Starting phenix.real_space_refine on Fri Jul 3 05:56:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7fd8_31536/07_2026/7fd8_31536.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fd8_31536/07_2026/7fd8_31536.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7fd8_31536/07_2026/7fd8_31536.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fd8_31536/07_2026/7fd8_31536.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7fd8_31536/07_2026/7fd8_31536.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7fd8_31536/07_2026/7fd8_31536.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7fd8_31536/07_2026/7fd8_31536.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fd8_31536/07_2026/7fd8_31536.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 7824 2.51 5 N 2004 2.21 5 O 2210 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12152 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 764, 6014 Classifications: {'peptide': 764} Link IDs: {'PTRANS': 32, 'TRANS': 731} Chain breaks: 2 Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 62 Unusual residues: {'NAG': 1, 'QUS': 1, 'Y01': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: B Time building chain proxies: 5.30, per 1000 atoms: 0.44 Number of scatterers: 12152 At special positions: 0 Unit cell: (77.43, 102.35, 173.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 114 16.00 O 2210 8.00 N 2004 7.00 C 7824 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 99 " distance=2.03 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 530 " distance=2.02 Simple disulfide: pdb=" SG CYS A 276 " - pdb=" SG CYS A 278 " distance=2.04 Simple disulfide: pdb=" SG CYS A 365 " - pdb=" SG CYS A 381 " distance=2.03 Simple disulfide: pdb=" SG CYS A 419 " - pdb=" SG CYS A 426 " distance=2.03 Simple disulfide: pdb=" SG CYS A 511 " - pdb=" SG CYS A 531 " distance=2.03 Simple disulfide: pdb=" SG CYS A 515 " - pdb=" SG CYS A 534 " distance=2.03 Simple disulfide: pdb=" SG CYS A 537 " - pdb=" SG CYS A 549 " distance=2.03 Simple disulfide: pdb=" SG CYS A 552 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 644 " - pdb=" SG CYS A 733 " distance=2.04 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 99 " distance=2.03 Simple disulfide: pdb=" SG CYS B 241 " - pdb=" SG CYS B 530 " distance=2.02 Simple disulfide: pdb=" SG CYS B 276 " - pdb=" SG CYS B 278 " distance=2.04 Simple disulfide: pdb=" SG CYS B 365 " - pdb=" SG CYS B 381 " distance=2.03 Simple disulfide: pdb=" SG CYS B 419 " - pdb=" SG CYS B 426 " distance=2.03 Simple disulfide: pdb=" SG CYS B 511 " - pdb=" SG CYS B 531 " distance=2.03 Simple disulfide: pdb=" SG CYS B 515 " - pdb=" SG CYS B 534 " distance=2.03 Simple disulfide: pdb=" SG CYS B 537 " - pdb=" SG CYS B 549 " distance=2.03 Simple disulfide: pdb=" SG CYS B 552 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 644 " - pdb=" SG CYS B 733 " distance=2.04 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 Links applied NAG-ASN " NAG A 901 " - " ASN A 210 " " NAG B 901 " - " ASN B 210 " Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 571.8 milliseconds 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2852 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 12 sheets defined 48.4% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 65 through 81 Processing helix chain 'A' and resid 101 through 113 Processing helix chain 'A' and resid 151 through 163 removed outlier: 3.800A pdb=" N LEU A 161 " --> pdb=" O GLN A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 181 removed outlier: 3.776A pdb=" N ASP A 181 " --> pdb=" O ASP A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 209 Processing helix chain 'A' and resid 221 through 238 Processing helix chain 'A' and resid 253 through 266 Processing helix chain 'A' and resid 279 through 293 Processing helix chain 'A' and resid 317 through 321 removed outlier: 3.521A pdb=" N ALA A 321 " --> pdb=" O GLN A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 342 Processing helix chain 'A' and resid 354 through 364 removed outlier: 3.815A pdb=" N PHE A 363 " --> pdb=" O TRP A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 419 Processing helix chain 'A' and resid 433 through 444 removed outlier: 3.669A pdb=" N LYS A 443 " --> pdb=" O GLU A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 604 removed outlier: 3.517A pdb=" N ALA A 583 " --> pdb=" O GLU A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 612 Processing helix chain 'A' and resid 614 through 636 removed outlier: 3.862A pdb=" N THR A 632 " --> pdb=" O GLY A 628 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N PHE A 633 " --> pdb=" O TYR A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 671 removed outlier: 3.737A pdb=" N ARG A 648 " --> pdb=" O CYS A 644 " (cutoff:3.500A) Proline residue: A 655 - end of helix Processing helix chain 'A' and resid 692 through 715 removed outlier: 3.943A pdb=" N GLN A 704 " --> pdb=" O LEU A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 736 through 760 Proline residue: A 743 - end of helix Processing helix chain 'A' and resid 765 through 788 removed outlier: 5.756A pdb=" N ALA A 771 " --> pdb=" O ASN A 767 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LYS A 772 " --> pdb=" O PHE A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 795 removed outlier: 4.274A pdb=" N PHE A 793 " --> pdb=" O VAL A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 797 through 816 Processing helix chain 'A' and resid 818 through 826 Processing helix chain 'B' and resid 65 through 81 Processing helix chain 'B' and resid 101 through 113 Processing helix chain 'B' and resid 151 through 163 removed outlier: 3.798A pdb=" N LEU B 161 " --> pdb=" O GLN B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 181 removed outlier: 3.776A pdb=" N ASP B 181 " --> pdb=" O ASP B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 209 Processing helix chain 'B' and resid 221 through 238 Processing helix chain 'B' and resid 253 through 266 Processing helix chain 