Starting phenix.real_space_refine on Thu Jul 2 17:19:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8t6u_41081/07_2026/8t6u_41081.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t6u_41081/07_2026/8t6u_41081.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t6u_41081/07_2026/8t6u_41081.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t6u_41081/07_2026/8t6u_41081.map" model { file = "/net/cci-nas-00/data/ceres_data/8t6u_41081/07_2026/8t6u_41081.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t6u_41081/07_2026/8t6u_41081.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8t6u_41081/07_2026/8t6u_41081.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8t6u_41081/07_2026/8t6u_41081.cif" } resolution = 3.13 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= -0.003 sd= 0.032 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 36 5.16 5 C 5826 2.51 5 N 1328 2.21 5 O 1446 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8638 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 516, 4071 Classifications: {'peptide': 516} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 29, 'TRANS': 486} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 4071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 516, 4071 Classifications: {'peptide': 516} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 29, 'TRANS': 486} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" 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 chiralities: 2 Chain: "L" 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 chiralities: 2 Chain: "A" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 256 Unusual residues: {'CLR': 4, 'H9F': 1, 'PC1': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 148 Unusual residues: {'CLR': 4, 'H9F': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "B" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Time building chain proxies: 1.90, per 1000 atoms: 0.22 Number of scatterers: 8638 At special positions: 0 Unit cell: (72.092, 132.348, 83.928, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 36 16.00 P 2 15.00 O 1446 8.00 N 1328 7.00 C 5826 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG D 1 " - " ASN A 642 " " NAG L 1 " - " ASN B 642 " Time building additional restraints: 1.08 Conformation dependent library (CDL) restraints added in 306.7 milliseconds 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1920 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 4 sheets defined 73.3% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 379 through 390 removed outlier: 3.515A pdb=" N VAL A 383 " --> pdb=" O PHE A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 393 No H-bonds generated for 'chain 'A' and resid 391 through 393' Processing helix chain 'A' and resid 394 through 399 Processing helix chain 'A' and resid 402 through 431 removed outlier: 3.709A pdb=" N PHE A 414 " --> pdb=" O ILE A 410 " (cutoff:3.500A) Proline residue: A 419 - end of helix Processing helix chain 'A' and resid 436 through 455 Processing helix chain 'A' and resid 465 through 483 Processing helix chain 'A' and resid 485 through 507 removed outlier: 3.521A pdb=" N VAL A 491 " --> pdb=" O ILE A 487 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TRP A 492 " --> pdb=" O VAL A 488 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE A 507 " --> pdb=" O LEU A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 515 Processing helix chain 'A' and resid 517 through 547 Processing helix chain 'A' and resid 569 through 593 removed outlier: 3.580A pdb=" N LEU A 573 " --> pdb=" O ASN A 569 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASN A 593 " --> pdb=" O ARG A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 608 Processing helix chain 'A' and resid 608 through 624 removed outlier: 3.535A pdb=" N ILE A 612 " --> pdb=" O PHE A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 667 Processing helix chain 'A' and resid 667 through 690 Processing helix chain 'A' and resid 701 through 717 removed outlier: 3.692A pdb=" N ASP A 705 " --> pdb=" O GLY A 701 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU A 706 " --> pdb=" O PHE A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 720 No H-bonds generated for 'chain 'A' and resid 718 through 720' Processing helix chain 'A' and resid 727 through 738 Processing helix chain 'A' and resid 760 through 772 Processing helix chain 'A' and resid 776 through 781 Processing helix chain 'A' and resid 784 through 799 removed outlier: 3.974A pdb=" N LEU A 788 " --> pdb=" O PRO