Starting phenix.real_space_refine on Fri Jun 20 06:04:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tai_41136/06_2025/8tai_41136_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tai_41136/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8tai_41136/06_2025/8tai_41136.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tai_41136/06_2025/8tai_41136.map" model { file = "/net/cci-nas-00/data/ceres_data/8tai_41136/06_2025/8tai_41136_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tai_41136/06_2025/8tai_41136_trim.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG: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: {'GLU:plan': 2, 'ARG:plan': 1} 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: 11.02, per 1000 atoms: 0.47 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: 5.61 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 2.00 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: 9.00 Time building geometry restraints manager: 6.98 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: 1.190 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: 0.370 Extract box with map and model: 0.880 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 49.470 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.120 ------------------------------------------------------------------------------- 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 : 7.88 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (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 TRP 0.023 0.001 TRP B 132 HIS 0.004 0.001 HIS B 108 PHE 0.015 0.001 PHE B 73 TYR 0.015 0.001 TYR A 306 ARG 0.008 0.000 ARG B 98 Details of bonding type rmsd link_NAG-ASN : bond 0.23200 ( 2) link_NAG-ASN : angle 21.00944 ( 6) hydrogen bonds : bond 0.12224 ( 694) hydrogen bonds : angle 5.11064 ( 2031) SS BOND : bond 0.00256 ( 10) SS BOND : angle 1.87441 ( 20) covalent geometry : bond 0.00312 (12236) covalent geometry : angle 0.55833 (16607) *********************** 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 : 1.700 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: 0.4710 time to fit residues: 129.9903 Evaluate side-chains 159 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 1.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 10.0000 chunk 109 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 37 optimal weight: 8.9990 chunk 73 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 43 optimal weight: 0.3980 chunk 68 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 chunk 130 optimal weight: 0.4980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN ** A 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 104 ASN B 621 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.208167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.152786 restraints weight = 40627.092| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 2.83 r_work: 0.3498 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.0923 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= 0.147 Angle : 0.544 7.710 16633 Z= 0.296 Chirality : 0.046 0.413 1821 Planarity : 0.005 0.054 2064 Dihedral : 5.559 56.193 1722 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.03 % Allowed : 5.32 % Favored : 93.65 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.22), residues: 1426 helix: 2.17 (0.17), residues: 829 sheet: -0.82 (0.70), residues: 64 loop : -1.25 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 132 HIS 0.003 0.001 HIS B 108 PHE 0.015 0.001 PHE A 461 TYR 0.014 0.001 TYR B 77 ARG 0.004 0.000 ARG B 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00133 ( 2) link_NAG-ASN : angle 3.12011 ( 6) hydrogen bonds : bond 0.05081 ( 694) hydrogen bonds : angle 4.55803 ( 2031) SS BOND : bond 0.00212 ( 10) SS BOND : angle 1.06652 ( 20) covalent geometry : bond 0.00330 (12236) covalent geometry : angle 0.54036 (16607) *********************** 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 179 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 166 time to evaluate : 1.710 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: 0.9318 (mt) cc_final: 0.9064 (mt) REVERT: B 235 ARG cc_start: 0.8178 (ttm-80) cc_final: 0.7626 (ttm110) outliers start: 13 outliers final: 9 residues processed: 170 average time/residue: 0.4743 time to fit residues: 121.4614 Evaluate side-chains 168 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 159 time to evaluate : 1.