'B' and resid 279 through 293 Processing helix chain 'B' and resid 317 through 321 removed outlier: 3.522A pdb=" N ALA B 321 " --> pdb=" O GLN B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 342 Processing helix chain 'B' and resid 354 through 364 removed outlier: 3.814A pdb=" N PHE B 363 " --> pdb=" O TRP B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 419 Processing helix chain 'B' and resid 433 through 444 removed outlier: 3.669A pdb=" N LYS B 443 " --> pdb=" O GLU B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 604 removed outlier: 3.517A pdb=" N ALA B 583 " --> pdb=" O GLU B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 612 Processing helix chain 'B' and resid 614 through 636 removed outlier: 3.862A pdb=" N THR B 632 " --> pdb=" O GLY B 628 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N PHE B 633 " --> pdb=" O TYR B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 671 removed outlier: 3.737A pdb=" N ARG B 648 " --> pdb=" O CYS B 644 " (cutoff:3.500A) Proline residue: B 655 - end of helix Processing helix chain 'B' and resid 692 through 715 removed outlier: 3.943A pdb=" N GLN B 704 " --> pdb=" O LEU B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 760 Proline residue: B 743 - end of helix Processing helix chain 'B' and resid 765 through 788 removed outlier: 5.757A pdb=" N ALA B 771 " --> pdb=" O ASN B 767 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LYS B 772 " --> pdb=" O PHE B 768 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 795 removed outlier: 4.275A pdb=" N PHE B 793 " --> pdb=" O VAL B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 797 through 816 Processing helix chain 'B' and resid 818 through 826 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 5.827A pdb=" N ILE A 35 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N GLU A 94 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE A 37 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N ARG A 96 " --> pdb=" O ILE A 37 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ALA A 39 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N ILE A 36 " --> pdb=" O VAL A 144 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL A 146 " --> pdb=" O ILE A 36 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N GLY A 38 " --> pdb=" O VAL A 146 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N ILE A 170 " --> pdb=" O VAL A 144 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL A 146 " --> pdb=" O ILE A 170 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 213 through 219 removed outlier: 7.713A pdb=" N VAL A 214 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N SER A 245 " --> pdb=" O VAL A 214 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ALA A 216 " --> pdb=" O SER A 245 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N LYS A 247 " --> pdb=" O ALA A 216 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N HIS A 218 " --> pdb=" O LYS A 247 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 274 through 276 removed outlier: 6.241A pdb=" N VAL A 274 " --> pdb=" O LEU A 302 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE A 325 " --> pdb=" O LEU A 301 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE A 327 " --> pdb=" O GLY A 303 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLY A 324 " --> pdb=" O PHE A 471 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N TYR A 466 " --> pdb=" O SER A 486 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N SER A 486 " --> pdb=" O TYR A 466 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ILE A 468 " --> pdb=" O VAL A 484 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 446 through 447 removed outlier: 3.523A pdb=" N PHE A 446 " --> pdb=" O ILE A 454 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 520 through 523 removed outlier: 3.571A pdb=" N THR A 535 " --> pdb=" O LYS A 521 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 719 through 722 Processing sheet with id=AA7, first strand: chain 'B' and resid 28 through 31 removed outlier: 5.827A pdb=" N ILE B 35 " --> pdb=" O GLY B 92 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N GLU B 94 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE B 37 " --> pdb=" O GLU B 94 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N ARG B 96 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ALA B 39 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N ILE B 36 " --> pdb=" O VAL B 144 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL B 146 " --> pdb=" O ILE B 36 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLY B 38 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N ILE B 170 " --> pdb=" O VAL B 144 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL B 146 " --> pdb=" O ILE B 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 213 through 219 removed outlier: 7.712A pdb=" N VAL B 214 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N SER B 245 " --> pdb=" O VAL B 214 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ALA B 216 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N LYS B 247 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N HIS B 218 " --> pdb=" O LYS B 247 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 274 through 276 removed outlier: 6.240A pdb=" N VAL B 274 " --> pdb=" O LEU B 302 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE B 325 " --> pdb=" O LEU B 301 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE B 327 " --> pdb=" O GLY B 303 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLY B 324 " --> pdb=" O PHE B 471 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N TYR B 466 " --> pdb=" O SER B 486 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N SER B 486 " --> pdb=" O TYR B 466 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ILE B 468 " --> pdb=" O VAL B 484 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 446 through 447 removed outlier: 3.523A pdb=" N PHE B 446 " --> pdb=" O ILE B 454 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 520 through 523 removed outlier: 3.570A pdb=" N THR B 535 " --> pdb=" O LYS B 521 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 719 through 722 576 hydrogen bonds defined for protein. 