Starting phenix.real_space_refine on Mon Jun 9 18:24:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6k7n_9942/06_2025/6k7n_9942.cif Found real_map, /net/cci-nas-00/data/ceres_data/6k7n_9942/06_2025/6k7n_9942.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6k7n_9942/06_2025/6k7n_9942.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6k7n_9942/06_2025/6k7n_9942.map" model { file = "/net/cci-nas-00/data/ceres_data/6k7n_9942/06_2025/6k7n_9942.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6k7n_9942/06_2025/6k7n_9942.cif" } resolution = 2.84 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= 0.005 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: 7 Type Number sf(0) Gaussians Al 1 5.89 5 Mg 1 5.21 5 S 56 5.16 5 C 6834 2.51 5 N 1745 2.21 5 O 1903 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 75 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 10544 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 983, 7821 Classifications: {'peptide': 983} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 952} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 2615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2615 Classifications: {'peptide': 325} Link IDs: {'PCIS': 3, 'PTRANS': 22, 'TRANS': 299} Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 41 Unusual residues: {' MG': 1, 'ALF': 1, 'Y01': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 10.85, per 1000 atoms: 1.03 Number of scatterers: 10544 At special positions: 0 Unit cell: (68.89, 109.56, 165.17, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 56 16.00 Al 1 13.00 Mg 1 11.99 F 4 9.00 O 1903 8.00 N 1745 7.00 C 6834 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS C 91 " - pdb=" SG CYS C 104 " distance=2.02 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 102 " distance=2.03 Simple disulfide: pdb=" SG CYS C 157 " - pdb=" SG CYS C 171 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-4 " NAG B 2 " - " MAN B 3 " BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG B 1 " - " ASN C 180 " " NAG C 401 " - " ASN C 294 " " NAG C 402 " - " ASN C 107 " Time building additional restraints: 2.73 Conformation dependent library (CDL) restraints added in 1.7 seconds 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2462 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 10 sheets defined 48.5% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 63 through 75 Processing helix chain 'A' and resid 75 through 88 Processing helix chain 'A' and resid 101 through 131 Processing helix chain 'A' and resid 176 through 178 No H-bonds generated for 'chain 'A' and resid 176 through 178' Processing helix chain 'A' and resid 210 through 215 Processing helix chain 'A' and resid 270 through 274 removed outlier: 3.616A pdb=" N ASP A 273 " --> pdb=" O THR A 270 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR A 274 " --> pdb=" O GLY A 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 270 through 274' Processing helix chain 'A' and resid 275 through 280 Processing helix chain 'A' and resid 288 through 324 Processing helix chain 'A' and resid 339 through 352 Processing helix chain 'A' and resid 353 through 355 No H-bonds generated for 'chain 'A' and resid 353 through 355' Processing helix chain 'A' and resid 358 through 377 Processing helix chain 'A' and resid 393 through 397 removed outlier: 4.119A pdb=" N LEU A 396 " --> pdb=" O THR A 393 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN A 397 " --> pdb=" O SER A 394 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 393 through 397' Processing helix chain 'A' and resid 398 through 401 Processing helix chain 'A' and resid 447 through 455 Processing helix chain 'A' and resid 462 through 466 removed outlier: 3.787A pdb=" N PHE A 465 " --> pdb=" O ILE A 462 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU A 466 " --> pdb=" O CYS A 463 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 462 through 466' Processing helix chain 'A' and resid 467 through 472 Processing helix chain 'A' and resid 490 through 503 Processing helix chain 'A' and resid 559 through 564 Processing helix chain 'A' and resid 570 through 588 removed outlier: 5.569A pdb=" N ILE A 576 " --> pdb=" O LYS A 572 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LYS A 579 " --> pdb=" O GLU A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 617 removed outlier: 4.154A pdb=" N GLU A 606 " --> pdb=" O SER A 602 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N TRP A 607 " --> pdb=" O ASP A 603 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA A 609 " --> pdb=" O GLN A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 630 Processing helix chain 'A' and resid 651 through 662 Processing helix chain 'A' and resid 673 through 685 removed outlier: 4.588A pdb=" N ASN A 679 " --> pdb=" O GLU A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 739 Processing helix chain 'A' and resid 742 through 751 removed outlier: 3.925A pdb=" N LEU A 749 " --> pdb=" O TYR A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 777 Processing helix chain 'A' and resid 787 through 797 removed outlier: 4.622A pdb=" N SER A 792 " --> pdb=" O ALA A 788 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N MET A 793 " --> pdb=" O ASN A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 815 Processing helix chain 'A' and resid 823 through 831 removed outlier: 4.252A pdb=" N ASN A 827 " --> pdb=" O LYS A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 856 Processing helix chain 'A' and resid 856 through 866 removed outlier: 3.657A pdb=" N PHE A 863 " --> pdb=" O ILE A 859 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL A 864 " --> pdb=" O TRP A 860 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 881 Processing helix chain 'A' and resid 887 through 896 removed outlier: 3.993A pdb=" N LEU A 891 " --> pdb=" O ALA A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 908 Processing helix chain 'A' and resid 910 through 919 removed outlier: 3.615A pdb=" N GLN A 916 " --> pdb=" O TYR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 948 Proline residue: A 944 - end of helix Processing helix chain 'A' and resid 961 through 985 removed