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 HIS 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 39 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 96 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 8.9990 chunk 24 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 = 0.4405 r_free = 0.4405 target = 0.202784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.144910 restraints weight = 41418.569| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 2.74 r_work: 0.3427 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 12248 Z= 0.259 Angle : 0.594 7.415 16633 Z= 0.329 Chirality : 0.048 0.422 1821 Planarity : 0.005 0.052 2064 Dihedral : 5.550 57.317 1722 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.14 % Favored : 95.79 % Rotamer: Outliers : 1.51 % Allowed : 6.67 % Favored : 91.83 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.22), residues: 1426 helix: 1.86 (0.17), residues: 825 sheet: -1.30 (0.68), residues: 64 loop : -1.45 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 132 HIS 0.005 0.001 HIS B 108 PHE 0.025 0.002 PHE B 675 TYR 0.012 0.002 TYR B 291 ARG 0.003 0.001 ARG B 813 Details of bonding type rmsd link_NAG-ASN : bond 0.00150 ( 2) link_NAG-ASN : angle 3.05051 ( 6) hydrogen bonds : bond 0.05793 ( 694) hydrogen bonds : angle 4.58822 ( 2031) SS BOND : bond 0.00218 ( 10) SS BOND : angle 1.10715 ( 20) covalent geometry : bond 0.00603 (12236) covalent geometry : angle 0.59022 (16607) *********************** 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 181 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 162 time to evaluate : 2.153 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 328 GLN cc_start: 0.8357 (mt0) cc_final: 0.8117 (mt0) REVERT: B 201 ASP cc_start: 0.7204 (t70) cc_final: 0.6993 (t0) REVERT: B 235 ARG cc_start: 0.8281 (ttm-80) cc_final: 0.7705 (ttm110) outliers start: 19 outliers final: 16 residues processed: 172 average time/residue: 0.5950 time to fit residues: 154.3572 Evaluate side-chains 174 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 158 time to evaluate : 2.243 ------------------------------------------------------------------------------- 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 334 SER 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 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 Chi-restraints excluded: chain B residue 805 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 111 optimal weight: 6.9990 chunk 104 optimal weight: 7.9990 chunk 119 optimal weight: 3.9990 chunk 60 optimal weight: 0.4980 chunk 66 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 38 optimal weight: 10.0000 chunk 92 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 123 optimal weight: 4.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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** 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 = 0.4431 r_free = 0.4431 target = 0.203825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.143016 restraints weight = 41049.279| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.45 r_work: 0.3487 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12248 Z= 0.124 Angle : 0.513 7.760 16633 Z= 0.279 Chirality : 0.045 0.412 1821 Planarity : 0.005 0.049 2064 Dihedral : 5.132 56.564 1722 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.27 % Allowed : 8.10 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.22), residues: 1426 helix: 2.18 (0.17), residues: 826 sheet: -1.50 (0.64), residues: 74 loop : -1.34 (0.26), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 397 HIS 0.003 0.001 HIS B 143 PHE 0.014 0.001 PHE A 461 TYR 0.011 0.001 TYR B 138 ARG 0.002 0.000 ARG B 235 Details of bonding type rmsd link_NAG-ASN : bond 0.00147 ( 2) link_NAG-ASN : angle 2.88103 ( 6) hydrogen bonds : bond 0.04812 ( 694) hydrogen bonds : angle 4.30689 ( 2031) SS BOND : bond 0.00106 ( 10) SS BOND : angle 0.59522 ( 20) covalent geometry : bond 0.00271 (12236) covalent geometry : angle 0.51000 (16607) *********************** 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 : 1.815 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: 0.7774 (m-40) cc_final: 0.7355 (m-40) REVERT: B 235 ARG cc_start: 0.8248 (ttm-80) cc_final: 0.7657 (ttm110) REVERT: B 265 GLU cc_start: 0.8478 (mt-10) cc_final: 0.8221 (mt-10) REVERT: B 721 ASP cc_start: 0.8218 (p0) cc_final: 0.7955 (p0) outliers start: 16 outliers final: 14 residues processed: 174 average time/residue: 0.5051 time to fit residues: 131.5257 Evaluate side-chains 170 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 156 time to evaluate : 1.662 ------------------------------------------------------------------------------- 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 349 CYS 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 Chi-restraints excluded: chain B residue 762 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 85 optimal weight: 10.0000 chunk 117 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 104 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 13 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 73 optimal weight: 8.9990 chunk 138 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 = 0.4397 r_free = 0.4397 target = 0.201789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.143383 restraints weight = 41953.356| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 2.58 r_work: 0.3463 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3326 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 12248 Z= 0.265 Angle : 0.580 7.372 16633 Z= 0.320 Chirality : 0.048 0.426 1821 Planarity : 0.005 0.046 2064 Dihedral : 5.259 54.650 1722 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.49 % Favored : 