Starting phenix.real_space_refine on Thu Feb 13 19:09:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d66_46586/02_2025/9d66_46586.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d66_46586/02_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_46586/02_2025/9d66_46586.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d66_46586/02_2025/9d66_46586.map" model { file = "/net/cci-nas-00/data/ceres_data/9d66_46586/02_2025/9d66_46586.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d66_46586/02_2025/9d66_46586.cif" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 6.25, per 1000 atoms: 0.67 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: 2.58 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.95 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: 5.15 Time building geometry restraints manager: 3.03 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: 0.03 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: 1.040 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 27.190 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.030 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:16.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.000 ------------------------------------------------------------------------------- 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= 0.232 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (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 TRP 0.006 0.002 TRP C 19 HIS 0.003 0.001 HIS C 296 PHE 0.018 0.002 PHE C 279 TYR 0.018 0.004 TYR A 98 ARG 0.013 0.002 ARG B 39 *********************** 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 : 1.066 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: 1.3438 time to fit residues: 296.0984 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 : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 0.6980 chunk 90 optimal weight: 0.3980 chunk 50 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 61 optimal weight: 0.0670 chunk 48 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 57 optimal weight: 0.1980 chunk 70 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 overall best weight: 0.3918 ------------------------------------------------------------------------------- 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 = 0.4099 r_free = 0.4099 target = 0.188123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.151391 restraints weight = 2538.375| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 0.72 r_work: 0.3148 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9417 Z= 0.188 Angle : 0.536 7.215 12783 Z= 0.284 Chirality : 0.040 0.153 1626 Planarity : 0.004 0.039 1557 Dihedral : 3.977 13.419 1281 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 2.56 % Allowed : 10.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.23), residues: 1200 helix: 0.66 (0.16), residues: 954 sheet: 0.42 (0.75), residues: 54 loop : 0.01 (0.43), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 19 HIS 0.001 0.000 HIS C 296 PHE 0.027 0.002 PHE B 222 TYR 0.010 0.002 TYR B 373 ARG 0.006 0.001 ARG C 280 *********************** 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 204 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 178 time to evaluate : 1.177 Fit side-chains REVERT: A 40 GLU cc_start: 0.7110 (mt-10) cc_final: 0.6759 (mt-10) REVERT: A 117 LYS cc_start: 0.8127 (mtpp) cc_final: 0.7911 (mttm) REVERT: A 163 LYS cc_start: 0.8214 (ttmm) cc_final: 0.7389 (pttp) REVERT: A 229 MET cc_start: 0.8779 (mtm) cc_final: 0.8485 (mtm) REVERT: A 256 TRP cc_start: 0.8509 (m100) cc_final: 0.7681 (m-10) REVERT: A 272 GLU cc_start: 0.7319 (mm-30) cc_final: 0.6831 (mt-10) REVERT: A 280 ARG cc_start: 0.6995 (ttp80) cc_final: 0.6485 (ttm170) REVERT: A 281 LYS cc_start: 0.6942 (tttt) cc_final: 0.6132 (mmtp) REVERT: A 286 MET cc_start: 0.8315 (mtp) cc_final: 0.7943 (mtm) REVERT: A 315 ARG cc_start: 0.7649 (tpp-160) cc_final: 0.7353 (ttm110) REVERT: A 318 MET cc_start: 0.7284 (tpt) cc_final: 0.6775 (ttp) REVERT: A 352 LYS cc_start: 0.7046 (tmtt) cc_final: 0.6709 (mttt) REVERT: A 356 ARG cc_start: 0.6543 (tpm170) cc_final: 0.6063 (ptp-110) REVERT: A 359 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8195 (mp) REVERT: A 368 ASP cc_start: 0.7964 (OUTLIER) cc_final: 0.7451 (m-30) REVERT: A 444 ASP cc_start: 0.7706 (t0) cc_final: 0.7496 (t0) REVERT: A 464 LYS cc_start: 0.7171 (tppp) cc_final: 0.6539 (tppt) REVERT: B 205 MET cc_start: 0.8477 (ptm) cc_final: 0.8185 (ptt) REVERT: B 232 LYS cc_start: 0.7903 (ttpt) cc_final: 0.7435 (mtpt) REVERT: B 272 GLU cc_start: 0.7267 (mm-30) cc_final: 0.6844 (mt-10) REVERT: B 281 LYS cc_start: 0.6746 (tttt) cc_final: 0.5841 (mmtp) REVERT: B 304 ILE cc_start: 0.7713 (pt) cc_final: 0.7317 (mt) REVERT: B 318 MET cc_start: 0.7177 (tpt) cc_final: 0.6570 (ttp) REVERT: B 352 LYS cc_start: 0.6988 (tmtt) cc_final: 0.6618 (mttt) REVERT: B 356 ARG cc_start: 0.6665 (tpm170) cc_final: 0.6083 (ptp-110) REVERT: C 232 LYS cc_start: 0.8009 (ttpt) cc_final: 0.7680 (mtmp) REVERT: C 256 TRP cc_start: 0.8492 (m100) cc_final: 0.7588 (m-10) REVERT: C 258 MET cc_start: 0.8155 (ttt) cc_final: 0.7868 (ttt) REVERT: C 280 ARG cc_start: 0.7351 (ttp80) cc_final: 0.6903 (ttm170) REVERT: C 281 LYS cc_start: 0.7159 (tttt) cc_final: 0.6407 (mmtp) REVERT: C 286 MET cc_start: 0.8240 (mtp) cc_final: 