Starting phenix.real_space_refine on Sun Aug 24 22:26:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tai_41136/08_2025/8tai_41136_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tai_41136/08_2025/8tai_41136.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8tai_41136/08_2025/8tai_41136_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tai_41136/08_2025/8tai_41136_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tai_41136/08_2025/8tai_41136.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tai_41136/08_2025/8tai_41136.map" } resolution = 3.1 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= 0.791 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 3 9.91 5 S 71 5.16 5 C 7824 2.51 5 N 1906 2.21 5 O 2105 1.98 5 H 11607 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23516 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 11239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 705, 11239 Classifications: {'peptide': 705} Link IDs: {'PTRANS': 32, 'TRANS': 672} Chain breaks: 6 Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2, 'TYR:plan': 2, 'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 69 Chain: "B" Number of atoms: 12190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 743, 12190 Classifications: {'peptide': 743} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 33, 'TRANS': 709} Chain breaks: 3 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' CA': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 44 Unusual residues: {' CA': 2, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.09, per 1000 atoms: 0.17 Number of scatterers: 23516 At special positions: 0 Unit cell: (135.079, 88.095, 119.977, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 3 19.99 S 71 16.00 O 2105 8.00 N 1906 7.00 C 7824 6.00 H 11607 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 372 " distance=2.04 Simple disulfide: pdb=" SG CYS A 338 " - pdb=" SG CYS A 365 " distance=2.04 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 807 " distance=2.03 Simple disulfide: pdb=" SG CYS A 352 " - pdb=" SG CYS A 356 " distance=2.03 Simple disulfide: pdb=" SG CYS A 596 " - pdb=" SG CYS A 601 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 372 " distance=2.03 Simple disulfide: pdb=" SG CYS B 338 " - pdb=" SG CYS B 365 " distance=2.03 Simple disulfide: pdb=" SG CYS B 349 " - pdb=" SG CYS B 807 " distance=2.03 Simple disulfide: pdb=" SG CYS B 352 " - pdb=" SG CYS B 356 " distance=2.03 Simple disulfide: pdb=" SG CYS B 596 " - pdb=" SG CYS B 601 " distance=2.03 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 Atom "HETATM23484 O5 NAG B 901 .*. O " rejected from bonding due to valence issues. Atom "HETATM23455 O5 NAG A 902 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 901 " - " ASN A 362 " " NAG A 902 " - " ASN A 785 " Time building additional restraints: 2.10 Conformation dependent library (CDL) restraints added in 549.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2758 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 6 sheets defined 63.5% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 92 through 108 Processing helix chain 'A' and resid 131 through 142 removed outlier: 3.700A pdb=" N MET A 142 " --> pdb=" O TYR A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 195 removed outlier: 5.732A pdb=" N ASN A 193 " --> pdb=" O SER A 190 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE A 195 " --> pdb=" O MET A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 220 Processing helix chain 'A' and resid 233 through 239 Processing helix chain 'A' and resid 264 through 274 Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 284 through 292 Processing helix chain 'A' and resid 293 through 327 removed outlier: 3.972A pdb=" N LEU A 312 " --> pdb=" O GLN A 308 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP A 327 " --> pdb=" O TYR A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 339 Processing helix chain 'A' and resid 364 through 375 removed outlier: 3.914A pdb=" N ILE A 373 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N PHE A 374 " --> pdb=" O LYS A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 408 removed outlier: 3.670A pdb=" N LEU A 380 " --> pdb=" O SER A 376 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL A 388 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N THR A 391 " --> pdb=" O GLY A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 486 Processing helix chain 'A' and resid 504 through 539 removed outlier: 3.875A pdb=" N THR A 526 " --> pdb=" O MET A 522 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE A 527 " --> pdb=" O ILE A 523 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU A 539 " --> pdb=" O ILE A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 573 removed outlier: 5.427A pdb=" N SER A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N CYS A 567 " --> pdb=" O TYR A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 638 removed outlier: 5.399A pdb=" N LEU A 627 " --> pdb=" O GLN A 623 " (cutoff:3.500A) Proline residue: A 628 - end of helix Processing helix chain 'A' and resid 648 through 656 removed outlier: 3.526A pdb=" N GLN A 652 " --> pdb=" O PRO