outlier: 3.832A pdb=" N LEU A 965 " --> pdb=" O ASP A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1011 Processing helix chain 'A' and resid 1020 through 1024 removed outlier: 3.577A pdb=" N SER A1024 " --> pdb=" O PRO A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1033 Processing helix chain 'A' and resid 1033 through 1062 removed outlier: 3.655A pdb=" N TRP A1037 " --> pdb=" O SER A1033 " (cutoff:3.500A) Proline residue: A1044 - end of helix removed outlier: 5.155A pdb=" N LEU A1050 " --> pdb=" O ALA A1046 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ASP A1051 " --> pdb=" O SER A1047 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE A1062 " --> pdb=" O LYS A1058 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 74 Proline residue: C 63 - end of helix Processing helix chain 'C' and resid 131 through 136 Processing helix chain 'C' and resid 139 through 144 Processing helix chain 'C' and resid 146 through 152 Processing helix chain 'C' and resid 172 through 177 Processing helix chain 'C' and resid 206 through 212 Processing helix chain 'C' and resid 222 through 227 Processing helix chain 'C' and resid 239 through 243 removed outlier: 3.530A pdb=" N LEU C 243 " --> pdb=" O VAL C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 253 removed outlier: 3.964A pdb=" N ILE C 253 " --> pdb=" O ASN C 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 250 through 253' Processing helix chain 'C' and resid 254 through 262 Processing helix chain 'C' and resid 323 through 350 Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 40 Processing sheet with id=AA2, first strand: chain 'A' and resid 156 through 159 removed outlier: 3.985A pdb=" N VAL A 263 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N HIS A 264 " --> pdb=" O LEU A 172 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 180 through 183 Processing sheet with id=AA4, first strand: chain 'A' and resid 390 through 391 removed outlier: 7.785A pdb=" N VAL A 801 " --> pdb=" O THR A 781 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ALA A 783 " --> pdb=" O VAL A 801 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N ILE A 803 " --> pdb=" O ALA A 783 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N GLY A 785 " --> pdb=" O ILE A 803 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N LEU A 782 " --> pdb=" O LYS A 404 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ILE A 406 " --> pdb=" O LEU A 782 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ILE A 784 " --> pdb=" O ILE A 406 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N SER A 408 " --> pdb=" O ILE A 784 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LYS A 404 " --> pdb=" O LYS A 665 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N TRP A 667 " --> pdb=" O LYS A 404 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ILE A 406 " --> pdb=" O TRP A 667 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N LEU A 669 " --> pdb=" O ILE A 406 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N SER A 408 " --> pdb=" O LEU A 669 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE A 666 " --> pdb=" O VAL A 756 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N CYS A 758 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ILE A 668 " --> pdb=" O CYS A 758 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU A 727 " --> pdb=" O ILE A 757 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N CYS A 759 " --> pdb=" O LEU A 727 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ILE A 729 " --> pdb=" O CYS A 759 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ILE A 728 " --> pdb=" O ILE A 694 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 415 through 425 removed outlier: 7.201A pdb=" N MET A 419 " --> pdb=" O LYS A 647 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N LYS A 647 " --> pdb=" O MET A 419 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N PHE A 421 " --> pdb=" O GLU A 645 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N GLU A 645 " --> pdb=" O PHE A 421 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS A 423 " --> pdb=" O ALA A 643 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA A 641 " --> pdb=" O THR A 425 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 514 through 517 Processing sheet with id=AA7, first strand: chain 'A' and resid 545 through 547 Processing sheet with id=AA8, first strand: chain 'C' and resid 77 through 81 removed outlier: 5.944A pdb=" N TYR C 122 " --> pdb=" O LEU C 272 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N LEU C 272 " --> pdb=" O TYR C 122 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LEU C 124 " --> pdb=" O ARG C 270 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N ARG C 270 " --> pdb=" O LEU C 124 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 102 through 110 removed outlier: 4.343A pdb=" N CYS C 102 " --> pdb=" O TYR C 297 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL C 295 " --> pdb=" O CYS C 104 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ARG C 290 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR C 182 " --> pdb=" O THR C 296 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 162 through 163 removed outlier: 3.573A pdb=" N LYS C 166 " --> pdb=" O ASN C 163 " (cutoff:3.500A) 472 hydrogen bonds defined for protein. 1368 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.60 Time building geometry restraints manager: 3.