A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 812 Processing helix chain 'A' and resid 822 through 828 Processing helix chain 'A' and resid 829 through 853 Processing helix chain 'A' and resid 858 through 865 removed outlier: 3.553A pdb=" N LEU A 865 " --> pdb=" O PHE A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 865 through 873 removed outlier: 3.534A pdb=" N ARG A 870 " --> pdb=" O THR A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 878 removed outlier: 3.821A pdb=" N ILE A 877 " --> pdb=" O LEU A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 887 Processing helix chain 'B' and resid 379 through 390 removed outlier: 3.513A pdb=" N VAL B 383 " --> pdb=" O PHE B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 393 No H-bonds generated for 'chain 'B' and resid 391 through 393' Processing helix chain 'B' and resid 394 through 399 Processing helix chain 'B' and resid 402 through 431 removed outlier: 3.706A pdb=" N PHE B 414 " --> pdb=" O ILE B 410 " (cutoff:3.500A) Proline residue: B 419 - end of helix Processing helix chain 'B' and resid 436 through 455 Processing helix chain 'B' and resid 465 through 483 Processing helix chain 'B' and resid 485 through 507 removed outlier: 3.520A pdb=" N VAL B 491 " --> pdb=" O ILE B 487 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TRP B 492 " --> pdb=" O VAL B 488 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE B 507 " --> pdb=" O LEU B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 515 Processing helix chain 'B' and resid 517 through 547 Processing helix chain 'B' and resid 569 through 593 removed outlier: 3.581A pdb=" N LEU B 573 " --> pdb=" O ASN B 569 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASN B 593 " --> pdb=" O ARG B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 608 Processing helix chain 'B' and resid 608 through 624 removed outlier: 3.536A pdb=" N ILE B 612 " --> pdb=" O PHE B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 667 Processing helix chain 'B' and resid 667 through 690 Processing helix chain 'B' and resid 701 through 717 removed outlier: 3.690A pdb=" N ASP B 705 " --> pdb=" O GLY B 701 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU B 706 " --> pdb=" O PHE B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 720 No H-bonds generated for 'chain 'B' and resid 718 through 720' Processing helix chain 'B' and resid 727 through 738 Processing helix chain 'B' and resid 760 through 772 Processing helix chain 'B' and resid 776 through 781 Processing helix chain 'B' and resid 784 through 799 removed outlier: 3.974A pdb=" N LEU B 788 " --> pdb=" O PRO B 784 " (cutoff:3.500A) Processing helix chain 'B' and resid 803 through 812 Processing helix chain 'B' and resid 822 through 828 Processing helix chain 'B' and resid 829 through 853 Processing helix chain 'B' and resid 858 through 865 removed outlier: 3.554A pdb=" N LEU B 865 " --> pdb=" O PHE B 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 865 through 873 removed outlier: 3.533A pdb=" N ARG B 870 " --> pdb=" O THR B 866 " (cutoff:3.500A) Processing helix chain 'B' and resid 873 through 878 removed outlier: 3.827A pdb=" N ILE B 877 " --> pdb=" O LEU B 873 " (cutoff:3.500A) Processing helix chain 'B' and resid 879 through 887 Processing sheet with id=AA1, first strand: chain 'A' and resid 462 through 463 Processing sheet with id=AA2, first strand: chain 'A' and resid 739 through 742 removed outlier: 7.366A pdb=" N VAL A 740 " --> pdb=" O GLN A 754 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN A 754 " --> pdb=" O VAL A 740 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN A 752 " --> pdb=" O GLY A 742 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 462 through 463 Processing sheet with id=AA4, first strand: chain 'B' and resid 739 through 742 removed outlier: 7.365A pdb=" N VAL B 740 " --> pdb=" O GLN B 754 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN B 754 " --> pdb=" O VAL B 740 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN B 752 " --> pdb=" O GLY B 742 " (cutoff:3.500A) 518 hydrogen bonds defined for protein. 