Starting phenix.real_space_refine on Fri May 16 09:32:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z27_39743/05_2025/8z27_39743.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z27_39743/05_2025/8z27_39743.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z27_39743/05_2025/8z27_39743.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z27_39743/05_2025/8z27_39743.map" model { file = "/net/cci-nas-00/data/ceres_data/8z27_39743/05_2025/8z27_39743.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z27_39743/05_2025/8z27_39743.cif" } resolution = 2.86 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= 0.001 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6946 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 31 5.16 5 C 5481 2.51 5 N 1418 2.21 5 O 1666 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 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: 8596 Number of models: 1 Model: "" Number of chains: 8 Chain: "a" Number of atoms: 1118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1118 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 4, 'TRANS': 137} Chain breaks: 2 Chain: "b" Number of atoms: 7292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 905, 7292 Classifications: {'peptide': 905} Link IDs: {'PTRANS': 43, 'TRANS': 861} Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" 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: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.33, per 1000 atoms: 0.62 Number of scatterers: 8596 At special positions: 0 Unit cell: (97.98, 124.2, 92.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 31 16.00 O 1666 8.00 N 1418 7.00 C 5481 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS a 72 " - pdb=" SG CYS a 131 " distance=2.03 Simple disulfide: pdb=" SG CYS a 86 " - pdb=" SG CYS a 99 " distance=2.03 Simple disulfide: pdb=" SG CYS a 114 " - pdb=" SG CYS a 141 " distance=2.03 Simple disulfide: pdb=" SG CYS b 769 " - pdb=" SG CYS b 776 " distance=2.04 Simple disulfide: pdb=" SG CYS b 806 " - pdb=" SG CYS b 842 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG A 2 " - " BMA A 3 " " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " BETA1-6 " NAG D 1 " - " FUC D 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A 1 " - " ASN a 58 " " NAG B 1 " - " ASN b 533 " " NAG C 1 " - " ASN b 633 " " NAG D 1 " - " ASN b 747 " " NAG E 1 " - " ASN b 689 " " NAG a 201 " - " ASN a 98 " Time building additional restraints: 2.23 Conformation dependent library (CDL) restraints added in 905.8 milliseconds 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2004 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 12 sheets defined 45.0% alpha, 14.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'a' and resid 100 through 104 Processing helix chain 'b' and resid 220 through 227 removed outlier: 4.490A pdb=" N ARG b 224 " --> pdb=" O ALA b 220 " (cutoff:3.500A) Processing helix chain 'b' and resid 311 through 318 Processing helix chain 'b' and resid 320 through 339 removed outlier: 4.037A pdb=" N GLY b 328 " --> pdb=" O LEU b 324 " (cutoff:3.500A) Proline residue: b 329 - end of helix Processing helix chain 'b' and resid 370 through 374 Processing helix chain 'b' and resid 381 through 400 removed outlier: 3.783A pdb=" N TRP b 400 " --> pdb=" O LEU b 396 " (cutoff:3.500A) Processing helix chain 'b' and resid 409 through 411 No H-bonds generated for 'chain 'b' and resid 409 through 411' Processing helix chain 'b' and resid 412 through 432 Processing helix chain 'b' and resid 436 through 445 removed outlier: 4.275A pdb=" N VAL b 442 " --> pdb=" O LYS b 438 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N LEU b 443 " --> pdb=" O ASP b 439 " (cutoff:3.500A) Processing helix chain 'b' and resid 445 through 455 removed outlier: 3.507A pdb=" N ALA b 451 " --> pdb=" O TYR b 447 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL b 452 " --> pdb=" O ARG b 448 " (cutoff:3.500A) Processing helix chain 'b' and resid 470 through 478 removed outlier: 3.907A pdb=" N PHE b 478 " --> pdb=" O ILE b 474 " (cutoff:3.500A) Processing helix chain 'b' and resid 479 through 497 removed outlier: 3.559A pdb=" N GLY b 486 " --> pdb=" O SER b 482 " (cutoff:3.500A) Processing helix chain 'b' and resid 499 through 513 Processing helix chain 'b' and resid 519 through 534 removed outlier: 3.817A pdb=" N LEU b 523 " --> pdb=" O ILE b 519 " (cutoff:3.500A) Processing helix chain 'b' and resid 542 through 553 removed outlier: 3.568A pdb=" N ARG b 549 " --> pdb=" O ALA b 545 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TRP b 550 " --> pdb=" O ILE b 546 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN b 553 " --> pdb=" O ARG b 549 " (cutoff:3.500A) Processing helix chain 'b' and resid 631 through 635 removed outlier: 3.867A pdb=" N THR b 635 " --> pdb=" O LEU b 632 " (cutoff:3.500A) Processing helix chain 'b' and resid 643 through 657 Processing helix chain 'b' and resid 662 through 679 Processing helix chain 'b' and resid 683 through 693 removed outlier: 3.559A pdb=" N ALA b 687 " --> pdb=" O PRO b 683 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N PHE b 693 " --> pdb=" O ASN b 689 " (cutoff:3.500A) Processing helix chain 'b' and resid 694 through 696 No H-bonds generated for 'chain 'b' and resid 694 through 696' Processing helix chain 'b' and resid 699 through 718 removed outlier: 3.632A pdb=" N TRP b 703 " --> pdb=" O GLU b 699 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N TYR b 712 " --> pdb=" O SER b 708 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N PHE b 713 " --> pdb=" O SER b 709 " (cutoff:3.500A) Processing helix chain 'b' and resid 722 through 745 Proline residue: b 736 - end of helix Processing helix chain 'b' and resid 754 through 771 Processing helix chain 'b' and resid 773 through 789 removed outlier: 3.673A pdb=" N LYS b 777 " --> pdb=" O VAL b 773 " (cutoff:3.500A) Processing helix chain 'b' and resid 800 through 812 Processing helix chain 'b' and resid 813 through 827 removed outlier: 3.546A pdb=" N TRP b 817 " --> pdb=" O GLY b 813 " (cutoff:3.500A) Processing helix chain 'b' and resid 829 through 841 removed outlier: 4.024A pdb=" N ALA b 841 " --> pdb=" O ARG b 837 " (cutoff:3.500A) Processing helix chain 'b' and resid 845 through 858 removed outlier: 4.198A pdb=" N LEU b 857 " --> pdb=" O LEU b 853 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ASN b 858 " --> pdb=" O SER b 854 " (cutoff:3.500A) Processing helix chain 'b' and resid 863 through 877 removed outlier: 4.145A pdb=" N ILE b 868 " --> pdb=" O LYS b 864 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N SER b 869 " --> pdb=" O GLN b 865 " (cutoff:3.500A) Processing helix chain 'b' and resid 877 through 891 removed outlier: 4.497A pdb=" N SER b 882 " --> pdb=" O VAL b 878 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LEU b 883 " --> pdb=" O ILE b 879 " (cutoff:3.500A) Processing helix chain 'b' and resid 891 through 900 Processing helix chain 'b' and resid 905 through 913 Processing helix chain 'b' and resid 919 through 933 Processing helix chain 'b' and resid 940 through 962 removed outlier: 4.675A pdb=" N ALA b 944 " --> pdb=" O SER b 940 " (cutoff:3.500A) Processing helix chain 'b' and resid 962 through 977 Processing sheet with id=AA1, first strand: chain 'a' and resid 51 through 53 removed outlier: 3.882A pdb=" N ILE a 52 " --> pdb=" O LYS a 44 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR a 38 " --> pdb=" O THR a 60 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'a' and resid 51 through 53 removed outlier: 3.882A pdb=" N ILE a 52 " --> pdb=" O LYS a 44 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG a 97 " --> pdb=" O SER a 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 106 through 109 removed outlier: 3.516A pdb=" N THR a 106 " --> pdb=" O ARG a 148 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ALA a 147 " --> pdb=" O VAL a 155 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N VAL a 155 " --> pdb=" O ALA a 147 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'b' and resid 143 through 146 removed outlier: 3.870A pdb=" N GLU b 183 " --> pdb=" O ARG b 146 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N THR b 118 " --> pdb=" O PRO b 88 " (cutoff:3.500A) removed outlier: 9.148A pdb=" N THR b 238 " --> pdb=" O ILE b 87 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N SER b 89 " --> pdb=" O THR b 238 " (cutoff:3.500A) removed outlier: 8.306A pdb=" N ASN b 240 " --> pdb=" O SER b 89 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N TYR b 91 " --> pdb=" O ASN b 240 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N THR b 242 " --> pdb=" O TYR b 91 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N VAL b 93 " --> pdb=" O THR b 242 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ILE b 244 " --> pdb=" O VAL b 93 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N LEU b 95 " --> pdb=" O ILE b 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'b' and resid 125 through 128 Processing sheet with id=AA6, first strand: chain 'b' and resid 199 through 206 Processing sheet with id=AA7, first strand: chain 'b' and resid 250 through 253 Processing sheet with id=AA8, first strand: chain 'b' and resid 294 through 295 removed outlier: 6.877A pdb=" N TRP b 309 " --> pdb=" O ALA b 351 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N ASP b 348 " --> pdb=" O VAL b 366 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N TYR b 368 " --> pdb=" O ASP b 348 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ILE b 350 " --> pdb=" O TYR b 368 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'b' and resid 401 through 402 Processing sheet with id=AB1, first strand: chain 'b' and resid 614 through 616 removed outlier: 7.576A pdb=" N ASN b 641 " --> pdb=" O PRO b 557 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N VAL b 559 " --> pdb=" O ASN b 641 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'b' and resid 593 through 595 Processing sheet with id=AB3, first strand: chain 'b' and resid 602 through 603 380 hydrogen bonds defined for protein. 1101 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: 2.67 Time building geometry restraints manager: 2.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2033 1.33 - 1.45: 2000 1.45 - 1.57: 4727 1.57 - 1.69: 1 1.69 - 1.81: 50 Bond restraints: 8811 Sorted by residual: bond pdb=" C THR b 216 " pdb=" N GLN b 217 " ideal model delta sigma weight residual 1.330 1.394 -0.064 1.39e-02 5.18e+03 2.13e+01 bond pdb=" CA GLN a 64 " pdb=" C GLN a 64 " ideal model delta sigma weight residual 1.525 1.486 0.038 1.28e-02 6.10e+03 8.96e+00 bond pdb=" C TRP b 958 " pdb=" O TRP b 958 " ideal model delta sigma weight residual 1.237 1.205 0.031 1.17e-02 7.31e+03 7.18e+00 bond pdb=" CA ASN a 128 " pdb=" C ASN a 128 " ideal model delta sigma weight residual 1.523 1.488 0.036 1.34e-02 5.57e+03 7.03e+00 bond pdb=" CA MET b 609 " pdb=" C MET b 609 " ideal model delta sigma weight residual 1.528 1.500 0.028 1.08e-02 8.57e+03 6.64e+00 ... (remaining 8806 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 11066 2.49 - 4.98: 775 4.98 - 7.47: 132 7.47 - 9.95: 26 9.95 - 12.44: 9 Bond angle restraints: 12008 Sorted by residual: angle pdb=" N TYR a 48 " pdb=" CA TYR a 48 " pdb=" C TYR a 48 " ideal model delta sigma weight residual 113.17 101.60 11.57 1.26e+00 6.30e-01 8.43e+01 angle pdb=" N TRP b 748 " pdb=" CA TRP b 748 " pdb=" C TRP b 748 " ideal model delta sigma weight residual 112.24 122.09 -9.85 1.28e+00 6.10e-01 5.92e+01 angle pdb=" N ASN a 67 " pdb=" CA ASN a 67 " pdb=" C ASN a 67 " ideal model delta sigma weight residual 108.73 120.84 -12.11 1.63e+00 3.76e-01 5.52e+01 angle pdb=" N GLY a 47 " pdb=" CA GLY a 47 " pdb=" C GLY a 47 " ideal model delta sigma weight residual 114.92 105.55 9.37 1.30e+00 5.92e-01 5.20e+01 angle pdb=" N THR b 844 " pdb=" CA THR b 844 " pdb=" C THR b 844 " ideal model delta sigma weight residual 111.36 119.15 -7.79 1.09e+00 8.42e-01 5.11e+01 ... (remaining 12003 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.37: 4394 21.37 - 42.74: 606 42.74 - 64.10: 345 64.10 - 85.47: 44 85.47 - 106.84: 12 Dihedral angle restraints: 5401 sinusoidal: 2306 harmonic: 3095 Sorted by residual: dihedral pdb=" N ARG b 307 " pdb=" C ARG b 307 " pdb=" CA ARG b 307 " pdb=" CB ARG b 307 " ideal model delta harmonic sigma weight residual 122.80 141.91 -19.11 0 2.50e+00 1.60e-01 5.84e+01 dihedral pdb=" C ARG b 307 " pdb=" N ARG b 307 " pdb=" CA ARG b 307 " pdb=" CB ARG b 307 " ideal model delta harmonic sigma weight residual -122.60 -141.56 18.96 0 2.50e+00 1.60e-01 5.75e+01 dihedral pdb=" C VAL a 80 " pdb=" N VAL a 80 " pdb=" CA VAL a 80 " pdb=" CB VAL a 80 " ideal model delta harmonic sigma weight residual -122.00 -139.81 17.81 0 2.50e+00 1.60e-01 5.07e+01 ... (remaining 5398 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.160: 1210 0.160 - 0.319: 147 0.319 - 0.479: 16 0.479 - 0.639: 5 0.639 - 0.798: 1 Chirality restraints: 1379 Sorted by residual: chirality pdb=" C1 BMA A 3 " pdb=" O4 NAG A 2 " pdb=" C2 BMA A 3 " pdb=" O5 BMA A 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-02 2.50e+03 1.10e+02 chirality pdb=" C1 NAG A 2 " pdb=" O4 NAG A 1 " pdb=" C2 NAG A 2 " pdb=" O5 NAG A 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-02 2.50e+03 9.25e+01 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 -2.21 -0.19 2.00e-02 2.50e+03 9.12e+01 ... (remaining 1376 not shown) Planarity restraints: 1521 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 2 " 0.358 2.00e-02 2.50e+03 3.08e-01 1.18e+03 pdb=" C7 NAG B 2 " -0.087 2.00e-02 2.50e+03 pdb=" C8 NAG B 2 " 0.124 2.00e-02 2.50e+03 pdb=" N2 NAG B 2 " -0.547 2.00e-02 2.50e+03 pdb=" O7 NAG B 2 " 0.152 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG a 201 " -0.309 2.00e-02 2.50e+03 2.60e-01 8.44e+02 pdb=" C7 NAG a 201 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG a 201 " -0.191 2.00e-02 2.50e+03 pdb=" N2 NAG a 201 " 0.446 2.00e-02 2.50e+03 pdb=" O7 NAG a 201 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " 0.196 2.00e-02 2.50e+03 1.62e-01 3.27e+02 pdb=" C7 NAG D 1 " -0.054 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " 0.143 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " -0.261 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " -0.023 2.00e-02 2.50e+03 ... (remaining 1518 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2515 2.81 - 3.33: 8038 3.33 - 3.86: 16703 3.86 - 4.38: 19679 4.38 - 4.90: 30103 Nonbonded interactions: 77038 Sorted by model distance: nonbonded pdb=" CG1 VAL b 262 " pdb=" OG1 THR b 265 " model vdw 2.290 3.460 nonbonded pdb=" CD1 ILE a 59 " pdb=" CD2 LEU a 61 " model vdw 2.312 3.880 nonbonded pdb=" CB VAL b 262 " pdb=" OG1 THR b 265 " model vdw 2.383 3.470 nonbonded pdb=" N TYR a 48 " pdb=" N GLY a 49 " model vdw 2.399 2.560 nonbonded pdb=" N LEU a 56 " pdb=" NH2 ARG a 157 " model vdw 2.419 3.200 ... (remaining 77033 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 'B' selection = chain 'C' selection = chain 'E' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.450 Find NCS groups from input model: 0.080 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:13.