Starting phenix.real_space_refine on Wed Sep 17 19:42:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6k7n_9942/09_2025/6k7n_9942.cif Found real_map, /net/cci-nas-00/data/ceres_data/6k7n_9942/09_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_9942/09_2025/6k7n_9942.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6k7n_9942/09_2025/6k7n_9942.map" model { file = "/net/cci-nas-00/data/ceres_data/6k7n_9942/09_2025/6k7n_9942.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6k7n_9942/09_2025/6k7n_9942.cif" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.92, per 1000 atoms: 0.28 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: 1.11 Conformation dependent library (CDL) restraints added in 528.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.33 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: 1.70 Time building geometry restraints manager: 1.35 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: 1.790 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: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.460 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.340 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.012 0.001 ARG A 214 TYR 0.031 0.004 TYR C 297 PHE 0.031 0.004 PHE C 179 TRP 0.026 0.004 TRP A 143 HIS 0.024 0.003 HIS C 302 Details of bonding type rmsd covalent geometry : bond 0.01283 (10790) covalent geometry : angle 1.53291 (14649) SS BOND : bond 0.00708 ( 3) SS BOND : angle 2.77414 ( 6) hydrogen bonds : bond 0.11587 ( 472) hydrogen bonds : angle 6.91537 ( 1368) 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) link_NAG-ASN : bond 0.01278 ( 3) link_NAG-ASN : angle 6.81563 ( 9) *********************** 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 : 0.416 Fit side-chains revert: symmetry clash REVERT: A 74 ARG cc_start: 0.6781 (tpt90) cc_final: 0.6262 (ttp-110) REVERT: A 119 GLU cc_start: 0.7207 (pt0) cc_final: 0.7004 (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 213 MET cc_start: 0.4081 (ttt) cc_final: 0.3549 (ptp) REVERT: A 469 MET cc_start: 0.0611 (pmm) cc_final: -0.0974 (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: 0.6275 time to fit residues: 82.9934 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 : 0.382 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.0770 chunk 66 optimal weight: 10.0000 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 30.0000 chunk 129 optimal weight: 0.8980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN 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 42 GLN 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 = 0.4218 r_free = 0.4218 target = 0.210147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.154788 restraints weight = 10162.155| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 1.51 r_work: 0.3115 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10798 Z= 0.141 Angle : 0.713 12.656 14670 Z= 0.363 Chirality : 0.045 0.193 1678 Planarity : 0.006 0.067 1828 Dihedral : 9.770 91.320 1589 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 2.53 % Allowed : 12.99 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.19 (0.22), residues: 1298 helix: -0.53 (0.20), residues: 575 sheet: -1.19 (0.39), residues: 158 loop : -2.52 (0.24), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 481 TYR 0.026 0.002 TYR A 611 PHE 0.017 0.002 PHE A 968 TRP 0.021 0.002 TRP A 876 HIS 0.014 0.001 HIS C 302 Details of bonding type rmsd covalent geometry : bond 0.00295 (10790) covalent geometry : angle 0.69858 (14649) SS BOND : bond 0.00183 ( 3) SS BOND : angle 0.90199 ( 6) hydrogen bonds : bond 0.04879 ( 472) hydrogen bonds : angle 5.56881 ( 1368) link_ALPHA1-4 : bond 0.01064 ( 1) link_ALPHA1-4 : angle 3.64598 ( 3) link_BETA1-4 : bond 0.00657 ( 1) link_BETA1-4 : angle 1.28869 ( 3) link_NAG-ASN : bond 0.00334 ( 3) link_NAG-ASN : angle 5.26842 ( 9) *********************** 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 139 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 110 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ARG cc_start: 0.7342 (tpt90) cc_final: 0.6611 (ttp-110) REVERT: A 79 SER cc_start: 0.8725 (p) cc_final: 0.8470 (m) REVERT: A 127 ASP cc_start: 0.7139 (t0) cc_final: 0.6390 (p0) REVERT: A 180 MET cc_start: 0.3532 (tpp) cc_final: 0.2228 (tpt) REVERT: A 654 GLU cc_start: 0.7202 (mp0) cc_final: 0.6979 (mp0) REVERT: A 693 MET cc_start: 0.3826 (mtp) cc_final: 0.3112 (mmt) REVERT: A 771 GLU cc_start: 0.7501 (mm-30) cc_final: 0.7022 (mt-10) REVERT: A 904 ASN cc_start: 0.8569 (m-40) cc_final: 0.8325 (m-40) REVERT: A 915 SER cc_start: 0.7274 (t) cc_final: 0.7061 (m) REVERT: C 184 GLU cc_start: 0.8412 (mt-10) cc_final: 0.8064 (mt-10) REVERT: C 195 ILE cc_start: 0.8733 (OUTLIER) cc_final: 0.8484 (pp) REVERT: C 242 MET cc_start: 0.8495 (mmm) cc_final: 0.8154 (mmp) REVERT: C 278 ARG cc_start: 0.7992 (ptp-170) cc_final: 0.7692 (ptm160) outliers start: 29 outliers final: 10 residues processed: 125 average time/residue: 0.5534 time to fit residues: 74.9675 Evaluate side-chains 103 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.402 ------------------------------------------------------------------------------- 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 858 GLU 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 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 64 optimal weight: 0.0170 chunk 110 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 72 optimal weight: 0.0770 chunk 32 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 61 optimal weight: 0.1980 chunk 34 optimal weight: 7.9990 chunk 127 optimal weight: 0.7980 chunk 52 optimal weight: 9.9990 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 ASN A 381 HIS A 580 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.212681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.156816 restraints weight = 10279.667| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 1.46 r_work: 0.3191 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1941 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= 0.121 Angle : 0.641 11.347 14670 Z= 0.323 Chirality : 0.043 0.165 1678 Planarity : 0.005 0.058 1828 Dihedral : 7.804 72.414 1586 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 2.88 % Allowed : 15.43 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.37 (0.23), residues: 1298 helix: 0.28 (0.22), residues: 566 sheet: -1.05 (0.37), residues: 190 loop : -2.14 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 540 TYR 0.024 0.001 TYR A 629 PHE 0.016 0.001 PHE A 968 TRP 0.018 0.001 TRP A 876 HIS 0.012 0.001 HIS C 302 Details of bonding type rmsd covalent geometry : bond 0.00253 (10790) covalent geometry : angle 0.62835 (14649) SS BOND : bond 0.00120 ( 3) SS BOND : angle 0.74783 ( 6) hydrogen bonds : bond 0.04286 ( 472) hydrogen bonds : angle 5.20270 ( 1368) link_ALPHA1-4 : bond 0.01554 ( 1) link_ALPHA1-4 : angle 3.52052 ( 3) link_BETA1-4 : bond 0.00366 ( 1) link_BETA1-4 : angle 1.27741 ( 3) link_NAG-ASN : bond 0.00358 ( 3) link_NAG-ASN : angle 4.70436 ( 9) *********************** 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 142 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 109 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 SER cc_start: 0.8695 (p) cc_final: 0.8470 (m) REVERT: A 180 MET cc_start: 0.3768 (tpp) cc_final: 0.2703 (tpt) REVERT: A 771 GLU cc_start: 0.7317 (mm-30) cc_final: 0.6929 (mt-10) REVERT: C 76 ARG cc_start: 0.8629 (mmp80) cc_final: 0.8255 (mmt-90) REVERT: C 86 GLU cc_start: 0.7521 (mp0) cc_final: 0.7172 (mt-10) REVERT: C 184 GLU cc_start: 0.8379 (mt-10) cc_final: 0.8005 (mt-10) REVERT: C 224 GLU cc_start: 0.7895 (tm-30) cc_final: 0.7651 (tp30) REVERT: C 278 ARG cc_start: 0.7975 (ptp-170) cc_final: 0.7698 (ptm160) outliers start: 33 outliers final: 8 residues processed: 131 average time/residue: 0.5559 time to fit residues: 78.7541 Evaluate side-chains 103 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 0.336 ------------------------------------------------------------------------------- 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 386 ASP Chi-restraints excluded: chain A residue 418 VAL 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 346 