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1846 1.32 - 1.44: 2834 1.44 - 1.57: 6020 1.57 - 1.69: 1 1.69 - 1.82: 89 Bond restraints: 10790 Sorted by residual: bond pdb=" F1 ALF A1301 " pdb="AL ALF A1301 " ideal model delta sigma weight residual 1.684 1.791 -0.107 2.00e-02 2.50e+03 2.88e+01 bond pdb=" F3 ALF A1301 " pdb="AL ALF A1301 " ideal model delta sigma weight residual 1.685 1.792 -0.107 2.00e-02 2.50e+03 2.87e+01 bond pdb=" F4 ALF A1301 " pdb="AL ALF A1301 " ideal model delta sigma weight residual 1.686 1.793 -0.107 2.00e-02 2.50e+03 2.87e+01 bond pdb=" F2 ALF A1301 " pdb="AL ALF A1301 " ideal model delta sigma weight residual 1.685 1.790 -0.105 2.00e-02 2.50e+03 2.76e+01 bond pdb=" C ILE C 62 " pdb=" N PRO C 63 " ideal model delta sigma weight residual 1.335 1.380 -0.045 1.36e-02 5.41e+03 1.09e+01 ... (remaining 10785 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.21: 14642 14.21 - 28.42: 5 28.42 - 42.63: 0 42.63 - 56.84: 0 56.84 - 71.05: 2 Bond angle restraints: 14649 Sorted by residual: angle pdb=" F1 ALF A1301 " pdb="AL ALF A1301 " pdb=" F2 ALF A1301 " ideal model delta sigma weight residual 108.68 179.73 -71.05 3.00e+00 1.11e-01 5.61e+02 angle pdb=" F3 ALF A1301 " pdb="AL ALF A1301 " pdb=" F4 ALF A1301 " ideal model delta sigma weight residual 109.63 177.39 -67.76 3.00e+00 1.11e-01 5.10e+02 angle pdb=" F2 ALF A1301 " pdb="AL ALF A1301 " pdb=" F4 ALF A1301 " ideal model delta sigma weight residual 110.21 88.85 21.36 3.00e+00 1.11e-01 5.07e+01 angle pdb=" F1 ALF A1301 " pdb="AL ALF A1301 " pdb=" F3 ALF A1301 " ideal model delta sigma weight residual 109.69 89.52 20.17 3.00e+00 1.11e-01 4.52e+01 angle pdb=" F2 ALF A1301 " pdb="AL ALF A1301 " pdb=" F3 ALF A1301 " ideal model delta sigma weight residual 109.59 90.70 18.89 3.00e+00 1.11e-01 3.96e+01 ... (remaining 14644 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.56: 5927 20.56 - 41.12: 513 41.12 - 61.68: 66 61.68 - 82.24: 14 82.24 - 102.80: 14 Dihedral angle restraints: 6534 sinusoidal: 2717 harmonic: 3817 Sorted by residual: dihedral pdb=" CA ARG A 479 " pdb=" C ARG A 479 " pdb=" N GLU A 480 " pdb=" CA GLU A 480 " ideal model delta harmonic sigma weight residual 180.00 146.31 33.69 0 5.00e+00 4.00e-02 4.54e+01 dihedral pdb=" CA THR A 535 " pdb=" C THR A 535 " pdb=" N SER A 536 " pdb=" CA SER A 536 " ideal model delta harmonic sigma weight residual -180.00 -146.87 -33.13 0 5.00e+00 4.00e-02 4.39e+01 dihedral pdb=" CA THR C 100 " pdb=" C THR C 100 " pdb=" N PRO C 101 " pdb=" CA PRO C 101 " ideal model delta harmonic sigma weight residual 0.00 32.24 -32.24 0 5.00e+00 4.00e-02 4.16e+01 ... (remaining 6531 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 1380 0.094 - 0.187: 276 0.187 - 0.281: 20 0.281 - 0.375: 1 0.375 - 0.468: 1 Chirality restraints: 1678 Sorted by residual: chirality pdb=" CB ILE A 694 " pdb=" CA ILE A 694 " pdb=" CG1 ILE A 694 " pdb=" CG2 ILE A 694 " both_signs ideal model delta sigma weight residual False 2.64 2.18 0.47 2.00e-01 2.50e+01 5.48e+00 chirality pdb=" CG LEU A 854 " pdb=" CB LEU A 854 " pdb=" CD1 LEU A 854 " pdb=" CD2 LEU A 854 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" CB ILE A 784 " pdb=" CA ILE A 784 " pdb=" CG1 ILE A 784 " pdb=" CG2 ILE A 784 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 1675 not shown) Planarity restraints: 1831 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 402 " -0.265 2.00e-02 2.50e+03 2.26e-01 6.40e+02 pdb=" C7 NAG C 402 " 0.065 2.00e-02 2.50e+03 pdb=" C8 NAG C 402 " -0.168 2.00e-02 2.50e+03 pdb=" N2 NAG C 402 " 0.391 2.00e-02 2.50e+03 pdb=" O7 NAG C 402 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 401 " 0.220 2.00e-02 2.50e+03 1.83e-01 4.17e+02 pdb=" C7 NAG C 401 " -0.058 2.00e-02 2.50e+03 pdb=" C8 NAG C 401 " 0.157 2.00e-02 2.50e+03 pdb=" N2 NAG C 401 " -0.300 2.00e-02 2.50e+03 pdb=" O7 NAG C 401 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 1 " -0.058 2.00e-02 2.50e+03 5.08e-02 3.22e+01 pdb=" C7 NAG B 1 " 0.009 2.00e-02 2.50e+03 pdb=" C8 NAG B 1 " 0.012 2.00e-02 2.50e+03 pdb=" N2 NAG B 1 " 0.084 2.00e-02 2.50e+03 pdb=" O7 NAG B 1 " -0.047 2.00e-02 2.50e+03 ... (remaining 1828 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 111 2.62 - 3.19: 8625 3.19 - 3.76: 17111 3.76 - 4.33: 24221 4.33 - 4.90: 38949 Nonbonded interactions: 89017 Sorted by model distance: nonbonded pdb=" F3 ALF A1301 " pdb="MG MG A1303 " model vdw 2.046 2.120 nonbonded pdb=" OD2 ASP A 409 " pdb="MG MG A1303 " model vdw 2.233 2.170 nonbonded pdb=" OH TYR C 134 " pdb=" OG SER C 177 " model vdw 2.243 3.040 nonbonded pdb=" OG SER A 767 " pdb=" OG SER A 792 " model vdw 2.293 3.040 nonbonded pdb=" O TYR A 881 " pdb=" OG1 THR A 886 " model vdw 2.297 3.040 ... (remaining 89012 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 96.810 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: 0.020 Extract box with map and model: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.160 Process input model: 33.910 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:27.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 159.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 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 : 0.013 0.107 10798 Z= 0.534 Angle : 1.543 71.046 14670 Z= 0.736 Chirality : 0.072 0.468 1678 Planarity : 0.011 0.226 1828 Dihedral : 16.045 102.800 4063 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.94 % Favored : 91.99 % Rotamer: Outliers : 0.44 % Allowed : 8.54 % Favored : 91.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.24 % 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: -3.74 (0.19), residues: 1298 helix: -2.16 (0.16), residues: 560 sheet: -1.53 (0.39), residues: 144 loop : -3.03 (0.21), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.004 TRP A 143 HIS 0.024 0.003 HIS C 302 PHE 0.031 0.004 PHE C 179 TYR 0.031 0.004 TYR C 297 ARG 0.012 0.001 ARG A 214 Details of bonding type rmsd link_NAG-ASN : bond 0.01278 ( 3) link_NAG-ASN : angle 6.81563 ( 9) link_ALPHA1-4 : bond 0.01223 ( 1) link_ALPHA1-4 : angle 3.42058 ( 3) link_BETA1-4 : bond 0.00316 ( 1) link_BETA1-4 : angle 2.87276 ( 3) hydrogen bonds : bond 0.11587 ( 472) hydrogen bonds : angle 6.91537 ( 1368) SS BOND : bond 0.00708 ( 3) SS BOND : angle 2.77414 ( 6) covalent geometry : bond 0.01283 (10790) covalent geometry : angle 1.53291 (14649) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 118 time to evaluate : 1.722 Fit side-chains revert: symmetry clash REVERT: A 74 ARG cc_start: 0.6781 (tpt90) cc_final: 0.6263 (ttp-110) REVERT: A 119 GLU cc_start: 0.7207 (pt0) cc_final: 0.7003 (pt0) REVERT: A 127 ASP cc_start: 0.6730 (t0) cc_final: 0.5991 (p0) REVERT: A 180 MET cc_start: 0.3435 (tpp) cc_final: 0.2468 (tpt) REVERT: A 469 MET cc_start: 0.0611 (pmm) cc_final: -0.0973 (mpp) REVERT: A 693 MET cc_start: 0.3923 (mtp) cc_final: 0.3220 (mmt) REVERT: A 771 GLU cc_start: 0.6974 (mm-30) cc_final: 0.6437 (mt-10) REVERT: A 875 ARG cc_start: 