A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 681 removed outlier: 4.103A pdb=" N PHE A 681 " --> pdb=" O PHE A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 710 removed outlier: 4.137A pdb=" N ARG A 701 " --> pdb=" O ILE A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 747 removed outlier: 4.340A pdb=" N ILE A 728 " --> pdb=" O ALA A 724 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL A 738 " --> pdb=" O ILE A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 760 Processing helix chain 'A' and resid 775 through 781 Processing helix chain 'A' and resid 787 through 789 No H-bonds generated for 'chain 'A' and resid 787 through 789' Processing helix chain 'A' and resid 825 through 856 Processing helix chain 'A' and resid 861 through 870 removed outlier: 4.247A pdb=" N LYS A 865 " --> pdb=" O SER A 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 108 removed outlier: 3.626A pdb=" N ASN B 91 " --> pdb=" O LYS B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 142 Processing helix chain 'B' and resid 188 through 195 removed outlier: 3.641A pdb=" N MET B 192 " --> pdb=" O LYS B 189 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ASN B 193 " --> pdb=" O SER B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 204 removed outlier: 3.534A pdb=" N PHE B 204 " --> pdb=" O ARG B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 220 Processing helix chain 'B' and resid 232 through 239 removed outlier: 3.679A pdb=" N LEU B 236 " --> pdb=" O GLY B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 273 Processing helix chain 'B' and resid 275 through 279 Processing helix chain 'B' and resid 284 through 293 Processing helix chain 'B' and resid 293 through 327 removed outlier: 3.928A pdb=" N TYR B 299 " --> pdb=" O LYS B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 339 Processing helix chain 'B' and resid 360 through 363 Processing helix chain 'B' and resid 364 through 375 Processing helix chain 'B' and resid 376 through 408 removed outlier: 3.745A pdb=" N LEU B 380 " --> pdb=" O SER B 376 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N THR B 391 " --> pdb=" O GLY B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 416 Processing helix chain 'B' and resid 456 through 488 removed outlier: 3.643A pdb=" N THR B 488 " --> pdb=" O VAL B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 539 removed outlier: 3.944A pdb=" N THR B 526 " --> pdb=" O MET B 522 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE B 527 " --> pdb=" O ILE B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 573 removed outlier: 5.229A pdb=" N SER B 566 " --> pdb=" O ASN B 562 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N CYS B 567 " --> pdb=" O TYR B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 638 Proline residue: B 628 - end of helix Processing helix chain 'B' and resid 648 through 654 Processing helix chain 'B' and resid 664 through 681 removed outlier: 3.906A pdb=" N PHE B 681 " --> pdb=" O PHE B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 710 removed outlier: 4.361A pdb=" N ARG B 701 " --> pdb=" O ILE B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 747 removed outlier: 3.992A pdb=" N ILE B 728 " --> pdb=" O ALA B 724 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL B 737 " --> pdb=" O ALA B 733 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N VAL B 738 " --> pdb=" O ILE B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 760 Processing helix chain 'B' and resid 775 through 781 Processing helix chain 'B' and resid 787 through 789 No H-bonds generated for 'chain 'B' and resid 787 through 789' Processing helix chain 'B' and resid 825 through 857 Processing helix chain 'B' and resid 861 through 868 Processing sheet with id=AA1, first strand: chain 'A' and resid 113 through 116 removed outlier: 3.571A pdb=" N ALA A 244 " --> pdb=" O VAL A 76 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 348 removed outlier: 3.682A pdb=" N TRP A 359 " --> pdb=" O MET A 348 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 784 through 785 Processing sheet with id=AA4, first strand: chain 'B' and resid 114 through 116 removed outlier: 3.578A pdb=" N PHE B 246 " --> pdb=" O ILE B 74 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA B 244 " --> pdb=" O VAL B 76 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 221 through 225 removed outlier: 4.207A pdb=" N GLN B 223 " --> pdb=" O LYS B 230 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS B 230 " --> pdb=" O GLN B 223 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET B 225 " --> pdb=" O VAL B 228 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 782 through 785 removed outlier: 3.535A pdb=" N TYR B 809 " --> pdb=" O SER B 782 " (cutoff:3.500A) 694 hydrogen bonds defined for protein. 2031 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: 4.57 Time building geometry restraints manager: 2.