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4785 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 : 0.007 0.064 8830 Z= 0.534 Angle : 1.413 12.443 12060 Z= 0.942 Chirality : 0.109 0.798 1379 Planarity : 0.016 0.308 1515 Dihedral : 24.392 106.837 3382 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.38 % Allowed : 1.44 % Favored : 98.17 % Rotamer: Outliers : 32.69 % Allowed : 18.16 % Favored : 49.15 % Cbeta Deviations : 0.90 % 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: 3.16 (0.25), residues: 1039 helix: 3.98 (0.22), residues: 426 sheet: 1.25 (0.37), residues: 186 loop : 0.52 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP b 969 HIS 0.005 0.001 HIS b 394 PHE 0.032 0.003 PHE b 496 TYR 0.022 0.002 TYR b 368 ARG 0.005 0.001 ARG b 142 Details of bonding type rmsd link_NAG-ASN : bond 0.00501 ( 6) link_NAG-ASN : angle 2.80140 ( 18) link_BETA1-4 : bond 0.00293 ( 7) link_BETA1-4 : angle 1.19858 ( 21) hydrogen bonds : bond 0.21957 ( 379) hydrogen bonds : angle 7.64993 ( 1101) link_BETA1-6 : bond 0.00104 ( 1) link_BETA1-6 : angle 0.82342 ( 3) SS BOND : bond 0.00452 ( 5) SS BOND : angle 0.79232 ( 10) covalent geometry : bond 0.00732 ( 8811) covalent geometry : angle 1.41071 (12008) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 306 poor density : 168 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 479 ASP cc_start: 0.5986 (OUTLIER) cc_final: 0.5298 (p0) outliers start: 306 outliers final: 43 residues processed: 415 average time/residue: 0.9079 time to fit residues: 406.6458 Evaluate side-chains 121 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 77 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 59 ILE Chi-restraints excluded: chain a residue 79 SER Chi-restraints excluded: chain a residue 101 ASP Chi-restraints excluded: chain a residue 111 THR Chi-restraints excluded: chain a residue 120 LYS Chi-restraints excluded: chain a residue 121 LEU Chi-restraints excluded: chain a residue 129 LYS Chi-restraints excluded: chain a residue 132 LEU Chi-restraints excluded: chain a residue 137 VAL Chi-restraints excluded: chain a residue 148 ARG Chi-restraints excluded: chain a residue 149 THR Chi-restraints excluded: chain a residue 159 LEU Chi-restraints excluded: chain a residue 165 GLU Chi-restraints excluded: chain a residue 170 VAL Chi-restraints excluded: chain b residue 85 THR Chi-restraints excluded: chain b residue 104 ASN Chi-restraints excluded: chain b residue 143 VAL Chi-restraints excluded: chain b residue 164 VAL Chi-restraints excluded: chain b residue 168 LEU Chi-restraints excluded: chain b residue 169 VAL Chi-restraints excluded: chain b residue 182 TYR Chi-restraints excluded: chain b residue 187 LYS Chi-restraints excluded: chain b residue 250 VAL Chi-restraints excluded: chain b residue 253 SER Chi-restraints excluded: chain b residue 258 ARG Chi-restraints excluded: chain b residue 265 THR Chi-restraints excluded: chain b residue 273 THR Chi-restraints excluded: chain b residue 326 VAL Chi-restraints excluded: chain b residue 442 VAL Chi-restraints excluded: chain b residue 479 ASP Chi-restraints excluded: chain b residue 483 TYR Chi-restraints excluded: chain b residue 544 ASN Chi-restraints excluded: chain b residue 561 VAL Chi-restraints excluded: chain b residue 591 TRP Chi-restraints excluded: chain b residue 690 SER Chi-restraints excluded: chain b residue 756 THR Chi-restraints excluded: chain b residue 789 LYS Chi-restraints excluded: chain b residue 802 SER Chi-restraints excluded: chain b residue 838 SER Chi-restraints excluded: chain b residue 864 LYS Chi-restraints excluded: chain b residue 876 SER Chi-restraints excluded: chain b residue 910 ILE Chi-restraints excluded: chain b residue 958 TRP Chi-restraints excluded: chain b residue 961 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 49 optimal weight: 5.9990 chunk 60 optimal weight: 20.0000 chunk 94 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 93 ASN a 154 GLN b 104 ASN ** b 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 171 HIS b 179 ASN b 295 ASN b 356 ASN b 399 GLN b 403 ASN b 733 GLN ** b 740 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 889 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.103096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.077377 restraints weight = 34809.625| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 4.77 r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.4324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 8830 Z= 0.262 Angle : 0.878 13.137 12060 Z= 0.463 Chirality : 0.052 0.264 1379 Planarity : 0.007 0.058 1515 Dihedral : 11.989 66.891 1499 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 19.84 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.41 % Favored : 97.50 % Rotamer: Outliers : 11.00 % Allowed : 28.85 % Favored : 60.15 % 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: 1.29 (0.25), residues: 1039 helix: 1.88 (0.23), residues: 441 sheet: 0.68 (0.37), residues: 183 loop : -0.10 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP b 892 HIS 0.009 0.002 HIS a 83 PHE 0.028 0.003 PHE b 784 TYR 0.026 0.002 TYR a 71 ARG 0.007 0.001 ARG b 549 Details of bonding type rmsd link_NAG-ASN : bond 0.00534 ( 6) link_NAG-ASN : angle 2.64993 ( 18) link_BETA1-4 : bond 0.00392 ( 7) link_BETA1-4 : angle 1.69186 ( 21) hydrogen bonds : bond 0.08157 ( 379) hydrogen bonds : angle 6.51617 ( 1101) link_BETA1-6 : bond 0.00239 ( 1) link_BETA1-6 : angle 1.49475 ( 3) SS BOND : bond 0.00689 ( 5) SS BOND : angle 1.48519 ( 10) covalent geometry : bond 0.00573 ( 8811) covalent geometry : angle 0.86938 (12008) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 85 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 118 PHE cc_start: 0.8802 (m-80) cc_final: 0.8466 (m-80) REVERT: a 128 ASN cc_start: 0.9416 (t0) cc_final: 0.9173 (m-40) REVERT: b 146 ARG cc_start: 0.1087 (OUTLIER) cc_final: 0.0855 (pmt170) REVERT: b 200 TYR cc_start: 0.8309 (p90) cc_final: 0.7890 (p90) REVERT: b 315 MET cc_start: 0.6909 (mmm) cc_final: 0.6678 (mmp) REVERT: b 449 VAL cc_start: 0.9605 (t) cc_final: 0.9390 (p) REVERT: b 675 ASP cc_start: 0.8600 (m-30) cc_final: 0.8273 (t70) REVERT: b 775 LYS cc_start: 0.6594 (OUTLIER) cc_final: 0.6120 (mtpp) REVERT: b 916 ARG cc_start: 0.8693 (OUTLIER) cc_final: 0.7934 (ttp-170) REVERT: b 958 TRP cc_start: 