95.44 % Rotamer: Outliers : 1.35 % Allowed : 9.21 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.22), residues: 1426 helix: 1.85 (0.17), residues: 826 sheet: -1.82 (0.61), residues: 75 loop : -1.45 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 132 HIS 0.005 0.001 HIS B 108 PHE 0.023 0.002 PHE B 675 TYR 0.012 0.002 TYR B 291 ARG 0.004 0.000 ARG B 289 Details of bonding type rmsd link_NAG-ASN : bond 0.00177 ( 2) link_NAG-ASN : angle 2.69667 ( 6) hydrogen bonds : bond 0.05620 ( 694) hydrogen bonds : angle 4.49351 ( 2031) SS BOND : bond 0.00227 ( 10) SS BOND : angle 0.90815 ( 20) covalent geometry : bond 0.00615 (12236) covalent geometry : angle 0.57690 (16607) *********************** 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 175 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 158 time to evaluate : 1.725 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: symmetry clash REVERT: B 53 GLU cc_start: 0.7619 (pt0) cc_final: 0.7188 (pt0) REVERT: B 104 ASN cc_start: 0.7846 (m-40) cc_final: 0.7621 (m110) REVERT: B 235 ARG cc_start: 0.8281 (ttm-80) cc_final: 0.7690 (ttm110) outliers start: 17 outliers final: 16 residues processed: 166 average time/residue: 0.4839 time to fit residues: 119.7863 Evaluate side-chains 167 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 151 time to evaluate : 1.929 ------------------------------------------------------------------------------- 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 124 VAL 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 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 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 124 optimal weight: 1.9990 chunk 46 optimal weight: 9.9990 chunk 143 optimal weight: 0.7980 chunk 141 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 117 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 142 optimal weight: 0.7980 chunk 4 optimal weight: 20.0000 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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** B 730 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.202659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.141935 restraints weight = 40550.689| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 2.42 r_work: 0.3541 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3402 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12248 Z= 0.124 Angle : 0.508 7.814 16633 Z= 0.276 Chirality : 0.045 0.416 1821 Planarity : 0.005 0.046 2064 Dihedral : 4.948 57.557 1722 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.59 % Allowed : 9.13 % Favored : 89.29 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.22), residues: 1426 helix: 2.18 (0.17), residues: 827 sheet: -1.75 (0.62), residues: 75 loop : -1.36 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 397 HIS 0.003 0.001 HIS B 108 PHE 0.016 0.001 PHE B 482 TYR 0.012 0.001 TYR A 528 ARG 0.002 0.000 ARG A 753 Details of bonding type rmsd link_NAG-ASN : bond 0.00125 ( 2) link_NAG-ASN : angle 2.55364 ( 6) hydrogen bonds : bond 0.04741 ( 694) hydrogen bonds : angle 4.25793 ( 2031) SS BOND : bond 0.00103 ( 10) SS BOND : angle 0.54628 ( 20) covalent geometry : bond 0.00272 (12236) covalent geometry : angle 0.50535 (16607) *********************** 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 183 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 163 time to evaluate : 1.782 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: symmetry clash REVERT: B 53 GLU cc_start: 0.7568 (pt0) cc_final: 0.7213 (pt0) REVERT: B 104 ASN cc_start: 0.7742 (m-40) cc_final: 0.7301 (m110) REVERT: B 123 LEU cc_start: 0.9115 (mm) cc_final: 0.8873 (mt) outliers start: 20 outliers final: 16 residues processed: 174 average time/residue: 0.4645 time to fit residues: 120.6888 Evaluate side-chains 172 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 156 time to evaluate : 1.863 ------------------------------------------------------------------------------- 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 767 ASP Chi-restraints excluded: chain B residue 141 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 89 optimal weight: 0.7980 chunk 137 optimal weight: 5.9990 chunk 112 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 133 optimal weight: 0.8980 chunk 83 optimal weight: 7.9990 chunk 77 optimal weight: 8.9990 chunk 104 optimal weight: 8.