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 11595 1.03 - 1.23: 266 1.23 - 1.43: 5068 1.43 - 1.63: 6802 1.63 - 1.83: 112 Bond restraints: 23843 Sorted by residual: bond pdb=" N PHE B 52 " pdb=" H1 PHE B 52 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" CG1 ILE B 472 " pdb=" CD1 ILE B 472 " ideal model delta sigma weight residual 1.513 1.443 0.070 3.90e-02 6.57e+02 3.18e+00 bond pdb=" CG MET A 309 " pdb=" SD MET A 309 " ideal model delta sigma weight residual 1.803 1.764 0.039 2.50e-02 1.60e+03 2.38e+00 bond pdb=" C1 NAG A 901 " pdb=" O5 NAG A 901 " ideal model delta sigma weight residual 1.406 1.431 -0.025 2.00e-02 2.50e+03 1.57e+00 bond pdb=" C1 NAG B 901 " pdb=" O5 NAG B 901 " ideal model delta sigma weight residual 1.406 1.429 -0.023 2.00e-02 2.50e+03 1.35e+00 ... (remaining 23838 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.16: 42921 7.16 - 14.33: 3 14.33 - 21.49: 0 21.49 - 28.66: 0 28.66 - 35.82: 24 Bond angle restraints: 42948 Sorted by residual: angle pdb=" N ILE B 141 " pdb=" CA ILE B 141 " pdb=" HA ILE B 141 " ideal model delta sigma weight residual 110.00 74.18 35.82 3.00e+00 1.11e-01 1.43e+02 angle pdb=" CB GLN A 94 " pdb=" CA GLN A 94 " pdb=" HA GLN A 94 " ideal model delta sigma weight residual 109.00 73.21 35.79 3.00e+00 1.11e-01 1.42e+02 angle pdb=" C ARG A 235 " pdb=" CA ARG A 235 " pdb=" HA ARG A 235 " ideal model delta sigma weight residual 109.00 73.68 35.32 3.00e+00 1.11e-01 1.39e+02 angle pdb=" CB PHE B 215 " pdb=" CA PHE B 215 " pdb=" HA PHE B 215 " ideal model delta sigma weight residual 109.00 73.72 35.28 3.00e+00 1.11e-01 1.38e+02 angle pdb=" N ASP A 286 " pdb=" CA ASP A 286 " pdb=" HA ASP A 286 " ideal model delta sigma weight residual 110.00 74.87 35.13 3.00e+00 1.11e-01 1.37e+02 ... (remaining 42943 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 10289 17.99 - 35.98: 864 35.98 - 53.97: 212 53.97 - 71.96: 47 71.96 - 89.95: 10 Dihedral angle restraints: 11422 sinusoidal: 6018 harmonic: 5404 Sorted by residual: dihedral pdb=" CB CYS A 338 " pdb=" SG CYS A 338 " pdb=" SG CYS A 365 " pdb=" CB CYS A 365 " ideal model delta sinusoidal sigma weight residual -86.00 -175.95 89.95 1 1.00e+01 1.00e-02 9.59e+01 dihedral pdb=" CB CYS A 352 " pdb=" SG CYS A 352 " pdb=" SG CYS A 356 " pdb=" CB CYS A 356 " ideal model delta sinusoidal sigma weight residual -86.00 -146.29 60.29 1 1.00e+01 1.00e-02 4.84e+01 dihedral pdb=" CB CYS B 352 " pdb=" SG CYS B 352 " pdb=" SG CYS B 356 " pdb=" CB CYS B 356 " ideal model delta sinusoidal sigma weight residual -86.00 -138.27 52.27 1 1.00e+01 1.00e-02 3.73e+01 ... (remaining 11419 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.309: 1812 0.309 - 0.618: 8 0.618 - 0.927: 0 0.927 - 1.236: 0 1.236 - 1.545: 1 Chirality restraints: 1821 Sorted by residual: chirality pdb=" C4 NAG A 901 " pdb=" C3 NAG A 901 " pdb=" C5 NAG A 901 " pdb=" O4 NAG A 901 " both_signs ideal model delta sigma weight residual False -2.53 -0.99 -1.55 2.00e-01 2.50e+01 5.97e+01 chirality pdb=" C1 NAG A 902 " pdb=" ND2 ASN A 785 " pdb=" C2 NAG A 902 " pdb=" O5 NAG A 902 " both_signs ideal model delta sigma weight residual False -2.40 -2.99 0.59 2.00e-01 2.50e+01 8.83e+00 chirality pdb=" CA CYS A 356 " pdb=" N CYS A 356 " pdb=" C CYS A 356 " pdb=" CB CYS A 356 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.24e+00 ... (remaining 1818 not shown) Planarity restraints: 3437 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 785 " -0.230 2.00e-02 2.50e+03 2.26e-01 6.37e+02 pdb=" CG ASN A 785 " 0.075 2.00e-02 2.50e+03 pdb=" OD1 ASN A 785 " 0.064 2.00e-02 2.50e+03 pdb=" ND2 ASN A 785 " 0.352 2.00e-02 2.50e+03 pdb=" C1 NAG A 902 " -0.262 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS A 349 " 0.039 5.00e-02 4.00e+02 5.96e-02 5.68e+00 pdb=" N PRO A 350 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 350 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 350 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 796 " 0.039 5.00e-02 4.00e+02 5.96e-02 5.68e+00 pdb=" N PRO B 797 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO B 797 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 797 " 0.033 5.00e-02 4.00e+02 ... (remaining 3434 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 1548 2.20 - 2.80: 46822 2.80 - 3.40: 64549 3.40 - 4.00: 80569 4.00 - 4.60: 125381 Nonbonded interactions: 318869 Sorted by model distance: nonbonded pdb=" O SER A 278 " pdb="HH21 ARG A 701 " model vdw 1.598 2.450 nonbonded pdb=" HA ARG B 235 " pdb=" HB3 ARG B 235 " model vdw 1.602 1.952 nonbonded pdb=" HA PHE B 215 " pdb=" HB3 PHE B 215 " model vdw 1.608 1.952 nonbonded pdb=" ND2 ASN B 362 " pdb=" O5 NAG B 901 " model vdw 1.625 2.950 nonbonded pdb=" HA ASP A 286 " pdb=" HB2 ASP A 286 " model vdw 1.630 1.952 ... (remaining 318864 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 59 through 868 or resid 901 through 902 or resid 904)) selection = (chain 'B' and (resid 59 through 82 or resid 91 through 93 or (resid 94 through \ 97 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 98 or (resid 99 and (name N or name CA or name C or name O or name CB \ or name H or name HA )) or resid 100 or (resid 101 through 107 and (name N or na \ me CA or name C or name O or name CB or name H or name HA )) or resid 108 throug \ h 115 or (resid 116 through 126 and (name N or name CA or name C or name O or na \ me CB or name H or name HA )) or resid 127 through 128 or (resid 129 and (name N \ or name CA or name C or name O or name CB or name H or name HA )) or resid 130 \ through 