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 19 optimal weight: 20.0000 chunk 122 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 108 optimal weight: 0.5980 chunk 123 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 127 optimal weight: 0.6980 chunk 8 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 94 optimal weight: 0.2980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 776 GLN A 810 GLN C 298 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.211377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.155449 restraints weight = 10341.069| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 1.56 r_work: 0.3104 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10798 Z= 0.138 Angle : 0.649 10.915 14670 Z= 0.324 Chirality : 0.044 0.163 1678 Planarity : 0.005 0.055 1828 Dihedral : 6.962 54.298 1585 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 2.35 % Allowed : 17.26 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.05 (0.23), residues: 1298 helix: 0.51 (0.22), residues: 572 sheet: -0.69 (0.40), residues: 176 loop : -2.01 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 214 TYR 0.025 0.001 TYR A 611 PHE 0.020 0.001 PHE A 351 TRP 0.017 0.001 TRP A 876 HIS 0.004 0.001 HIS A 936 Details of bonding type rmsd covalent geometry : bond 0.00304 (10790) covalent geometry : angle 0.63656 (14649) SS BOND : bond 0.00209 ( 3) SS BOND : angle 1.03488 ( 6) hydrogen bonds : bond 0.04402 ( 472) hydrogen bonds : angle 5.10214 ( 1368) link_ALPHA1-4 : bond 0.01694 ( 1) link_ALPHA1-4 : angle 3.72742 ( 3) link_BETA1-4 : bond 0.00076 ( 1) link_BETA1-4 : angle 1.33646 ( 3) link_NAG-ASN : bond 0.00160 ( 3) link_NAG-ASN : angle 4.62069 ( 9) *********************** 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 122 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 95 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 SER cc_start: 0.8717 (p) cc_final: 0.8487 (m) REVERT: A 180 MET cc_start: 0.3578 (tpp) cc_final: 0.2632 (tpt) REVERT: A 777 VAL cc_start: 0.8565 (t) cc_final: 0.8270 (m) REVERT: A 884 MET cc_start: 0.8945 (OUTLIER) cc_final: 0.8721 (ttt) REVERT: C 184 GLU cc_start: 0.8460 (mt-10) cc_final: 0.8076 (mt-10) REVERT: C 195 ILE cc_start: 0.8691 (OUTLIER) cc_final: 0.8490 (pp) REVERT: C 224 GLU cc_start: 0.8050 (tm-30) cc_final: 0.7794 (tp30) REVERT: C 278 ARG cc_start: 0.7985 (ptp-170) cc_final: 0.7673 (ptm160) outliers start: 27 outliers final: 14 residues processed: 109 average time/residue: 0.4942 time to fit residues: 58.9964 Evaluate side-chains 107 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.392 ------------------------------------------------------------------------------- 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 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 670 THR Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 798 HIS Chi-restraints excluded: chain A residue 884 MET 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 346 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 28 optimal weight: 4.9990 chunk 128 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 chunk 85 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 76 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 1 optimal weight: 20.0000 chunk 91 optimal weight: 0.7980 chunk 100 optimal weight: 4.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 92 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.207373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.151986 restraints weight = 10182.823| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 1.52 r_work: 0.3050 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 10798 Z= 0.243 Angle : 0.722 11.487 14670 Z= 0.362 Chirality : 0.048 0.176 1678 Planarity : 0.005 0.055 1828 Dihedral : 6.846 52.989 1585 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 3.75 % Allowed : 16.74 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.21 (0.23), residues: 1298 helix: 0.32 (0.21), residues: 572 sheet: -0.76 (0.40), residues: 175 loop : -2.03 (0.26), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 613 TYR 0.022 0.002 TYR A 629 PHE 