILE cc_start: 0.7438 (OUTLIER) cc_final: 0.7189 (OUTLIER) REVERT: B 352 LYS cc_start: 0.6874 (tmtt) cc_final: 0.6597 (mttt) REVERT: B 356 ARG cc_start: 0.6695 (tpm170) cc_final: 0.6113 (ptp-110) REVERT: B 357 PHE cc_start: 0.8042 (t80) cc_final: 0.7753 (t80) REVERT: B 419 MET cc_start: 0.8298 (OUTLIER) cc_final: 0.7946 (tpp) REVERT: C 40 GLU cc_start: 0.7220 (mt-10) cc_final: 0.6843 (mp0) REVERT: C 42 SER cc_start: 0.8514 (t) cc_final: 0.8293 (t) REVERT: C 92 LEU cc_start: 0.7168 (OUTLIER) cc_final: 0.6721 (mm) REVERT: C 232 LYS cc_start: 0.7698 (ttpt) cc_final: 0.7412 (mtmt) REVERT: C 256 TRP cc_start: 0.8558 (m100) cc_final: 0.7650 (m-10) REVERT: C 258 MET cc_start: 0.8236 (OUTLIER) cc_final: 0.7891 (ttt) REVERT: C 274 GLU cc_start: 0.7122 (mm-30) cc_final: 0.6567 (tp30) REVERT: C 280 ARG cc_start: 0.7424 (ttp80) cc_final: 0.6982 (ttm170) REVERT: C 281 LYS cc_start: 0.7174 (tttt) cc_final: 0.6232 (mmmm) REVERT: C 286 MET cc_start: 0.8181 (mtp) cc_final: 0.7883 (mtm) REVERT: C 307 ILE cc_start: 0.7538 (OUTLIER) cc_final: 0.7309 (mt) REVERT: C 315 ARG cc_start: 0.7413 (tpp-160) cc_final: 0.6903 (ttm170) REVERT: C 318 MET cc_start: 0.7332 (tpt) cc_final: 0.6932 (ptt) REVERT: C 352 LYS cc_start: 0.7084 (tmtt) cc_final: 0.6754 (mttt) REVERT: C 385 ASN cc_start: 0.8164 (m-40) cc_final: 0.7886 (m110) REVERT: C 445 ARG cc_start: 0.8271 (mtt90) cc_final: 0.8035 (mmt180) outliers start: 32 outliers final: 16 residues processed: 171 average time/residue: 0.4997 time to fit residues: 91.6358 Evaluate side-chains 177 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 258 MET Chi-restraints excluded: chain C residue 269 CYS Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 403 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 0 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 103 optimal weight: 7.9990 chunk 65 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 98 optimal weight: 0.6980 chunk 108 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.172861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.131623 restraints weight = 2732.811| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 0.84 r_work: 0.3340 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9417 Z= 0.168 Angle : 0.534 6.172 12783 Z= 0.280 Chirality : 0.041 0.172 1626 Planarity : 0.004 0.036 1557 Dihedral : 3.661 16.252 1281 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 3.25 % Allowed : 16.27 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.24), residues: 1200 helix: 1.16 (0.17), residues: 948 sheet: 1.66 (0.75), residues: 48 loop : -0.43 (0.40), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 353 TYR 0.009 0.001 TYR A 285 PHE 0.015 0.002 PHE C 240 TRP 0.003 0.001 TRP A 256 HIS 0.002 0.001 HIS C 296 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 9417) covalent geometry : angle 0.53407 (12783) hydrogen bonds : bond 0.04767 ( 725) hydrogen bonds : angle 4.75750 ( 2130) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 162 time to evaluate : 0.358 Fit side-chains REVERT: A 92 LEU cc_start: 0.6897 (OUTLIER) cc_final: 0.6465 (mm) REVERT: A 256 TRP cc_start: 0.8550 (m100) cc_final: 0.7718 (m-10) REVERT: A 272 GLU cc_start: 0.7394 (mm-30) cc_final: 0.6878 (mt-10) REVERT: A 274 GLU cc_start: 0.7306 (mm-30) cc_final: 0.6965 (tp30) REVERT: A 280 ARG cc_start: 0.7316 (ttp80) cc_final: 0.6828 (ttm170) REVERT: A 281 LYS cc_start: 0.7250 (tttt) cc_final: 0.6164 (mmtp) REVERT: A 286 MET cc_start: 0.8313 (mtp) cc_final: 0.8046 (mtm) REVERT: A 307 ILE cc_start: 0.7531 (OUTLIER) cc_final: 0.7259 (mt) REVERT: A 318 MET cc_start: 0.7230 (tpt) cc_final: 0.6899 (ttp) REVERT: A 347 ASN cc_start: 0.8322 (OUTLIER) cc_final: 0.8029 (m110) REVERT: A 356 ARG cc_start: 0.6823 (tpm170) cc_final: 0.6263 (ptp-110) REVERT: A 357 PHE cc_start: 0.8293 (t80) cc_final: 0.8031 (t80) REVERT: A 368 ASP cc_start: 0.8142 (OUTLIER) cc_final: 0.7472 (m-30) REVERT: B 40 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.6992 (mt-10) REVERT: B 42 SER cc_start: 0.8462 (t) cc_final: 0.8230 (m) REVERT: B 142 MET cc_start: 0.8270 (mmm) cc_final: 0.7800 (tpp) REVERT: B 205 MET cc_start: 0.8586 (ptm) cc_final: 0.8271 (ptt) REVERT: B 269 CYS cc_start: 0.7495 (t) cc_final: 0.7069 (t) REVERT: B 272 GLU cc_start: 0.7169 (mm-30) cc_final: 0.6871 (mm-30) REVERT: B 281 LYS cc_start: 0.7053 (tttt) cc_final: 0.5860 (mmtp) REVERT: B 307 ILE cc_start: 0.7507 (OUTLIER) cc_final: 0.7255 (OUTLIER) REVERT: B 352 LYS cc_start: 0.6960 (tmtt) cc_final: 0.6670 (mttt) REVERT: B 353 ARG cc_start: 0.8043 (mtm-85) cc_final: 0.7824 (mpp80) REVERT: B 356 ARG cc_start: 0.6789 (tpm170) cc_final: 0.6208 (ptp-110) REVERT: B 419 MET cc_start: 0.8354 (OUTLIER) cc_final: 0.8072 (tpp) REVERT: B 444 ASP cc_start: 0.7693 (t0) cc_final: 0.7396 (t0) REVERT: C 40 GLU cc_start: 0.7230 (mt-10) cc_final: 0.6856 (mp0) REVERT: C 42 SER cc_start: 0.8459 (t) cc_final: 0.8222 (t) REVERT: C 92 LEU cc_start: 0.7290 (OUTLIER) cc_final: 0.6834 (mm) REVERT: C 232 LYS cc_start: 0.7837 (ttpt) cc_final: 0.7547 (mtmt) REVERT: C 256 TRP cc_start: 0.8548 (m100) cc_final: 0.7681 (m-10) REVERT: C 258 MET cc_start: 0.8297 (OUTLIER) cc_final: 0.7942 (ttt) REVERT: C 274 GLU cc_start: 0.7283 (mm-30) cc_final: 0.6673 (tp30) REVERT: C 280 ARG cc_start: 0.7458 (ttp80) cc_final: 0.7037 (ttm170) REVERT: C 281 LYS cc_start: 0.7236 (tttt) cc_final: 0.6291 (mmmm) REVERT: C 286 MET cc_start: 0.8228 (mtp) cc_final: 0.7936 (mtm) REVERT: C 307 ILE cc_start: 0.7579 (OUTLIER) cc_final: 0.7364 (mt) REVERT: C 315 ARG cc_start: 0.7577 (tpp-160) cc_final: 0.7097 (ttm170) REVERT: C 318 MET cc_start: 0.7340 (tpt) cc_final: 0.6873 (ptt) REVERT: C 352 LYS cc_start: 0.7179 (tmtt) cc_final: 0.6856 (mttt) REVERT: C 385 ASN cc_start: 0.8142 (m-40) cc_final: 0.7870 (m110) REVERT: C 419 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.7175 (tmm) REVERT: C 445 ARG cc_start: 0.8380 (mtt90) cc_final: 0.8118 (mmt180) outliers start: 33 outliers final: 18 residues processed: 177 average time/residue: 0.4930 time to fit residues: 93.6507 Evaluate side-chains 185 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 157 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 258 MET Chi-restraints excluded: chain C residue 269 CYS Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 