134 or (resid 135 through 137 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 138 through 140 or (resid 141 and ( \ name N or name CA or name C or name O or name CB or name H or name HA )) or resi \ d 142 or (resid 143 and (name N or name CA or name C or name O or name CB or nam \ e H or name HA )) or resid 144 through 147 or resid 185 through 222 or resid 232 \ through 235 or (resid 236 through 239 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 240 or (resid 241 and (name N or n \ ame CA or name C or name O or name CB or name H or name HA )) or resid 242 throu \ gh 423 or resid 457 through 487 or resid 503 through 589 or (resid 590 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 59 \ 1 through 638 or resid 645 through 660 or (resid 661 and (name N or name CA or n \ ame C or name O or name CB or name H or name HA )) or resid 662 through 777 or ( \ resid 778 and (name N or name CA or name C or name O or name CB or name CG or na \ me OD1 or name ND2 or name H or name HA or name HB2 or name HB3)) or resid 779 t \ hrough 784 or (resid 785 and (name N or name CA or name C or name O or name CB o \ r name CG or name OD1 or name ND2 or name H or name HA or name HB2 or name HB3)) \ or resid 786 through 857 or (resid 858 and (name N or name CA or name C or name \ O or name CB or name CG or name CD )) or (resid 859 and (name N or name CA or n \ ame C or name O or name CB or name CG or name OD1 or name OD2)) or resid 860 thr \ ough 868 or resid 902 through 903 or resid 905)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.410 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: 0.130 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 19.550 Find NCS groups from input model: 0.260 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: 0.010 Load rotamer database and sin/cos tables:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.328 12248 Z= 0.205 Angle : 0.689 50.568 16633 Z= 0.337 Chirality : 0.059 1.545 1821 Planarity : 0.004 0.060 2064 Dihedral : 13.720 89.498 4503 Min Nonbonded Distance : 1.625 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.32 (0.22), residues: 1426 helix: 2.26 (0.17), residues: 822 sheet: -0.83 (0.78), residues: 58 loop : -1.16 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 98 TYR 0.015 0.001 TYR A 306 PHE 0.015 0.001 PHE B 73 TRP 0.023 0.001 TRP B 132 HIS 0.004 0.001 HIS B 108 Details of bonding type rmsd covalent geometry : bond 0.00312 (12236) covalent geometry : angle 0.55833 (16607) SS BOND : bond 0.00256 ( 10) SS BOND : angle 1.87441 ( 20) hydrogen bonds : bond 0.12224 ( 694) hydrogen bonds : angle 5.11064 ( 2031) link_NAG-ASN : bond 0.23200 ( 2) link_NAG-ASN : angle 21.00944 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 184 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 396 PHE cc_start: 0.7208 (m-10) cc_final: 0.6822 (m-10) REVERT: A 479 LEU cc_start: 0.9037 (mt) cc_final: 0.8786 (mt) REVERT: B 235 ARG cc_start: 0.7989 (ttm-80) cc_final: 0.7402 (ttm110) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.1775 time to fit residues: 49.3500 Evaluate side-chains 160 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 30.0000 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN B 104 ASN B 621 ASN B 652 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.206285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.145926 restraints weight = 40993.537| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 2.45 r_work: 0.3596 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3460 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.0901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12248 Z= 0.124 Angle : 0.531 7.869 16633 Z= 0.286 Chirality : 0.045 0.411 1821 Planarity : 0.005 0.053 2064 Dihedral : 5.498 53.317 1722 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.11 % Allowed : 5.16 % Favored : 93.73 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.33 (0.22), residues: 1426 helix: 2.26 (0.17), residues: 831 sheet: -0.76 (0.70), residues: 64 loop : -1.20 (0.26), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 98 TYR 0.014 0.001 TYR B 77 PHE 0.015 0.001 PHE A 461 TRP 0.012 0.001 TRP B 132 HIS 0.003 0.001 HIS B 108 Details of bonding type rmsd covalent geometry : bond 0.00266 (12236) covalent geometry : angle 0.52544 (16607) SS BOND : bond 0.00235 ( 10) SS BOND : angle 1.05740 ( 20) hydrogen bonds : bond 0.05017 ( 694) hydrogen bonds : angle 4.52289 ( 2031) link_NAG-ASN : bond 0.00281 ( 2) link_NAG-ASN : angle 3.55913 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 180 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 166 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 479 LEU cc_start: 0.9275 (mt) cc_final: 0.9018 (mt) REVERT: B 143 HIS cc_start: 0.7481 (m170) cc_final: 0.7243 (m-70) REVERT: B 235 ARG cc_start: 0.8181 (ttm-80) cc_final: 0.7624 (ttm110) outliers start: 14 outliers final: 10 residues processed: 170 average time/residue: 0.1794 time to fit residues: 45.7818 Evaluate side-chains 169 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 159 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 624 GLU Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 717 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 24 optimal weight: 4.9990 chunk 125 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 123 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 117 optimal weight: 0.6980 chunk 96 optimal weight: 4.