0.031 0.002 PHE A 351 TRP 0.022 0.002 TRP A 876 HIS 0.006 0.001 HIS A 936 Details of bonding type rmsd covalent geometry : bond 0.00577 (10790) covalent geometry : angle 0.70698 (14649) SS BOND : bond 0.00332 ( 3) SS BOND : angle 1.53869 ( 6) hydrogen bonds : bond 0.05404 ( 472) hydrogen bonds : angle 5.30210 ( 1368) link_ALPHA1-4 : bond 0.01297 ( 1) link_ALPHA1-4 : angle 4.65255 ( 3) link_BETA1-4 : bond 0.00294 ( 1) link_BETA1-4 : angle 2.09672 ( 3) link_NAG-ASN : bond 0.00466 ( 3) link_NAG-ASN : angle 5.01749 ( 9) *********************** 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 138 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 95 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 SER cc_start: 0.8743 (p) cc_final: 0.8492 (m) REVERT: A 180 MET cc_start: 0.3661 (tpp) cc_final: 0.2698 (tpt) REVERT: A 213 MET cc_start: 0.5889 (tpt) cc_final: 0.5224 (tpt) REVERT: A 228 LEU cc_start: 0.6160 (OUTLIER) cc_final: 0.5919 (mp) REVERT: A 693 MET cc_start: 0.3857 (mtp) cc_final: 0.3197 (mmt) REVERT: A 771 GLU cc_start: 0.7492 (mm-30) cc_final: 0.6905 (mt-10) REVERT: A 777 VAL cc_start: 0.8679 (t) cc_final: 0.8379 (m) REVERT: A 884 MET cc_start: 0.9030 (OUTLIER) cc_final: 0.8653 (ttt) REVERT: C 184 GLU cc_start: 0.8442 (mt-10) cc_final: 0.8061 (mt-10) REVERT: C 195 ILE cc_start: 0.8672 (OUTLIER) cc_final: 0.8452 (pp) REVERT: C 278 ARG cc_start: 0.8011 (ptp-170) cc_final: 0.7663 (ptm160) REVERT: C 290 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.7805 (mtm-85) outliers start: 43 outliers final: 21 residues processed: 124 average time/residue: 0.4956 time to fit residues: 67.3565 Evaluate side-chains 114 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 89 time to evaluate : 0.257 ------------------------------------------------------------------------------- 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 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 469 MET Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 657 GLU Chi-restraints excluded: chain A residue 670 THR 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 884 MET 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 65 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 47 optimal weight: 20.0000 chunk 46 optimal weight: 6.9990 chunk 39 optimal weight: 30.0000 chunk 114 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 72 optimal weight: 0.2980 chunk 96 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.208882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.146666 restraints weight = 10263.919| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 1.60 r_work: 0.3107 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10798 Z= 0.178 Angle : 0.681 12.672 14670 Z= 0.339 Chirality : 0.045 0.171 1678 Planarity : 0.005 0.053 1828 Dihedral : 6.512 51.287 1585 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 3.40 % Allowed : 17.96 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.04 (0.23), residues: 1298 helix: 0.47 (0.21), residues: 573 sheet: -0.70 (0.40), residues: 178 loop : -1.95 (0.26), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 613 TYR 0.022 0.002 TYR A 611 PHE 0.022 0.002 PHE A 351 TRP 0.021 0.002 TRP A 876 HIS 0.004 0.001 HIS A 264 Details of bonding type rmsd covalent geometry : bond 0.00410 (10790) covalent geometry : angle 0.66796 (14649) SS BOND : bond 0.00274 ( 3) SS BOND : angle 1.25037 ( 6) hydrogen bonds : bond 0.04850 ( 472) hydrogen bonds : angle 5.17705 ( 1368) link_ALPHA1-4 : bond 0.01594 ( 1) link_ALPHA1-4 : angle 4.57749 ( 3) link_BETA1-4 : bond 0.00154 ( 1) link_BETA1-4 : angle 1.68635 ( 3) link_NAG-ASN : bond 0.00182 ( 3) link_NAG-ASN : angle 4.62863 ( 9) *********************** 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 132 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 93 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 SER cc_start: 0.8682 (p) cc_final: 0.8447 (m) REVERT: A 180 MET cc_start: 0.3482 (tpp) cc_final: 0.2225 (tpt) REVERT: A 213 MET cc_start: 0.5855 (tpt) cc_final: 0.5228 (tpt) REVERT: A 228 LEU cc_start: 0.6275 (OUTLIER) cc_final: 0.5972 (mp) REVERT: A 693 MET cc_start: 0.4018 (mtp) cc_final: 0.3292 (mmt) REVERT: A 771 GLU cc_start: 0.7368 (mm-30) cc_final: 0.6822 (mt-10) REVERT: A 776 GLN cc_start: 0.8560 (tp40) cc_final: 0.8278 (mm-40) REVERT: A 777 VAL cc_start: 0.8676 (t) cc_final: 0.8379 (m) REVERT: C 184 GLU cc_start: 0.8406 (mt-10) cc_final: 0.8016 (mt-10) REVERT: C 195 ILE cc_start: 0.8670 (OUTLIER) cc_final: 0.8429 (pp) REVERT: C 278 ARG cc_start: 0.7932 (ptp-170) cc_final: 0.7578 (ptm160) outliers start: 39 outliers final: 23 residues processed: 121 average time/residue: 0.5065 time to fit residues: 67.2895 Evaluate side-chains 118 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 93 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 65 LEU 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 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 485 ILE Chi-restraints excluded: chain A residue 670 THR 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 195 ILE Chi-restraints excluded: chain C residue 281 ASP Chi-restraints excluded: chain C residue 315 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 45 optimal weight: 0.9980 chunk 40 optimal weight: 0.0670 chunk 111 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 86 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 79 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 overall best weight: 0.7518 ------------------------------------------------------------------------------- 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 = 0.4229 r_free = 0.4229 target = 0.211171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.149411 restraints weight = 10226.388| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 1.52 r_work: 0.3142 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2406 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= 0.125 Angle : 0.628 11.367 14670 Z= 0.312 Chirality : 0.043 0.160 1678 Planarity : 0.004 0.053 1828 Dihedral : 6.077 51.743 1585 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 3.49 % Allowed : 17.79 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.76 (0.24), residues: 1298 helix: 0.74 (0.22), residues: 572 sheet: -0.56 (0.41), residues: 173 loop : -1.83 (0.26), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 613 TYR 0.022 0.001 TYR A 611 PHE 0.018 0.001 PHE A 968 TRP 0.018 0.001 TRP A 876 HIS 0.004 0.001 HIS A 264 Details of bonding type rmsd covalent geometry : bond 0.00271 (10790) covalent geometry : angle 0.61636 (14649) SS BOND : bond 0.00163 ( 3) SS BOND : angle 0.90804 ( 6) hydrogen bonds : bond 0.04268 ( 472) hydrogen bonds : angle 5.00131 ( 1368) link_ALPHA1-4 : bond 0.01632 ( 1) link_ALPHA1-4 : angle 4.18400 ( 3) link_BETA1-4 : bond 0.00034 ( 1) link_BETA1-4 : angle 1.40833 ( 3) link_NAG-ASN : bond 0.00084 ( 3) link_NAG-ASN : angle 4.22151 ( 9) *********************** 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 147 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 107 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 SER cc_start: 0.8685 (p) cc_final: 0.8435 (m) REVERT: A 180 MET cc_start: 0.3557 (tpp) cc_final: 0.2683 (tpt) REVERT: A 228 LEU cc_start: 0.6285 (OUTLIER) cc_final: 0.6025 (mp) REVERT: A 661 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.8112 (mttm) REVERT: A 776 GLN cc_start: 0.8549 (tp40) cc_final: 0.8237 (mm-40) REVERT: A 777 VAL cc_start: 0.8653 (t) cc_final: 0.8383 (m) REVERT: C 76 ARG cc_start: 0.8412 (mmp80) cc_final: 0.8103 (mmt-90) REVERT: C 86 GLU cc_start: 0.7619 (mp0) cc_final: 0.7202 (mt-10) REVERT: C 184 GLU cc_start: 0.8421 (mt-10) cc_final: 0.8040 (mt-10) REVERT: C 195 ILE cc_start: 0.8680 (OUTLIER) cc_final: 0.8439 (pp) REVERT: C 224 GLU cc_start: 0.8019 (tm-30) cc_final: 0.7804 (tp30) REVERT: C 278 ARG cc_start: 0.7925 (ptp-170) cc_final: 0.7597 (ptm160) outliers start: 40 outliers final: 20 residues processed: 132 average time/residue: 0.5777 time to fit residues: 82.8015 Evaluate side-chains 110 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 87 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 65 LEU 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 