0.7906 (mtm) REVERT: C 304 ILE cc_start: 0.7450 (pt) cc_final: 0.7118 (mt) REVERT: C 315 ARG cc_start: 0.7620 (tpp-160) cc_final: 0.7290 (ttm110) REVERT: C 318 MET cc_start: 0.7373 (tpt) cc_final: 0.6835 (ttp) REVERT: C 329 MET cc_start: 0.8213 (mmt) cc_final: 0.8010 (mpp) REVERT: C 348 ASN cc_start: 0.8164 (m-40) cc_final: 0.7910 (m-40) REVERT: C 352 LYS cc_start: 0.7190 (tmtt) cc_final: 0.6782 (mttt) REVERT: C 356 ARG cc_start: 0.6376 (tpm170) cc_final: 0.6172 (ptp90) outliers start: 26 outliers final: 8 residues processed: 191 average time/residue: 1.3503 time to fit residues: 274.2159 Evaluate side-chains 176 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 166 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 368 ASP 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 359 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 104 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 116 optimal weight: 0.0770 chunk 93 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 ASN B 348 ASN C 252 GLN C 312 ASN C 348 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.183807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.144034 restraints weight = 2661.893| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 0.82 r_work: 0.3456 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9417 Z= 0.186 Angle : 0.498 6.127 12783 Z= 0.261 Chirality : 0.039 0.161 1626 Planarity : 0.004 0.034 1557 Dihedral : 3.703 12.076 1281 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 2.56 % Allowed : 11.74 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.24), residues: 1200 helix: 1.13 (0.16), residues: 960 sheet: 0.64 (0.76), residues: 54 loop : 0.22 (0.45), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 19 HIS 0.001 0.001 HIS C 296 PHE 0.015 0.002 PHE A 222 TYR 0.010 0.001 TYR A 162 ARG 0.005 0.001 ARG C 353 *********************** 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 192 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 166 time to evaluate : 0.968 Fit side-chains REVERT: A 40 GLU cc_start: 0.7126 (mt-10) cc_final: 0.6835 (mt-10) REVERT: A 60 MET cc_start: 0.8483 (mmm) cc_final: 0.8150 (mmm) REVERT: A 229 MET cc_start: 0.8756 (mtm) cc_final: 0.8521 (mtm) REVERT: A 256 TRP cc_start: 0.8452 (m100) cc_final: 0.7646 (m-10) REVERT: A 272 GLU cc_start: 0.7302 (mm-30) cc_final: 0.6763 (mt-10) REVERT: A 280 ARG cc_start: 0.6973 (ttp80) cc_final: 0.6520 (ttm170) REVERT: A 281 LYS cc_start: 0.7137 (tttt) cc_final: 0.6200 (mmtp) REVERT: A 286 MET cc_start: 0.8233 (mtp) cc_final: 0.7986 (mtm) REVERT: A 315 ARG cc_start: 0.7567 (tpp-160) cc_final: 0.7334 (tpt170) REVERT: A 318 MET cc_start: 0.7178 (tpt) cc_final: 0.6714 (ttp) REVERT: A 347 ASN cc_start: 0.8341 (OUTLIER) cc_final: 0.7990 (m110) REVERT: A 352 LYS cc_start: 0.7047 (tmtt) cc_final: 0.6751 (mttt) REVERT: A 356 ARG cc_start: 0.6634 (tpm170) cc_final: 0.6097 (ptp-110) REVERT: A 357 PHE cc_start: 0.8152 (t80) cc_final: 0.7928 (t80) REVERT: A 359 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8131 (mp) REVERT: A 368 ASP cc_start: 0.7993 (OUTLIER) cc_final: 0.7474 (m-30) REVERT: B 40 GLU cc_start: 0.7249 (OUTLIER) cc_final: 0.6886 (mt-10) REVERT: B 99 PHE cc_start: 0.7952 (t80) cc_final: 0.7586 (t80) REVERT: B 205 MET cc_start: 0.8503 (ptm) cc_final: 0.8188 (ptt) REVERT: B 269 CYS cc_start: 0.7407 (t) cc_final: 0.7039 (t) REVERT: B 272 GLU cc_start: 0.7205 (mm-30) cc_final: 0.6762 (mt-10) REVERT: B 281 LYS cc_start: 0.6941 (tttt) cc_final: 0.5980 (mmtp) REVERT: B 318 MET cc_start: 0.7274 (tpt) cc_final: 0.6870 (ttp) REVERT: B 352 LYS cc_start: 0.6981 (tmtt) cc_final: 0.6659 (mttt) REVERT: B 356 ARG cc_start: 0.6672 (tpm170) cc_final: 0.6100 (ptp-110) REVERT: B 444 ASP cc_start: 0.7734 (t0) cc_final: 0.7398 (t0) REVERT: C 232 LYS cc_start: 0.7886 (ttpt) cc_final: 0.7643 (mtmt) REVERT: C 256 TRP cc_start: 0.8483 (m100) cc_final: 0.7568 (m-10) REVERT: C 258 MET cc_start: 0.8223 (ttt) cc_final: 0.7926 (ttt) REVERT: C 280 ARG cc_start: 0.7382 (ttp80) cc_final: 0.6937 (ttm170) REVERT: C 281 LYS cc_start: 0.7174 (tttt) cc_final: 0.6422 (mmtp) REVERT: C 286 MET cc_start: 0.8163 (mtp) cc_final: 0.7896 (mtm) REVERT: C 315 ARG cc_start: 0.7603 (tpp-160) cc_final: 0.7354 (ttm110) REVERT: C 318 MET cc_start: 0.7428 (tpt) cc_final: 0.6893 (ttp) REVERT: C 352 LYS cc_start: 0.7177 (tmtt) cc_final: 0.6800 (mttt) outliers start: 26 outliers final: 12 residues processed: 178 average time/residue: 1.2656 time to fit residues: 240.1838 Evaluate side-chains 172 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 156 time to evaluate : 1.414 ------------------------------------------------------------------------------- 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 347 ASN Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 22 LEU 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 365 ILE Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain C residue 92 LEU 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 91 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 106 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 93 optimal weight: 0.9990 chunk 95 optimal weight: 0.7980 chunk 58 optimal weight: 0.6980 chunk 109 optimal weight: 0.0970 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN A 348 ASN C 252 