1692 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.74 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1946 1.30 - 1.43: 3302 1.43 - 1.56: 7022 1.56 - 1.69: 0 1.69 - 1.82: 164 Bond restraints: 12434 Sorted by residual: bond pdb=" CAY Y01 B 903 " pdb=" OAG Y01 B 903 " ideal model delta sigma weight residual 1.207 1.422 -0.215 2.00e-02 2.50e+03 1.15e+02 bond pdb=" CAY Y01 A 903 " pdb=" OAG Y01 A 903 " ideal model delta sigma weight residual 1.207 1.422 -0.215 2.00e-02 2.50e+03 1.15e+02 bond pdb=" CAI Y01 B 903 " pdb=" CAZ Y01 B 903 " ideal model delta sigma weight residual 1.332 1.498 -0.166 2.00e-02 2.50e+03 6.93e+01 bond pdb=" CAI Y01 A 903 " pdb=" CAZ Y01 A 903 " ideal model delta sigma weight residual 1.332 1.498 -0.166 2.00e-02 2.50e+03 6.93e+01 bond pdb=" C01 QUS A 902 " pdb=" C02 QUS A 902 " ideal model delta sigma weight residual 1.556 1.458 0.098 2.00e-02 2.50e+03 2.41e+01 ... (remaining 12429 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 14746 2.01 - 4.03: 1950 4.03 - 6.04: 134 6.04 - 8.05: 22 8.05 - 10.06: 10 Bond angle restraints: 16862 Sorted by residual: angle pdb=" C LYS B 379 " pdb=" N THR B 380 " pdb=" CA THR B 380 " ideal model delta sigma weight residual 121.31 127.44 -6.13 1.49e+00 4.50e-01 1.69e+01 angle pdb=" C LYS A 379 " pdb=" N THR A 380 " pdb=" CA THR A 380 " ideal model delta sigma weight residual 121.31 127.36 -6.05 1.49e+00 4.50e-01 1.65e+01 angle pdb=" N LYS B 517 " pdb=" CA LYS B 517 " pdb=" C LYS B 517 " ideal model delta sigma weight residual 112.57 108.07 4.50 1.13e+00 7.83e-01 1.58e+01 angle pdb=" N LYS A 517 " pdb=" CA LYS A 517 " pdb=" C LYS A 517 " ideal model delta sigma weight residual 112.57 108.09 4.48 1.13e+00 7.83e-01 1.57e+01 angle pdb=" C TYR A 317 " pdb=" N GLN A 318 " pdb=" CA GLN A 318 " ideal model delta sigma weight residual 120.28 125.90 -5.62 1.44e+00 4.82e-01 1.52e+01 ... (remaining 16857 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.63: 7186 22.63 - 45.25: 227 45.25 - 67.88: 23 67.88 - 90.50: 6 90.50 - 113.13: 2 Dihedral angle restraints: 7444 sinusoidal: 2996 harmonic: 4448 Sorted by residual: dihedral pdb=" CB CYS B 537 " pdb=" SG CYS B 537 " pdb=" SG CYS B 549 " pdb=" CB CYS B 549 " ideal model delta sinusoidal sigma weight residual 93.00 156.64 -63.64 1 1.00e+01 1.00e-02 5.34e+01 dihedral pdb=" CB CYS A 537 " pdb=" SG CYS A 537 " pdb=" SG CYS A 549 " pdb=" CB CYS A 549 " ideal model delta sinusoidal sigma weight residual 93.00 156.63 -63.63 1 1.00e+01 1.00e-02 5.34e+01 dihedral pdb=" CB CYS A 552 " pdb=" SG CYS A 552 " pdb=" SG CYS A 565 " pdb=" CB CYS A 565 " ideal model delta sinusoidal sigma weight residual -86.00 -129.41 43.41 1 1.00e+01 1.00e-02 2.63e+01 ... (remaining 7441 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.345: 1892 0.345 - 0.689: 4 0.689 - 1.033: 0 1.033 - 1.378: 0 1.378 - 1.722: 2 Chirality restraints: 1898 Sorted by residual: chirality pdb=" C02 QUS B 902 " pdb=" C01 QUS B 902 " pdb=" C03 QUS B 902 " pdb=" NP3 QUS B 902 " both_signs ideal model delta sigma weight residual False 2.50 0.78 1.72 2.00e-01 2.50e+01 7.41e+01 chirality pdb=" C02 QUS A 902 " pdb=" C01 QUS A 902 " pdb=" C03 QUS A 902 " pdb=" NP3 QUS A 902 " both_signs ideal model delta sigma weight residual False 2.50 0.78 1.72 2.00e-01 2.50e+01 7.38e+01 chirality pdb=" C1 NAG B 901 " pdb=" ND2 ASN B 210 " pdb=" C2 NAG B 901 " pdb=" O5 NAG B 901 " both_signs ideal model delta sigma weight residual False -2.40 -1.88 -0.52 2.00e-01 2.50e+01 6.75e+00 ... (remaining 1895 not shown) Planarity restraints: 2116 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CAM Y01 B 903 " -0.025 2.00e-02 2.50e+03 4.43e-02 1.97e+01 pdb=" CAY Y01 B 903 " 0.077 2.00e-02 2.50e+03 pdb=" OAG Y01 B 903 " -0.027 2.00e-02 2.50e+03 pdb=" OAW Y01 B 903 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAM Y01 A 903 " 0.025 2.00e-02 2.50e+03 4.35e-02 1.89e+01 pdb=" CAY Y01 A 903 " -0.075 2.00e-02 2.50e+03 pdb=" OAG Y01 A 903 " 0.027 2.00e-02 2.50e+03 pdb=" OAW Y01 A 903 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C01 QUS B 902 " -0.046 2.00e-02 2.50e+03 2.64e-02 6.99e+00 pdb=" C02 QUS B 902 " 0.013 2.00e-02 2.50e+03 pdb=" O16 QUS B 902 " 0.016 2.00e-02 2.50e+03 pdb=" O17 QUS B 902 " 0.017 2.00e-02 2.50e+03 ... (remaining 2113 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 3556 2.84 - 3.36: 11937 3.36 - 3.87: 20567 3.87 - 4.39: 23303 4.39 - 4.90: 39011 Nonbonded interactions: 98374 Sorted by model distance: nonbonded pdb=" OG SER B 250 " pdb=" OE2 GLU B 279 " model vdw 2.327 3.040 nonbonded pdb=" OG SER A 250 " pdb=" OE2 GLU A 279 " model vdw 2.328 3.040 nonbonded pdb=" O GLY B 253 " pdb=" OG SER B 256 " model vdw 2.331 3.040 nonbonded pdb=" O GLY A 253 " pdb=" OG SER A 256 " model vdw 2.332 3.040 nonbonded pdb=" OG SER A 152 " pdb=" OG SER A 176 " model vdw 2.339 3.040 ... (remaining 98369 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' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 5.330 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.030 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 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 : 0.008 0.215 12456 Z= 0.494 Angle : 1.403 10.063 16908 Z= 0.935 Chirality : 0.108 1.722 1898 Planarity : 0.004 0.044 2114 Dihedral : 11.636 113.126 4532 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.58 % Favored : 91.29 % Rotamer: Outliers : 0.61 % Allowed : 2.88 % Favored : 96.52 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.25 (0.19), residues: 1516 helix: -0.64 (0.16), residues: 706 sheet: -2.08 (0.37), residues: 160 loop : -2.24 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 351 TYR 0.019 0.002 TYR B 223 PHE 0.020 0.002 PHE B 337 TRP 0.014 0.003 TRP A 575 HIS 0.010 0.002 HIS B 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00800 / 0.49 (12434) covalent geometry : angle 1.39914 / 0.93 (16862) SS BOND : bond 0.00335 / 0.24 ( 20) SS BOND : angle 1.52857 / 1.04 ( 40) hydrogen bonds : bond 0.12851 / 8.52 ( 576) hydrogen bonds : angle 5.79304 / 4.05 ( 1692) link_NAG-ASN : bond 0.00930 / 0.47 ( 2) link_NAG-ASN : angle 5.28140 / 2.78 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 127 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 414 MET cc_start: 0.8661 (ttt) cc_final: 0.8382 (tmm) REVERT: A 429 MET cc_start: 0.7534 (mpp) cc_final: 0.7218 (mpp) REVERT: A 592 LEU cc_start: 0.8961 (mt) cc_final: 0.8749 (tt) REVERT: A 714 MET cc_start: 0.6865 (mmt) cc_final: 0.5929 (ttp) REVERT: B 414 MET cc_start: 0.8632 (ttt) cc_final: 0.8427 (tmm) REVERT: B 429 MET cc_start: 0.7558 (mpp) cc_final: 0.7267 (mpp) REVERT: B 592 LEU cc_start: 0.8903 (mt) cc_final: 0.8700 (tt) REVERT: B 714 MET cc_start: 0.7060 (mmt) cc_final: 0.6244 (ttp) outliers start: 8 outliers final: 0 residues processed: 135 average time/residue: 0.1054 time to fit residues: 20.7275 Evaluate side-chains 72 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 7.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 159 GLN A 222 ASN B 159 GLN B 222 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.064005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.047799 restraints weight = 64393.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.047207 restraints weight = 37499.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.047719 restraints weight = 29640.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.047934 restraints weight = 23946.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.048105 restraints weight = 22006.540| |-----------------------------------------------------------------------------| r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12456 Z= 0.248 Angle : 0.684 10.581 16908 Z= 0.344 Chirality : 0.045 0.225 1898 Planarity : 0.004 0.040 2114 Dihedral : 7.474 101.439 1704 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.74 % Favored : 94.13 % Rotamer: Outliers : 0.76 % Allowed : 7.50 % Favored : 91.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.21), residues: 1516 helix: 0.45 (0.19), residues: 720 sheet: -2.32 (0.32), residues: 178 loop : -1.79 (0.26), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 310 TYR 0.013 0.001 TYR B 317 PHE 0.018 0.002 PHE A 337 TRP 0.017 0.002 TRP A 532 HIS 0.006 0.001 HIS B 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.25 (12434) covalent geometry : angle 0.68132 / 0.34 (16862) SS BOND : bond 0.00362 / 0.18 ( 20) SS BOND : angle 0.91370 / 0.61 ( 40) hydrogen bonds : bond 0.04286 / 2.99 ( 576) hydrogen bonds : angle 4.75060 / 3.33 ( 1692) link_NAG-ASN : bond 0.00232 / 0.12 ( 2) link_NAG-ASN : angle 3.13188 / 1.54 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 414 MET cc_start: 0.9108 (ttt) cc_final: 0.8658 (tmm) REVERT: A 714 MET cc_start: 0.7017 (mmt) cc_final: 0.6261 (ttp) REVERT: B 414 MET cc_start: 0.9097 (ttt) cc_final: 0.8649 (tmm) REVERT: B 714 MET cc_start: 0.7169 (mmt) cc_final: 0.6283 (ttp) outliers start: 10 outliers final: 8 residues processed: 89 average time/residue: 0.0934 time to fit residues: 13.1954 Evaluate side-chains 75 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 TYR Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain A residue 819 VAL Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 699 ILE Chi-restraints excluded: chain B residue 819 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 146 optimal weight: 7.9990 chunk 145 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 61 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 chunk 50 optimal weight: 9.9990 chunk 140 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 132 optimal weight: 1.9990 chunk 126 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 704 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.063454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.046753 restraints weight = 65310.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.046650 restraints weight = 37435.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.047038 restraints weight = 28921.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.047237 restraints weight = 24598.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.047474 restraints weight = 22114.619| |-----------------------------------------------------------------------------| r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 12456 Z= 0.275 Angle : 0.675 9.001 16908 Z= 0.341 Chirality : 0.045 0.213 1898 Planarity : 0.004 0.039 2114 Dihedral : 7.554 99.622 1704 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.93 % Favored : 92.94 % Rotamer: Outliers : 2.05 % Allowed : 9.17 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.22), residues: 1516 helix: 0.85 (0.19), residues: 708 sheet: -2.07 (0.35), residues: 166 loop : -1.68 (0.26), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 310 TYR 0.011 0.001 TYR B 341 PHE 0.019 0.002 PHE A 596 TRP 0.015 0.002 TRP B 532 HIS 0.005 0.001 HIS B 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00589 / 0.28 (12434) covalent geometry : angle 0.67305 / 0.34 (16862) SS BOND : bond 0.00374 / 0.19 ( 20) SS BOND : angle 0.91381 / 0.61 ( 40) hydrogen bonds : bond 0.04056 / 2.82 ( 576) hydrogen bonds : angle 4.75058 / 3.33 ( 1692) link_NAG-ASN : bond 0.00168 / 0.08 ( 2) link_NAG-ASN : angle 2.54254 / 1.26 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 68 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 414 MET cc_start: 0.9135 (ttt) cc_final: 0.8780 (tmm) REVERT: A 429 MET cc_start: 0.8018 (mpp) cc_final: 0.7761 (mpp) REVERT: A 714 MET cc_start: 0.7020 (mmt) cc_final: 0.6245 (ttp) REVERT: B 414 MET cc_start: 0.9124 (ttt) cc_final: 0.8749 (tmm) REVERT: B 429 MET cc_start: 0.8022 (mpp) cc_final: 0.7761 (mpp) REVERT: B 714 MET cc_start: 0.7174 (mmt) cc_final: 0.6264 (ttp) REVERT: B 783 ILE cc_start: 0.8758 (mt) cc_final: 0.8487 (tt) outliers start: 27 outliers final: 15 residues processed: 93 average time/residue: 0.0905 time to fit residues: 13.1008 Evaluate side-chains 81 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 405 TYR Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 575 TRP Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain A residue 819 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 575 TRP Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 699 ILE Chi-restraints excluded: chain B residue 819 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 42 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 chunk 121 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 115 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 704 GLN B 704 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.065335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.048523 restraints weight = 63864.