419 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 22 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 72 optimal weight: 0.9980 chunk 96 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 117 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 ASN B 252 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.177465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.137298 restraints weight = 2702.042| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 0.81 r_work: 0.3068 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 9417 Z= 0.150 Angle : 0.523 8.775 12783 Z= 0.275 Chirality : 0.040 0.173 1626 Planarity : 0.004 0.036 1557 Dihedral : 3.610 18.165 1281 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.96 % Allowed : 16.77 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.33 (0.24), residues: 1200 helix: 1.19 (0.17), residues: 948 sheet: 1.44 (0.74), residues: 48 loop : -0.43 (0.41), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 353 TYR 0.008 0.001 TYR A 285 PHE 0.013 0.002 PHE C 240 TRP 0.003 0.001 TRP A 276 HIS 0.001 0.001 HIS C 296 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 9417) covalent geometry : angle 0.52333 (12783) hydrogen bonds : bond 0.04563 ( 725) hydrogen bonds : angle 4.71711 ( 2130) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2400 Ramachandran restraints generated. 1200 Oldfield, 0 Emsley, 1200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 161 time to evaluate : 0.302 Fit side-chains REVERT: A 92 LEU cc_start: 0.6719 (OUTLIER) cc_final: 0.6307 (mm) REVERT: A 256 TRP cc_start: 0.8496 (m100) cc_final: 0.7631 (m-10) REVERT: A 272 GLU cc_start: 0.7328 (mm-30) cc_final: 0.6809 (mt-10) REVERT: A 274 GLU cc_start: 0.7239 (mm-30) cc_final: 0.6901 (tp30) REVERT: A 280 ARG cc_start: 0.7270 (ttp80) cc_final: 0.6782 (ttm170) REVERT: A 281 LYS cc_start: 0.7162 (tttt) cc_final: 0.6069 (mmtp) REVERT: A 286 MET cc_start: 0.8242 (mtp) cc_final: 0.7967 (mtm) REVERT: A 307 ILE cc_start: 0.7431 (OUTLIER) cc_final: 0.7154 (mt) REVERT: A 318 MET cc_start: 0.7139 (tpt) cc_final: 0.6800 (ttp) REVERT: A 347 ASN cc_start: 0.8242 (OUTLIER) cc_final: 0.7932 (m110) REVERT: A 356 ARG cc_start: 0.6787 (tpm170) cc_final: 0.6122 (ptp-110) REVERT: A 368 ASP cc_start: 0.8021 (OUTLIER) cc_final: 0.7358 (m-30) REVERT: B 40 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.6943 (mt-10) REVERT: B 42 SER cc_start: 0.8451 (t) cc_final: 0.8216 (m) REVERT: B 142 MET cc_start: 0.8226 (mmm) cc_final: 0.7732 (tpp) REVERT: B 205 MET cc_start: 0.8556 (ptm) cc_final: 0.8240 (ptt) REVERT: B 269 CYS cc_start: 0.7302 (t) cc_final: 0.6826 (t) REVERT: B 272 GLU cc_start: 0.7091 (mm-30) cc_final: 0.6785 (mm-30) REVERT: B 281 LYS cc_start: 0.6916 (tttt) cc_final: 0.5730 (mmtp) REVERT: B 307 ILE cc_start: 0.7423 (OUTLIER) cc_final: 0.7174 (OUTLIER) REVERT: B 352 LYS cc_start: 0.6787 (tmtt) cc_final: 0.6464 (mttt) REVERT: B 356 ARG cc_start: 0.6657 (tpm170) cc_final: 0.5971 (ptp-110) REVERT: B 419 MET cc_start: 0.8265 (OUTLIER) cc_final: 0.7922 (tpp) REVERT: B 444 ASP cc_start: 0.7602 (t0) cc_final: 0.7302 (t0) REVERT: C 40 GLU cc_start: 0.7144 (mt-10) cc_final: 0.6743 (mp0) REVERT: C 42 SER cc_start: 0.8458 (t) cc_final: 0.8209 (t) REVERT: C 92 LEU cc_start: 0.7133 (OUTLIER) cc_final: 0.6695 (mm) REVERT: C 232 LYS cc_start: 0.7769 (ttpt) cc_final: 0.7466 (mtmt) REVERT: C 256 TRP cc_start: 0.8537 (m100) cc_final: 0.7607 (m-10) REVERT: C 258 MET cc_start: 0.8271 (OUTLIER) cc_final: 0.7919 (ttt) REVERT: C 274 GLU cc_start: 0.7244 (mm-30) cc_final: 0.6631 (tp30) REVERT: C 280 ARG cc_start: 0.7398 (ttp80) cc_final: 0.6996 (ttm170) REVERT: C 281 LYS cc_start: 0.7172 (tttt) cc_final: 0.6218 (mmmm) REVERT: C 286 MET cc_start: 0.8150 (mtp) cc_final: 0.7847 (mtm) REVERT: C 307 ILE cc_start: 0.7388 (OUTLIER) cc_final: 0.7177 (mt) REVERT: C 315 ARG cc_start: 0.7489 (tpp-160) cc_final: 0.6994 (ttm110) REVERT: C 318 MET cc_start: 0.7303 (tpt) cc_final: 0.6787 (ptt) REVERT: C 352 LYS cc_start: 0.7077 (tmtt) cc_final: 0.6742 (mttt) REVERT: C 385 ASN cc_start: 0.8096 (m-40) cc_final: 0.7833 (m110) REVERT: C 419 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.7092 (tmm) REVERT: C 445 ARG cc_start: 0.8196 (mtt90) cc_final: 0.7970 (mmt180) outliers start: 30 outliers final: 16 residues processed: 175 average time/residue: 0.5030 time to fit residues: 94.6107 Evaluate side-chains 184 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 158 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 364 THR Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain B residue 419 MET Chi-restraints excluded: chain B residue 422 VAL Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 258 MET Chi-restraints excluded: chain C residue 269 CYS Chi-restraints excluded: chain C residue 307 ILE Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 403 SER Chi-restraints excluded: chain C residue 419 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 82 optimal weight: 0.0980 chunk 15 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 60 optimal weight: 0.1980 chunk 71 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 ASN B 241 ASN B 252 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.173054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.130577 restraints weight = 2758.096| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 0.89 r_work: 0.3131 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9417 Z= 0.126 Angle : 0.499 9.909 12783 Z= 0.262 Chirality : 0.039 0.170 1626 Planarity : 0.004 0.035 1557 Dihedral : 3.495 18.358 1281 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.96 % Allowed : 16.77 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.54 (0.24), residues: 1200 helix: 1.34 (0.17), residues: 948 sheet: 1.40 (0.74), residues: 48 loop : -0.33 (0.41), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 353 TYR 0.008 0.001 TYR A 162 PHE 0.011 0.001 PHE B 222 TRP 0.004 0.001 TRP A 19 HIS 0.001 0.000 HIS C 296 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 9417) covalent geometry : angle 0.49894 (12783) hydrogen bonds : bond 0.04222 ( 725) hydrogen bonds : angle 4.63678 ( 2130) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3157.66 seconds wall clock time: 54 minutes 25.70 seconds (3265.70 seconds total)