0.7760 (mtt-85) cc_final: 0.7374 (mtt90) REVERT: A 901 ARG cc_start: 0.7153 (ttp-110) cc_final: 0.6915 (ttm110) REVERT: C 184 GLU cc_start: 0.7702 (mt-10) cc_final: 0.7385 (mt-10) REVERT: C 278 ARG cc_start: 0.7618 (ptp-170) cc_final: 0.7410 (ptm160) outliers start: 5 outliers final: 2 residues processed: 123 average time/residue: 1.4685 time to fit residues: 195.3791 Evaluate side-chains 93 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 91 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 419 MET Chi-restraints excluded: chain C residue 83 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 0.7980 chunk 98 optimal weight: 0.9990 chunk 54 optimal weight: 8.9990 chunk 33 optimal weight: 0.6980 chunk 66 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 chunk 39 optimal weight: 30.0000 chunk 61 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 118 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 124 HIS A 227 HIS A 234 ASN A 433 GLN A 454 ASN A 605 GLN A 612 GLN A 682 HIS A 765 GLN A 936 HIS A 967 ASN C 176 ASN C 222 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.208325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.151425 restraints weight = 10124.563| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 1.46 r_work: 0.3082 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10798 Z= 0.171 Angle : 0.734 13.098 14670 Z= 0.375 Chirality : 0.047 0.193 1678 Planarity : 0.006 0.068 1828 Dihedral : 10.056 95.237 1589 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 2.62 % Allowed : 13.08 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % 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: -2.31 (0.21), residues: 1298 helix: -0.64 (0.20), residues: 573 sheet: -1.22 (0.39), residues: 158 loop : -2.57 (0.24), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 876 HIS 0.014 0.001 HIS C 302 PHE 0.019 0.002 PHE A 968 TYR 0.026 0.002 TYR A 611 ARG 0.005 0.001 ARG A 481 Details of bonding type rmsd link_NAG-ASN : bond 0.00485 ( 3) link_NAG-ASN : angle 5.55102 ( 9) link_ALPHA1-4 : bond 0.01466 ( 1) link_ALPHA1-4 : angle 3.91653 ( 3) link_BETA1-4 : bond 0.00061 ( 1) link_BETA1-4 : angle 1.53781 ( 3) hydrogen bonds : bond 0.05264 ( 472) hydrogen bonds : angle 5.67234 ( 1368) SS BOND : bond 0.00226 ( 3) SS BOND : angle 1.14664 ( 6) covalent geometry : bond 0.00380 (10790) covalent geometry : angle 0.71866 (14649) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 108 time to evaluate : 1.083 Fit side-chains revert: symmetry clash REVERT: A 74 ARG cc_start: 0.7309 (tpt90) cc_final: 0.6544 (ttp-110) REVERT: A 180 MET cc_start: 0.3628 (tpp) cc_final: 0.2304 (tpt) REVERT: A 469 MET cc_start: 0.0621 (pmm) cc_final: -0.0242 (mmt) REVERT: A 654 GLU cc_start: 0.7262 (mp0) cc_final: 0.7042 (mp0) REVERT: A 693 MET cc_start: 0.3920 (mtp) cc_final: 0.3193 (mmt) REVERT: A 771 GLU cc_start: 0.7491 (mm-30) cc_final: 0.6979 (mt-10) REVERT: A 875 ARG cc_start: 0.8206 (mtt-85) cc_final: 0.7978 (mtt90) REVERT: A 904 ASN cc_start: 0.8591 (m-40) cc_final: 0.8365 (m-40) REVERT: A 915 SER cc_start: 0.7251 (t) cc_final: 0.7014 (m) REVERT: C 184 GLU cc_start: 0.8397 (mt-10) cc_final: 0.8043 (mt-10) REVERT: C 195 ILE cc_start: 0.8662 (OUTLIER) cc_final: 0.8447 (pp) REVERT: C 242 MET cc_start: 0.8482 (mmm) cc_final: 0.8134 (mmp) REVERT: C 278 ARG cc_start: 0.8016 (ptp-170) cc_final: 0.7727 (ptm160) REVERT: C 290 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.7910 (mtm-85) outliers start: 30 outliers final: 10 residues processed: 126 average time/residue: 1.2599 time to fit residues: 171.9723 Evaluate side-chains 104 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 798 HIS Chi-restraints excluded: chain A residue 899 SER Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 281 ASP Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 318 MET Chi-restraints excluded: chain C residue 346 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 6 optimal weight: 4.9990 chunk 17 optimal weight: 0.0770 chunk 102 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 112 optimal weight: 0.6980 chunk 70 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 62 optimal weight: 20.0000 chunk 45 optimal weight: 20.0000 chunk 80 optimal weight: 0.7980 overall best weight: 1.0540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 381 HIS A 580 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.209643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.153543 restraints weight = 10233.617| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 1.54 r_work: 0.3088 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10798 Z= 0.151 Angle : 0.679 12.195 14670 Z= 0.343 Chirality : 0.045 0.171 1678 Planarity : 0.005 0.058 1828 Dihedral : 8.463 83.246 1586 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 2.79 % Allowed : 15.52 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % 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: -1.59 (0.23), residues: 1298 helix: 0.07 (0.21), residues: 573 sheet: -1.05 (0.37), residues: 186 loop : -2.28 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 876 HIS 0.012 0.001 HIS C 302 PHE 0.018 0.001 PHE A 968 TYR 0.024 0.002 TYR A 629 ARG 0.004 0.000 ARG A 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00170 ( 3) link_NAG-ASN : angle 5.11188 ( 9) link_ALPHA1-4 : bond 0.01569 ( 1) link_ALPHA1-4 : angle 3.67574 ( 3) link_BETA1-4 : bond 0.00090 ( 1) link_BETA1-4 : angle 1.49893 ( 3) hydrogen bonds : bond 0.04792 ( 472) hydrogen bonds : angle 5.36531 ( 1368) SS BOND : bond 0.00196 ( 3) SS BOND : angle 1.02813 ( 6) covalent geometry : bond 0.00338 (10790) covalent geometry : angle 0.66435 (14649) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 103 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 ARG cc_start: 0.7316 (tpt90) cc_final: 0.6609 (ttp-110) REVERT: A 79 SER cc_start: 0.8734 (p) cc_final: 0.8492 (m) REVERT: A 180 MET cc_start: 0.3749 (tpp) cc_final: 0.2380 (tpt) REVERT: A 693 MET cc_start: 0.3730 (mtp) cc_final: 0.3095 (mmt) REVERT: A 771 GLU cc_start: 0.7453 (mm-30) cc_final: 0.7005 (mt-10) REVERT: A 915 SER cc_start: 0.7322 (t) cc_final: 0.7120 (m) REVERT: C 184 GLU cc_start: 0.8451 (mt-10) cc_final: 