0.4734 (OUTLIER) cc_final: 0.3490 (t-100) outliers start: 103 outliers final: 40 residues processed: 171 average time/residue: 0.8406 time to fit residues: 156.9761 Evaluate side-chains 110 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 66 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 31 THR Chi-restraints excluded: chain a residue 55 THR Chi-restraints excluded: chain a residue 78 PHE Chi-restraints excluded: chain a residue 79 SER Chi-restraints excluded: chain a residue 97 ARG Chi-restraints excluded: chain a residue 111 THR Chi-restraints excluded: chain a residue 119 ASP Chi-restraints excluded: chain a residue 121 LEU Chi-restraints excluded: chain a residue 132 LEU Chi-restraints excluded: chain a residue 137 VAL Chi-restraints excluded: chain a residue 149 THR Chi-restraints excluded: chain a residue 165 GLU Chi-restraints excluded: chain b residue 85 THR Chi-restraints excluded: chain b residue 89 SER Chi-restraints excluded: chain b residue 108 THR Chi-restraints excluded: chain b residue 130 SER Chi-restraints excluded: chain b residue 146 ARG Chi-restraints excluded: chain b residue 164 VAL Chi-restraints excluded: chain b residue 168 LEU Chi-restraints excluded: chain b residue 181 GLN Chi-restraints excluded: chain b residue 187 LYS Chi-restraints excluded: chain b residue 205 THR Chi-restraints excluded: chain b residue 215 THR Chi-restraints excluded: chain b residue 236 LYS Chi-restraints excluded: chain b residue 250 VAL Chi-restraints excluded: chain b residue 273 THR Chi-restraints excluded: chain b residue 326 VAL Chi-restraints excluded: chain b residue 479 ASP Chi-restraints excluded: chain b residue 544 ASN Chi-restraints excluded: chain b residue 561 VAL Chi-restraints excluded: chain b residue 591 TRP Chi-restraints excluded: chain b residue 623 THR Chi-restraints excluded: chain b residue 649 LYS Chi-restraints excluded: chain b residue 682 VAL Chi-restraints excluded: chain b residue 775 LYS Chi-restraints excluded: chain b residue 809 ILE Chi-restraints excluded: chain b residue 831 ASN Chi-restraints excluded: chain b residue 844 THR Chi-restraints excluded: chain b residue 864 LYS Chi-restraints excluded: chain b residue 876 SER Chi-restraints excluded: chain b residue 907 SER Chi-restraints excluded: chain b residue 913 VAL Chi-restraints excluded: chain b residue 916 ARG Chi-restraints excluded: chain b residue 958 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 92 optimal weight: 0.8980 chunk 49 optimal weight: 10.0000 chunk 100 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 20.0000 chunk 23 optimal weight: 40.0000 chunk 37 optimal weight: 10.0000 chunk 81 optimal weight: 1.9990 chunk 4 optimal weight: 8.9990 chunk 63 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 646 ASN b 680 GLN ** b 740 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 758 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.102800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.077178 restraints weight = 35050.217| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 4.72 r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.5189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8830 Z= 0.187 Angle : 0.748 9.818 12060 Z= 0.391 Chirality : 0.047 0.240 1379 Planarity : 0.005 0.046 1515 Dihedral : 8.882 58.381 1452 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 17.19 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.60 % Favored : 97.31 % Rotamer: Outliers : 7.69 % Allowed : 29.38 % Favored : 62.93 % 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: 0.73 (0.25), residues: 1039 helix: 1.41 (0.24), residues: 441 sheet: 0.03 (0.35), residues: 216 loop : -0.20 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP b 892 HIS 0.008 0.001 HIS a 83 PHE 0.022 0.002 PHE a 143 TYR 0.020 0.002 TYR b 284 ARG 0.009 0.001 ARG a 148 Details of bonding type rmsd link_NAG-ASN : bond 0.00302 ( 6) link_NAG-ASN : angle 1.96909 ( 18) link_BETA1-4 : bond 0.00385 ( 7) link_BETA1-4 : angle 1.66134 ( 21) hydrogen bonds : bond 0.06390 ( 379) hydrogen bonds : angle 6.06584 ( 1101) link_BETA1-6 : bond 0.00373 ( 1) link_BETA1-6 : angle 1.02231 ( 3) SS BOND : bond 0.00411 ( 5) SS BOND : angle 1.07321 ( 10) covalent geometry : bond 0.00412 ( 8811) covalent geometry : angle 0.74149 (12008) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 73 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 118 PHE cc_start: 0.8717 (m-80) cc_final: 0.8373 (m-80) REVERT: a 128 ASN cc_start: 0.9366 (t0) cc_final: 0.9120 (m-40) REVERT: b 200 TYR cc_start: 0.8173 (p90) cc_final: 0.7844 (p90) REVERT: b 252 LEU cc_start: 0.6916 (mt) cc_final: 0.6499 (mt) REVERT: b 281 MET cc_start: 0.6371 (ptp) cc_final: 0.5856 (ppp) REVERT: b 450 MET cc_start: 0.8659 (mmt) cc_final: 0.8421 (mmt) REVERT: b 479 ASP cc_start: 0.6448 (OUTLIER) cc_final: 0.5589 (p0) REVERT: b 490 LEU cc_start: 0.8769 (tp) cc_final: 0.8443 (mp) REVERT: b 675 ASP cc_start: 0.8597 (m-30) cc_final: 0.8319 (t70) REVERT: b 775 LYS cc_start: 0.6511 (OUTLIER) cc_final: 0.6297 (mtpp) outliers start: 72 outliers final: 33 residues processed: 134 average time/residue: 0.8305 time to fit residues: 121.9088 Evaluate side-chains 97 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 62 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 55 THR Chi-restraints excluded: chain a residue 78 PHE Chi-restraints excluded: chain a residue 79 SER Chi-restraints excluded: chain a residue 111 THR Chi-restraints excluded: chain a residue 113 THR Chi-restraints excluded: chain a residue 119 ASP Chi-restraints excluded: chain a residue 121 LEU Chi-restraints excluded: chain a residue 137 VAL Chi-restraints excluded: chain a residue 149 THR Chi-restraints excluded: chain a residue 159 LEU Chi-restraints excluded: chain a residue 165 GLU Chi-restraints excluded: chain b residue 85 THR Chi-restraints excluded: chain b residue 89 SER Chi-restraints excluded: chain b residue 130 SER Chi-restraints excluded: chain b residue 164 VAL Chi-restraints excluded: chain b residue 169 VAL Chi-restraints excluded: chain b residue 181 GLN Chi-restraints excluded: chain b residue 186 SER Chi-restraints excluded: chain b residue 205 THR Chi-restraints excluded: chain b residue 215 THR Chi-restraints excluded: chain b residue 308 ILE Chi-restraints excluded: chain b residue 326 VAL Chi-restraints excluded: chain b residue 479 ASP Chi-restraints excluded: chain b residue 494 SER Chi-restraints excluded: chain b residue 554 MET Chi-restraints excluded: chain b residue 561 VAL Chi-restraints excluded: chain b residue 575 LEU Chi-restraints excluded: chain b residue 591 TRP Chi-restraints excluded: chain b residue 649 LYS Chi-restraints excluded: chain b residue 682 VAL Chi-restraints excluded: chain b residue 775 LYS Chi-restraints excluded: chain b residue 803 THR Chi-restraints excluded: chain b residue 809 ILE Chi-restraints excluded: chain b residue 869 SER Chi-restraints excluded: chain b residue 876 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 103 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 26 optimal weight: 8.9990 chunk 97 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 44 