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 ASN B 730 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.207436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.150451 restraints weight = 41470.833| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 2.65 r_work: 0.3505 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3365 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12248 Z= 0.149 Angle : 0.522 7.875 16633 Z= 0.284 Chirality : 0.045 0.419 1821 Planarity : 0.004 0.053 2064 Dihedral : 5.205 56.126 1722 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.27 % Allowed : 6.35 % Favored : 92.38 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.22), residues: 1426 helix: 2.26 (0.17), residues: 830 sheet: -0.92 (0.70), residues: 64 loop : -1.24 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 289 TYR 0.012 0.001 TYR B 138 PHE 0.016 0.001 PHE B 675 TRP 0.012 0.001 TRP B 132 HIS 0.004 0.001 HIS B 108 Details of bonding type rmsd covalent geometry : bond 0.00337 (12236) covalent geometry : angle 0.51784 (16607) SS BOND : bond 0.00123 ( 10) SS BOND : angle 0.81337 ( 20) hydrogen bonds : bond 0.04936 ( 694) hydrogen bonds : angle 4.36201 ( 2031) link_NAG-ASN : bond 0.00029 ( 2) link_NAG-ASN : angle 3.13464 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 179 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 163 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 104 ASN cc_start: 0.7704 (m-40) cc_final: 0.7248 (m-40) REVERT: B 235 ARG cc_start: 0.8178 (ttm-80) cc_final: 0.7621 (ttm110) outliers start: 16 outliers final: 12 residues processed: 170 average time/residue: 0.1811 time to fit residues: 46.1044 Evaluate side-chains 169 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 157 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 624 GLU Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 767 ASP Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 405 GLU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 717 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 142 optimal weight: 4.9990 chunk 13 optimal weight: 9.9990 chunk 89 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 2 optimal weight: 0.0040 chunk 30 optimal weight: 7.9990 chunk 12 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 chunk 67 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 674 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 = 0.4473 r_free = 0.4473 target = 0.207762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.145649 restraints weight = 40738.627| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 2.51 r_work: 0.3615 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3464 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12248 Z= 0.105 Angle : 0.492 8.061 16633 Z= 0.264 Chirality : 0.044 0.415 1821 Planarity : 0.004 0.054 2064 Dihedral : 4.847 55.776 1722 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.27 % Allowed : 7.06 % Favored : 91.67 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.46 (0.22), residues: 1426 helix: 2.44 (0.17), residues: 830 sheet: -1.31 (0.63), residues: 74 loop : -1.21 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 289 TYR 0.011 0.001 TYR B 77 PHE 0.015 0.001 PHE A 461 TRP 0.009 0.001 TRP A 273 HIS 0.003 0.001 HIS B 143 Details of bonding type rmsd covalent geometry : bond 0.00221 (12236) covalent geometry : angle 0.48855 (16607) SS BOND : bond 0.00131 ( 10) SS BOND : angle 0.59502 ( 20) hydrogen bonds : bond 0.04373 ( 694) hydrogen bonds : angle 4.17082 ( 2031) link_NAG-ASN : bond 0.00111 ( 2) link_NAG-ASN : angle 2.87721 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 181 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 165 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 104 ASN cc_start: 0.7812 (m-40) cc_final: 0.7575 (m110) REVERT: B 221 LYS cc_start: 0.8309 (ptmt) cc_final: 0.7691 (ttpt) REVERT: B 235 ARG cc_start: 0.8240 (ttm-80) cc_final: 0.7659 (ttm110) outliers start: 16 outliers final: 14 residues processed: 171 average time/residue: 0.1856 time to fit residues: 47.1517 Evaluate side-chains 169 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 155 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 624 GLU Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 767 ASP Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 717 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 51 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 86 optimal weight: 0.6980 chunk 33 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 chunk 47 optimal weight: 20.0000 chunk 91 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 101 optimal weight: 2.9990 chunk 87 optimal weight: 0.2980 chunk 53 optimal weight: 3.