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.183413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.142781 restraints weight = 2788.468| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 0.85 r_work: 0.3101 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2528 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= 0.194 Angle : 0.484 5.514 12783 Z= 0.254 Chirality : 0.039 0.152 1626 Planarity : 0.004 0.034 1557 Dihedral : 3.599 12.058 1281 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 3.06 % Allowed : 13.51 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.24), residues: 1200 helix: 1.30 (0.17), residues: 960 sheet: 0.64 (0.74), residues: 54 loop : 0.18 (0.45), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 276 HIS 0.001 0.000 HIS C 296 PHE 0.018 0.002 PHE B 357 TYR 0.009 0.001 TYR B 373 ARG 0.006 0.001 ARG C 353 *********************** 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 198 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 167 time to evaluate : 1.099 Fit side-chains REVERT: A 229 MET cc_start: 0.8746 (mtm) cc_final: 0.8483 (mtm) REVERT: A 231 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7293 (tm-30) REVERT: A 256 TRP cc_start: 0.8495 (m100) cc_final: 0.7628 (m-10) REVERT: A 272 GLU cc_start: 0.7307 (mm-30) cc_final: 0.6722 (mt-10) REVERT: A 280 ARG cc_start: 0.6976 (ttp80) cc_final: 0.6487 (ttm170) REVERT: A 281 LYS cc_start: 0.7027 (tttt) cc_final: 0.6020 (mmtp) REVERT: A 286 MET cc_start: 0.8187 (mtp) cc_final: 0.7962 (mtm) REVERT: A 318 MET cc_start: 0.7253 (tpt) cc_final: 0.6831 (ttp) REVERT: A 352 LYS cc_start: 0.6985 (tmtt) cc_final: 0.6751 (mttt) REVERT: A 356 ARG cc_start: 0.6661 (tpm170) cc_final: 0.6092 (ptp-110) REVERT: A 357 PHE cc_start: 0.8128 (t80) cc_final: 0.7855 (t80) REVERT: A 368 ASP cc_start: 0.8045 (OUTLIER) cc_final: 0.7487 (m-30) REVERT: A 419 MET cc_start: 0.8353 (OUTLIER) cc_final: 0.6797 (tmm) REVERT: B 40 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.7098 (mt-10) REVERT: B 99 PHE cc_start: 0.7943 (t80) cc_final: 0.7553 (t80) REVERT: B 142 MET cc_start: 0.8266 (mmm) cc_final: 0.7793 (tpp) REVERT: B 205 MET cc_start: 0.8599 (ptm) cc_final: 0.8296 (ptt) REVERT: B 231 GLU cc_start: 0.8005 (tt0) cc_final: 0.7610 (tm-30) REVERT: B 269 CYS cc_start: 0.7278 (t) cc_final: 0.6882 (t) REVERT: B 272 GLU cc_start: 0.7128 (mm-30) cc_final: 0.6719 (mt-10) REVERT: B 281 LYS cc_start: 0.6890 (tttt) cc_final: 0.5856 (mmtp) REVERT: B 318 MET cc_start: 0.7224 (tpt) cc_final: 0.6840 (ttp) REVERT: B 352 LYS cc_start: 0.6860 (tmtt) cc_final: 0.6591 (mttt) REVERT: B 356 ARG cc_start: 0.6680 (tpm170) cc_final: 0.6038 (ptp-110) REVERT: B 444 ASP cc_start: 0.7678 (t0) cc_final: 0.7355 (t0) REVERT: C 40 GLU cc_start: 0.7348 (mt-10) cc_final: 0.6895 (mp0) REVERT: C 232 LYS cc_start: 0.7802 (ttpt) cc_final: 0.7541 (mtmt) REVERT: C 256 TRP cc_start: 0.8504 (m100) cc_final: 0.7556 (m-10) REVERT: C 258 MET cc_start: 0.8252 (OUTLIER) cc_final: 0.7909 (ttt) REVERT: C 280 ARG cc_start: 0.7319 (ttp80) cc_final: 0.6852 (ttm170) REVERT: C 281 LYS cc_start: 0.7089 (tttt) cc_final: 0.6228 (mmmm) REVERT: C 286 MET cc_start: 0.8110 (mtp) cc_final: 0.7831 (mtm) REVERT: C 307 ILE cc_start: 0.7423 (OUTLIER) cc_final: 0.7179 (mt) REVERT: C 315 ARG cc_start: 0.7502 (tpp-160) cc_final: 0.7197 (ttm110) REVERT: C 318 MET cc_start: 0.7426 (tpt) cc_final: 0.6893 (ttp) REVERT: C 352 LYS cc_start: 0.7055 (tmtt) cc_final: 0.6783 (mttt) REVERT: C 368 ASP cc_start: 0.7913 (OUTLIER) cc_final: 0.7602 (m-30) outliers start: 31 outliers final: 8 residues processed: 177 average time/residue: 1.2102 time to fit residues: 229.4427 Evaluate side-chains 175 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 160 time to evaluate : 0.979 ------------------------------------------------------------------------------- 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 231 GLU 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 309 VAL Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain C residue 258 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 34 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 108 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 94 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 C 348 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.187094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.150773 restraints weight = 2717.000| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 0.70 r_work: 0.3140 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9417 Z= 0.237 Angle : 0.506 5.459 12783 Z= 0.265 Chirality : 0.040 0.144 1626 Planarity : 0.004 0.035 1557 Dihedral : 3.617 11.695 1281 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 3.25 % Allowed : 14.20 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.24), residues: 1200 helix: 1.24 (0.17), residues: 960 sheet: 0.63 (0.75), residues: 54 loop : 0.03 (0.44), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 276 HIS 0.002 0.001 HIS A 296 PHE 0.014 0.002 PHE C 240 TYR 0.008 0.001 TYR A 162 ARG 0.006 0.001 ARG C 353 *********************** 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 192 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 159 time to evaluate : 0.960 Fit side-chains REVERT: A 40 GLU cc_start: 0.7225 (mt-10) cc_final: 0.7011 (mt-10) REVERT: A 60 MET