267 VAL Chi-restraints excluded: chain A residue 305 LEU 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 485 ILE Chi-restraints excluded: chain A residue 661 LYS Chi-restraints excluded: chain A residue 670 THR 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 89 SER 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 346 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 0.2980 chunk 92 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 58 optimal weight: 10.0000 chunk 8 optimal weight: 0.6980 chunk 1 optimal weight: 0.0070 chunk 32 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 104 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 overall best weight: 0.4998 ------------------------------------------------------------------------------- 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 = 0.4245 r_free = 0.4245 target = 0.213031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.157480 restraints weight = 10237.525| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 1.61 r_work: 0.3160 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2652 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= 0.114 Angle : 0.626 11.660 14670 Z= 0.309 Chirality : 0.042 0.156 1678 Planarity : 0.004 0.054 1828 Dihedral : 5.728 52.242 1585 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 2.79 % Allowed : 18.48 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.24), residues: 1298 helix: 0.91 (0.22), residues: 573 sheet: -0.48 (0.41), residues: 177 loop : -1.71 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 613 TYR 0.022 0.001 TYR A 611 PHE 0.017 0.001 PHE A 968 TRP 0.016 0.001 TRP A 927 HIS 0.004 0.001 HIS C 302 Details of bonding type rmsd covalent geometry : bond 0.00241 (10790) covalent geometry : angle 0.61625 (14649) SS BOND : bond 0.00143 ( 3) SS BOND : angle 0.81303 ( 6) hydrogen bonds : bond 0.04021 ( 472) hydrogen bonds : angle 4.86691 ( 1368) link_ALPHA1-4 : bond 0.01888 ( 1) link_ALPHA1-4 : angle 3.93188 ( 3) link_BETA1-4 : bond 0.00273 ( 1) link_BETA1-4 : angle 1.33163 ( 3) link_NAG-ASN : bond 0.00098 ( 3) link_NAG-ASN : angle 3.75734 ( 9) *********************** 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 133 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 101 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 SER cc_start: 0.8693 (p) cc_final: 0.8456 (m) REVERT: A 180 MET cc_start: 0.3535 (tpp) cc_final: 0.2656 (tpt) REVERT: A 364 GLU cc_start: 0.8339 (mt-10) cc_final: 0.8002 (mt-10) REVERT: A 419 MET cc_start: 0.3510 (mpm) cc_final: 0.0201 (ppp) REVERT: A 469 MET cc_start: 0.0977 (OUTLIER) cc_final: 0.0689 (mtm) REVERT: A 776 GLN cc_start: 0.8572 (tp40) cc_final: 0.8264 (mm110) REVERT: A 777 VAL cc_start: 0.8698 (t) cc_final: 0.8431 (m) REVERT: C 76 ARG cc_start: 0.8456 (mmp80) cc_final: 0.8105 (mmt-90) REVERT: C 86 GLU cc_start: 0.7733 (mp0) cc_final: 0.7303 (mt-10) REVERT: C 184 GLU cc_start: 0.8509 (mt-10) cc_final: 0.8107 (mt-10) REVERT: C 224 GLU cc_start: 0.7951 (tm-30) cc_final: 0.7748 (tp30) REVERT: C 278 ARG cc_start: 0.7913 (ptp-170) cc_final: 0.7580 (ptm160) REVERT: C 281 ASP cc_start: 0.7639 (OUTLIER) cc_final: 0.7419 (m-30) REVERT: C 290 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.7772 (mtm-85) REVERT: C 298 ASN cc_start: 0.8486 (m-40) cc_final: 0.8227 (m110) outliers start: 32 outliers final: 12 residues processed: 122 average time/residue: 0.5898 time to fit residues: 78.1256 Evaluate side-chains 107 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.419 ------------------------------------------------------------------------------- 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 305 LEU Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 670 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 36 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 chunk 6 optimal weight: 0.0470 chunk 23 optimal weight: 1.9990 chunk 46 optimal weight: 20.0000 chunk 42 optimal weight: 20.0000 chunk 109 optimal weight: 3.9990 chunk 54 optimal weight: 20.0000 chunk 108 optimal weight: 0.4980 chunk 88 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 