1518 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: 1.31 Time building geometry restraints manager: 1.28 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: 1333 1.32 - 1.45: 2348 1.45 - 1.58: 5084 1.58 - 1.71: 5 1.71 - 1.84: 66 Bond restraints: 8836 Sorted by residual: bond pdb=" C5 H9F B2203 " pdb=" N8 H9F B2203 " ideal model delta sigma weight residual 1.348 1.508 -0.160 2.00e-02 2.50e+03 6.37e+01 bond pdb=" C5 H9F A2204 " pdb=" N8 H9F A2204 " ideal model delta sigma weight residual 1.348 1.487 -0.139 2.00e-02 2.50e+03 4.86e+01 bond pdb=" C2 H9F B2203 " pdb=" N7 H9F B2203 " ideal model delta sigma weight residual 1.360 1.490 -0.130 2.00e-02 2.50e+03 4.24e+01 bond pdb=" C2 H9F A2204 " pdb=" N7 H9F A2204 " ideal model delta sigma weight residual 1.360 1.482 -0.122 2.00e-02 2.50e+03 3.70e+01 bond pdb=" C6 H9F B2203 " pdb=" N6 H9F B2203 " ideal model delta sigma weight residual 1.364 1.471 -0.107 2.00e-02 2.50e+03 2.86e+01 ... (remaining 8831 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 8760 1.47 - 2.93: 2470 2.93 - 4.40: 733 4.40 - 5.86: 64 5.86 - 7.33: 9 Bond angle restraints: 12036 Sorted by residual: angle pdb=" C ILE B 493 " pdb=" N GLY B 494 " pdb=" CA GLY B 494 " ideal model delta sigma weight residual 119.98 125.48 -5.50 1.11e+00 8.12e-01 2.45e+01 angle pdb=" C ILE A 493 " pdb=" N GLY A 494 " pdb=" CA GLY A 494 " ideal model delta sigma weight residual 119.98 125.42 -5.44 1.11e+00 8.12e-01 2.41e+01 angle pdb=" N GLN A 434 " pdb=" CA GLN A 434 " pdb=" C GLN A 434 " ideal model delta sigma weight residual 111.28 106.09 5.19 1.09e+00 8.42e-01 2.27e+01 angle pdb=" N PRO A 722 " pdb=" CA PRO A 722 " pdb=" C PRO A 722 " ideal model delta sigma weight residual 110.55 117.88 -7.33 1.63e+00 3.76e-01 2.02e+01 angle pdb=" N PRO B 722 " pdb=" CA PRO B 722 " pdb=" C PRO B 722 " ideal model delta sigma weight residual 110.55 117.72 -7.17 1.63e+00 3.76e-01 1.94e+01 ... (remaining 12031 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.06: 4971 34.06 - 68.12: 153 68.12 - 102.18: 16 102.18 - 136.24: 3 136.24 - 170.30: 1 Dihedral angle restraints: 5144 sinusoidal: 2168 harmonic: 2976 Sorted by residual: dihedral pdb=" C18 H9F A2204 " pdb=" C19 H9F A2204 " pdb=" N7 H9F A2204 " pdb=" C2 H9F A2204 " ideal model delta sinusoidal sigma weight residual 90.87 -98.83 -170.30 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C17 H9F A2204 " pdb=" C18 H9F A2204 " pdb=" C19 H9F A2204 " pdb=" N7 H9F A2204 " ideal model delta sinusoidal sigma weight residual 55.70 -69.79 125.49 1 3.00e+01 1.11e-03 1.69e+01 dihedral pdb=" C21 H9F B2203 " pdb=" C22 H9F B2203 " pdb=" C23 H9F B2203 " pdb=" C24 H9F B2203 " ideal model delta sinusoidal sigma weight residual -64.51 52.53 -117.04 1 3.00e+01 1.11e-03 1.55e+01 ... (remaining 5141 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.848: 1434 0.848 - 1.697: 0 1.697 - 2.545: 0 2.545 - 3.393: 0 3.393 - 4.241: 2 Chirality restraints: 1436 Sorted by residual: chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 1.84 -4.24 2.00e-02 2.50e+03 4.50e+04 chirality pdb=" C1 NAG L 2 " pdb=" O4 NAG L 1 " pdb=" C2 NAG L 2 " pdb=" O5 NAG L 2 " both_signs ideal model delta sigma weight residual False -2.40 1.83 -4.23 2.00e-02 2.50e+03 4.48e+04 chirality pdb=" CB ILE A 493 " pdb=" CA ILE A 493 " pdb=" CG1 ILE A 493 " pdb=" CG2 ILE A 493 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 1433 not shown) Planarity restraints: 1406 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " 0.072 2.00e-02 2.50e+03 6.31e-02 4.98e+01 pdb=" C7 NAG D 1 " -0.056 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " 0.065 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " -0.085 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG L 1 " -0.068 2.00e-02 2.50e+03 5.99e-02 4.48e+01 pdb=" C7 NAG L 1 " 0.054 2.00e-02 2.50e+03 pdb=" C8 NAG L 1 " -0.062 2.00e-02 2.50e+03 pdb=" N2 NAG L 1 " 0.081 2.00e-02 2.50e+03 pdb=" O7 NAG L 1 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 878 " -0.042 2.00e-02 2.50e+03 3.28e-02 1.88e+01 pdb=" CG PHE A 878 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE A 878 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE A 878 " 0.053 2.00e-02 2.50e+03 pdb=" CE1 PHE A 878 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 PHE A 878 " -0.038 2.00e-02 2.50e+03 pdb=" CZ PHE A 878 " -0.020 2.00e-02 2.50e+03 ... (remaining 1403 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 895 2.78 - 3.31: 9182 3.31 - 3.84: 14079 3.84 - 4.37: 18538 4.37 - 4.90: 30013 Nonbonded interactions: 72707 Sorted by model distance: nonbonded pdb=" OH TYR A 555 " pdb=" OH TYR B 555 " model vdw 2.246 3.040 nonbonded pdb=" NH2 ARG A 646 " pdb=" CA GLY A 720 " model vdw 2.373 3.520 nonbonded pdb=" NH2 ARG A 879 " pdb=" OE2 GLU A 882 " model vdw 2.403 3.120 nonbonded pdb=" NH2 ARG B 879 " pdb=" OE2 GLU B 882 " model vdw 2.417 3.120 nonbonded pdb=" OG1 THR B 739 " pdb=" O HOH B2301 " model vdw 2.449 3.040 ... (remaining 72702 