cc_start: 0.8535 (mmm) cc_final: 0.8187 (mmm) REVERT: A 229 MET cc_start: 0.8776 (mtm) cc_final: 0.8546 (mtm) REVERT: A 256 TRP cc_start: 0.8514 (m100) cc_final: 0.7713 (m-10) REVERT: A 269 CYS cc_start: 0.7409 (t) cc_final: 0.7100 (t) REVERT: A 272 GLU cc_start: 0.7393 (mm-30) cc_final: 0.6821 (mt-10) REVERT: A 280 ARG cc_start: 0.7084 (ttp80) cc_final: 0.6595 (ttm170) REVERT: A 281 LYS cc_start: 0.7149 (tttt) cc_final: 0.6096 (mmtp) REVERT: A 286 MET cc_start: 0.8362 (mtp) cc_final: 0.8140 (mtm) REVERT: A 318 MET cc_start: 0.7261 (tpt) cc_final: 0.6917 (ttp) REVERT: A 347 ASN cc_start: 0.8411 (OUTLIER) cc_final: 0.8150 (m110) REVERT: A 352 LYS cc_start: 0.6913 (tmtt) cc_final: 0.6704 (mttt) REVERT: A 356 ARG cc_start: 0.6689 (tpm170) cc_final: 0.6286 (ptp-110) REVERT: A 359 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8212 (mp) REVERT: A 367 MET cc_start: 0.8954 (OUTLIER) cc_final: 0.8445 (mtm) REVERT: A 368 ASP cc_start: 0.8183 (OUTLIER) cc_final: 0.7550 (m-30) REVERT: A 419 MET cc_start: 0.8492 (OUTLIER) cc_final: 0.6934 (tmm) REVERT: B 99 PHE cc_start: 0.7987 (t80) cc_final: 0.7607 (t80) REVERT: B 142 MET cc_start: 0.8321 (mmm) cc_final: 0.7872 (tpp) REVERT: B 205 MET cc_start: 0.8548 (ptm) cc_final: 0.8253 (ptt) REVERT: B 269 CYS cc_start: 0.7381 (t) cc_final: 0.6999 (t) REVERT: B 281 LYS cc_start: 0.7098 (tttt) cc_final: 0.5965 (mmtp) REVERT: B 307 ILE cc_start: 0.7538 (mm) cc_final: 0.7275 (mt) REVERT: B 318 MET cc_start: 0.7253 (tpt) cc_final: 0.6992 (ttp) REVERT: B 352 LYS cc_start: 0.6946 (tmtt) cc_final: 0.6691 (mttt) REVERT: B 356 ARG cc_start: 0.6733 (tpm170) cc_final: 0.6222 (ptp-110) REVERT: B 444 ASP cc_start: 0.7718 (t0) cc_final: 0.7435 (t0) REVERT: C 40 GLU cc_start: 0.7352 (mt-10) cc_final: 0.6988 (mp0) REVERT: C 232 LYS cc_start: 0.7896 (ttpt) cc_final: 0.7640 (mtmt) REVERT: C 256 TRP cc_start: 0.8580 (m100) cc_final: 0.7712 (m-10) REVERT: C 258 MET cc_start: 0.8258 (OUTLIER) cc_final: 0.7910 (ttt) REVERT: C 280 ARG cc_start: 0.7352 (ttp80) cc_final: 0.6925 (ttm170) REVERT: C 281 LYS cc_start: 0.7176 (tttt) cc_final: 0.6300 (mmmm) REVERT: C 286 MET cc_start: 0.8202 (mtp) cc_final: 0.7943 (mtm) REVERT: C 307 ILE cc_start: 0.7608 (mm) cc_final: 0.7368 (mt) REVERT: C 315 ARG cc_start: 0.7611 (tpp-160) cc_final: 0.7290 (ttm170) REVERT: C 318 MET cc_start: 0.7576 (tpt) cc_final: 0.7130 (ttp) REVERT: C 352 LYS cc_start: 0.7192 (tmtt) cc_final: 0.6860 (mttt) REVERT: C 353 ARG cc_start: 0.7781 (mpp80) cc_final: 0.7571 (mpp80) REVERT: C 444 ASP cc_start: 0.7673 (t0) cc_final: 0.7071 (t70) outliers start: 33 outliers final: 12 residues processed: 174 average time/residue: 1.1985 time to fit residues: 223.7825 Evaluate side-chains 172 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 154 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ILE 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 347 ASN Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 365 ILE 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 92 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 403 SER Chi-restraints excluded: chain C residue 258 MET Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 403 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 66 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 24 optimal weight: 0.0980 chunk 119 optimal weight: 2.9990 chunk 117 optimal weight: 0.5980 chunk 73 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 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 312 ASN C 252 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.191210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.154945 restraints weight = 2714.208| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 0.71 r_work: 0.3144 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2761 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= 0.180 Angle : 0.477 5.001 12783 Z= 0.250 Chirality : 0.039 0.205 1626 Planarity : 0.004 0.034 1557 Dihedral : 3.483 11.610 1281 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 3.16 % Allowed : 14.99 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.24), residues: 1200 helix: 1.43 (0.17), residues: 948 sheet: 1.89 (0.73), residues: 48 loop : -0.17 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 276 HIS 0.001 0.000 HIS C 296 PHE 0.010 0.001 PHE C 240 TYR 0.008 0.001 TYR A 162 ARG 0.007 0.000 ARG B 353 *********************** 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 194 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 162 time to evaluate : 1.080 Fit side-chains REVERT: A 256 TRP cc_start: 0.8502 (m100) cc_final: 0.7681 (m-10) REVERT: A 269 CYS cc_start: 0.7418 (t) cc_final: 0.7045 (t) REVERT: A 272 GLU cc_start: 0.7417 (mm-30) cc_final: 0.6846 (mt-10) REVERT: A 280 ARG cc_start: 0.7201 (ttp80) cc_final: 0.6768 (ttm170) REVERT: A 281 LYS cc_start: 0.7169 (tttt) cc_final: 0.6134 (mmtp) REVERT: A 286 MET cc_start: 0.8334 (mtp) cc_final: 0.8107 (mtm) REVERT: A 318 MET cc_start: 0.7225 (tpt) cc_final: 0.6858 (ttp) REVERT: A 356 ARG cc_start: 0.6691 (tpm170) cc_final: 0.6158 (ptp-110) REVERT: A 357 PHE cc_start: 0.8195 (t80) cc_final: 0.7977 (t80) REVERT: A 359 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8072 (mp) REVERT: A 367 MET cc_start: 0.8908 (OUTLIER) cc_final: 0.8357 (mtm) REVERT: A 368 ASP cc_start: 0.8088 (OUTLIER) cc_final: 0.7473 (m-30) REVERT: A 419 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.6963 (tmm) REVERT: B 99 PHE cc_start: 0.7991 (t80) cc_final: 0.7605 (t80) REVERT: B 142 MET cc_start: 0.8291 (mmm) cc_final: 0.7917 (tpp) REVERT: B 205 MET cc_start: 0.8568 (ptm) cc_final: 0.8268 (ptt) REVERT: B 231 GLU cc_start: 0.8060 (tt0) cc_final: 0.7669 (tm-30) REVERT: B 269 CYS cc_start: 0.7356 (t) cc_final: 0.6974 (t) REVERT: B 281 LYS cc_start: 0.7079 (tttt) cc_final: 0.5902 (mmtp) REVERT: B 307 ILE cc_start: 0.7472 (OUTLIER) cc_final: 0.7205 (mt) REVERT: B 318 MET cc_start: 0.7193 (tpt) cc_final: 0.6933 (ttp) REVERT: B 352 LYS cc_start: 0.6907 (tmtt) cc_final: 0.6628 (mttt) REVERT: B 356 ARG cc_start: 0.6744 (tpm170) cc_final: 0.6174 (ptp-110) REVERT: B 359 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.8015 (mp) REVERT: C 40 GLU cc_start: 0.7251 (mt-10) cc_final: 0.6911 (mp0) REVERT: C 232 LYS cc_start: 0.7815 (ttpt) cc_final: 0.7562 (mtmt) REVERT: C 256 TRP cc_start: 0.8571 (m100) cc_final: 0.7693 (m-10) REVERT: C 258 MET cc_start: 0.8265 (OUTLIER) cc_final: 0.7917 (ttt) REVERT: C 280 ARG cc_start: 0.7384 (ttp80) cc_final: 0.6979 (ttm170) REVERT: C 281 LYS cc_start: 0.7192 (tttt) cc_final: 0.6285 (mmmm) REVERT: C 286 MET cc_start: 0.8181 (mtp) cc_final: 0.7917 (mtm) REVERT: C 307 ILE cc_start: 0.7539 (OUTLIER) cc_final: 0.7308 (mt) REVERT: C 315 ARG cc_start: 0.7597 (tpp-160) cc_final: 0.7081 (ttm170) REVERT: C 318 MET cc_start: 0.7470 (tpt) cc_final: 0.7027 (ptt) REVERT: C 352 LYS cc_start: 0.7174 (tmtt) cc_final: 0.6788 (mttt) REVERT: C 368 ASP cc_start: 0.7945 (OUTLIER) cc_final: 0.7635 (m-30) outliers start: 32 outliers final: 9 residues processed: 178 average time/residue: 1.1584 time to fit residues: 221.4037 Evaluate side-chains 174 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 156 time to evaluate : 0.953 ------------------------------------------------------------------------------- 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 359 LEU 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 92 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 359 LEU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 90 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 111 optimal weight: 4.9990 chunk 67 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 312 ASN ** C 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.174184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.131565 restraints weight = 2839.907| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 0.90 r_work: 0.3464 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9417 Z= 0.237 Angle : 0.509 5.093 12783 Z= 0.266 Chirality : 0.040 0.173 1626 Planarity : 0.004 0.034 1557 Dihedral : 3.555 11.622 1281 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.66 % Allowed : 16.37 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.24), residues: 1200 helix: 1.32 (0.17), residues: 948 sheet: 1.80 (0.73), residues: 48 loop : -0.28 (0.41), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 276 HIS 0.002 0.001 HIS B 296 PHE 0.015 0.002 PHE C 240 TYR 0.008 0.001 TYR A 285 ARG 0.006 0.001 ARG B 353 *********************** 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 186 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 159 time to evaluate : 1.084 Fit side-chains REVERT: A 60 MET cc_start: 0.8464 (mmm) cc_final: 0.8131 (mmm) REVERT: A 231 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7422 (tm-30) REVERT: A 256 TRP cc_start: 0.8409 (m100) cc_final: 0.7547 (m-10) REVERT: A 269 CYS cc_start: 0.7253 (t) cc_final: 0.6906 (t) REVERT: A 272 GLU cc_start: 0.7389 (mm-30) cc_final: 0.6825 (mt-10) REVERT: A 280 ARG cc_start: 0.7192 (ttp80) cc_final: 0.6749 (ttm170) REVERT: A 281 LYS cc_start: 0.7101 (tttt) cc_final: 0.6015 (mmtp) REVERT: A 286 MET cc_start: 0.8278 (mtp) cc_final: 0.8030 (mtm) REVERT: A 318 MET cc_start: 0.7194 (tpt) cc_final: 0.6836 (ttp) REVERT: A 356 ARG cc_start: 0.6733 (tpm170) cc_final: 0.6164 (ptp-110) REVERT: A 367 MET cc_start: 0.8947 (OUTLIER) cc_final: 0.8415 (mtm) REVERT: A 368 ASP cc_start: 0.8153 (OUTLIER) cc_final: 0.7464 (m-30) REVERT: B 42 SER cc_start: 0.8431 (t) cc_final: 0.8194 (m) REVERT: B 99 PHE cc_start: 0.7877 (t80) cc_final: 0.7496 (t80) REVERT: B 142 MET cc_start: 0.8230 (mmm) cc_final: 0.7824 (tpp) REVERT: B 205 MET cc_start: 0.8588 (ptm) cc_final: 0.8264 (ptt) REVERT: B 269 CYS cc_start: 0.7330 (t) cc_final: 0.6931 (t) REVERT: B 272 GLU cc_start: 0.7245 (mm-30) cc_final: 0.6961 (mt-10) REVERT: B 281 LYS cc_start: 0.7100 (tttt) cc_final: 0.5890 (mmtp) REVERT: B 307 ILE cc_start: 0.7411 (OUTLIER) cc_final: 0.7156 (mt) REVERT: B 318 MET cc_start: 0.7263 (tpt) cc_final: 0.6934 (ttp) REVERT: B 346 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6575 (mt-10) REVERT: B 352 LYS cc_start: 0.6839 (tmtt) cc_final: 0.6567 (mttt) REVERT: B 356 ARG cc_start: 0.6761 (tpm170) cc_final: 0.6093 (ptp-110) REVERT: B 444 ASP cc_start: 0.7681 (t0) cc_final: 0.7436 (t0) REVERT: C 40 GLU cc_start: 0.7223 (mt-10) cc_final: 0.6846 (mp0) REVERT: C 92 LEU cc_start: 0.7289 (OUTLIER) cc_final: 0.6805 (mm) REVERT: C 232 LYS cc_start: 0.7778 (ttpt) cc_final: 0.7498 (mtmt) REVERT: C 256 TRP cc_start: 0.8482 (m100) cc_final: 0.7561 (m-10) REVERT: C 258 MET cc_start: 0.8236 (OUTLIER) cc_final: 