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.048796 restraints weight = 36773.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.049250 restraints weight = 25596.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.049430 restraints weight = 22385.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.049540 restraints weight = 19763.157| |-----------------------------------------------------------------------------| r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12456 Z= 0.111 Angle : 0.578 10.126 16908 Z= 0.285 Chirality : 0.042 0.222 1898 Planarity : 0.003 0.042 2114 Dihedral : 7.027 99.019 1704 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.08 % Favored : 94.79 % Rotamer: Outliers : 0.76 % Allowed : 9.39 % Favored : 89.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.22), residues: 1516 helix: 1.29 (0.19), residues: 722 sheet: -1.87 (0.36), residues: 170 loop : -1.70 (0.26), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 574 TYR 0.007 0.001 TYR B 340 PHE 0.012 0.001 PHE B 337 TRP 0.009 0.001 TRP A 532 HIS 0.003 0.001 HIS B 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (12434) covalent geometry : angle 0.57554 / 0.28 (16862) SS BOND : bond 0.00175 / 0.11 ( 20) SS BOND : angle 0.85300 / 0.58 ( 40) hydrogen bonds : bond 0.03461 / 2.41 ( 576) hydrogen bonds : angle 4.33465 / 3.04 ( 1692) link_NAG-ASN : bond 0.00540 / 0.27 ( 2) link_NAG-ASN : angle 2.36416 / 1.19 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 414 MET cc_start: 0.9128 (ttt) cc_final: 0.8744 (tmm) REVERT: A 429 MET cc_start: 0.8007 (mpp) cc_final: 0.7684 (mpp) REVERT: A 714 MET cc_start: 0.7106 (mmt) cc_final: 0.6232 (ttp) REVERT: B 414 MET cc_start: 0.9134 (ttt) cc_final: 0.8732 (tmm) REVERT: B 429 MET cc_start: 0.7957 (mpp) cc_final: 0.7619 (mpp) REVERT: B 657 MET cc_start: 0.9301 (ptt) cc_final: 0.8880 (ppp) REVERT: B 714 MET cc_start: 0.7212 (mmt) cc_final: 0.6342 (ttp) REVERT: B 783 ILE cc_start: 0.8694 (mt) cc_final: 0.8413 (tt) outliers start: 10 outliers final: 3 residues processed: 81 average time/residue: 0.0865 time to fit residues: 11.0448 Evaluate side-chains 76 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 73 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 PHE Chi-restraints excluded: chain A residue 819 VAL Chi-restraints excluded: chain B residue 112 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 71 optimal weight: 8.9990 chunk 18 optimal weight: 7.9990 chunk 149 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 chunk 39 optimal weight: 0.9980 chunk 126 optimal weight: 0.9990 chunk 70 optimal weight: 6.9990 chunk 99 optimal weight: 5.9990 chunk 83 optimal weight: 7.9990 chunk 117 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.063435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.046597 restraints weight = 64589.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.046813 restraints weight = 34867.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.047208 restraints weight = 25946.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.047341 restraints weight = 22812.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.047482 restraints weight = 20575.811| |-----------------------------------------------------------------------------| r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 12456 Z= 0.279 Angle : 0.662 8.502 16908 Z= 0.335 Chirality : 0.044 0.214 1898 Planarity : 0.004 0.041 2114 Dihedral : 7.330 99.504 1704 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.00 % Favored : 93.87 % Rotamer: Outliers : 2.05 % Allowed : 9.62 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.22), residues: 1516 helix: 1.16 (0.19), residues: 720 sheet: -1.99 (0.35), residues: 176 loop : -1.55 (0.27), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 310 TYR 0.010 0.001 TYR B 340 PHE 0.016 0.002 PHE A 596 TRP 0.015 0.002 TRP B 532 HIS 0.006 0.001 HIS B 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00599 / 0.28 (12434) covalent geometry : angle 0.66045 / 0.33 (16862) SS BOND : bond 0.00355 / 0.20 ( 20) SS BOND : angle 0.82927 / 0.55 ( 40) hydrogen bonds : bond 0.03808 / 2.64 ( 576) hydrogen bonds : angle 4.64992 / 3.27 ( 1692) link_NAG-ASN : bond 0.00061 / 0.03 ( 2) link_NAG-ASN : angle 2.06932 / 1.02 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 68 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 407 MET cc_start: 0.9303 (tpp) cc_final: 0.9021 (tpp) REVERT: A 414 MET cc_start: 0.9137 (ttt) cc_final: 0.8796 (tmm) REVERT: A 429 MET cc_start: 0.7998 (mpp) cc_final: 0.7713 (mpp) REVERT: A 657 MET cc_start: 0.9382 (ptt) cc_final: 0.8912 (ppp) REVERT: A 714 MET cc_start: 0.7149 (mmt) cc_final: 0.6293 (ttp) REVERT: B 407 MET cc_start: 0.9305 (tpp) cc_final: 0.9023 (tpp) REVERT: B 414 MET cc_start: 0.9149 (ttt) cc_final: 0.8794 (tmm) REVERT: B 429 MET cc_start: 0.7899 (mpp) cc_final: 0.7672 (mpp) REVERT: B 657 MET cc_start: 0.9310 (ptt) cc_final: 0.8822 (ppp) REVERT: B 714 MET cc_start: 0.7268 (mmt) cc_final: 0.6349 (ttp) REVERT: B 783 ILE cc_start: 0.8906 (mt) cc_final: 0.8675 (tt) outliers start: 27 outliers final: 21 residues processed: 94 average