0.8083 (mt-10) REVERT: C 195 ILE cc_start: 0.8736 (OUTLIER) cc_final: 0.8499 (pp) REVERT: C 242 MET cc_start: 0.8527 (mmm) cc_final: 0.8316 (mmp) REVERT: C 278 ARG cc_start: 0.8026 (ptp-170) cc_final: 0.7697 (ptm160) REVERT: C 290 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.7854 (mtm-85) outliers start: 32 outliers final: 14 residues processed: 125 average time/residue: 1.5827 time to fit residues: 217.8541 Evaluate side-chains 110 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 798 HIS Chi-restraints excluded: chain A residue 899 SER Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 281 ASP Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 346 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 27 optimal weight: 4.9990 chunk 16 optimal weight: 20.0000 chunk 24 optimal weight: 8.9990 chunk 19 optimal weight: 20.0000 chunk 100 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 119 optimal weight: 0.0670 chunk 91 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 overall best weight: 2.1924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 ASN C 92 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.207277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.144869 restraints weight = 10163.662| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 1.54 r_work: 0.3029 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 10798 Z= 0.222 Angle : 0.726 12.496 14670 Z= 0.365 Chirality : 0.047 0.171 1678 Planarity : 0.005 0.055 1828 Dihedral : 8.072 79.301 1586 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 3.40 % Allowed : 16.30 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % 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: -1.41 (0.23), residues: 1298 helix: 0.17 (0.21), residues: 573 sheet: -0.92 (0.38), residues: 185 loop : -2.16 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 876 HIS 0.005 0.001 HIS A 832 PHE 0.024 0.002 PHE A 351 TYR 0.023 0.002 TYR A 611 ARG 0.003 0.001 ARG A 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00371 ( 3) link_NAG-ASN : angle 5.35081 ( 9) link_ALPHA1-4 : bond 0.01521 ( 1) link_ALPHA1-4 : angle 3.95188 ( 3) link_BETA1-4 : bond 0.00375 ( 1) link_BETA1-4 : angle 1.89714 ( 3) hydrogen bonds : bond 0.05346 ( 472) hydrogen bonds : angle 5.37644 ( 1368) SS BOND : bond 0.00268 ( 3) SS BOND : angle 1.36975 ( 6) covalent geometry : bond 0.00524 (10790) covalent geometry : angle 0.71143 (14649) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 90 time to evaluate : 3.436 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 ARG cc_start: 0.7353 (tpt90) cc_final: 0.7142 (tpt90) REVERT: A 79 SER cc_start: 0.8727 (p) cc_final: 0.8474 (m) REVERT: A 180 MET cc_start: 0.3597 (tpp) cc_final: 0.2326 (tpt) REVERT: A 228 LEU cc_start: 0.6270 (OUTLIER) cc_final: 0.5950 (mp) REVERT: A 277 MET cc_start: 0.7239 (mmm) cc_final: 0.7022 (mmm) REVERT: A 541 MET cc_start: 0.1791 (OUTLIER) cc_final: 0.1334 (mtt) REVERT: A 661 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.8200 (mttm) REVERT: A 693 MET cc_start: 0.3879 (mtp) cc_final: 0.3146 (mmt) REVERT: A 771 GLU cc_start: 0.7454 (mm-30) cc_final: 0.6760 (mt-10) REVERT: A 777 VAL cc_start: 0.8552 (t) cc_final: 0.8256 (m) REVERT: A 884 MET cc_start: 0.9028 (OUTLIER) cc_final: 0.8652 (ttt) REVERT: A 904 ASN cc_start: 0.8485 (m-40) cc_final: 0.8245 (m110) REVERT: A 915 SER cc_start: 0.7356 (t) cc_final: 0.7097 (m) REVERT: C 45 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8482 (mp) REVERT: C 184 GLU cc_start: 0.8413 (mt-10) cc_final: 0.8024 (mt-10) REVERT: C 195 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.8438 (pp) REVERT: C 242 MET cc_start: 0.8507 (mmm) cc_final: 0.8126 (mmp) REVERT: C 278 ARG cc_start: 0.8060 (ptp-170) cc_final: 0.7713 (ptm160) outliers start: 39 outliers final: 18 residues processed: 116 average time/residue: 1.8795 time to fit residues: 239.7355 Evaluate side-chains 112 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 88 time to evaluate : 2.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 541 MET Chi-restraints excluded: chain A residue 661 LYS Chi-restraints excluded: chain A residue 798 HIS Chi-restraints excluded: chain A residue 875 ARG Chi-restraints excluded: chain A residue 884 MET Chi-restraints excluded: chain A residue 899 SER Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 89 SER Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 281 ASP Chi-restraints excluded: chain C residue 318 MET Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 346 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 30 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 69 optimal weight: 0.1980 chunk 65 optimal weight: 10.0000 chunk 56 optimal weight: 20.0000 chunk 67 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 55 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN A 810 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.209330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.153582 restraints weight = 10105.429| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 1.42 r_work: 0.3138 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10798 Z= 0.164 Angle : 0.661 11.727 14670 Z= 0.332 Chirality : 0.045 0.170 1678 Planarity : 0.005 0.054 1828 Dihedral : 7.302 64.441 1586 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 3.75 % Allowed : 16.56 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % 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: -1.13 (0.23), residues: 1298 helix: 0.43 (0.22), residues: 573 sheet: -0.82 (0.39), residues: 182 loop : -2.01 (0.26), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 876 HIS 0.004 0.001 HIS C 302 PHE 0.021 0.002 PHE A 351 TYR 0.023 0.002 TYR A 629 ARG 0.003 0.000 ARG A 540 Details of bonding type rmsd link_NAG-ASN : bond 0.00160 ( 3) link_NAG-ASN : angle 4.85748 ( 9) link_ALPHA1-4 : bond 0.01627 ( 1) link_ALPHA1-4 : angle 3.69241 ( 3) link_BETA1-4 : bond 0.00176 ( 1) link_BETA1-4 : angle 1.48403 ( 3) hydrogen bonds : bond 0.04759 ( 472) hydrogen bonds : angle 5.18297 ( 1368) SS BOND : bond 0.00205 ( 3) SS BOND : angle 1.08169 ( 6) covalent geometry : bond 0.00375 (10790) covalent geometry : angle 0.64768 (14649) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 94 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 SER cc_start: 0.8698 (p) cc_final: 0.8440 (m) REVERT: A 180 MET cc_start: 0.3709 (tpp) cc_final: 0.2741 (tpt) REVERT: A 654 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.6472 (mp0) REVERT: A 693 MET cc_start: 0.4046 (mtp) cc_final: 0.3312 (mmt) REVERT: A 771 GLU cc_start: 0.7446 (mm-30) cc_final: 0.6955 (mt-10) REVERT: A 777 VAL cc_start: 0.8681 (t) cc_final: 0.8417 (m) REVERT: A 904 ASN cc_start: 0.8471 (m-40) cc_final: 0.8186 (m110) REVERT: C 184 GLU cc_start: 0.8376 (mt-10) cc_final: 0.8002 (mt-10) REVERT: C 195 ILE cc_start: 0.8700 (OUTLIER) cc_final: 0.8500 (pp) REVERT: C 215 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.7919 (mmt180) REVERT: C 242 MET cc_start: 0.8486 (mmm) cc_final: 0.8088 (mmp) REVERT: C 278 ARG cc_start: 0.7997 (ptp-170) cc_final: 0.7661 (ptm160) REVERT: C 290 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.7755 (mtm-85) outliers start: 43 outliers final: 21 residues processed: 123 average time/residue: 1.0597 time to fit residues: 144.1443 Evaluate side-chains 113 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 88 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 798 HIS Chi-restraints excluded: chain A residue 875 ARG Chi-restraints excluded: chain A residue 899 SER Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 89 SER Chi-restraints excluded: chain C residue 195 ILE Chi-restraints excluded: chain C residue 215 ARG Chi-restraints excluded: chain C residue 281 ASP Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 318 MET Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 346 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 2 optimal weight: 8.9990 chunk 30 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 42 optimal weight: 9.9990 chunk 73 optimal weight: 0.4980 chunk 80 optimal weight: 0.1980 chunk 105 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.213792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.158619 restraints weight = 10128.351| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 1.49 r_work: 0.3168 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 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 0.028 10798 Z= 0.122 Angle : 0.638 12.937 14670 Z= 0.316 Chirality : 0.043 0.160 1678 Planarity : 0.004 0.053 1828 Dihedral : 6.387 51.910 1586 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 3.05 % Allowed : 17.87 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % 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: -0.83 (0.24), residues: 1298 helix: 0.69 (0.22), residues: 572 sheet: -0.65 (0.40), residues: 179 loop : -1.86 (0.26), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 876 HIS 0.004 0.001 HIS A 264 PHE 0.017 0.001 PHE A 968 TYR 0.022 0.001 TYR A 629 ARG 0.003 0.000 ARG A 540 Details of bonding type rmsd link_NAG-ASN : bond 0.00182 ( 3) link_NAG-ASN : angle 4.42090 ( 9) link_ALPHA1-4 : bond 0.01913 ( 1) link_ALPHA1-4 : angle 4.02112 ( 3) link_BETA1-4 : bond 0.00094 ( 1) link_BETA1-4 : angle 1.20253 ( 3) hydrogen bonds : bond 0.04204 ( 472) hydrogen bonds : angle 5.02939 ( 1368) SS BOND : bond 0.00124 ( 3) SS BOND : angle 0.77570 ( 6) covalent geometry : bond 0.00263 (10790) covalent geometry : angle 0.62583 (14649) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 91 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 SER cc_start: 0.8692 (p) cc_final: 0.8453 (m) REVERT: A 180 MET cc_start: 0.3696 (tpp) cc_final: 0.2704 (tpt) REVERT: A 213 MET cc_start: 0.6044 (tpt) cc_final: 0.4980 (mmm) REVERT: A 228 LEU cc_start: 0.6331 (OUTLIER) cc_final: 0.6070 (mp) REVERT: A 469 MET cc_start: 0.1127 (OUTLIER) cc_final: 0.0730 (ptm) REVERT: A 777 VAL cc_start: 0.8738 (t) cc_final: 0.8473 (m) REVERT: A 904 ASN cc_start: 0.8450 (m-40) cc_final: 0.8164 (m110) REVERT: C 184 GLU cc_start: 0.8445 (mt-10) cc_final: 0.8076 (mt-10) REVERT: C 242 MET cc_start: 0.8523 (mmm) cc_final: 0.8148 (mmp) REVERT: C 278 ARG cc_start: 0.7982 (ptp-170) cc_final: 0.7635 (ptm160) outliers start: 35 outliers final: 15 residues processed: 112 average time/residue: 1.0198 time to fit residues: 126.4093 Evaluate side-chains 104 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 798 HIS Chi-restraints excluded: chain A residue 875 ARG Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 281 ASP Chi-restraints excluded: chain C residue 318 MET Chi-restraints excluded: chain C residue 346 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 119 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 125 optimal weight: 0.6980 chunk 86 optimal weight: 0.6980 chunk 66 optimal weight: 5.9990 chunk 114 optimal weight: 0.4980 chunk 29 optimal weight: 0.0170 chunk 89 optimal weight: 1.9990 chunk 24 optimal weight: 9.9990 chunk 123 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- 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 = 0.4239 r_free = 0.4239 target = 0.212293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.157247 restraints weight = 10319.732| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 1.57 r_work: 0.3161 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10798 Z= 0.117 Angle : 0.618 10.963 14670 Z= 0.307 Chirality : 0.043 0.160 1678 Planarity : 0.004 0.054 1828 Dihedral : 5.951 52.239 1586 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 2.70 % Allowed : 18.57 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % 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: -0.65 (0.24), residues: 1298 helix: 0.81 (0.22), residues: 574 sheet: -0.50 (0.41), residues: 176 loop : -1.76 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 876 HIS 0.004 0.001 HIS A 264 PHE 0.017 0.001 PHE A 968 TYR 0.021 0.001 TYR A 629 ARG 0.003 0.000 ARG A 540 Details of bonding type rmsd link_NAG-ASN : bond 0.00151 ( 3) link_NAG-ASN : angle 4.02857 ( 9) link_ALPHA1-4 : bond 0.01762 ( 1) link_ALPHA1-4 : angle 4.18236 ( 3) link_BETA1-4 : bond 0.00176 ( 1) link_BETA1-4 : angle 1.29879 ( 3) hydrogen bonds : bond 0.04090 ( 472) hydrogen bonds : angle 4.90135 ( 1368) SS BOND : bond 0.00125 ( 3) SS BOND : angle 0.77273 ( 6) covalent geometry : bond 0.00249 (10790) covalent