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- 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 = 0.4014 r_free = 0.4014 target = 0.178021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.116068 restraints weight = 40771.851| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.35 r_work: 0.2955 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 12248 Z= 0.212 Angle : 0.549 7.524 16633 Z= 0.302 Chirality : 0.047 0.425 1821 Planarity : 0.005 0.047 2064 Dihedral : 5.046 54.587 1722 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.35 % Allowed : 9.84 % Favored : 88.81 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.22), residues: 1426 helix: 2.00 (0.17), residues: 826 sheet: -1.94 (0.60), residues: 75 loop : -1.39 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 397 HIS 0.005 0.001 HIS B 108 PHE 0.020 0.002 PHE B 675 TYR 0.010 0.001 TYR B 138 ARG 0.002 0.000 ARG B 200 Details of bonding type rmsd link_NAG-ASN : bond 0.00133 ( 2) link_NAG-ASN : angle 2.41348 ( 6) hydrogen bonds : bond 0.05252 ( 694) hydrogen bonds : angle 4.36739 ( 2031) SS BOND : bond 0.00176 ( 10) SS BOND : angle 0.74873 ( 20) covalent geometry : bond 0.00492 (12236) covalent geometry : angle 0.54668 (16607) *********************** 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 178 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 161 time to evaluate : 1.900 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: A 529 GLU cc_start: 0.8221 (mm-30) cc_final: 0.7991 (mm-30) REVERT: B 53 GLU cc_start: 0.7666 (pt0) cc_final: 0.7410 (pt0) REVERT: B 104 ASN cc_start: 0.7777 (m-40) cc_final: 0.7327 (m-40) REVERT: B 221 LYS cc_start: 0.8444 (ptmt) cc_final: 0.8070 (ptmt) REVERT: B 235 ARG cc_start: 0.8273 (ttm-80) cc_final: 0.8049 (ttm-80) outliers start: 17 outliers final: 17 residues processed: 170 average time/residue: 0.5016 time to fit residues: 128.6112 Evaluate side-chains 172 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 155 time to evaluate : 1.855 ------------------------------------------------------------------------------- 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 672 ILE 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 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 805 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 14 optimal weight: 10.0000 chunk 82 optimal weight: 5.9990 chunk 143 optimal weight: 0.9990 chunk 118 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 16 optimal weight: 7.9990 chunk 136 optimal weight: 0.7980 chunk 78 optimal weight: 6.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 730 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.180475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.123927 restraints weight = 40581.413| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.37 r_work: 0.3010 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 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 0.039 12248 Z= 0.117 Angle : 0.504 7.726 16633 Z= 0.274 Chirality : 0.044 0.416 1821 Planarity : 0.004 0.046 2064 Dihedral : 4.801 54.815 1722 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.43 % Allowed : 9.76 % Favored : 88.81 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.22), residues: 1426 helix: 2.24 (0.17), residues: 827 sheet: -1.71 (0.62), residues: 74 loop : -1.31 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 397 HIS 0.002 0.001 HIS B 108 PHE 0.016 0.001 PHE B 482 TYR 0.010 0.001 TYR B 138 ARG 0.002 0.000 ARG A 753 Details of bonding type rmsd link_NAG-ASN : bond 0.00118 ( 2) link_NAG-ASN : angle 2.31113 ( 6) hydrogen bonds : bond 0.04619 ( 694) hydrogen bonds : angle 4.21432 ( 2031) SS BOND : bond 0.00096 ( 10) SS BOND : angle 0.51010 ( 20) covalent geometry : bond 0.00251 (12236) covalent geometry : angle 0.50227 (16607) *********************** 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 178 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 160 time to evaluate : 1.857 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 104 ASN cc_start: 0.7779 (m-40) cc_final: 0.7343 (m110) REVERT: B 221 LYS cc_start: 0.8473 (ptmt) cc_final: 0.8105 (ptmt) REVERT: B 479 LEU cc_start: 0.9342 (mt) cc_final: 0.9141 (mt) outliers start: 18 outliers final: 18 residues processed: 168 average time/residue: 0.4637 time to fit residues: 117.2797 Evaluate side-chains 174 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 156 time to evaluate : 1.934 ------------------------------------------------------------------------------- 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 672 ILE 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 109 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 131 optimal weight: 1.9990 chunk 48 optimal weight: 10.0000 chunk 136 optimal weight: 6.9990 chunk 102 optimal weight: 8.9990 chunk 89 optimal weight: 0.6980 chunk 123 optimal weight: 3.9990 chunk 90 optimal weight: 0.5980 chunk 41 optimal weight: 3.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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 = 0.4035 r_free = 0.4035 target = 0.180042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.119104 restraints weight = 40373.781| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.34 r_work: 0.2982 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 12248 Z= 0.134 Angle : 0.506 7.652 16633 Z= 0.275 Chirality : 0.045 0.419 1821 Planarity : 0.005 0.047 2064 Dihedral : 4.774 55.026 1722 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.43 % Allowed : 9.92 % Favored : 88.65 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.22), residues: 1426 helix: 2.28 (0.17), residues: 827 sheet: -1.68 (0.62), residues: 74 loop : -1.32 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 397 HIS 0.003 0.001 HIS B 108 PHE 0.017 