optimal weight: 9.9990 chunk 15 optimal weight: 20.0000 chunk 1 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 171 HIS b 207 ASN b 297 GLN b 644 GLN ** b 740 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 793 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.099954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.074323 restraints weight = 35695.749| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 4.65 r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.5805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 8830 Z= 0.223 Angle : 0.739 9.549 12060 Z= 0.389 Chirality : 0.046 0.194 1379 Planarity : 0.006 0.047 1515 Dihedral : 7.310 56.982 1434 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 18.60 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.18 % Favored : 96.73 % Rotamer: Outliers : 6.73 % Allowed : 31.20 % Favored : 62.07 % 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: 0.35 (0.26), residues: 1039 helix: 1.02 (0.24), residues: 441 sheet: -0.04 (0.36), residues: 209 loop : -0.39 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP b 77 HIS 0.007 0.002 HIS b 671 PHE 0.019 0.002 PHE b 970 TYR 0.023 0.002 TYR b 712 ARG 0.007 0.001 ARG a 157 Details of bonding type rmsd link_NAG-ASN : bond 0.00522 ( 6) link_NAG-ASN : angle 2.02810 ( 18) link_BETA1-4 : bond 0.00259 ( 7) link_BETA1-4 : angle 1.41410 ( 21) hydrogen bonds : bond 0.06880 ( 379) hydrogen bonds : angle 5.98348 ( 1101) link_BETA1-6 : bond 0.00701 ( 1) link_BETA1-6 : angle 1.06114 ( 3) SS BOND : bond 0.00996 ( 5) SS BOND : angle 1.54240 ( 10) covalent geometry : bond 0.00497 ( 8811) covalent geometry : angle 0.73230 (12008) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 65 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 118 PHE cc_start: 0.8630 (m-80) cc_final: 0.8264 (m-80) REVERT: a 128 ASN cc_start: 0.9350 (t0) cc_final: 0.9051 (m-40) REVERT: b 200 TYR cc_start: 0.8183 (p90) cc_final: 0.7940 (p90) REVERT: b 479 ASP cc_start: 0.6498 (OUTLIER) cc_final: 0.5692 (p0) REVERT: b 490 LEU cc_start: 0.8838 (tp) cc_final: 0.8499 (mp) REVERT: b 675 ASP cc_start: 0.8627 (m-30) cc_final: 0.8372 (t70) REVERT: b 681 ILE cc_start: 0.8985 (OUTLIER) cc_final: 0.8771 (tp) outliers start: 63 outliers final: 37 residues processed: 121 average time/residue: 0.8199 time to fit residues: 109.2023 Evaluate side-chains 96 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 57 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 55 THR Chi-restraints excluded: chain a residue 70 VAL Chi-restraints excluded: chain a residue 78 PHE Chi-restraints excluded: chain a residue 79 SER Chi-restraints excluded: chain a residue 97 ARG Chi-restraints excluded: chain a residue 113 THR Chi-restraints excluded: chain a residue 119 ASP Chi-restraints excluded: chain a residue 121 LEU Chi-restraints excluded: chain a residue 137 VAL Chi-restraints excluded: chain a residue 141 CYS Chi-restraints excluded: chain a residue 149 THR Chi-restraints excluded: chain a residue 165 GLU Chi-restraints excluded: chain b residue 108 THR Chi-restraints excluded: chain b residue 130 SER Chi-restraints excluded: chain b residue 164 VAL Chi-restraints excluded: chain b residue 169 VAL Chi-restraints excluded: chain b residue 187 LYS Chi-restraints excluded: chain b residue 205 THR Chi-restraints excluded: chain b residue 213 LEU Chi-restraints excluded: chain b residue 215 THR Chi-restraints excluded: chain b residue 308 ILE Chi-restraints excluded: chain b residue 326 VAL Chi-restraints excluded: chain b residue 479 ASP Chi-restraints excluded: chain b residue 497 LEU Chi-restraints excluded: chain b residue 554 MET Chi-restraints excluded: chain b residue 561 VAL Chi-restraints excluded: chain b residue 575 LEU Chi-restraints excluded: chain b residue 591 TRP Chi-restraints excluded: chain b residue 628 VAL Chi-restraints excluded: chain b residue 681 ILE Chi-restraints excluded: chain b residue 682 VAL Chi-restraints excluded: chain b residue 766 SER Chi-restraints excluded: chain b residue 803 THR Chi-restraints excluded: chain b residue 809 ILE Chi-restraints excluded: chain b residue 831 ASN Chi-restraints excluded: chain b residue 844 THR Chi-restraints excluded: chain b residue 869 SER Chi-restraints excluded: chain b residue 876 SER Chi-restraints excluded: chain b residue 926 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 12 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 chunk 96 optimal weight: 0.8980 chunk 13 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 5 optimal weight: 30.0000 chunk 83 optimal weight: 0.9980 chunk 50 optimal weight: 0.0370 chunk 87 optimal weight: 2.9990 chunk 10 optimal weight: 0.0370 overall best weight: 0.7938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 646 ASN b 680 GLN ** b 740 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.102589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.077337 restraints weight = 35022.835| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 4.77 r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.6076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8830 Z= 0.138 Angle : 0.668 10.552 12060 Z= 0.346 Chirality : 0.044 0.218 1379 Planarity : 0.005 0.058 1515 Dihedral : 6.470 58.621 1432 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.98 % Favored : 96.92 % Rotamer: Outliers : 5.77 % Allowed : 32.16 % Favored : 62.07 % 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: 0.53 (0.26), residues: 1039 helix: 1.31 (0.24), residues: 441 sheet: 0.05 (0.36), residues: 204 loop : -0.48 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP b 77 HIS 0.005 0.001 HIS a 83 PHE 0.020 0.002 PHE b 496 TYR 0.018 0.001 TYR a 163 ARG 0.008 0.001 ARG a 148 Details of bonding type rmsd link_NAG-ASN : bond 0.00284 ( 6) link_NAG-ASN : angle 1.42581 ( 18) link_BETA1-4 : bond 0.00298 ( 7) link_BETA1-4 : angle 1.17890 ( 21) hydrogen bonds : bond 0.04891 ( 379) hydrogen bonds : angle 5.58676 ( 1101) link_BETA1-6 : bond 0.01018 ( 1) link_BETA1-6 : angle 1.11675 ( 3) SS BOND : bond 0.00267 ( 5) SS BOND : angle 1.26984 ( 10) covalent geometry : bond 0.00301 ( 8811) covalent geometry : angle 0.66387 (12008) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 68 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 128 ASN cc_start: 0.9319 (t0) cc_final: 0.8946 (m-40) REVERT: b 200 TYR cc_start: 0.8168 (p90) cc_final: 0.7905 (p90) REVERT: b 252 LEU cc_start: 0.7121 (mt) cc_final: 0.6676 (mt) REVERT: b 281 MET cc_start: 0.6308 (ptp) cc_final: 0.5542 (tmm) REVERT: b 315 MET cc_start: 0.7460 (mmp) cc_final: 0.7129 (mmp) REVERT: b 479 ASP cc_start: 0.6343 (OUTLIER) cc_final: 0.5568 (p0) REVERT: b 490 LEU cc_start: 0.8773 (tp) cc_final: 0.8556 (mp) REVERT: b 675 ASP cc_start: 0.8588 (m-30) cc_final: 0.8328 (t70) outliers start: 54 outliers final: 29 residues processed: 115 average time/residue: 0.7931 time to fit residues: 101.0090 Evaluate side-chains 88 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 58 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 55 THR Chi-restraints excluded: chain a residue 70 VAL Chi-restraints excluded: chain a residue 78 PHE Chi-restraints excluded: chain a residue 79 SER Chi-restraints excluded: chain a residue 119 ASP Chi-restraints excluded: chain a residue 121 LEU Chi-restraints excluded: chain a residue 137 VAL Chi-restraints excluded: chain a residue 141 CYS Chi-restraints excluded: chain a residue 149 THR Chi-restraints excluded: chain a residue 159 LEU Chi-restraints excluded: chain a residue 165 GLU Chi-restraints excluded: chain b residue 130 SER Chi-restraints excluded: chain b residue 164 VAL Chi-restraints excluded: chain b residue 187 LYS Chi-restraints excluded: chain b residue 205 THR Chi-restraints excluded: chain b residue 213 LEU Chi-restraints excluded: chain b residue 215 THR Chi-restraints excluded: chain b residue 242 THR Chi-restraints excluded: chain b residue 308 ILE Chi-restraints excluded: chain b residue 326 VAL Chi-restraints excluded: chain b residue 479 ASP Chi-restraints excluded: chain b residue 497 LEU Chi-restraints excluded: chain b residue 554 MET Chi-restraints excluded: chain b residue 561 VAL Chi-restraints excluded: chain b residue 575 LEU Chi-restraints excluded: chain b residue 591 TRP Chi-restraints excluded: chain b residue 681 ILE Chi-restraints excluded: chain b residue 682 VAL Chi-restraints excluded: chain b residue 869 SER Chi-restraints excluded: chain b residue 876 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 1 optimal weight: 1.9990 chunk 89 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 20 optimal weight: 8.9990 chunk 46 optimal weight: 20.0000 chunk 42 optimal weight: 20.0000 chunk 10 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 chunk 59 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 181 GLN ** b 740 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.099800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.074276 restraints weight = 35903.470| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 4.59 r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.6353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 8830 Z= 0.216 Angle : 0.712 10.877 12060 Z= 0.371 Chirality : 0.045 0.229 1379 Planarity : 0.005 0.059 1515 Dihedral : 6.504 57.903 1432 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 17.01 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.27 % Favored : 96.63 % Rotamer: Outliers : 5.77 % Allowed : 32.69 % Favored : 61.54 % 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: 0.31 (0.26), residues: 1039 helix: 1.16 (0.24), residues: 440 sheet: -0.06 (0.36), residues: 199 loop : -0.64 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP b 77 HIS 0.007 0.001 HIS b 671 PHE 0.020 0.002 PHE b 496 TYR 0.016 0.002 TYR b 899 ARG 0.009 0.001 ARG a 148 Details of bonding type rmsd link_NAG-ASN : bond 0.00393 ( 6) link_NAG-ASN : angle 1.71376 ( 18) link_BETA1-4 : bond 0.00242 ( 7) link_BETA1-4 : angle 1.33134 ( 21) hydrogen bonds : bond 0.06299 ( 379) hydrogen bonds : angle 5.73013 ( 1101) link_BETA1-6 : bond 0.00620 ( 1) link_BETA1-6 : angle 0.74186 ( 3) SS BOND : bond 0.00351 ( 5) SS BOND : angle 1.89516 ( 10) covalent geometry : bond 0.00492 ( 8811) covalent geometry : angle 0.70624 (12008) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 61 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 59 ILE cc_start: 0.9176 (tt) cc_final: 0.8824 (pp) REVERT: b 200 TYR cc_start: 0.8145 (p90) cc_final: 0.7913 (p90) REVERT: b 252 LEU cc_start: 0.7295 (mt) cc_final: 0.6835 (mt) REVERT: b 479 ASP cc_start: 0.6516 (OUTLIER) cc_final: 0.5801 (p0) REVERT: b 490 LEU cc_start: 0.8808 (tp) cc_final: 0.8536 (mp) REVERT: b 675 ASP cc_start: 0.8648 (m-30) cc_final: 0.8392 (t70) REVERT: b 681 ILE cc_start: 0.8948 (OUTLIER) cc_final: 0.8695 (tp) REVERT: b 775 LYS cc_start: 0.7138 (OUTLIER) cc_final: 0.6800 (mmmm) outliers start: 54 outliers final: 33 residues processed: 109 average time/residue: 0.7749 time to fit residues: 93.7024 Evaluate side-chains 91 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 55 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 55 THR Chi-restraints excluded: chain a residue 70 VAL Chi-restraints excluded: chain a residue 78 PHE Chi-restraints excluded: chain a residue 79 SER Chi-restraints excluded: chain a residue 121 LEU Chi-restraints excluded: chain a residue 137 VAL Chi-restraints excluded: chain a residue 141 CYS Chi-restraints excluded: chain a residue 149 THR Chi-restraints excluded: chain a residue 165 GLU Chi-restraints excluded: chain b residue 108 THR Chi-restraints excluded: chain b residue 130 SER Chi-restraints excluded: chain b residue 164 VAL Chi-restraints excluded: chain b residue 169 VAL Chi-restraints excluded: chain b residue 181 GLN Chi-restraints excluded: chain b residue 186 SER Chi-restraints excluded: chain b residue 187 LYS Chi-restraints excluded: chain b residue 205 THR Chi-restraints excluded: chain b residue 213 LEU Chi-restraints excluded: chain b residue 215 THR Chi-restraints excluded: chain b residue 242 THR Chi-restraints excluded: chain b residue 308 ILE Chi-restraints excluded: chain b residue 326 VAL Chi-restraints excluded: chain b residue 479 ASP Chi-restraints excluded: chain b residue 494 SER Chi-restraints excluded: chain b residue 497 LEU Chi-restraints excluded: chain b residue 554 MET Chi-restraints excluded: chain b residue 561 VAL Chi-restraints excluded: chain b residue 575 LEU Chi-restraints excluded: chain b residue 591 TRP Chi-restraints excluded: chain b residue 681 ILE Chi-restraints excluded: chain b residue 682 VAL Chi-restraints excluded: chain b residue 775 LYS Chi-restraints excluded: chain b residue 803 THR Chi-restraints excluded: chain b residue 831 ASN Chi-restraints excluded: chain b residue 844 THR Chi-restraints excluded: chain b residue 869 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 59 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 68 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 12 optimal weight: 10.0000 chunk 103 optimal weight: 1.9990 chunk 61 optimal weight: 0.0770 chunk 4 optimal weight: 30.0000 chunk 46 optimal weight: 9.9990 chunk 40 optimal weight: 8.9990 chunk 18 optimal weight: 40.0000 overall best weight: 4.