geometry : angle 0.60732 (14649) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 94 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 SER cc_start: 0.8690 (p) cc_final: 0.8451 (m) REVERT: A 180 MET cc_start: 0.3677 (tpp) cc_final: 0.2812 (tpt) REVERT: A 213 MET cc_start: 0.5951 (tpt) cc_final: 0.5205 (tpt) REVERT: A 228 LEU cc_start: 0.6327 (OUTLIER) cc_final: 0.6125 (mp) REVERT: A 469 MET cc_start: 0.1241 (OUTLIER) cc_final: 0.0920 (ptm) REVERT: A 654 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.6511 (mp0) REVERT: A 693 MET cc_start: 0.3400 (mtp) cc_final: 0.3181 (mpp) REVERT: A 777 VAL cc_start: 0.8728 (t) cc_final: 0.8467 (m) REVERT: A 904 ASN cc_start: 0.8399 (m-40) cc_final: 0.8110 (m110) REVERT: C 76 ARG cc_start: 0.8560 (mmp80) cc_final: 0.8126 (mmt-90) REVERT: C 184 GLU cc_start: 0.8533 (mt-10) cc_final: 0.8147 (mt-10) REVERT: C 278 ARG cc_start: 0.7954 (ptp-170) cc_final: 0.7603 (ptm160) REVERT: C 281 ASP cc_start: 0.7605 (OUTLIER) cc_final: 0.7400 (m-30) REVERT: C 290 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.7814 (mtm-85) REVERT: C 298 ASN cc_start: 0.8538 (m-40) cc_final: 0.8327 (m110) outliers start: 31 outliers final: 11 residues processed: 115 average time/residue: 1.0558 time to fit residues: 133.9372 Evaluate side-chains 104 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 798 HIS Chi-restraints excluded: chain C residue 281 ASP Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 346 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 96 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 21 optimal weight: 6.9990 chunk 39 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 chunk 28 optimal weight: 0.2980 chunk 128 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 129 optimal weight: 4.9990 chunk 106 optimal weight: 6.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 259 ASN ** 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 = 0.4233 r_free = 0.4233 target = 0.211801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.156272 restraints weight = 10193.577| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 1.56 r_work: 0.3114 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10798 Z= 0.126 Angle : 0.632 11.211 14670 Z= 0.314 Chirality : 0.043 0.154 1678 Planarity : 0.004 0.053 1828 Dihedral : 5.800 52.102 1585 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 2.01 % Allowed : 19.53 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % 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: -0.53 (0.24), residues: 1298 helix: 0.88 (0.22), residues: 574 sheet: -0.40 (0.41), residues: 179 loop : -1.68 (0.27), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 876 HIS 0.004 0.001 HIS A 264 PHE 0.032 0.001 PHE A 351 TYR 0.021 0.001 TYR A 611 ARG 0.004 0.000 ARG A 875 Details of bonding type rmsd link_NAG-ASN : bond 0.00079 ( 3) link_NAG-ASN : angle 3.82043 ( 9) link_ALPHA1-4 : bond 0.01636 ( 1) link_ALPHA1-4 : angle 3.95126 ( 3) link_BETA1-4 : bond 0.00077 ( 1) link_BETA1-4 : angle 1.39228 ( 3) hydrogen bonds : bond 0.04211 ( 472) hydrogen bonds : angle 4.88009 ( 1368) SS BOND : bond 0.00145 ( 3) SS BOND : angle 0.85438 ( 6) covalent geometry : bond 0.00275 (10790) covalent geometry : angle 0.62186 (14649) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 92 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 SER cc_start: 0.8705 (p) cc_final: 0.8450 (m) REVERT: A 180 MET cc_start: 0.3363 (tpp) cc_final: 0.2532 (tpt) REVERT: A 364 GLU cc_start: 0.8376 (mt-10) cc_final: 0.8084 (mt-10) REVERT: A 419 MET cc_start: 0.3347 (mpm) cc_final: 0.0026 (ppp) REVERT: A 469 MET cc_start: 0.1108 (OUTLIER) cc_final: 0.0824 (ptm) REVERT: A 691 MET cc_start: 0.2233 (mmt) cc_final: 0.2013 (mmt) REVERT: A 777 VAL cc_start: 0.8656 (t) cc_final: 0.8357 (m) REVERT: A 904 ASN cc_start: 0.8336 (m-40) cc_final: 0.8049 (m110) REVERT: C 76 ARG cc_start: 0.8609 (mmp80) cc_final: 0.8158 (mmt-90) REVERT: C 184 GLU cc_start: 0.8501 (mt-10) cc_final: 0.8091 (mt-10) REVERT: C 278 ARG cc_start: 0.7892 (ptp-170) cc_final: 0.7527 (ptm160) REVERT: C 281 ASP cc_start: 0.7625 (OUTLIER) cc_final: 0.7406 (m-30) REVERT: C 290 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.7819 (mtm-85) outliers start: 23 outliers final: 13 residues processed: 106 average time/residue: 1.0052 time to fit residues: 117.0272 Evaluate side-chains 105 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 798 HIS Chi-restraints excluded: chain C residue 281 ASP Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 346 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 42 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 2 optimal weight: 8.9990 chunk 82 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN ** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 810 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.209212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.153873 restraints weight = 10318.438| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 1.64 r_work: 0.3063 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10798 Z= 0.171 Angle : 0.667 10.826 14670 Z= 0.330 Chirality : 0.045 0.172 1678 Planarity : 0.004 0.053 1828 Dihedral : 5.903 51.739 1585 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 2.18 % Allowed : 19.62 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % 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: -0.64 (0.24), residues: 1298 helix: 0.76 (0.22), residues: 573 sheet: -0.46 (0.41), residues: 180 loop : -1.72 (0.27), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 876 HIS 0.004 0.001 HIS A 936 PHE 0.034 0.002 PHE A 351 TYR 0.022 0.002 TYR A 611 ARG 0.004 0.000 ARG A 875 Details of bonding type rmsd link_NAG-ASN : bond 0.00287 ( 3) link_NAG-ASN : angle 3.94599 ( 9) link_ALPHA1-4 : bond 0.01513 ( 1) link_ALPHA1-4 : angle 4.24056 ( 3) link_BETA1-4 : bond 0.00057 ( 1) link_BETA1-4 : angle 1.68417 ( 3) hydrogen bonds : bond 0.04720 ( 472) hydrogen bonds : angle 4.99631 ( 1368) SS BOND : bond 0.00195 ( 3) SS BOND : angle 1.09608 ( 6) covalent geometry : bond 0.00394 (10790) covalent geometry : angle 0.65693 (14649) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 87 