Starting phenix.real_space_refine on Mon May 12 22:51:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t6u_41081/05_2025/8t6u_41081.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t6u_41081/05_2025/8t6u_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_41081/05_2025/8t6u_41081.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t6u_41081/05_2025/8t6u_41081.map" model { file = "/net/cci-nas-00/data/ceres_data/8t6u_41081/05_2025/8t6u_41081.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t6u_41081/05_2025/8t6u_41081.cif" } resolution = 3.13 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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 dihedrals: 6 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 dihedrals: 6 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: 6.38, per 1000 atoms: 0.74 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: 2.29 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 0.85 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: 2.28 Time building geometry restraints manager: 2.62 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: 5507 34.06 - 68.12: 167 68.12 - 102.18: 16 102.18 - 136.24: 3 136.24 - 170.30: 1 Dihedral angle restraints: 5694 sinusoidal: 2718 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 5691 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 891 or resid 2201 through 2202 or resid 2205)) \ selection = (chain 'B' and (resid 369 through 891 or resid 2201 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: 2.750 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: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 23.320 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 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 : 15.188 170.302 3774 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 4.28 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.15 (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 TRP 0.036 0.009 TRP B 723 HIS 0.018 0.006 HIS B 819 PHE 0.053 0.007 PHE A 878 TYR 0.036 0.009 TYR A 596 ARG 0.014 0.003 ARG B 389 Details of bonding type rmsd link_NAG-ASN : bond 0.00476 ( 2) link_NAG-ASN : angle 2.84904 ( 6) link_BETA1-4 : bond 0.06733 ( 2) link_BETA1-4 : angle 16.96308 ( 6) hydrogen bonds : bond 0.22884 ( 518) hydrogen bonds : angle 8.61015 ( 1518) covalent geometry : bond 0.01129 ( 8836) covalent geometry : angle 1.48528 (12036) *********************** 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 : 0.912 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: 0.2197 time to fit residues: 40.0497 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 : 0.974 ------------------------------------------------------------------------------- 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 86 optimal weight: 1.9990 chunk 77 optimal weight: 0.0470 chunk 42 optimal weight: 0.0770 chunk 26 optimal weight: 0.0670 chunk 52 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 overall best weight: 0.3574 ------------------------------------------------------------------------------- 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 = 0.3247 r_free = 0.3247 target = 0.073407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.062397 restraints weight = 24622.970| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 2.99 r_work: 0.2860 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8840 Z= 0.130 Angle : 0.596 7.298 12048 Z= 0.296 Chirality : 0.039 0.132 1436 Planarity : 0.005 0.047 1404 Dihedral : 12.303 149.154 1877 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.90 % Allowed : 10.38 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.25), residues: 1024 helix: 1.07 (0.19), residues: 700 sheet: None (None), residues: 0 loop : -1.64 (0.31), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 831 HIS 0.002 0.001 HIS B 734 PHE 0.025 0.001 PHE B 411 TYR 0.010 0.002 TYR B 818 ARG 0.007 0.001 ARG A 879 Details of bonding type rmsd link_NAG-ASN : bond 0.00106 ( 2) link_NAG-ASN : angle 1.34771 ( 6) link_BETA1-4 : bond 0.00180 ( 2) link_BETA1-4 : angle 2.03343 ( 6) hydrogen bonds : bond 0.04475 ( 518) hydrogen bonds : angle 4.77229 ( 1518) covalent geometry : bond 0.00286 ( 8836) covalent geometry : angle 0.59399 (12036) *********************** 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 91 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 0.837 Fit side-chains REVERT: A 406 LEU cc_start: 0.9039 (tt) cc_final: 0.8838 (tp) REVERT: A 554 ASN cc_start: 0.8426 (t0) cc_final: 0.8093 (t0) REVERT: A 721 MET cc_start: 0.8875 (mpp) cc_final: 0.8651 (mpp) REVERT: B 554 ASN cc_start: 0.8412 (t0) cc_final: 0.8080 (t0) REVERT: B 721 MET cc_start: 0.8889 (mpp) cc_final: 0.8687 (mpp) outliers start: 17 outliers final: 8 residues processed: 80 average time/residue: 0.2070 time to fit residues: 24.5737 Evaluate side-chains 66 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.942 ------------------------------------------------------------------------------- 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 697 VAL 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 34 optimal weight: 0.2980 chunk 82 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 99 optimal weight: 0.4980 chunk 64 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.3198 r_free = 0.3198 target = 0.070437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.059464 restraints weight = 25700.896| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 2.96 r_work: 0.2805 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8840 Z= 0.188 Angle : 0.586 6.699 12048 Z= 0.285 Chirality : 0.040 0.149 1436 Planarity : 0.005 0.051 1404 Dihedral : 11.591 139.269 1875 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.56 % Allowed : 11.38 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.26), residues: 1024 helix: 1.58 (0.20), residues: 708 sheet: None (None), residues: 0 loop : -1.28 (0.32), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 831 HIS 0.002 0.001 HIS B 734 PHE 0.012 0.001 PHE B 411 TYR 0.017 0.002 TYR B 818 ARG 0.004 0.001 ARG B 879 Details of bonding type rmsd link_NAG-ASN : bond 0.00046 ( 2) link_NAG-ASN : angle 0.96732 ( 6) link_BETA1-4 : bond 0.00669 ( 2) link_BETA1-4 : angle 1.64522 ( 6) hydrogen bonds : bond 0.04150 ( 518) hydrogen bonds : angle 4.36180 ( 1518) covalent geometry : bond 0.00446 ( 8836) covalent geometry : angle 0.58435 (12036) *********************** 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 72 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.921 Fit side-chains REVERT: A 554 ASN cc_start: 0.8409 (t0) cc_final: 0.8112 (t0) REVERT: B 554 ASN cc_start: 0.8392 (t0) cc_final: 0.8100 (t0) outliers start: 14 outliers final: 10 residues processed: 65 average time/residue: 0.1876 time to fit residues: 18.2576 Evaluate side-chains 63 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.867 ------------------------------------------------------------------------------- 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 78 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 88 optimal weight: 3.9990 chunk 95 optimal weight: 0.0010 chunk 89 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 overall best weight: 1.1190 ------------------------------------------------------------------------------- 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 = 0.3201 r_free = 0.3201 target = 0.070697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.059746 restraints weight = 25568.960| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 2.95 r_work: 0.2811 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8840 Z= 0.159 Angle : 0.550 5.860 12048 Z= 0.268 Chirality : 0.039 0.142 1436 Planarity : 0.005 0.051 1404 Dihedral : 10.743 130.734 1875 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.01 % Allowed : 10.71 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.26), residues: 1024 helix: 1.73 (0.20), residues: 710 sheet: None (None), residues: 0 loop : -1.03 (0.32), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 831 HIS 0.001 0.001 HIS B 547 PHE 0.013 0.001 PHE B 411 TYR 0.017 0.001 TYR A 824 ARG 0.003 0.000 ARG B 656 Details of bonding type rmsd link_NAG-ASN : bond 0.00026 ( 2) link_NAG-ASN : angle 0.95777 ( 6) link_BETA1-4 : bond 0.00356 ( 2) link_BETA1-4 : angle 0.92807 ( 6) hydrogen bonds : bond 0.03874 ( 518) hydrogen bonds : angle 4.21859 ( 1518) covalent geometry : bond 0.00376 ( 8836) covalent geometry : angle 0.54965 (12036) *********************** 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 75 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 57 time to evaluate : 0.907 Fit side-chains REVERT: A 406 LEU cc_start: 0.9173 (tt) cc_final: 0.8960 (tp) REVERT: A 554 ASN cc_start: 0.8388 (t0) cc_final: 0.8113 (t0) REVERT: B 554 ASN cc_start: 0.8380 (t0) cc_final: 0.8110 (t0) outliers start: 18 outliers final: 12 residues processed: 65 average time/residue: 0.1859 time to fit residues: 18.1044 Evaluate side-chains 67 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.962 ------------------------------------------------------------------------------- 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 843 CYS 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 780 LEU 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 91 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 80 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 chunk 54 