time/residue: 0.1009 time to fit residues: 14.7631 Evaluate side-chains 90 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 69 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 112 PHE Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 405 TYR Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 575 TRP Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 699 ILE Chi-restraints excluded: chain A residue 819 VAL Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 112 PHE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 575 TRP Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 695 VAL Chi-restraints excluded: chain B residue 699 ILE Chi-restraints excluded: chain B residue 819 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 45 optimal weight: 7.9990 chunk 130 optimal weight: 10.0000 chunk 30 optimal weight: 0.6980 chunk 113 optimal weight: 0.5980 chunk 80 optimal weight: 0.9990 chunk 56 optimal weight: 7.9990 chunk 73 optimal weight: 10.0000 chunk 90 optimal weight: 0.8980 chunk 119 optimal weight: 6.9990 chunk 136 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.064783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.048157 restraints weight = 63833.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.048207 restraints weight = 38673.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.048881 restraints weight = 27184.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.048982 restraints weight = 22256.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.049134 restraints weight = 20795.440| |-----------------------------------------------------------------------------| r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12456 Z= 0.138 Angle : 0.581 9.427 16908 Z= 0.287 Chirality : 0.042 0.221 1898 Planarity : 0.003 0.042 2114 Dihedral : 7.013 98.947 1704 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.88 % Favored : 94.99 % Rotamer: Outliers : 1.21 % Allowed : 10.61 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.22), residues: 1516 helix: 1.40 (0.19), residues: 720 sheet: -1.53 (0.37), residues: 166 loop : -1.50 (0.26), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 574 TYR 0.007 0.001 TYR B 340 PHE 0.012 0.001 PHE A 337 TRP 0.010 0.001 TRP A 532 HIS 0.003 0.001 HIS B 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (12434) covalent geometry : angle 0.57942 / 0.29 (16862) SS BOND : bond 0.00181 / 0.10 ( 20) SS BOND : angle 0.78518 / 0.53 ( 40) hydrogen bonds : bond 0.03449 / 2.38 ( 576) hydrogen bonds : angle 4.36964 / 3.06 ( 1692) link_NAG-ASN : bond 0.00412 / 0.21 ( 2) link_NAG-ASN : angle 2.08223 / 1.04 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 414 MET cc_start: 0.9136 (ttt) cc_final: 0.8758 (tmm) REVERT: A 657 MET cc_start: 0.9372 (ptt) cc_final: 0.8896 (ppp) REVERT: A 714 MET cc_start: 0.7124 (mmt) cc_final: 0.6275 (ttp) REVERT: B 414 MET cc_start: 0.9135 (ttt) cc_final: 0.8758 (tmm) REVERT: B 657 MET cc_start: 0.9288 (ptt) cc_final: 0.8820 (ppp) REVERT: B 714 MET cc_start: 0.7222 (mmt) cc_final: 0.6605 (mtp) REVERT: B 783 ILE cc_start: 0.8834 (mt) cc_final: 0.8595 (tt) outliers start: 16 outliers final: 13 residues processed: 88 average time/residue: 0.1015 time to fit residues: 13.8990 Evaluate side-chains 82 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 405 TYR Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 819 VAL Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 112 PHE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 575 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 40 optimal weight: 0.0980 chunk 75 optimal weight: 9.9990 chunk 84 optimal weight: 4.9990 chunk 25 optimal weight: 0.0000 chunk 151 optimal weight: 0.9980 chunk 146 optimal weight: 9.9990 chunk 28 optimal weight: 0.0020 chunk 66 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 138 optimal weight: 9.9990 chunk 98 optimal weight: 5.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.065464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.049439 restraints weight = 63386.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.049128 restraints weight = 37711.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.049563 restraints weight = 28751.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.049784 restraints weight = 23684.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.050342 restraints weight = 20719.300| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 12456 Z= 0.103 Angle : 0.563 9.267 16908 Z= 0.276 Chirality : 0.042 0.222 1898 Planarity : 0.003 0.041 2114 Dihedral : 6.750 99.288 1704 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.95 % Favored : 94.92 % Rotamer: Outliers : 1.67 % Allowed : 10.83 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.22), residues: 1516 helix: 1.58 (0.19), residues: 714 sheet: -1.28 (0.38), residues: 166 loop : -1.33 (0.26), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 574 TYR 0.008 0.001 TYR A 757 PHE 0.010 0.001 PHE B 337 TRP 0.008 0.001 TRP B 532 HIS 0.002 0.001 HIS A 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 (12434) covalent geometry : angle 0.56182 / 0.28 (16862) SS BOND : bond 0.00147 / 0.09 ( 20) SS BOND : angle 0.77600 / 0.53 ( 40) hydrogen bonds : bond 0.03248 / 2.25 ( 576) hydrogen bonds : angle 4.25605 / 2.97 ( 1692) link_NAG-ASN : bond 0.00458 / 0.23 ( 2) link_NAG-ASN : angle 1.92686 / 0.95 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 72 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 414 MET cc_start: 0.9139 (ttt) cc_final: 0.8714 (tmm) REVERT: A 601 PHE cc_start: 0.7174 (m-80) cc_final: 0.6964 (m-80) REVERT: A 657 MET cc_start: 0.9331 (ptt) cc_final: 0.8853 (ppp) REVERT: A 714 MET cc_start: 0.7175 (mmt) cc_final: 0.6507 (ttp) REVERT: B 414 MET cc_start: 0.9149 (ttt) cc_final: 0.8716 (tmm) REVERT: B 657 MET cc_start: 0.9262 (ptt) cc_final: 0.8973 (ppp) REVERT: B 714 MET cc_start: 0.7187 (mmt) cc_final: 0.6649 (mtp) REVERT: B 783 ILE cc_start: 0.8744 (mt) cc_final: 0.8488 (tt) outliers start: 22 outliers final: 