0.7863 (ttt) REVERT: C 280 ARG cc_start: 0.7384 (ttp80) cc_final: 0.6989 (ttm170) REVERT: C 281 LYS cc_start: 0.7143 (tttt) cc_final: 0.6206 (mmmm) REVERT: C 286 MET cc_start: 0.8143 (mtp) cc_final: 0.7862 (mtm) REVERT: C 307 ILE cc_start: 0.7461 (OUTLIER) cc_final: 0.7236 (mt) REVERT: C 315 ARG cc_start: 0.7556 (tpp-160) cc_final: 0.7029 (ttm170) REVERT: C 318 MET cc_start: 0.7464 (tpt) cc_final: 0.6938 (ptt) REVERT: C 352 LYS cc_start: 0.7091 (tmtt) cc_final: 0.6703 (mttt) REVERT: C 444 ASP cc_start: 0.7539 (t0) cc_final: 0.6946 (t70) outliers start: 27 outliers final: 9 residues processed: 171 average time/residue: 1.1623 time to fit residues: 213.6813 Evaluate side-chains 174 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 157 time to evaluate : 1.116 ------------------------------------------------------------------------------- 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 231 GLU Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 368 ASP 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 346 GLU Chi-restraints excluded: chain B residue 368 ASP Chi-restraints excluded: chain B residue 403 SER 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 15 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 105 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 252 GLN C 348 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.190120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.155006 restraints weight = 2665.643| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 0.67 r_work: 0.3131 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9417 Z= 0.219 Angle : 0.500 6.107 12783 Z= 0.262 Chirality : 0.040 0.166 1626 Planarity : 0.004 0.035 1557 Dihedral : 3.523 11.843 1281 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 3.35 % Allowed : 15.98 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.24), residues: 1200 helix: 1.35 (0.17), residues: 948 sheet: 1.75 (0.74), residues: 48 loop : -0.30 (0.41), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 276 HIS 0.002 0.001 HIS B 296 PHE 0.013 0.001 PHE C 240 TYR 0.008 0.001 TYR A 285 ARG 0.006 0.001 ARG C 353 *********************** 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 192 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 158 time to evaluate : 1.001 Fit side-chains REVERT: A 60 MET cc_start: 0.8525 (mmm) cc_final: 0.8198 (mmm) REVERT: A 92 LEU cc_start: 0.6843 (OUTLIER) cc_final: 0.6405 (mm) REVERT: A 256 TRP cc_start: 0.8517 (m100) cc_final: 0.7721 (m-10) REVERT: A 269 CYS cc_start: 0.7406 (t) cc_final: 0.7023 (t) REVERT: A 272 GLU cc_start: 0.7390 (mm-30) cc_final: 0.6886 (mt-10) REVERT: A 280 ARG cc_start: 0.7244 (ttp80) cc_final: 0.6811 (ttm170) REVERT: A 281 LYS cc_start: 0.7225 (tttt) cc_final: 0.6173 (mmtp) REVERT: A 286 MET cc_start: 0.8377 (mtp) cc_final: 0.8137 (mtm) REVERT: A 318 MET cc_start: 0.7284 (tpt) cc_final: 0.6935 (ttp) REVERT: A 347 ASN cc_start: 0.8399 (OUTLIER) cc_final: 0.8090 (m110) REVERT: A 356 ARG cc_start: 0.6746 (tpm170) cc_final: 0.6265 (ptp-110) REVERT: A 359 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8189 (mp) REVERT: A 367 MET cc_start: 0.8959 (OUTLIER) cc_final: 0.8459 (mtm) REVERT: A 368 ASP cc_start: 0.8190 (OUTLIER) cc_final: 0.7531 (m-30) REVERT: B 99 PHE cc_start: 0.7998 (t80) cc_final: 0.7633 (t80) REVERT: B 142 MET cc_start: 0.8304 (mmm) cc_final: 0.7943 (tpp) REVERT: B 205 MET cc_start: 0.8560 (ptm) cc_final: 0.8261 (ptt) REVERT: B 269 CYS cc_start: 0.7566 (t) cc_final: 0.7166 (t) REVERT: B 281 LYS cc_start: 0.7200 (tttt) cc_final: 0.5987 (mmtp) REVERT: B 307 ILE cc_start: 0.7553 (OUTLIER) cc_final: 0.7296 (mt) REVERT: B 318 MET cc_start: 0.7384 (tpt) cc_final: 0.7115 (ttp) REVERT: B 346 GLU cc_start: 0.7212 (OUTLIER) cc_final: 0.6612 (mt-10) REVERT: B 352 LYS cc_start: 0.6958 (tmtt) cc_final: 0.6696 (mttt) REVERT: B 356 ARG cc_start: 0.6791 (tpm170) cc_final: 0.6254 (ptp-110) REVERT: B 419 MET cc_start: 0.8367 (OUTLIER) cc_final: 0.8011 (tpp) REVERT: C 40 GLU cc_start: 0.7241 (mt-10) cc_final: 0.6905 (mp0) REVERT: C 92 LEU cc_start: 0.7352 (OUTLIER) cc_final: 0.6883 (mm) REVERT: C 232 LYS cc_start: 0.7761 (ttpt) cc_final: 0.7480 (mtmt) REVERT: C 256 TRP cc_start: 0.8589 (m100) cc_final: 0.7745 (m-10) REVERT: C 258 MET cc_start: 0.8258 (OUTLIER) cc_final: 0.7892 (ttt) REVERT: C 280 ARG cc_start: 0.7450 (ttp80) cc_final: 0.7057 (ttm170) REVERT: C 281 LYS cc_start: 0.7216 (tttt) cc_final: 0.6304 (mmmm) REVERT: C 286 MET cc_start: 0.8219 (mtp) cc_final: 0.7950 (mtm) REVERT: C 307 ILE cc_start: 0.7592 (OUTLIER) cc_final: 0.7364 (mt) REVERT: C 315 ARG cc_start: 0.7602 (tpp-160) cc_final: 0.7103 (ttm170) REVERT: C 318 MET cc_start: 0.7470 (tpt) cc_final: 0.7037 (ptt) REVERT: C 352 LYS cc_start: 0.7199 (tmtt) cc_final: 0.6847 (mttt) REVERT: C 444 ASP cc_start: 0.7552 (t0) cc_final: 0.6962 (t70) outliers start: 34 outliers final: 12 residues processed: 171 average time/residue: 1.1522 time to fit residues: 212.0194 Evaluate side-chains 177 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 154 time to evaluate : 1.015 ------------------------------------------------------------------------------- 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 347 ASN Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 418 THR 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 