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 369 through 2202 or resid 2205)) selection = (chain 'B' and (resid 369 through 2202 or resid 2205)) } ncs_group { reference = chain 'D' selection = chain 'L' } 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: 3.720 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.230 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 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 : 0.011 0.160 8840 Z= 0.708 Angle : 1.533 27.809 12048 Z= 1.032 Chirality : 0.175 4.241 1436 Planarity : 0.009 0.096 1404 Dihedral : 15.930 170.302 3224 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.64 % Favored : 97.17 % Rotamer: Outliers : 0.33 % Allowed : 5.02 % Favored : 94.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.15 (0.20), residues: 1024 helix: -1.70 (0.15), residues: 704 sheet: None (None), residues: 0 loop : -2.66 (0.27), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.003 ARG B 389 TYR 0.036 0.009 TYR A 596 PHE 0.053 0.007 PHE A 878 TRP 0.036 0.009 TRP B 723 HIS 0.018 0.006 HIS B 819 Details of bonding type rmsd/Z covalent geometry : bond 0.01129 / 0.71 ( 8836) covalent geometry : angle 1.48528 / 1.02 (12036) hydrogen bonds : bond 0.22884 / 15.13 ( 518) hydrogen bonds : angle 8.61015 / 6.18 ( 1518) link_BETA1-4 : bond 0.06733 / 3.37 ( 2) link_BETA1-4 : angle 16.96308 / 8.26 ( 6) link_NAG-ASN : bond 0.00476 / 0.23 ( 2) link_NAG-ASN : angle 2.84904 / 1.46 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 132 time to evaluate : 0.263 Fit side-chains revert: symmetry clash REVERT: A 406 LEU cc_start: 0.9412 (tt) cc_final: 0.9208 (tp) REVERT: A 554 ASN cc_start: 0.8690 (t0) cc_final: 0.8470 (t0) REVERT: B 406 LEU cc_start: 0.9404 (tt) cc_final: 0.9197 (tp) REVERT: B 554 ASN cc_start: 0.8692 (t0) cc_final: 0.8476 (t0) REVERT: B 712 MET cc_start: 0.8731 (mtm) cc_final: 0.8526 (mtm) outliers start: 3 outliers final: 3 residues processed: 135 average time/residue: 0.1056 time to fit residues: 19.4312 Evaluate side-chains 65 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 62 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 825 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.072624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.061536 restraints weight = 25063.555| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 2.97 r_work: 0.2846 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8840 Z= 0.150 Angle : 0.606 6.692 12048 Z= 0.299 Chirality : 0.039 0.135 1436 Planarity : 0.005 0.047 1404 Dihedral : 13.414 148.269 1327 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.79 % Allowed : 10.27 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.26), residues: 1024 helix: 1.08 (0.19), residues: 700 sheet: None (None), residues: 0 loop : -1.55 (0.31), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 879 TYR 0.010 0.002 TYR B 818 PHE 0.024 0.001 PHE B 411 TRP 0.019 0.001 TRP B 831 HIS 0.002 0.001 HIS A 734 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 ( 8836) covalent geometry : angle 0.60506 / 0.30 (12036) hydrogen bonds : bond 0.04332 / 2.82 ( 518) hydrogen bonds : angle 4.71473 / 3.41 ( 1518) link_BETA1-4 : bond 0.00639 / 0.30 ( 2) link_BETA1-4 : angle 1.48788 / 0.95 ( 6) link_NAG-ASN : bond 0.00050 / 0.02 ( 2) link_NAG-ASN : angle 1.41639 / 0.79 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.277 Fit side-chains REVERT: A 406 LEU cc_start: 0.9076 (tt) cc_final: 0.8866 (tp) REVERT: A 554 ASN cc_start: 0.8454 (t0) cc_final: 0.8141 (t0) REVERT: A 721 MET cc_start: 0.8853 (mpp) cc_final: 0.8623 (mpp) REVERT: B 406 LEU cc_start: 0.9034 (tt) cc_final: 0.8819 (tp) REVERT: B 554 ASN cc_start: 0.8428 (t0) cc_final: 0.8110 (t0) REVERT: B 721 MET cc_start: 0.8869 (mpp) cc_final: 0.8660 (mpp) outliers start: 16 outliers final: 7 residues processed: 75 average time/residue: 0.0851 time to fit residues: 9.4929 Evaluate side-chains 65 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 833 MET Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 833 MET Chi-restraints excluded: chain B residue 873 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 37 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 95 optimal weight: 8.9990 chunk 73 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 26 optimal weight: 0.0980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.072073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.061167 restraints weight = 24990.810| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 2.91 r_work: 0.2849 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8840 