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 730 GLN B 785 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.203977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.143377 restraints weight = 40607.582| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 2.79 r_work: 0.3535 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3396 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12248 Z= 0.165 Angle : 0.521 7.782 16633 Z= 0.284 Chirality : 0.045 0.423 1821 Planarity : 0.005 0.049 2064 Dihedral : 4.834 59.749 1722 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.11 % Allowed : 8.25 % Favored : 90.63 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.22), residues: 1426 helix: 2.36 (0.17), residues: 825 sheet: -1.46 (0.62), residues: 74 loop : -1.30 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 753 TYR 0.011 0.001 TYR B 138 PHE 0.018 0.001 PHE B 675 TRP 0.012 0.001 TRP B 132 HIS 0.004 0.001 HIS B 108 Details of bonding type rmsd covalent geometry : bond 0.00377 (12236) covalent geometry : angle 0.51878 (16607) SS BOND : bond 0.00142 ( 10) SS BOND : angle 0.66985 ( 20) hydrogen bonds : bond 0.04816 ( 694) hydrogen bonds : angle 4.24305 ( 2031) link_NAG-ASN : bond 0.00055 ( 2) link_NAG-ASN : angle 2.65087 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 171 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 157 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 104 ASN cc_start: 0.7863 (m-40) cc_final: 0.7390 (m-40) REVERT: B 235 ARG cc_start: 0.8258 (ttm-80) cc_final: 0.7685 (ttm110) REVERT: B 271 ARG cc_start: 0.8046 (mmm-85) cc_final: 0.7482 (mmm160) REVERT: B 282 LYS cc_start: 0.8004 (tptt) cc_final: 0.7573 (tppt) REVERT: B 546 ASP cc_start: 0.8657 (m-30) cc_final: 0.8415 (m-30) outliers start: 14 outliers final: 14 residues processed: 163 average time/residue: 0.1821 time to fit residues: 44.3743 Evaluate side-chains 169 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 155 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 624 GLU Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 767 ASP Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 717 GLU Chi-restraints excluded: chain B residue 805 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 43 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 126 optimal weight: 0.4980 chunk 137 optimal weight: 0.9980 chunk 82 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 12 optimal weight: 20.0000 chunk 123 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 674 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 = 0.4457 r_free = 0.4457 target = 0.206090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.145462 restraints weight = 40691.723| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 2.44 r_work: 0.3582 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3447 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12248 Z= 0.106 Angle : 0.485 7.905 16633 Z= 0.261 Chirality : 0.044 0.414 1821 Planarity : 0.004 0.047 2064 Dihedral : 4.596 59.789 1722 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.43 % Allowed : 8.17 % Favored : 90.40 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.50 (0.22), residues: 1426 helix: 2.52 (0.17), residues: 826 sheet: -1.37 (0.61), residues: 74 loop : -1.23 (0.26), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 753 TYR 0.011 0.001 TYR B 77 PHE 0.011 0.001 PHE A 461 TRP 0.009 0.001 TRP B 397 HIS 0.003 0.001 HIS B 143 Details of bonding type rmsd covalent geometry : bond 0.00227 (12236) covalent geometry : angle 0.48278 (16607) SS BOND : bond 0.00101 ( 10) SS BOND : angle 0.47865 ( 20) hydrogen bonds : bond 0.04333 ( 694) hydrogen bonds : angle 4.11833 ( 2031) link_NAG-ASN : bond 0.00096 ( 2) link_NAG-ASN : angle 2.51095 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 177 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 159 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 53 GLU cc_start: 0.7457 (pt0) cc_final: 0.7057 (pt0) REVERT: B 104 ASN cc_start: 0.7860 (m-40) cc_final: 0.7428 (m-40) REVERT: B 123 LEU cc_start: 0.9057 (mm) cc_final: 0.8829 (mt) REVERT: B 235 ARG cc_start: 0.8196 (ttm-80) cc_final: 0.7631 (ttm110) REVERT: B 271 ARG cc_start: 0.7946 (mmm-85) cc_final: 0.7461 (mmm160) REVERT: B 546 ASP cc_start: 0.8612 (m-30) cc_final: 0.8369 (m-30) REVERT: B 721 ASP cc_start: 0.8056 (p0) cc_final: 0.7749 (p0) outliers start: 18 outliers final: 15 residues processed: 167 average time/residue: 0.1864 time to fit residues: 46.0779 Evaluate side-chains 170 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 155 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 624 GLU Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 767 ASP Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 717 GLU Chi-restraints excluded: chain B residue 762 ILE Chi-restraints excluded: chain B residue 805 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 85 optimal weight: 8.9990 chunk 94 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 135 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 730 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.182071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.120295 restraints weight = 40353.950| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 2.69 r_work: 0.2990 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12248 Z= 0.144 Angle : 0.502 7.788 16633 Z= 0.272 Chirality : 0.045 0.421 1821 Planarity : 0.004 0.046 2064 Dihedral : 4.599 57.398 