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 SER cc_start: 0.8729 (p) cc_final: 0.8485 (m) REVERT: A 180 MET cc_start: 0.3684 (tpp) cc_final: 0.2820 (tpt) REVERT: A 469 MET cc_start: 0.0917 (OUTLIER) cc_final: 0.0524 (ptm) REVERT: A 654 GLU cc_start: 0.7404 (OUTLIER) cc_final: 0.6540 (mp0) REVERT: A 691 MET cc_start: 0.1973 (mmt) cc_final: 0.1742 (mmt) REVERT: A 771 GLU cc_start: 0.7441 (mm-30) cc_final: 0.6900 (mt-10) REVERT: A 777 VAL cc_start: 0.8693 (t) cc_final: 0.8374 (m) REVERT: A 884 MET cc_start: 0.8959 (OUTLIER) cc_final: 0.8533 (ttt) REVERT: A 904 ASN cc_start: 0.8381 (m-40) cc_final: 0.8071 (m110) REVERT: C 76 ARG cc_start: 0.8649 (mmp80) cc_final: 0.8301 (mmt-90) REVERT: C 184 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8144 (mt-10) REVERT: C 278 ARG cc_start: 0.8007 (ptp-170) cc_final: 0.7621 (ptm160) REVERT: C 281 ASP cc_start: 0.7642 (OUTLIER) cc_final: 0.7392 (m-30) REVERT: C 290 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.7859 (mtm-85) outliers start: 25 outliers final: 13 residues processed: 101 average time/residue: 1.1018 time to fit residues: 122.3088 Evaluate side-chains 104 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 798 HIS Chi-restraints excluded: chain A residue 884 MET Chi-restraints excluded: chain C residue 281 ASP Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 346 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 101 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 114 optimal weight: 0.3980 chunk 100 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 7.9990 chunk 74 optimal weight: 1.9990 chunk 128 optimal weight: 0.9980 chunk 78 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 810 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.211785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.158912 restraints weight = 10178.441| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 1.62 r_work: 0.3110 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10798 Z= 0.130 Angle : 0.630 11.082 14670 Z= 0.313 Chirality : 0.043 0.170 1678 Planarity : 0.004 0.054 1828 Dihedral : 5.685 51.846 1585 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 1.66 % Allowed : 19.97 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % 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: -0.55 (0.24), residues: 1298 helix: 0.85 (0.22), residues: 573 sheet: -0.36 (0.41), residues: 179 loop : -1.70 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 876 HIS 0.004 0.001 HIS A 264 PHE 0.030 0.001 PHE A 351 TYR 0.021 0.001 TYR A 611 ARG 0.003 0.000 ARG A 875 Details of bonding type rmsd link_NAG-ASN : bond 0.00034 ( 3) link_NAG-ASN : angle 3.69555 ( 9) link_ALPHA1-4 : bond 0.01624 ( 1) link_ALPHA1-4 : angle 3.98920 ( 3) link_BETA1-4 : bond 0.00033 ( 1) link_BETA1-4 : angle 1.39497 ( 3) hydrogen bonds : bond 0.04274 ( 472) hydrogen bonds : angle 4.92420 ( 1368) SS BOND : bond 0.00154 ( 3) SS BOND : angle 0.87717 ( 6) covalent geometry : bond 0.00285 (10790) covalent geometry : angle 0.62100 (14649) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2596 Ramachandran restraints generated. 1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 SER cc_start: 0.8741 (p) cc_final: 0.8475 (m) REVERT: A 180 MET cc_start: 0.3692 (tpp) cc_final: 0.2817 (tpt) REVERT: A 469 MET cc_start: 0.0909 (OUTLIER) cc_final: 0.0514 (ptm) REVERT: A 654 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.6479 (mp0) REVERT: A 771 GLU cc_start: 0.7496 (mm-30) cc_final: 0.6921 (mt-10) REVERT: A 777 VAL cc_start: 0.8680 (t) cc_final: 0.8376 (m) REVERT: A 904 ASN cc_start: 0.8411 (m-40) cc_final: 0.8134 (m110) REVERT: C 76 ARG cc_start: 0.8631 (mmp80) cc_final: 0.8289 (mmt-90) REVERT: C 86 GLU cc_start: 0.7602 (mp0) cc_final: 0.7205 (mt-10) REVERT: C 184 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8139 (mt-10) REVERT: C 224 GLU cc_start: 0.8081 (tm-30) cc_final: 0.7864 (tp30) REVERT: C 228 LYS cc_start: 0.7500 (ttmp) cc_final: 0.7229 (ptmm) REVERT: C 278 ARG cc_start: 0.7955 (ptp-170) cc_final: 0.7581 (ptm160) REVERT: C 281 ASP cc_start: 0.7664 (OUTLIER) cc_final: 0.7425 (m-30) outliers start: 19 outliers final: 11 residues processed: 109 average time/residue: 1.2464 time to fit residues: 147.4378 Evaluate side-chains 104 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 798 HIS Chi-restraints excluded: chain C residue 281 ASP Chi-restraints excluded: chain C residue 346 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 65 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 chunk 36 optimal weight: 3.9990 chunk 76 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 80 optimal weight: 0.5980 chunk 1 optimal weight: 8.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 GLN A 810 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.211294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.154582 restraints weight = 10149.057| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 1.58 r_work: 0.3142 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10798 Z= 0.127 Angle : 0.626 11.000 14670 Z= 0.310 Chirality : 0.043 0.143 1678 Planarity : 0.004 0.053 1828 Dihedral : 5.561 52.059 1585 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 1.48 % Allowed : 20.31 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % 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: -0.50 (0.24), residues: 1298 helix: 0.90 (0.22), residues: 573 sheet: -0.36 (0.41), residues: 179 loop : -1.67 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 876 HIS 0.004 0.001 HIS A 264 PHE 0.033 0.001 PHE A 351 TYR 0.022 0.001 TYR A 611 ARG 0.004 0.000 ARG A 540 Details of bonding type rmsd link_NAG-ASN : bond 0.00067 ( 3) link_NAG-ASN : angle 3.54593 ( 9) link_ALPHA1-4 : bond 0.01704 ( 1) link_ALPHA1-4 : angle 3.86840 ( 3) link_BETA1-4 : bond 0.00058 ( 1) link_BETA1-4 : angle 1.41355 ( 3) hydrogen bonds : bond 0.04240 ( 472) hydrogen bonds : angle 4.88641 ( 1368) SS BOND : bond 0.00184 ( 3) SS BOND : angle 0.92463 ( 6) covalent geometry : bond 0.00279 (10790) covalent geometry : angle 0.61749 (14649) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9727.77 seconds wall clock time: 171 minutes 22.14 seconds (10282.14 seconds total)