13 residues processed: 91 average time/residue: 0.0901 time to fit residues: 13.1659 Evaluate side-chains 81 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 PHE Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 819 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 278 CYS Chi-restraints excluded: chain B residue 573 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 0.8980 chunk 83 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 91 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 58 optimal weight: 10.0000 chunk 63 optimal weight: 5.9990 chunk 84 optimal weight: 0.8980 chunk 20 optimal weight: 0.0060 chunk 125 optimal weight: 6.9990 chunk 94 optimal weight: 0.9980 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 157 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.065874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.050071 restraints weight = 63997.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.049334 restraints weight = 36701.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.050202 restraints weight = 29543.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.050441 restraints weight = 21468.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.050609 restraints weight = 20698.070| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12456 Z= 0.106 Angle : 0.571 9.036 16908 Z= 0.277 Chirality : 0.042 0.220 1898 Planarity : 0.003 0.043 2114 Dihedral : 6.640 99.654 1704 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.55 % Favored : 95.32 % Rotamer: Outliers : 1.59 % Allowed : 11.06 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.22), residues: 1516 helix: 1.69 (0.19), residues: 718 sheet: -1.12 (0.40), residues: 166 loop : -1.31 (0.26), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 574 TYR 0.008 0.001 TYR B 340 PHE 0.009 0.001 PHE A 337 TRP 0.008 0.001 TRP A 532 HIS 0.003 0.001 HIS A 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (12434) covalent geometry : angle 0.56987 / 0.28 (16862) SS BOND : bond 0.00122 / 0.08 ( 20) SS BOND : angle 0.79460 / 0.53 ( 40) hydrogen bonds : bond 0.03168 / 2.19 ( 576) hydrogen bonds : angle 4.15723 / 2.92 ( 1692) link_NAG-ASN : bond 0.00433 / 0.22 ( 2) link_NAG-ASN : angle 1.86194 / 0.93 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 70 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 305 ASP cc_start: 0.8426 (p0) cc_final: 0.8217 (p0) REVERT: A 414 MET cc_start: 0.9118 (ttt) cc_final: 0.8793 (tmm) REVERT: A 601 PHE cc_start: 0.7300 (m-80) cc_final: 0.7085 (m-80) REVERT: A 657 MET cc_start: 0.9298 (ptt) cc_final: 0.8874 (ppp) REVERT: A 714 MET cc_start: 0.7113 (mmt) cc_final: 0.6462 (ttm) REVERT: B 106 LEU cc_start: 0.9445 (OUTLIER) cc_final: 0.8919 (tt) REVERT: B 305 ASP cc_start: 0.8447 (p0) cc_final: 0.8210 (p0) REVERT: B 414 MET cc_start: 0.9148 (ttt) cc_final: 0.8713 (tmm) REVERT: B 657 MET cc_start: 0.9242 (ptt) cc_final: 0.8820 (ppp) REVERT: B 714 MET cc_start: 0.7163 (mmt) cc_final: 0.6529 (ttp) REVERT: B 783 ILE cc_start: 0.8743 (mt) cc_final: 0.8489 (tt) outliers start: 21 outliers final: 15 residues processed: 89 average time/residue: 0.0971 time to fit residues: 13.8423 Evaluate side-chains 85 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 PHE Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 819 VAL Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 112 PHE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 278 CYS Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain B residue 573 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 114 optimal weight: 4.9990 chunk 136 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 80 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 96 optimal weight: 6.9990 chunk 125 optimal weight: 10.0000 chunk 141 optimal weight: 9.9990 chunk 83 optimal weight: 3.9990 chunk 137 optimal weight: 6.9990 chunk 123 optimal weight: 0.9980 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.064837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.048195 restraints weight = 63691.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.048258 restraints weight = 40237.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.048489 restraints weight = 28559.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.049057 restraints weight = 24454.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.049081 restraints weight = 21083.883| |-----------------------------------------------------------------------------| r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12456 Z= 0.166 Angle : 0.590 8.646 16908 Z= 0.291 Chirality : 0.042 0.218 1898 Planarity : 0.003 0.046 2114 Dihedral : 6.764 99.721 1704 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.82 % Favored : 95.05 % Rotamer: Outliers : 1.44 % Allowed : 11.29 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.22), residues: 1516 helix: 1.67 (0.19), residues: 716 sheet: -1.11 (0.40), residues: 166 loop : -1.19 (0.27), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 574 TYR 0.009 0.001 TYR B 340 PHE 0.013 0.001 PHE A 337 TRP 0.010 0.001 TRP A 532 HIS 0.004 0.001 HIS A 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.17 (12434) covalent geometry : angle 0.58822 / 0.29 (16862) SS BOND : bond 0.00203 / 0.11 ( 20) SS BOND : angle 0.78846 / 0.53 ( 40) hydrogen bonds : bond 0.03329 / 2.30 ( 576) hydrogen bonds : angle 4.29714 / 3.03 ( 1692) link_NAG-ASN : bond 0.00234 / 0.12 ( 2) link_NAG-ASN : angle 1.76071 / 0.87 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 69 time to evaluate : 0.511 Fit side-chains REVERT: A 106 LEU cc_start: 0.9461 (OUTLIER) cc_final: 0.8914 (tt) REVERT: A 414 MET cc_start: 0.9155 (ttt) cc_final: 0.8736 (tmm) REVERT: A 601 PHE cc_start: 0.7291 (m-80) cc_final: 0.7090 (m-80) REVERT: A 657 MET cc_start: 0.9298 (ptt) cc_final: 0.8864 (ppp) REVERT: A 714 MET cc_start: 0.7065 (mmt) cc_final: 0.6382 (ttm) REVERT: B 106 LEU cc_start: 0.9471 (OUTLIER) cc_final: 0.8910 (tt) REVERT: B 414 MET cc_start: 0.9146 (ttt) cc_final: 0.8720 (tmm) REVERT: B 657 MET cc_start: 0.9249 (ptt) cc_final: 0.8935 (ppp) REVERT: B 714 MET cc_start: 0.7173 (mmt) cc_final: 0.6472 (ttp) REVERT: B 783 ILE cc_start: 0.8967 (mt) cc_final: 0.8747 (tt) outliers start: 19 outliers final: 17 residues processed: 85 average time/residue: 0.0971 time to fit residues: 13.1473 Evaluate side-chains 87 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 68 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 112 PHE Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 405 TYR Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 819 VAL Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 112 PHE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 278 CYS Chi-restraints excluded: chain B residue 405 TYR Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 819 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 125 optimal weight: 10.0000 chunk 114 optimal weight: 1.9990 chunk 70 optimal weight: 0.0870 chunk 130 optimal weight: 20.0000 chunk 45 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 96 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 74 optimal weight: 8.9990 chunk 115 optimal weight: 1.9990 chunk 118 optimal weight: 5.9990 overall best weight: 1.1562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.065604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.050178 restraints weight = 64860.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.049083 restraints weight = 39381.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.049875 restraints weight = 31889.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.050182 restraints weight = 23299.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.050241 restraints weight = 21739.695| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12456 Z= 0.123 Angle : 0.580 8.977 16908 Z= 0.284 Chirality : 0.042 0.220 1898 Planarity : 0.003 0.043 2114 Dihedral : 6.649 99.466 1704 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.55 % Favored : 95.32 % Rotamer: Outliers : 1.29 % Allowed : 11.59 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.22), residues: 1516 helix: 1.71 (0.19), residues: 716 sheet: -1.00 (0.40), residues: 166 loop : -1.18 (0.27), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 524 TYR 0.007 0.001 TYR B 340 PHE 0.010 0.001 PHE B 337 TRP 0.011 0.001 TRP B 532 HIS 0.002 0.001 HIS A 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (12434) covalent geometry : angle 0.57837 / 0.28 (16862) SS BOND : bond 0.00162 / 0.09 ( 20) SS BOND : angle 0.83984 / 0.56 ( 40) hydrogen bonds : bond 0.03231 / 2.23 ( 576) hydrogen bonds : angle 4.19768 / 2.95 ( 1692) link_NAG-ASN : bond 0.00375 / 0.19 ( 2) link_NAG-ASN : angle 1.80180 / 0.89 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3032 Ramachandran restraints generated. 1516 Oldfield, 0 Emsley, 1516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 0.444 Fit side-chains revert: symmetry clash REVERT: A 414 MET cc_start: 0.9147 (ttt) cc_final: 0.8717 (tmm) REVERT: A 601 PHE cc_start: 0.7313 (m-80) cc_final: 0.7110 (m-80) REVERT: A 657 MET cc_start: 0.9268 (ptt) cc_final: 0.8885 (ppp) REVERT: A 714 MET cc_start: 0.7117 (mmt) cc_final: 0.6417 (ttm) REVERT: B 414 MET cc_start: 0.9146 (ttt) cc_final: 0.8710 (tmm) REVERT: B 657 MET cc_start: 0.9248 (ptt) cc_final: 0.8955 (ppp) REVERT: B 714 MET cc_start: 0.7198 (mmt) cc_final: 0.6557 (ttp) REVERT: B 783 ILE cc_start: 0.8838 (mt) cc_final: 0.8603 (tt) outliers start: 17 outliers final: 17 residues processed: 85 average time/residue: 0.0951 time to fit residues: 12.9479 Evaluate side-chains 85 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 PHE Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 278 CYS Chi-restraints excluded: chain A residue 405 TYR Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 819 VAL Chi-restraints excluded: chain B residue 112 PHE Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 278 CYS Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 819 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 64 optimal weight: 20.0000 chunk 72 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 75 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 132 optimal weight: 20.0000 chunk 66 optimal weight: 7.9990 chunk 101 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 721 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.064140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.046733 restraints weight = 64683.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.047474 restraints weight = 36621.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.047604 restraints weight = 24635.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.047990 restraints weight = 22088.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.048107 restraints weight = 20067.678| |-----------------------------------------------------------------------------| r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 12456 Z= 0.235 Angle : 0.651 11.297 16908 Z= 0.327 Chirality : 0.044 0.225 1898 Planarity : 0.004 0.042 2114 Dihedral : 6.935 99.752 1704 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.34 % Favored : 94.53 % Rotamer: Outliers : 1.59 % Allowed : 11.36 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.22), residues: 1516 helix: 1.54 (0.19), residues: 718 sheet: -1.13 (0.40), residues: 166 loop : -1.20 (0.27), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 96 TYR 0.016 0.001 TYR A 779 PHE 0.013 0.002 PHE B 337 TRP 0.015 0.002 TRP A 532 HIS 0.005 0.001 HIS B 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.24 (12434) covalent geometry : angle 0.64991 / 0.33 (16862) SS BOND : bond 0.00319 / 0.17 ( 20) SS BOND : angle 0.83901 / 0.56 ( 40) hydrogen bonds : bond 0.03599 / 2.48 ( 576) hydrogen bonds : angle 4.49893 / 3.15 ( 1692) link_NAG-ASN : bond 0.00079 / 0.04 ( 2) link_NAG-ASN : angle 1.74575 / 0.86 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1720.10 seconds wall clock time: 30 minutes 51.05 seconds (1851.05 seconds total)