1722 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.19 % Allowed : 8.97 % Favored : 89.84 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.22), residues: 1426 helix: 2.47 (0.17), residues: 827 sheet: -1.41 (0.62), residues: 74 loop : -1.27 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 753 TYR 0.010 0.001 TYR B 138 PHE 0.016 0.001 PHE B 675 TRP 0.010 0.001 TRP B 132 HIS 0.004 0.001 HIS B 108 Details of bonding type rmsd covalent geometry : bond 0.00329 (12236) covalent geometry : angle 0.50024 (16607) SS BOND : bond 0.00109 ( 10) SS BOND : angle 0.57423 ( 20) hydrogen bonds : bond 0.04567 ( 694) hydrogen bonds : angle 4.15290 ( 2031) link_NAG-ASN : bond 0.00058 ( 2) link_NAG-ASN : angle 2.32418 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 176 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 161 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 53 GLU cc_start: 0.7500 (pt0) cc_final: 0.6972 (pt0) REVERT: B 104 ASN cc_start: 0.7896 (m-40) cc_final: 0.7416 (m-40) REVERT: B 143 HIS cc_start: 0.7312 (m170) cc_final: 0.7101 (m-70) REVERT: B 235 ARG cc_start: 0.8196 (ttm-80) cc_final: 0.7614 (ttm110) REVERT: B 271 ARG cc_start: 0.8070 (mmm-85) cc_final: 0.7554 (mmm160) REVERT: B 546 ASP cc_start: 0.8688 (m-30) cc_final: 0.8413 (m-30) outliers start: 15 outliers final: 15 residues processed: 167 average time/residue: 0.1756 time to fit residues: 43.9867 Evaluate side-chains 171 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 156 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 624 GLU Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 721 ASP Chi-restraints excluded: chain A residue 767 ASP Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 717 GLU Chi-restraints excluded: chain B residue 805 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 12 optimal weight: 9.9990 chunk 2 optimal weight: 20.0000 chunk 17 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 chunk 83 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 13 optimal weight: 8.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.180643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.118956 restraints weight = 40387.438| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 2.36 r_work: 0.2988 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12248 Z= 0.168 Angle : 0.524 7.617 16633 Z= 0.284 Chirality : 0.045 0.420 1821 Planarity : 0.005 0.047 2064 Dihedral : 4.712 55.036 1722 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.35 % Allowed : 8.89 % Favored : 89.76 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.22), residues: 1426 helix: 2.35 (0.17), residues: 827 sheet: -1.47 (0.63), residues: 74 loop : -1.31 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 200 TYR 0.017 0.001 TYR A 528 PHE 0.016 0.001 PHE B 675 TRP 0.009 0.001 TRP B 132 HIS 0.004 0.001 HIS B 108 Details of bonding type rmsd covalent geometry : bond 0.00386 (12236) covalent geometry : angle 0.52185 (16607) SS BOND : bond 0.00126 ( 10) SS BOND : angle 0.60320 ( 20) hydrogen bonds : bond 0.04778 ( 694) hydrogen bonds : angle 4.20246 ( 2031) link_NAG-ASN : bond 0.00125 ( 2) link_NAG-ASN : angle 2.24880 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 174 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 157 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 53 GLU cc_start: 0.7512 (pt0) cc_final: 0.7014 (pt0) REVERT: B 104 ASN cc_start: 0.7902 (m-40) cc_final: 0.7425 (m-40) REVERT: B 271 ARG cc_start: 0.8020 (mmm-85) cc_final: 0.7492 (mmm160) REVERT: B 546 ASP cc_start: 0.8713 (m-30) cc_final: 0.8419 (m-30) outliers start: 17 outliers final: 15 residues processed: 165 average time/residue: 0.1732 time to fit residues: 42.6151 Evaluate side-chains 170 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 155 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 624 GLU Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 767 ASP Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 717 GLU Chi-restraints excluded: chain B residue 805 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 111 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 119 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 134 optimal weight: 0.7980 chunk 108 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.180526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.124155 restraints weight = 40322.052| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.43 r_work: 0.3055 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12248 Z= 0.156 Angle : 0.512 7.625 16633 Z= 0.279 Chirality : 0.045 0.419 1821 Planarity : 0.005 0.048 2064 Dihedral : 4.761 55.170 1722 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.43 % Allowed : 9.13 % Favored : 89.44 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.31 (0.22), residues: 1426 helix: 2.37 (0.17), residues: 827 sheet: -1.49 (0.62), residues: 74 loop : -1.31 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 235 TYR 0.016 0.001 TYR A 528 PHE 0.015 0.001 PHE B 675 TRP 0.008 0.001 TRP B 397 HIS 0.004 0.001 HIS B 108 Details of bonding type rmsd covalent geometry : bond 0.00356 (12236) covalent geometry : angle 0.51000 (16607) SS BOND : bond 0.00122 ( 10) SS BOND : angle 