Z= 0.127 Angle : 0.536 7.826 12048 Z= 0.262 Chirality : 0.038 0.143 1436 Planarity : 0.005 0.050 1404 Dihedral : 12.473 137.665 1325 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.79 % Allowed : 11.27 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.26), residues: 1024 helix: 1.72 (0.20), residues: 706 sheet: None (None), residues: 0 loop : -1.22 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 879 TYR 0.016 0.001 TYR B 818 PHE 0.014 0.001 PHE A 411 TRP 0.012 0.001 TRP B 831 HIS 0.002 0.001 HIS A 734 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 ( 8836) covalent geometry : angle 0.53526 / 0.26 (12036) hydrogen bonds : bond 0.03881 / 2.54 ( 518) hydrogen bonds : angle 4.29304 / 3.12 ( 1518) link_BETA1-4 : bond 0.00652 / 0.33 ( 2) link_BETA1-4 : angle 1.23597 / 0.62 ( 6) link_NAG-ASN : bond 0.00240 / 0.12 ( 2) link_NAG-ASN : angle 0.78874 / 0.60 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 0.314 Fit side-chains REVERT: A 406 LEU cc_start: 0.9100 (tt) cc_final: 0.8889 (tp) REVERT: A 554 ASN cc_start: 0.8378 (t0) cc_final: 0.8068 (t0) REVERT: B 406 LEU cc_start: 0.9071 (tt) cc_final: 0.8864 (tp) REVERT: B 554 ASN cc_start: 0.8372 (t0) cc_final: 0.8066 (t0) outliers start: 16 outliers final: 10 residues processed: 69 average time/residue: 0.0809 time to fit residues: 8.3932 Evaluate side-chains 66 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain B residue 697 VAL Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 833 MET Chi-restraints excluded: chain B residue 843 CYS Chi-restraints excluded: chain B residue 873 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 52 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 82 optimal weight: 0.6980 chunk 21 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.072038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.061145 restraints weight = 25855.579| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 2.98 r_work: 0.2843 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8840 Z= 0.124 Angle : 0.516 5.750 12048 Z= 0.253 Chirality : 0.038 0.142 1436 Planarity : 0.005 0.050 1404 Dihedral : 11.735 130.846 1325 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.90 % Allowed : 10.71 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.26), residues: 1024 helix: 1.83 (0.20), residues: 710 sheet: None (None), residues: 0 loop : -1.08 (0.32), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 656 TYR 0.017 0.001 TYR A 824 PHE 0.012 0.001 PHE A 411 TRP 0.010 0.001 TRP B 492 HIS 0.001 0.000 HIS B 819 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.12 ( 8836) covalent geometry : angle 0.51590 / 0.25 (12036) hydrogen bonds : bond 0.03681 / 2.41 ( 518) hydrogen bonds : angle 4.15211 / 3.02 ( 1518) link_BETA1-4 : bond 0.00417 / 0.21 ( 2) link_BETA1-4 : angle 0.98266 / 0.47 ( 6) link_NAG-ASN : bond 0.00079 / 0.04 ( 2) link_NAG-ASN : angle 0.89705 / 0.65 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 57 time to evaluate : 0.414 Fit side-chains REVERT: A 406 LEU cc_start: 0.9155 (tt) cc_final: 0.8944 (tp) REVERT: A 554 ASN cc_start: 0.8386 (t0) cc_final: 0.8093 (t0) REVERT: B 406 LEU cc_start: 0.9137 (tt) cc_final: 0.8930 (tp) REVERT: B 554 ASN cc_start: 0.8375 (t0) cc_final: 0.8086 (t0) outliers start: 17 outliers final: 10 residues processed: 65 average time/residue: 0.0836 time to fit residues: 8.2603 Evaluate side-chains 65 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 833 MET Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain B residue 697 VAL Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 843 CYS Chi-restraints excluded: chain B residue 873 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 35 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 447 GLN B 447 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.069981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.058930 restraints weight = 26041.747| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 3.03 r_work: 0.2789 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8840 Z= 0.178 Angle : 0.568 6.803 12048 Z= 0.276 Chirality : 0.039 0.141 1436 Planarity : 0.005 0.050 1404 Dihedral : 11.138 115.937 1325 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.79 % Allowed : 10.94 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.26), residues: 1024 helix: 1.81 (0.20), residues: 722 sheet: None (None), residues: 0 loop : -0.90 (0.32), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 603 TYR 0.014 0.001 TYR A 824 PHE 0.011 0.001 PHE A 471 TRP 0.012 0.001 TRP B 