346 GLU Chi-restraints excluded: chain B residue 359 LEU 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 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 52 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 2 optimal weight: 0.0030 chunk 53 optimal weight: 0.0000 chunk 102 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 ASN A 413 GLN B 252 GLN C 348 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.180035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.140306 restraints weight = 2727.184| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 0.81 r_work: 0.3133 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2964 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= 0.179 Angle : 0.487 6.848 12783 Z= 0.255 Chirality : 0.039 0.193 1626 Planarity : 0.004 0.034 1557 Dihedral : 3.414 11.613 1281 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 3.06 % Allowed : 16.27 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.24), residues: 1200 helix: 1.48 (0.17), residues: 948 sheet: 1.80 (0.74), residues: 48 loop : -0.21 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 19 HIS 0.001 0.000 HIS C 296 PHE 0.011 0.001 PHE C 240 TYR 0.008 0.001 TYR A 285 ARG 0.006 0.000 ARG C 353 *********************** 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 190 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 159 time to evaluate : 1.023 Fit side-chains REVERT: A 256 TRP cc_start: 0.8475 (m100) cc_final: 0.7629 (m-10) REVERT: A 272 GLU cc_start: 0.7296 (mm-30) cc_final: 0.6827 (mt-10) REVERT: A 280 ARG cc_start: 0.7190 (ttp80) cc_final: 0.6751 (ttm170) REVERT: A 281 LYS cc_start: 0.7137 (tttt) cc_final: 0.6065 (mmtp) REVERT: A 286 MET cc_start: 0.8301 (mtp) cc_final: 0.8054 (mtm) REVERT: A 318 MET cc_start: 0.7174 (tpt) cc_final: 0.6799 (ttp) REVERT: A 347 ASN cc_start: 0.8292 (m110) cc_final: 0.8007 (m110) REVERT: A 348 ASN cc_start: 0.8203 (m-40) cc_final: 0.7973 (m-40) REVERT: A 356 ARG cc_start: 0.6700 (tpm170) cc_final: 0.6114 (ptp-110) REVERT: A 357 PHE cc_start: 0.8062 (t80) cc_final: 0.7847 (t80) REVERT: A 359 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.8014 (mp) REVERT: A 368 ASP cc_start: 0.8059 (OUTLIER) cc_final: 0.7429 (m-30) REVERT: B 40 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7069 (mt-10) REVERT: B 99 PHE cc_start: 0.7905 (t80) cc_final: 0.7495 (t80) REVERT: B 142 MET cc_start: 0.8064 (mmm) cc_final: 0.7700 (tpp) REVERT: B 205 MET cc_start: 0.8555 (ptm) cc_final: 0.8242 (ptt) REVERT: B 231 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7592 (tm-30) REVERT: B 269 CYS cc_start: 0.7559 (t) cc_final: 0.7120 (t) REVERT: B 272 GLU cc_start: 0.7126 (mm-30) cc_final: 0.6821 (mm-30) REVERT: B 281 LYS cc_start: 0.7082 (tttt) cc_final: 0.5845 (mmtp) REVERT: B 307 ILE cc_start: 0.7388 (OUTLIER) cc_final: 0.7130 (mt) REVERT: B 318 MET cc_start: 0.7140 (tpt) cc_final: 0.6891 (ttp) REVERT: B 352 LYS cc_start: 0.6864 (tmtt) cc_final: 0.6550 (mttt) REVERT: B 356 ARG cc_start: 0.6767 (tpm170) cc_final: 0.6118 (ptp-110) REVERT: C 40 GLU cc_start: 0.7215 (mt-10) cc_final: 0.6831 (mp0) REVERT: C 92 LEU cc_start: 0.7164 (OUTLIER) cc_final: 0.6716 (mm) REVERT: C 232 LYS cc_start: 0.7670 (ttpt) cc_final: 0.7387 (mtmt) REVERT: C 256 TRP cc_start: 0.8552 (m100) cc_final: 0.7637 (m-10) REVERT: C 258 MET cc_start: 0.8253 (OUTLIER) cc_final: 0.7879 (ttt) REVERT: C 280 ARG cc_start: 0.7430 (ttp80) cc_final: 0.7008 (ttm170) REVERT: C 281 LYS cc_start: 0.7135 (tttt) cc_final: 0.6195 (mmmm) REVERT: C 286 MET cc_start: 0.8128 (mtp) cc_final: 0.7867 (mtm) REVERT: C 307 ILE cc_start: 0.7478 (OUTLIER) cc_final: 0.7272 (mt) REVERT: C 315 ARG cc_start: 0.7523 (tpp-160) cc_final: 0.7010 (ttm170) REVERT: C 318 MET cc_start: 0.7282 (tpt) cc_final: 0.6817 (ptt) REVERT: C 352 LYS cc_start: 0.7102 (tmtt) cc_final: 0.6724 (mttt) REVERT: C 368 ASP cc_start: 0.7848 (OUTLIER) cc_final: 0.7549 (m-30) REVERT: C 385 ASN cc_start: 0.8002 (m-40) cc_final: 0.7713 (m110) outliers start: 31 outliers final: 11 residues processed: 174 average time/residue: 1.2857 time to fit residues: 239.2455 Evaluate side-chains 175 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 155 time to evaluate : 1.125 ------------------------------------------------------------------------------- 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 359 LEU 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 107 ILE Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 359 LEU 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 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 13 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 77 optimal weight: 0.0770 chunk 104 optimal weight: 0.2980 chunk 86 optimal weight: 0.7980 chunk 80 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 ASN A 413 GLN B 252 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.178686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.138728 restraints weight = 2757.438| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 0.81 r_work: 0.3106 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2947 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= 0.222 Angle : 0.514 8.635 12783 Z= 0.268 Chirality : 0.040 0.166 1626 Planarity : 0.004 0.034 1557 Dihedral : 3.474 11.841 1281 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.37 % Allowed : 17.