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 447 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.071221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.060373 restraints weight = 25379.265| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 2.95 r_work: 0.2828 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2753 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= 0.129 Angle : 0.524 6.442 12048 Z= 0.255 Chirality : 0.038 0.137 1436 Planarity : 0.005 0.051 1404 Dihedral : 10.305 120.545 1875 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.45 % Allowed : 11.72 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.26), residues: 1024 helix: 1.91 (0.20), residues: 710 sheet: None (None), residues: 0 loop : -0.85 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 492 HIS 0.001 0.000 HIS A 547 PHE 0.012 0.001 PHE A 411 TYR 0.014 0.001 TYR A 824 ARG 0.003 0.000 ARG B 656 Details of bonding type rmsd link_NAG-ASN : bond 0.00082 ( 2) link_NAG-ASN : angle 1.00770 ( 6) link_BETA1-4 : bond 0.00349 ( 2) link_BETA1-4 : angle 0.73434 ( 6) hydrogen bonds : bond 0.03723 ( 518) hydrogen bonds : angle 4.08566 ( 1518) covalent geometry : bond 0.00305 ( 8836) covalent geometry : angle 0.52365 (12036) *********************** 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 74 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 1.083 Fit side-chains REVERT: A 406 LEU cc_start: 0.9158 (tt) cc_final: 0.8950 (tp) REVERT: A 554 ASN cc_start: 0.8350 (t0) cc_final: 0.8083 (t0) REVERT: B 554 ASN cc_start: 0.8342 (t0) cc_final: 0.7866 (t0) outliers start: 13 outliers final: 10 residues processed: 68 average time/residue: 0.1828 time to fit residues: 18.7024 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 : 0.973 ------------------------------------------------------------------------------- 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 843 CYS 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 843 CYS Chi-restraints excluded: chain B residue 873 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 16 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.070832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.059977 restraints weight = 25225.434| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 2.94 r_work: 0.2823 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8840 Z= 0.131 Angle : 0.532 7.287 12048 Z= 0.257 Chirality : 0.038 0.141 1436 Planarity : 0.005 0.050 1404 Dihedral : 9.569 93.463 1874 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.79 % Allowed : 11.61 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.27), residues: 1024 helix: 1.99 (0.20), residues: 710 sheet: None (None), residues: 0 loop : -0.76 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 492 HIS 0.001 0.000 HIS B 547 PHE 0.012 0.001 PHE A 411 TYR 0.015 0.001 TYR A 824 ARG 0.005 0.000 ARG A 603 Details of bonding type rmsd link_NAG-ASN : bond 0.00056 ( 2) link_NAG-ASN : angle 1.05738 ( 6) link_BETA1-4 : bond 0.00432 ( 2) link_BETA1-4 : angle 0.76499 ( 6) hydrogen bonds : bond 0.03663 ( 518) hydrogen bonds : angle 4.03109 ( 1518) covalent geometry : bond 0.00310 ( 8836) covalent geometry : angle 0.53187 (12036) *********************** 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 77 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 0.988 Fit side-chains REVERT: A 406 LEU cc_start: 0.9189 (tt) cc_final: 0.8979 (tp) REVERT: A 554 ASN cc_start: 0.8350 (t0) cc_final: 0.7885 (t0) REVERT: B 554 ASN cc_start: 0.8355 (t0) cc_final: 0.7897 (t0) outliers start: 16 outliers final: 15 residues processed: 71 average time/residue: 0.1759 time to fit residues: 18.9756 Evaluate side-chains 69 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 0.899 ------------------------------------------------------------------------------- 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 780 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 23 optimal weight: 4.9990 chunk 22 optimal weight: 0.5980 chunk 98 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 100 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 69 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3211 r_free = 0.3211 target = 0.071151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.060360 restraints weight = 25379.032| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 2.93 r_work: 0.2825 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8840 Z= 0.125 Angle : 0.522 7.313 12048 Z= 0.252 Chirality : 0.038 0.151 1436 Planarity : 0.005 0.050 1404 Dihedral : 9.128 87.123 1874 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.90 % Allowed : 12.