831 HIS 0.002 0.001 HIS B 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 ( 8836) covalent geometry : angle 0.56770 / 0.28 (12036) hydrogen bonds : bond 0.03964 / 2.59 ( 518) hydrogen bonds : angle 4.11566 / 2.99 ( 1518) link_BETA1-4 : bond 0.00254 / 0.13 ( 2) link_BETA1-4 : angle 0.98383 / 0.49 ( 6) link_NAG-ASN : bond 0.00070 / 0.04 ( 2) link_NAG-ASN : angle 0.92081 / 0.66 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 57 time to evaluate : 0.277 Fit side-chains REVERT: A 554 ASN cc_start: 0.8379 (t0) cc_final: 0.8110 (t0) REVERT: B 406 LEU cc_start: 0.9151 (tt) cc_final: 0.8931 (tp) REVERT: B 554 ASN cc_start: 0.8363 (t0) cc_final: 0.7887 (t0) outliers start: 16 outliers final: 13 residues processed: 64 average time/residue: 0.0828 time to fit residues: 7.9927 Evaluate side-chains 66 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 833 MET Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain B residue 697 VAL Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain B residue 843 CYS Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 877 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 13 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 99 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.070911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.059930 restraints weight = 25653.917| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 2.99 r_work: 0.2812 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8840 Z= 0.132 Angle : 0.528 6.525 12048 Z= 0.256 Chirality : 0.038 0.141 1436 Planarity : 0.005 0.050 1404 Dihedral : 10.281 83.507 1324 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.67 % Allowed : 11.16 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.27), residues: 1024 helix: 1.99 (0.20), residues: 710 sheet: None (None), residues: 0 loop : -0.73 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 603 TYR 0.015 0.001 TYR A 824 PHE 0.012 0.001 PHE A 411 TRP 0.010 0.001 TRP B 831 HIS 0.001 0.001 HIS A 703 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 ( 8836) covalent geometry : angle 0.52808 / 0.26 (12036) hydrogen bonds : bond 0.03689 / 2.43 ( 518) hydrogen bonds : angle 4.03134 / 2.93 ( 1518) link_BETA1-4 : bond 0.00306 / 0.15 ( 2) link_BETA1-4 : angle 0.73008 / 0.40 ( 6) link_NAG-ASN : bond 0.00047 / 0.02 ( 2) link_NAG-ASN : angle 0.95321 / 0.65 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.272 Fit side-chains REVERT: A 406 LEU cc_start: 0.9186 (tt) cc_final: 0.8975 (tp) REVERT: A 435 MET cc_start: 0.9034 (mtp) cc_final: 0.8820 (ttt) REVERT: A 554 ASN cc_start: 0.8360 (t0) cc_final: 0.7887 (t0) REVERT: A 777 GLU cc_start: 0.9080 (tm-30) cc_final: 0.8879 (tm-30) REVERT: B 406 LEU cc_start: 0.9150 (tt) cc_final: 0.8940 (tp) REVERT: B 554 ASN cc_start: 0.8340 (t0) cc_final: 0.7872 (t0) outliers start: 15 outliers final: 14 residues processed: 70 average time/residue: 0.0803 time to fit residues: 8.4546 Evaluate side-chains 69 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 55 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 843 CYS Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 889 ASP Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 833 MET Chi-restraints excluded: chain B residue 843 CYS Chi-restraints excluded: chain B residue 873 LEU Chi-restraints excluded: chain B residue 889 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 24 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 89 optimal weight: 0.9990 chunk 73 optimal weight: 0.5980 chunk 23 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.071139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.060321 restraints weight = 25581.781| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 2.95 r_work: 0.2824 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8840 Z= 0.125 Angle : 0.530 7.428 12048 Z= 0.255 Chirality : 0.038 0.151 1436 Planarity : 0.005 0.050 1404 Dihedral : 9.891 83.744 1324 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.01 % Allowed : 11.61 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.27), residues: 1024 helix: 1.96 (0.20), residues: 722 sheet: None (None), residues: 0 loop : -0.62 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 603 TYR 0.014 0.001 TYR A 824 PHE 0.011 0.001 PHE A 411 TRP 0.010 0.001 TRP B 492 HIS 0.001 0.001 HIS A 703 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.12 ( 8836) covalent geometry : angle 0.52932 / 0.26 (12036) hydrogen bonds : bond 0.03615 / 2.38 ( 518) hydrogen bonds : angle 4.00107 / 2.91 ( 1518) link_BETA1-4 : bond 