0.57006 ( 20) hydrogen bonds : bond 0.04720 ( 694) hydrogen bonds : angle 4.20530 ( 2031) link_NAG-ASN : bond 0.00110 ( 2) link_NAG-ASN : angle 2.15775 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 175 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 157 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 53 GLU cc_start: 0.7518 (pt0) cc_final: 0.7308 (pt0) REVERT: B 104 ASN cc_start: 0.7855 (m-40) cc_final: 0.7395 (m-40) REVERT: B 271 ARG cc_start: 0.8008 (mmm-85) cc_final: 0.7507 (mmm160) REVERT: B 546 ASP cc_start: 0.8672 (m-30) cc_final: 0.8383 (m-30) outliers start: 18 outliers final: 18 residues processed: 166 average time/residue: 0.2076 time to fit residues: 51.0605 Evaluate side-chains 170 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 152 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 624 GLU Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 721 ASP Chi-restraints excluded: chain A residue 767 ASP Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 717 GLU Chi-restraints excluded: chain B residue 762 ILE Chi-restraints excluded: chain B residue 805 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 2 optimal weight: 20.0000 chunk 33 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 138 optimal weight: 0.9990 chunk 137 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 104 optimal weight: 7.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 674 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 = 0.4053 r_free = 0.4053 target = 0.181730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.120270 restraints weight = 40513.398| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.36 r_work: 0.3003 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12248 Z= 0.119 Angle : 0.493 7.774 16633 Z= 0.267 Chirality : 0.044 0.416 1821 Planarity : 0.004 0.048 2064 Dihedral : 4.739 58.850 1722 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.27 % Allowed : 9.21 % Favored : 89.52 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.45 (0.22), residues: 1426 helix: 2.47 (0.17), residues: 829 sheet: -1.45 (0.62), residues: 73 loop : -1.24 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 235 TYR 0.017 0.001 TYR A 528 PHE 0.015 0.001 PHE B 789 TRP 0.010 0.001 TRP B 397 HIS 0.003 0.001 HIS B 108 Details of bonding type rmsd covalent geometry : bond 0.00264 (12236) covalent geometry : angle 0.49201 (16607) SS BOND : bond 0.00106 ( 10) SS BOND : angle 0.49396 ( 20) hydrogen bonds : bond 0.04445 ( 694) hydrogen bonds : angle 4.12511 ( 2031) link_NAG-ASN : bond 0.00109 ( 2) link_NAG-ASN : angle 2.04767 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 170 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 154 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 53 GLU cc_start: 0.7533 (pt0) cc_final: 0.7094 (pt0) REVERT: B 104 ASN cc_start: 0.7875 (m-40) cc_final: 0.7404 (m-40) REVERT: B 271 ARG cc_start: 0.8007 (mmm-85) cc_final: 0.7500 (mmm160) REVERT: B 546 ASP cc_start: 0.8644 (m-30) cc_final: 0.8283 (m-30) outliers start: 16 outliers final: 16 residues processed: 162 average time/residue: 0.1809 time to fit residues: 43.8999 Evaluate side-chains 164 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 148 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 HIS Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 624 GLU Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 721 ASP Chi-restraints excluded: chain A residue 767 ASP Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 717 GLU Chi-restraints excluded: chain B residue 762 ILE Chi-restraints excluded: chain B residue 805 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 74 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 115 optimal weight: 0.8980 chunk 131 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 85 optimal weight: 0.8980 chunk 114 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 674 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 = 0.4057 r_free = 0.4057 target = 0.182086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.122441 restraints weight = 40266.991| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.57 r_work: 0.3024 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 12248 Z= 0.117 Angle : 0.489 7.793 16633 Z= 0.264 Chirality : 0.044 0.416 1821 Planarity : 0.004 0.048 2064 Dihedral : 4.687 57.848 1722 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.27 % Allowed : 9.29 % Favored : 89.44 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.50 (0.22), residues: 1426 helix: 2.51 (0.17), residues: 829 sheet: -1.43 (0.62), residues: 73 loop : -1.22 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 235 TYR 0.014 0.001 TYR A 528 PHE 0.012 0.001 PHE A 393 TRP 0.010 0.001 TRP B 397 HIS 0.003 0.001 HIS B 108 Details of bonding type rmsd covalent geometry : bond 0.00261 (12236) covalent geometry : angle 0.48760 (16607) SS BOND : bond 0.00094 ( 10) SS BOND : angle 0.48198 ( 20) hydrogen bonds : bond 0.04356 ( 694) hydrogen bonds : angle 4.10883 ( 2031) link_NAG-ASN : bond 0.00102 ( 2) link_NAG-ASN : angle 1.96456 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5873.08 seconds wall clock time: 99 minutes 49.35 seconds (5989.35 seconds total)