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.27), residues: 1024 helix: 1.96 (0.20), residues: 722 sheet: None (None), residues: 0 loop : -0.66 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 492 HIS 0.001 0.000 HIS B 547 PHE 0.010 0.001 PHE B 411 TYR 0.014 0.001 TYR A 824 ARG 0.004 0.000 ARG B 603 Details of bonding type rmsd link_NAG-ASN : bond 0.00069 ( 2) link_NAG-ASN : angle 1.07872 ( 6) link_BETA1-4 : bond 0.00319 ( 2) link_BETA1-4 : angle 0.68085 ( 6) hydrogen bonds : bond 0.03627 ( 518) hydrogen bonds : angle 3.99717 ( 1518) covalent geometry : bond 0.00296 ( 8836) covalent geometry : angle 0.52185 (12036) *********************** 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 73 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 56 time to evaluate : 1.022 Fit side-chains REVERT: A 406 LEU cc_start: 0.9162 (tt) cc_final: 0.8952 (tp) REVERT: A 554 ASN cc_start: 0.8360 (t0) cc_final: 0.7904 (t0) REVERT: B 554 ASN cc_start: 0.8366 (t0) cc_final: 0.7913 (t0) outliers start: 17 outliers final: 13 residues processed: 66 average time/residue: 0.1799 time to fit residues: 17.8796 Evaluate side-chains 67 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 0.939 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 4 optimal weight: 1.9990 chunk 11 optimal weight: 0.0030 chunk 23 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 92 optimal weight: 0.9990 chunk 95 optimal weight: 7.9990 chunk 30 optimal weight: 0.8980 overall best weight: 0.6994 ------------------------------------------------------------------------------- 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 = 0.3222 r_free = 0.3222 target = 0.071505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.060581 restraints weight = 25799.641| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 2.98 r_work: 0.2830 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.3133 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= 0.123 Angle : 0.538 8.045 12048 Z= 0.257 Chirality : 0.039 0.239 1436 Planarity : 0.005 0.050 1404 Dihedral : 8.933 87.019 1874 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.79 % Allowed : 12.28 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.27), residues: 1024 helix: 1.93 (0.20), residues: 722 sheet: None (None), residues: 0 loop : -0.53 (0.35), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 492 HIS 0.001 0.000 HIS A 703 PHE 0.010 0.001 PHE A 411 TYR 0.014 0.001 TYR A 824 ARG 0.003 0.000 ARG B 603 Details of bonding type rmsd link_NAG-ASN : bond 0.00042 ( 2) link_NAG-ASN : angle 1.11510 ( 6) link_BETA1-4 : bond 0.00324 ( 2) link_BETA1-4 : angle 0.72198 ( 6) hydrogen bonds : bond 0.03632 ( 518) hydrogen bonds : angle 4.01811 ( 1518) covalent geometry : bond 0.00290 ( 8836) covalent geometry : angle 0.53780 (12036) *********************** 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 73 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 57 time to evaluate : 0.968 Fit side-chains REVERT: A 406 LEU cc_start: 0.9184 (tt) cc_final: 0.8979 (tp) REVERT: A 554 ASN cc_start: 0.8362 (t0) cc_final: 0.7910 (t0) REVERT: A 721 MET cc_start: 0.8679 (OUTLIER) cc_final: 0.8042 (mpp) REVERT: B 554 ASN cc_start: 0.8357 (t0) cc_final: 0.7911 (t0) outliers start: 16 outliers final: 14 residues processed: 67 average time/residue: 0.1805 time to fit residues: 18.2133 Evaluate side-chains 72 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 57 time to evaluate : 0.960 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 84 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 44 optimal weight: 0.0570 chunk 22 optimal weight: 0.0070 chunk 95 optimal weight: 7.9990 chunk 85 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- 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 = 0.3228 r_free = 0.3228 target = 0.071901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.061149 restraints weight = 25234.570| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 2.94 r_work: 0.2843 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8840 Z= 0.118 Angle : 0.543 8.893 12048 Z= 0.258 Chirality : 0.039 0.237 1436 Planarity : 0.005 0.050 1404 Dihedral : 8.708 86.969 1874 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.79 % Allowed : 12.39 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.27), residues: 1024 helix: 2.06 (0.20), residues: 706 sheet: None (None), residues: 0 loop : -0.21 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 492 HIS 0.001 0.000 HIS A 703 PHE 0.010 0.001 PHE A 411 TYR 0.014 0.001 TYR A 824 ARG 0.004 0.000 ARG B 603 Details of bonding type rmsd link_NAG-ASN : bond 0.00054 ( 2) link_NAG-ASN : angle 1.15265 ( 6) link_BETA1-4 : bond 0.00291 ( 2) link_BETA1-4 : angle 0.72930 ( 6) hydrogen bonds : bond 0.03588 ( 518) hydrogen bonds : angle 4.03786 ( 1518) covalent geometry : bond 0.00278 ( 8836) covalent geometry : angle 0.54221 (12036) *********************** 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 74 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 58 time to evaluate : 0.998 Fit side-chains REVERT: A 554 ASN cc_start: 0.8374 (t0) cc_final: 0.7922 (t0) REVERT: A 721 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.7956 (mpp) REVERT: B 554 ASN cc_start: 0.8359 (t0) cc_final: 0.7909 (t0) outliers start: 16 outliers final: 13 residues processed: 67 average time/residue: 0.1825 time to fit residues: 18.4402 Evaluate side-chains 72 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.998 ------------------------------------------------------------------------------- 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 721 MET Chi-restraints excluded: chain A residue 833 MET 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 42 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 chunk 54 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 = 0.3211 r_free = 0.3211 target = 0.071232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.060410 restraints weight = 25550.683| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 2.95 r_work: 0.2827 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8840 Z= 0.138 Angle : 0.563 8.970 12048 Z= 0.266 Chirality : 0.039 0.175 1436 Planarity : 0.005 0.050 1404 Dihedral : 8.563 86.635 1874 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.56 % Allowed : 12.61 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.27), residues: 1024 helix: 2.04 (0.20), residues: 706 sheet: None (None), residues: 0 loop : -0.14 (0.36), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 492 HIS 0.002 0.001 HIS B 819 PHE 0.010 0.001 PHE A 411 TYR 0.014 0.001 TYR A 824 ARG 0.009 0.000 ARG A 603 Details of bonding type rmsd link_NAG-ASN : bond 0.00040 ( 2) link_NAG-ASN : angle 1.13576 ( 6) link_BETA1-4 : bond 0.00388 ( 2) link_BETA1-4 : angle 0.87677 ( 6) hydrogen bonds : bond 0.03682 ( 518) hydrogen bonds : angle 4.05647 ( 1518) covalent geometry : bond 0.00329 ( 8836) covalent geometry : angle 0.56255 (12036) ********************** 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 71 residues out of total 898 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 1.140 Fit side-chains REVERT: A 554 ASN cc_start: 0.8380 (t0) cc_final: 0.7928 (t0) REVERT: A 603 ARG cc_start: 0.8515 (ttp80) cc_final: 0.8233 (mtm-85) REVERT: A 721 MET cc_start: 0.8602 (OUTLIER) cc_final: 0.7929 (mpp) REVERT: B 554 ASN cc_start: 0.8358 (t0) cc_final: 0.7912 (t0) REVERT: B 603 ARG cc_start: 0.8498 (ttp80) cc_final: 0.8224 (mtm-85) outliers start: 14 outliers final: 13 residues processed: 65 average time/residue: 0.2100 time to fit residues: 20.5733 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 : 1.024 ------------------------------------------------------------------------------- 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 721 MET Chi-restraints excluded: chain A residue 833 MET 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 873 LEU 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 20 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 88 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 23 optimal weight: 6.9990 chunk 78 optimal weight: 0.0370 chunk 33 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- 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 = 0.3229 r_free = 0.3229 target = 0.072002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.061307 restraints weight = 25406.105| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 2.91 r_work: 0.2842 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8840 Z= 0.116 Angle : 0.551 8.854 12048 Z= 0.260 Chirality : 0.038 0.141 1436 Planarity : 0.005 0.049 1404 Dihedral : 8.440 86.952 1874 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.67 % Allowed : 12.28 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.27), residues: 1024 helix: 2.10 (0.20), residues: 706 sheet: None (None), residues: 0 loop : -0.11 (0.36), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 492 HIS 0.001 0.000 HIS B 703 PHE 0.010 0.001 PHE A 411 TYR 0.014 0.001 TYR A 824 ARG 0.007 0.000 ARG A 603 Details of bonding type rmsd link_NAG-ASN : bond 0.00057 ( 2) link_NAG-ASN : angle 1.17781 ( 6) link_BETA1-4 : bond 0.00366 ( 2) link_BETA1-4 : angle 0.81339 ( 6) hydrogen bonds : bond 0.03538 ( 518) hydrogen bonds : angle 3.99831 ( 1518) covalent geometry : bond 0.00270 ( 8836) covalent geometry : angle 0.55026 (12036) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3228.37 seconds wall clock time: 57 minutes 20.37 seconds (3440.37 seconds total)