0.00293 / 0.14 ( 2) link_BETA1-4 : angle 0.73505 / 0.42 ( 6) link_NAG-ASN : bond 0.00065 / 0.03 ( 2) link_NAG-ASN : angle 1.02054 / 0.68 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 58 time to evaluate : 0.350 Fit side-chains REVERT: A 406 LEU cc_start: 0.9194 (tt) cc_final: 0.8985 (tp) REVERT: A 554 ASN cc_start: 0.8357 (t0) cc_final: 0.7893 (t0) REVERT: A 721 MET cc_start: 0.8558 (OUTLIER) cc_final: 0.7921 (mpp) REVERT: A 777 GLU cc_start: 0.9043 (tm-30) cc_final: 0.8842 (tm-30) REVERT: B 406 LEU cc_start: 0.9159 (tt) cc_final: 0.8951 (tp) REVERT: B 554 ASN cc_start: 0.8342 (t0) cc_final: 0.7883 (t0) outliers start: 18 outliers final: 15 residues processed: 69 average time/residue: 0.0779 time to fit residues: 8.2286 Evaluate side-chains 72 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 56 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 833 MET Chi-restraints excluded: chain A residue 843 CYS Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 889 ASP Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain B residue 833 MET Chi-restraints excluded: chain B residue 843 CYS Chi-restraints excluded: chain B residue 889 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 55 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.070028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.059134 restraints weight = 25567.436| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 2.95 r_work: 0.2799 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8840 Z= 0.166 Angle : 0.562 8.029 12048 Z= 0.270 Chirality : 0.039 0.158 1436 Planarity : 0.005 0.050 1404 Dihedral : 9.750 84.811 1324 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.01 % Allowed : 12.17 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.27), residues: 1024 helix: 1.91 (0.20), residues: 722 sheet: None (None), residues: 0 loop : -0.51 (0.35), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 603 TYR 0.014 0.001 TYR A 824 PHE 0.009 0.001 PHE A 471 TRP 0.011 0.001 TRP B 831 HIS 0.001 0.001 HIS A 703 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 ( 8836) covalent geometry : angle 0.56184 / 0.27 (12036) hydrogen bonds : bond 0.03811 / 2.52 ( 518) hydrogen bonds : angle 4.04055 / 2.93 ( 1518) link_BETA1-4 : bond 0.00226 / 0.11 ( 2) link_BETA1-4 : angle 0.85061 / 0.50 ( 6) link_NAG-ASN : bond 0.00066 / 0.03 ( 2) link_NAG-ASN : angle 1.00939 / 0.68 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 56 time to evaluate : 0.376 Fit side-chains REVERT: A 406 LEU cc_start: 0.9191 (tt) cc_final: 0.8979 (tp) REVERT: A 554 ASN cc_start: 0.8362 (t0) cc_final: 0.7910 (t0) REVERT: A 777 GLU cc_start: 0.9076 (tm-30) cc_final: 0.8874 (tm-30) REVERT: B 406 LEU cc_start: 0.9169 (tt) cc_final: 0.8954 (tp) REVERT: B 554 ASN cc_start: 0.8347 (t0) cc_final: 0.7903 (t0) outliers start: 18 outliers final: 15 residues processed: 68 average time/residue: 0.0819 time to fit residues: 8.4343 Evaluate side-chains 71 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 833 MET Chi-restraints excluded: chain A residue 843 CYS Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 889 ASP Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain B residue 833 MET Chi-restraints excluded: chain B residue 843 CYS Chi-restraints excluded: chain B residue 889 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 25 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.070736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.059847 restraints weight = 25328.196| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 2.95 r_work: 0.2810 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8840 Z= 0.142 Angle : 0.574 9.153 12048 Z= 0.271 Chirality : 0.040 0.334 1436 Planarity : 0.004 0.050 1404 Dihedral : 9.614 84.943 1324 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.90 % Allowed : 12.39 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.84 (0.27), residues: 1024 helix: 1.90 (0.20), residues: 722 sheet: None (None), residues: 0 loop : -0.42 (0.36), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 603 TYR 0.014 0.001 TYR A 824 PHE 0.011 0.001 PHE A 411 TRP 0.010 0.001 TRP B 831 HIS 0.001 0.000 HIS B 819 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 ( 8836) covalent geometry : angle 0.57306 / 0.27 (12036) hydrogen bonds : bond 0.03702 / 2.45 ( 518) hydrogen bonds : angle 4.03783 / 2.94 ( 1518) link_BETA1-4 : bond 0.00321 / 0.16 ( 2) link_BETA1-4 : angle 0.80616 / 0.49 ( 6) link_NAG-ASN : bond 0.00050 / 0.02 ( 2) link_NAG-ASN : angle 1.06368 / 0.70 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 