overall best weight: 1.1084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.210940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.148237 restraints weight = 10198.346| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 1.49 r_work: 0.3093 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10798 Z= 0.144 Angle : 0.650 11.265 14670 Z= 0.321 Chirality : 0.044 0.159 1678 Planarity : 0.004 0.054 1828 Dihedral : 5.740 51.961 1585 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 2.35 % Allowed : 19.18 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.24), residues: 1298 helix: 0.88 (0.22), residues: 574 sheet: -0.42 (0.41), residues: 177 loop : -1.71 (0.27), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 613 TYR 0.022 0.001 TYR A 611 PHE 0.020 0.001 PHE A 351 TRP 0.016 0.001 TRP A 876 HIS 0.004 0.001 HIS A 264 Details of bonding type rmsd covalent geometry : bond 0.00326 (10790) covalent geometry : angle 0.64028 (14649) SS BOND : bond 0.00210 ( 3) SS BOND : angle 1.05622 ( 6) hydrogen bonds : bond 0.04395 ( 472) hydrogen bonds : angle 4.90918 ( 1368) link_ALPHA1-4 : bond 0.01602 ( 1) link_ALPHA1-4 : angle 4.01718 ( 3) link_BETA1-4 : bond 0.00005 ( 1) link_BETA1-4 : angle 1.51625 ( 3) link_NAG-ASN : bond 0.00200 ( 3) link_NAG-ASN : angle 3.77700 ( 9) *********************** 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 122 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 95 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 SER cc_start: 0.8704 (p) cc_final: 0.8451 (m) REVERT: A 180 MET cc_start: 0.3462 (tpp) cc_final: 0.2649 (tpt) REVERT: A 691 MET cc_start: 0.2184 (mmt) cc_final: 0.1927 (mmt) REVERT: A 771 GLU cc_start: 0.7395 (mm-30) cc_final: 0.6836 (mt-10) REVERT: A 776 GLN cc_start: 0.8540 (tp40) cc_final: 0.8208 (mm110) REVERT: A 777 VAL cc_start: 0.8624 (t) cc_final: 0.8340 (m) REVERT: C 76 ARG cc_start: 0.8343 (mmp80) cc_final: 0.8130 (mmt-90) REVERT: C 86 GLU cc_start: 0.7679 (mp0) cc_final: 0.7252 (mt-10) REVERT: C 112 LYS cc_start: 0.8069 (ttpp) cc_final: 0.7229 (pmtt) REVERT: C 184 GLU cc_start: 0.8461 (mt-10) cc_final: 0.8072 (mt-10) REVERT: C 224 GLU cc_start: 0.8012 (tm-30) cc_final: 0.7792 (tp30) REVERT: C 228 LYS cc_start: 0.7490 (tttp) cc_final: 0.7199 (ptmm) REVERT: C 278 ARG cc_start: 0.7917 (ptp-170) cc_final: 0.7568 (ptm160) REVERT: C 281 ASP cc_start: 0.7616 (OUTLIER) cc_final: 0.7396 (m-30) REVERT: C 290 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.7778 (mtm-85) outliers start: 27 outliers final: 17 residues processed: 114 average time/residue: 0.5844 time to fit residues: 72.4974 Evaluate side-chains 107 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.417 ------------------------------------------------------------------------------- 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 305 LEU Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 770 VAL Chi-restraints excluded: chain A residue 798 HIS Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 281 ASP Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 318 MET 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 18 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 117 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 chunk 125 optimal weight: 0.0770 chunk 116 optimal weight: 0.9990 overall best weight: 1.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.212379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.156826 restraints weight = 10095.113| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 1.56 r_work: 0.3128 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10798 Z= 0.150 Angle : 0.656 11.256 14670 Z= 0.324 Chirality : 0.044 0.173 1678 Planarity : 0.004 0.054 1828 Dihedral : 5.717 51.745 1585 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 1.83 % Allowed : 19.62 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.24), residues: 1298 helix: 0.87 (0.22), residues: 572 sheet: -0.41 (0.41), residues: 177 loop : -1.71 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 613 TYR 0.022 0.002 TYR A 611 PHE 0.021 0.001 PHE A 351 TRP 0.017 