0.001 PHE B 482 TYR 0.010 0.001 TYR B 138 ARG 0.002 0.000 ARG B 235 Details of bonding type rmsd link_NAG-ASN : bond 0.00099 ( 2) link_NAG-ASN : angle 2.20153 ( 6) hydrogen bonds : bond 0.04635 ( 694) hydrogen bonds : angle 4.21749 ( 2031) SS BOND : bond 0.00102 ( 10) SS BOND : angle 0.53362 ( 20) covalent geometry : bond 0.00303 (12236) covalent geometry : angle 0.50458 (16607) *********************** 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 173 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 155 time to evaluate : 1.826 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: A 529 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7955 (mm-30) REVERT: B 104 ASN cc_start: 0.7804 (m-40) cc_final: 0.7347 (m110) REVERT: B 221 LYS cc_start: 0.8439 (ptmt) cc_final: 0.8071 (ptmt) outliers start: 18 outliers final: 18 residues processed: 162 average time/residue: 0.5170 time to fit residues: 127.0187 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 : 1.819 ------------------------------------------------------------------------------- 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 672 ILE 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 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 105 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 4 optimal weight: 9.9990 chunk 62 optimal weight: 7.9990 chunk 47 optimal weight: 9.9990 chunk 90 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 29 optimal weight: 10.0000 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 = 0.4035 r_free = 0.4035 target = 0.179994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.118838 restraints weight = 40502.432| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 2.35 r_work: 0.2995 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 12248 Z= 0.136 Angle : 0.508 7.617 16633 Z= 0.275 Chirality : 0.045 0.418 1821 Planarity : 0.004 0.047 2064 Dihedral : 4.750 55.076 1722 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.51 % Allowed : 10.16 % Favored : 88.33 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.22), residues: 1426 helix: 2.27 (0.17), residues: 827 sheet: -1.59 (0.62), residues: 74 loop : -1.31 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 397 HIS 0.003 0.001 HIS B 108 PHE 0.015 0.001 PHE B 482 TYR 0.020 0.001 TYR A 528 ARG 0.002 0.000 ARG B 235 Details of bonding type rmsd link_NAG-ASN : bond 0.00102 ( 2) link_NAG-ASN : angle 2.13436 ( 6) hydrogen bonds : bond 0.04613 ( 694) hydrogen bonds : angle 4.22207 ( 2031) SS BOND : bond 0.00103 ( 10) SS BOND : angle 0.53968 ( 20) covalent geometry : bond 0.00309 (12236) covalent geometry : angle 0.50604 (16607) ********************** 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 176 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 157 time to evaluate : 1.866 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: 0.7808 (m-40) cc_final: 0.7352 (m110) REVERT: B 221 LYS cc_start: 0.8440 (ptmt) cc_final: 0.8078 (ptmt) outliers start: 19 outliers final: 18 residues processed: 166 average time/residue: 0.4611 time to fit residues: 114.9900 Evaluate side-chains 171 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 153 time to evaluate : 1.716 ------------------------------------------------------------------------------- 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 672 ILE 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 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 88 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 138 optimal weight: 0.6980 chunk 73 optimal weight: 8.9990 chunk 72 optimal weight: 3.9990 chunk 104 optimal weight: 9.9990 chunk 140 optimal weight: 1.9990 chunk 4 optimal weight: 9.9990 chunk 40 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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 = 0.4038 r_free = 0.4038 target = 0.180228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.118752 restraints weight = 40462.209| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 2.37 r_work: 0.2990 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 12248 Z= 0.132 Angle : 0.505 7.613 16633 Z= 0.274 Chirality : 0.045 0.418 1821 Planarity : 0.004 0.047 2064 Dihedral : 4.720 55.120 1722 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.43 % Allowed : 10.32 % Favored : 88.25 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.22), residues: 1426 helix: 2.27 (0.17), residues: 829 sheet: -1.58 (0.62), residues: 74 loop : -1.30 (0.26), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 397 HIS 0.003 0.001 HIS B 108 PHE 0.016 0.001 PHE B 482 TYR 0.021 0.001 TYR A 528 ARG 0.003 0.000 ARG B 235 Details of bonding type rmsd link_NAG-ASN : bond 0.00103 ( 2) link_NAG-ASN : angle 2.07500 ( 6) hydrogen bonds : bond 0.04565 ( 694) hydrogen bonds : angle 4.20361 ( 2031) SS BOND : bond 0.00106 ( 10) SS BOND : angle 0.53074 ( 20) covalent geometry : bond 0.00300 (12236) covalent geometry : angle 0.50310 (16607) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15033.26 seconds wall clock time: 257 minutes 8.60 seconds (15428.60 seconds total)