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.24), residues: 1200 helix: 1.40 (0.17), residues: 948 sheet: 1.54 (0.74), residues: 48 loop : -0.25 (0.41), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 276 HIS 0.001 0.001 HIS B 296 PHE 0.013 0.001 PHE C 240 TYR 0.008 0.001 TYR A 285 ARG 0.006 0.001 ARG C 353 ********************** 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 176 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 152 time to evaluate : 1.023 Fit side-chains REVERT: A 92 LEU cc_start: 0.6744 (OUTLIER) cc_final: 0.6301 (mm) REVERT: A 231 GLU cc_start: 0.7893 (tt0) cc_final: 0.7413 (tm-30) REVERT: A 256 TRP cc_start: 0.8476 (m100) cc_final: 0.7632 (m-10) REVERT: A 269 CYS cc_start: 0.7351 (t) cc_final: 0.6976 (t) REVERT: A 272 GLU cc_start: 0.7328 (mm-30) cc_final: 0.6772 (mt-10) REVERT: A 274 GLU cc_start: 0.7323 (mm-30) cc_final: 0.6956 (tp30) REVERT: A 280 ARG cc_start: 0.7199 (ttp80) cc_final: 0.6757 (ttm170) REVERT: A 281 LYS cc_start: 0.7103 (tttt) cc_final: 0.6006 (mmtp) REVERT: A 286 MET cc_start: 0.8308 (mtp) cc_final: 0.8060 (mtm) REVERT: A 307 ILE cc_start: 0.7481 (OUTLIER) cc_final: 0.7247 (mt) REVERT: A 318 MET cc_start: 0.7198 (tpt) cc_final: 0.6823 (ttp) REVERT: A 347 ASN cc_start: 0.8284 (m110) cc_final: 0.8009 (m110) REVERT: A 356 ARG cc_start: 0.6764 (tpm170) cc_final: 0.6206 (ptp-110) REVERT: A 359 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8121 (mp) REVERT: A 368 ASP cc_start: 0.8118 (OUTLIER) cc_final: 0.7485 (m-30) REVERT: B 40 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7110 (mt-10) REVERT: B 99 PHE cc_start: 0.7923 (t80) cc_final: 0.7544 (t80) REVERT: B 142 MET cc_start: 0.8054 (mmm) cc_final: 0.7708 (tpp) REVERT: B 205 MET cc_start: 0.8576 (ptm) cc_final: 0.8270 (ptt) REVERT: B 231 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7625 (tm-30) REVERT: B 269 CYS cc_start: 0.7373 (t) cc_final: 0.6935 (t) REVERT: B 272 GLU cc_start: 0.7127 (mm-30) cc_final: 0.6829 (mt-10) REVERT: B 281 LYS cc_start: 0.7099 (tttt) cc_final: 0.5861 (mmtp) REVERT: B 307 ILE cc_start: 0.7417 (OUTLIER) cc_final: 0.7164 (mt) REVERT: B 318 MET cc_start: 0.7244 (tpt) cc_final: 0.6959 (ttp) REVERT: B 352 LYS cc_start: 0.6857 (tmtt) cc_final: 0.6557 (mttt) REVERT: B 356 ARG cc_start: 0.6783 (tpm170) cc_final: 0.6138 (ptp-110) REVERT: B 419 MET cc_start: 0.8302 (OUTLIER) cc_final: 0.7941 (tpp) REVERT: C 92 LEU cc_start: 0.7271 (OUTLIER) cc_final: 0.6825 (mm) REVERT: C 232 LYS cc_start: 0.7733 (ttpt) cc_final: 0.7432 (mtmt) REVERT: C 256 TRP cc_start: 0.8544 (m100) cc_final: 0.7642 (m-10) REVERT: C 258 MET cc_start: 0.8241 (OUTLIER) cc_final: 0.7869 (ttt) REVERT: C 280 ARG cc_start: 0.7430 (ttp80) cc_final: 0.7008 (ttm170) REVERT: C 281 LYS cc_start: 0.7150 (tttt) cc_final: 0.6206 (mmmm) REVERT: C 286 MET cc_start: 0.8129 (mtp) cc_final: 0.7865 (mtm) REVERT: C 307 ILE cc_start: 0.7513 (OUTLIER) cc_final: 0.7294 (mt) REVERT: C 315 ARG cc_start: 0.7525 (tpp-160) cc_final: 0.7008 (ttm170) REVERT: C 318 MET cc_start: 0.7329 (tpt) cc_final: 0.6789 (ptt) REVERT: C 352 LYS cc_start: 0.7111 (tmtt) cc_final: 0.6726 (mttt) REVERT: C 368 ASP cc_start: 0.7980 (OUTLIER) cc_final: 0.7653 (m-30) REVERT: C 385 ASN cc_start: 0.8045 (m-40) cc_final: 0.7779 (m110) REVERT: C 444 ASP cc_start: 0.7460 (t0) cc_final: 0.6869 (t70) outliers start: 24 outliers final: 11 residues processed: 162 average time/residue: 1.2138 time to fit residues: 210.5870 Evaluate side-chains 173 residues out of total 1014 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 150 time to evaluate : 1.047 ------------------------------------------------------------------------------- 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 307 ILE Chi-restraints excluded: chain A residue 359 LEU 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 231 GLU Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 359 LEU 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 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 39 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 42 optimal weight: 0.1980 chunk 22 optimal weight: 0.8980 chunk 92 optimal weight: 0.3980 chunk 62 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 82 optimal weight: 0.3980 chunk 93 optimal weight: 0.0980 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 GLN B 252 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.193720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.159155 restraints weight = 2606.342| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 0.66 r_work: 0.3211 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9417 Z= 0.161 Angle : 0.482 10.078 12783 Z= 0.252 Chirality : 0.039 0.171 1626 Planarity : 0.004 0.033 1557 Dihedral : 3.325 11.389 1281 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 2.37 % Allowed : 17.16 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.24), residues: 1200 helix: 1.59 (0.17), residues: 951 sheet: 1.61 (0.75), residues: 48 loop : -0.27 (0.42), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 19 HIS 0.001 0.000 HIS C 296 PHE 0.010 0.001 PHE B 218 TYR 0.007 0.001 TYR A 162 ARG 0.007 0.000 ARG C 353 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6748.00 seconds wall clock time: 119 minutes 33.14 seconds (7173.14 seconds total)