0.001 TRP A 876 HIS 0.004 0.001 HIS A 264 Details of bonding type rmsd covalent geometry : bond 0.00338 (10790) covalent geometry : angle 0.64623 (14649) SS BOND : bond 0.00221 ( 3) SS BOND : angle 1.07956 ( 6) hydrogen bonds : bond 0.04469 ( 472) hydrogen bonds : angle 4.92877 ( 1368) link_ALPHA1-4 : bond 0.01632 ( 1) link_ALPHA1-4 : angle 4.01678 ( 3) link_BETA1-4 : bond 0.00075 ( 1) link_BETA1-4 : angle 1.50284 ( 3) link_NAG-ASN : bond 0.00202 ( 3) link_NAG-ASN : angle 3.71683 ( 9) ********************** 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 114 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 93 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 SER cc_start: 0.8695 (p) cc_final: 0.8434 (m) REVERT: A 180 MET cc_start: 0.3625 (tpp) cc_final: 0.2768 (tpt) REVERT: A 291 GLU cc_start: 0.7935 (tt0) cc_final: 0.7484 (tp30) REVERT: A 419 MET cc_start: 0.3720 (mpm) cc_final: 0.0418 (ppp) REVERT: A 771 GLU cc_start: 0.7511 (mm-30) cc_final: 0.6968 (mt-10) REVERT: A 776 GLN cc_start: 0.8567 (tp40) cc_final: 0.8334 (mm110) REVERT: A 777 VAL cc_start: 0.8651 (t) cc_final: 0.8370 (m) REVERT: C 76 ARG cc_start: 0.8379 (mmp80) cc_final: 0.8141 (mmt-90) REVERT: C 86 GLU cc_start: 0.7687 (mp0) cc_final: 0.7270 (mt-10) REVERT: C 112 LYS cc_start: 0.8040 (ttpp) cc_final: 0.7252 (pmtt) REVERT: C 184 GLU cc_start: 0.8478 (mt-10) cc_final: 0.8088 (mt-10) REVERT: C 224 GLU cc_start: 0.8006 (tm-30) cc_final: 0.7799 (tp30) REVERT: C 278 ARG cc_start: 0.7939 (ptp-170) cc_final: 0.7585 (ptm160) REVERT: C 281 ASP cc_start: 0.7591 (OUTLIER) cc_final: 0.7363 (m-30) REVERT: C 290 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.7798 (mtm-85) outliers start: 21 outliers final: 16 residues processed: 106 average time/residue: 0.5992 time to fit residues: 69.0660 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 : 0.430 ------------------------------------------------------------------------------- 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 305 LEU Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 469 MET Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 485 ILE Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 798 HIS Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 281 ASP Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 318 MET 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 93 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 99 optimal weight: 0.0370 chunk 8 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 54 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 overall best weight: 1.0064 ------------------------------------------------------------------------------- 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 = 0.4223 r_free = 0.4223 target = 0.210597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.147495 restraints weight = 10085.666| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 1.54 r_work: 0.3100 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10798 Z= 0.138 Angle : 0.642 11.249 14670 Z= 0.318 Chirality : 0.044 0.155 1678 Planarity : 0.004 0.053 1828 Dihedral : 5.622 51.806 1585 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 1.83 % Allowed : 19.44 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.53 (0.24), residues: 1298 helix: 0.88 (0.22), residues: 576 sheet: -0.41 (0.41), residues: 177 loop : -1.69 (0.27), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 613 TYR 0.022 0.001 TYR A 611 PHE 0.038 0.001 PHE A 351 TRP 0.017 0.001 TRP A 876 HIS 0.004 0.001 HIS A 264 Details of bonding type rmsd covalent geometry : bond 0.00307 (10790) covalent geometry : angle 0.63266 (14649) SS BOND : bond 0.00202 ( 3) SS BOND : angle 1.01053 ( 6) hydrogen bonds : bond 0.04382 ( 472) hydrogen bonds : angle 4.90145 ( 1368) link_ALPHA1-4 : bond 0.01636 ( 1) link_ALPHA1-4 : angle 3.91804 ( 3) link_BETA1-4 : bond 0.00026 ( 1) link_BETA1-4 : angle 1.47404 ( 3) link_NAG-ASN : bond 0.00132 ( 3) link_NAG-ASN : angle 3.60186 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4476.30 seconds wall clock time: 77 minutes 0.04 seconds (4620.04 seconds total)