58 time to evaluate : 0.354 Fit side-chains REVERT: A 406 LEU cc_start: 0.9210 (tt) cc_final: 0.9004 (tp) REVERT: A 554 ASN cc_start: 0.8348 (t0) cc_final: 0.7902 (t0) REVERT: A 721 MET cc_start: 0.8657 (OUTLIER) cc_final: 0.7957 (mpp) REVERT: B 554 ASN cc_start: 0.8330 (t0) cc_final: 0.7893 (t0) outliers start: 17 outliers final: 15 residues processed: 68 average time/residue: 0.0790 time to fit residues: 8.1455 Evaluate side-chains 73 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 57 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 833 MET Chi-restraints excluded: chain A residue 843 CYS Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 889 ASP Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain B residue 833 MET Chi-restraints excluded: chain B residue 843 CYS Chi-restraints excluded: chain B residue 889 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 39 optimal weight: 0.2980 chunk 38 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 101 optimal weight: 0.0070 chunk 49 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.071541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.060669 restraints weight = 25503.088| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 2.96 r_work: 0.2829 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8840 Z= 0.122 Angle : 0.567 10.078 12048 Z= 0.268 Chirality : 0.040 0.291 1436 Planarity : 0.005 0.050 1404 Dihedral : 9.454 85.174 1324 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.67 % Allowed : 12.83 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.27), residues: 1024 helix: 1.89 (0.20), residues: 722 sheet: None (None), residues: 0 loop : -0.36 (0.36), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 603 TYR 0.013 0.001 TYR A 824 PHE 0.011 0.001 PHE A 411 TRP 0.010 0.001 TRP A 492 HIS 0.001 0.000 HIS B 819 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 ( 8836) covalent geometry : angle 0.56657 / 0.27 (12036) hydrogen bonds : bond 0.03624 / 2.40 ( 518) hydrogen bonds : angle 4.03658 / 2.95 ( 1518) link_BETA1-4 : bond 0.00315 / 0.16 ( 2) link_BETA1-4 : angle 0.78638 / 0.51 ( 6) link_NAG-ASN : bond 0.00061 / 0.03 ( 2) link_NAG-ASN : angle 1.06953 / 0.69 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2048 Ramachandran restraints generated. 1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 0.392 Fit side-chains REVERT: A 554 ASN cc_start: 0.8329 (t0) cc_final: 0.7879 (t0) REVERT: B 554 ASN cc_start: 0.8321 (t0) cc_final: 0.7882 (t0) outliers start: 15 outliers final: 13 residues processed: 69 average time/residue: 0.0887 time to fit residues: 9.2870 Evaluate side-chains 72 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 843 CYS Chi-restraints excluded: chain A residue 889 ASP Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain B residue 833 MET Chi-restraints excluded: chain B residue 843 CYS Chi-restraints excluded: chain B residue 889 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 26 optimal weight: 4.9990 chunk 77 optimal weight: 0.0000 chunk 22 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 88 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 78 optimal weight: 0.0670 chunk 38 optimal weight: 0.6980 overall best weight: 0.4322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.071951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.061110 restraints weight = 25226.781| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 2.92 r_work: 0.2845 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8840 Z= 0.110 Angle : 0.569 10.544 12048 Z= 0.265 Chirality : 0.039 0.296 1436 Planarity : 0.005 0.050 1404 Dihedral : 9.310 85.216 1324 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.67 % Allowed : 12.39 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.10 (0.27), residues: 1024 helix: 2.07 (0.20), residues: 706 sheet: None (None), residues: 0 loop : -0.12 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 603 TYR 0.014 0.001 TYR A 824 PHE 0.011 0.001 PHE A 411 TRP 0.010 0.001 TRP B 492 HIS 0.001 0.000 HIS B 703 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 ( 8836) covalent geometry : angle 0.56808 / 0.26 (12036) hydrogen bonds : bond 0.03524 / 2.33 ( 518) hydrogen bonds : angle 4.01574 / 2.93 ( 1518) link_BETA1-4 : bond 0.00315 / 0.16 ( 2) link_BETA1-4 : angle 0.77303 / 0.51 ( 6) link_NAG-ASN : bond 0.00079 / 0.04 ( 2) link_NAG-ASN : angle 1.09762 / 0.71 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1656.95 seconds wall clock time: 29 minutes 26.53 seconds (1766.53 seconds total)