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 399 GLN ** b 740 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 889 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.097742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.072161 restraints weight = 36858.968| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 4.57 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.6698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 8830 Z= 0.268 Angle : 0.765 11.163 12060 Z= 0.403 Chirality : 0.048 0.318 1379 Planarity : 0.006 0.063 1515 Dihedral : 6.718 53.204 1431 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 17.95 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.33 % Favored : 95.57 % Rotamer: Outliers : 5.66 % Allowed : 32.80 % Favored : 61.54 % 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: -0.12 (0.25), residues: 1039 helix: 0.79 (0.24), residues: 433 sheet: -0.20 (0.37), residues: 200 loop : -0.86 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP b 77 HIS 0.013 0.002 HIS b 740 PHE 0.022 0.003 PHE b 970 TYR 0.023 0.002 TYR b 182 ARG 0.011 0.001 ARG a 148 Details of bonding type rmsd link_NAG-ASN : bond 0.00463 ( 6) link_NAG-ASN : angle 1.85392 ( 18) link_BETA1-4 : bond 0.00320 ( 7) link_BETA1-4 : angle 1.39553 ( 21) hydrogen bonds : bond 0.07196 ( 379) hydrogen bonds : angle 5.96722 ( 1101) link_BETA1-6 : bond 0.00692 ( 1) link_BETA1-6 : angle 0.81321 ( 3) SS BOND : bond 0.00403 ( 5) SS BOND : angle 1.73836 ( 10) covalent geometry : bond 0.00603 ( 8811) covalent geometry : angle 0.75977 (12008) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 63 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 59 ILE cc_start: 0.9210 (tt) cc_final: 0.8910 (pp) REVERT: a 81 TYR cc_start: 0.7824 (m-10) cc_final: 0.7604 (m-80) REVERT: a 127 PHE cc_start: 0.6993 (t80) cc_final: 0.6778 (t80) REVERT: a 163 TYR cc_start: 0.8131 (t80) cc_final: 0.7815 (t80) REVERT: b 200 TYR cc_start: 0.8153 (p90) cc_final: 0.7915 (p90) REVERT: b 252 LEU cc_start: 0.7372 (mt) cc_final: 0.6943 (mt) REVERT: b 281 MET cc_start: 0.6806 (ptp) cc_final: 0.5939 (tmm) REVERT: b 360 MET cc_start: 0.6853 (mmm) cc_final: 0.6635 (mmm) REVERT: b 479 ASP cc_start: 0.6789 (OUTLIER) cc_final: 0.6265 (p0) REVERT: b 490 LEU cc_start: 0.8826 (tp) cc_final: 0.8511 (mp) REVERT: b 592 ILE cc_start: 0.7843 (OUTLIER) cc_final: 0.7358 (pp) REVERT: b 649 LYS cc_start: 0.9305 (OUTLIER) cc_final: 0.8841 (ttpp) REVERT: b 675 ASP cc_start: 0.8661 (m-30) cc_final: 0.8419 (t70) REVERT: b 681 ILE cc_start: 0.8948 (OUTLIER) cc_final: 0.8719 (tp) outliers start: 53 outliers final: 38 residues processed: 111 average time/residue: 0.6860 time to fit residues: 85.2752 Evaluate side-chains 99 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 57 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 55 THR Chi-restraints excluded: chain a residue 70 VAL Chi-restraints excluded: chain a residue 78 PHE Chi-restraints excluded: chain a residue 79 SER Chi-restraints excluded: chain a residue 89 SER Chi-restraints excluded: chain a residue 113 THR Chi-restraints excluded: chain a residue 119 ASP Chi-restraints excluded: chain a residue 121 LEU Chi-restraints excluded: chain a residue 141 CYS Chi-restraints excluded: chain a residue 149 THR Chi-restraints excluded: chain a residue 158 SER Chi-restraints excluded: chain a residue 159 LEU Chi-restraints excluded: chain a residue 165 GLU Chi-restraints excluded: chain b residue 108 THR Chi-restraints excluded: chain b residue 130 SER Chi-restraints excluded: chain b residue 164 VAL Chi-restraints excluded: chain b residue 168 LEU Chi-restraints excluded: chain b residue 169 VAL Chi-restraints excluded: chain b residue 186 SER Chi-restraints excluded: chain b residue 187 LYS Chi-restraints excluded: chain b residue 213 LEU Chi-restraints excluded: chain b residue 215 THR Chi-restraints excluded: chain b residue 242 THR Chi-restraints excluded: chain b residue 308 ILE Chi-restraints excluded: chain b residue 326 VAL Chi-restraints excluded: chain b residue 446 VAL Chi-restraints excluded: chain b residue 479 ASP Chi-restraints excluded: chain b residue 494 SER Chi-restraints excluded: chain b residue 561 VAL Chi-restraints excluded: chain b residue 575 LEU Chi-restraints excluded: chain b residue 591 TRP Chi-restraints excluded: chain b residue 592 ILE Chi-restraints excluded: chain b residue 628 VAL Chi-restraints excluded: chain b residue 649 LYS Chi-restraints excluded: chain b residue 681 ILE Chi-restraints excluded: chain b residue 682 VAL Chi-restraints excluded: chain b residue 803 THR Chi-restraints excluded: chain b residue 831 ASN Chi-restraints excluded: chain b residue 844 THR Chi-restraints excluded: chain b residue 869 SER Chi-restraints excluded: chain b residue 901 THR Chi-restraints excluded: chain b residue 926 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 63 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 90 optimal weight: 0.8980 chunk 18 optimal weight: 9.9990 chunk 27 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 57 optimal weight: 20.0000 chunk 9 optimal weight: 0.0570 chunk 49 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 overall best weight: 1.5702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 181 GLN ** b 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 740 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 973 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.100086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.074602 restraints weight = 36412.664| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 4.77 r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.6861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8830 Z= 0.150 Angle : 0.700 11.536 12060 Z= 0.360 Chirality : 0.045 0.296 1379 Planarity : 0.005 0.057 1515 Dihedral : 6.383 49.826 1430 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.95 % Favored : 95.96 % Rotamer: Outliers : 4.91 % Allowed : 33.76 % Favored : 61.32 % 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: 0.13 (0.25), residues: 1039 helix: 1.15 (0.24), residues: 439 sheet: -0.19 (0.37), residues: 199 loop : -0.90 (0.29), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP b 77 HIS 0.012 0.001 HIS b 740 PHE 0.020 0.002 PHE b 496 TYR 0.020 0.001 TYR a 163 ARG 0.011 0.001 ARG a 148 Details of bonding type rmsd link_NAG-ASN : bond 0.00249 ( 6) link_NAG-ASN : angle 1.42359 ( 18) link_BETA1-4 : bond 0.00316 ( 7) link_BETA1-4 : angle 1.27935 ( 21) hydrogen bonds : bond 0.05375 ( 379) hydrogen bonds : angle 5.66092 ( 1101) link_BETA1-6 : bond 0.00627 ( 1) link_BETA1-6 : angle 0.79573 ( 3) SS BOND : bond 0.00261 ( 5) SS BOND : angle 1.35137 ( 10) covalent geometry : bond 0.00329 ( 8811) covalent geometry : angle 0.69589 (12008) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 65 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 81 TYR cc_start: 0.7877 (m-10) cc_final: 0.7650 (m-80) REVERT: a 127 PHE cc_start: 0.6958 (t80) cc_final: 0.6639 (t80) REVERT: a 163 TYR cc_start: 0.8137 (t80) cc_final: 0.7857 (t80) REVERT: b 200 TYR cc_start: 0.8098 (p90) cc_final: 0.7849 (p90) REVERT: b 217 GLN cc_start: 0.8972 (tm-30) cc_final: 0.8521 (tm-30) REVERT: b 252 LEU cc_start: 0.7441 (mt) cc_final: 0.6982 (mt) REVERT: b 281 MET cc_start: 0.6841 (ptp) cc_final: 0.5992 (tmm) REVERT: b 479 ASP cc_start: 0.6640 (OUTLIER) cc_final: 0.6190 (p0) REVERT: b 490 LEU cc_start: 0.8831 (tp) cc_final: 0.8598 (mp) REVERT: b 621 LYS cc_start: 0.7729 (OUTLIER) cc_final: 0.7325 (tmmm) REVERT: b 675 ASP cc_start: 0.8592 (m-30) cc_final: 0.8375 (t70) REVERT: b 681 ILE cc_start: 0.8918 (OUTLIER) cc_final: 0.8671 (tp) outliers start: 46 outliers final: 29 residues processed: 106 average time/residue: 0.6849 time to fit residues: 81.2618 Evaluate side-chains 91 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 59 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 55 THR Chi-restraints excluded: chain a residue 70 VAL Chi-restraints excluded: chain a residue 78 PHE Chi-restraints excluded: chain a residue 79 SER Chi-restraints excluded: chain a residue 113 THR Chi-restraints excluded: chain a residue 119 ASP Chi-restraints excluded: chain a residue 121 LEU Chi-restraints excluded: chain a residue 141 CYS Chi-restraints excluded: chain a residue 149 THR Chi-restraints excluded: chain a residue 159 LEU Chi-restraints excluded: chain a residue 165 GLU Chi-restraints excluded: chain b residue 130 SER Chi-restraints excluded: chain b residue 164 VAL Chi-restraints excluded: chain b residue 168 LEU Chi-restraints excluded: chain b residue 186 SER Chi-restraints excluded: chain b residue 187 LYS Chi-restraints excluded: chain b residue 205 THR Chi-restraints excluded: chain b residue 213 LEU Chi-restraints excluded: chain b residue 215 THR Chi-restraints excluded: chain b residue 242 THR Chi-restraints excluded: chain b residue 308 ILE Chi-restraints excluded: chain b residue 446 VAL Chi-restraints excluded: chain b residue 479 ASP Chi-restraints excluded: chain b residue 561 VAL Chi-restraints excluded: chain b residue 575 LEU Chi-restraints excluded: chain b residue 591 TRP Chi-restraints excluded: chain b residue 621 LYS Chi-restraints excluded: chain b residue 628 VAL Chi-restraints excluded: chain b residue 681 ILE Chi-restraints excluded: chain b residue 682 VAL Chi-restraints excluded: chain b residue 831 ASN Chi-restraints excluded: chain b residue 869 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 45 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 7 optimal weight: 0.6980 chunk 92 optimal weight: 0.8980 chunk 64 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 chunk 80 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 181 GLN ** b 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 740 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 889 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.100377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.074921 restraints weight = 35968.962| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 4.67 r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.7012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8830 Z= 0.147 Angle : 0.697 11.799 12060 Z= 0.356 Chirality : 0.044 0.289 1379 Planarity : 0.005 0.067 1515 Dihedral : 6.028 52.379 1429 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.04 % Favored : 95.86 % Rotamer: Outliers : 3.85 % Allowed : 34.51 % Favored : 61.65 % 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: 0.14 (0.25), residues: 1039 helix: 1.23 (0.24), residues: 439 sheet: -0.23 (0.37), residues: 199 loop : -0.94 (0.29), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP b 77 HIS 0.011 0.001 HIS b 740 PHE 0.019 0.002 PHE b 496 TYR 0.019 0.002 TYR a 163 ARG 0.015 0.001 ARG a 148 Details of bonding type rmsd link_NAG-ASN : bond 0.00195 ( 6) link_NAG-ASN : angle 1.35090 ( 18) link_BETA1-4 : bond 0.00377 ( 7) link_BETA1-4 : angle 1.35522 ( 21) hydrogen bonds : bond 0.05163 ( 379) hydrogen bonds : angle 5.53560 ( 1101) link_BETA1-6 : bond 0.00462 ( 1) link_BETA1-6 : angle 0.66926 ( 3) SS BOND : bond 0.00257 ( 5) SS BOND : angle 1.58801 ( 10) covalent geometry : bond 0.00326 ( 8811) covalent geometry : angle 0.69310 (12008) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 62 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 127 PHE cc_start: 0.6983 (t80) cc_final: 0.6686 (t80) REVERT: a 148 ARG cc_start: 0.7566 (mtp-110) cc_final: 0.7330 (ptm160) REVERT: b 200 TYR cc_start: 0.8144 (p90) cc_final: 0.7887 (p90) REVERT: b 217 GLN cc_start: 0.8799 (tm-30) cc_final: 0.8399 (tm-30) REVERT: b 252 LEU cc_start: 0.7397 (mt) cc_final: 0.6914 (mt) REVERT: b 281 MET cc_start: 0.6732 (ptp) cc_final: 0.5940 (tmm) REVERT: b 479 ASP cc_start: 0.6546 (OUTLIER) cc_final: 0.6120 (p0) REVERT: b 490 LEU cc_start: 0.8833 (tp) cc_final: 0.8568 (mp) REVERT: b 621 LYS cc_start: 0.7786 (OUTLIER) cc_final: 0.7382 (tmmm) REVERT: b 675 ASP cc_start: 0.8580 (m-30) cc_final: 0.8369 (t70) REVERT: b 681 ILE cc_start: 0.8934 (OUTLIER) cc_final: 0.8720 (tp) outliers start: 36 outliers final: 27 residues processed: 96 average time/residue: 0.7329 time to fit residues: 78.3132 Evaluate side-chains 89 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 59 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 55 THR Chi-restraints excluded: chain a residue 78 PHE Chi-restraints excluded: chain a residue 79 SER Chi-restraints excluded: chain a residue 113 THR Chi-restraints excluded: chain a residue 119 ASP Chi-restraints excluded: chain a residue 121 LEU Chi-restraints excluded: chain a residue 141 CYS Chi-restraints excluded: chain a residue 149 THR Chi-restraints excluded: chain a residue 158 SER Chi-restraints excluded: chain a residue 165 GLU Chi-restraints excluded: chain b residue 130 SER Chi-restraints excluded: chain b residue 164 VAL Chi-restraints excluded: chain b residue 168 LEU Chi-restraints excluded: chain b residue 169 VAL Chi-restraints excluded: chain b residue 187 LYS Chi-restraints excluded: chain b residue 205 THR Chi-restraints excluded: chain b residue 213 LEU Chi-restraints excluded: chain b residue 215 THR Chi-restraints excluded: chain b residue 242 THR Chi-restraints excluded: chain b residue 308 ILE Chi-restraints excluded: chain b residue 479 ASP Chi-restraints excluded: chain b residue 561 VAL Chi-restraints excluded: chain b residue 575 LEU Chi-restraints excluded: chain b residue 591 TRP Chi-restraints excluded: chain b residue 621 LYS Chi-restraints excluded: chain b residue 628 VAL Chi-restraints excluded: chain b residue 681 ILE Chi-restraints excluded: chain b residue 682 VAL Chi-restraints excluded: chain b residue 831 ASN Chi-restraints excluded: chain b residue 869 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 58 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 88 optimal weight: 0.4980 chunk 102 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 chunk 79 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 22 optimal weight: 9.9990 chunk 86 optimal weight: 1.9990 chunk 52 optimal weight: 10.0000 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 181 GLN ** b 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 517 ASN ** b 740 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 889 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.098316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.072519 restraints weight = 36892.715| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 4.69 r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.7162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 8830 Z= 0.212 Angle : 0.740 12.553 12060 Z= 0.380 Chirality : 0.046 0.223 1379 Planarity : 0.006 0.066 1515 Dihedral : 6.259 50.088 1429 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.72 % Favored : 95.19 % Rotamer: Outliers : 4.06 % Allowed : 34.62 % Favored : 61.32 % 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: -0.05 (0.25), residues: 1039 helix: 1.03 (0.24), residues: 433 sheet: -0.26 (0.37), residues: 199 loop : -1.00 (0.29), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP b 524 HIS 0.010 0.002 HIS b 740 PHE 0.018 0.002 PHE b 970 TYR 0.015 0.002 TYR b 204 ARG 0.012 0.001 ARG a 148 Details of bonding type rmsd link_NAG-ASN : bond 0.00286 ( 6) link_NAG-ASN : angle 1.64203 ( 18) link_BETA1-4 : bond 0.00303 ( 7) link_BETA1-4 : angle 1.43001 ( 21) hydrogen bonds : bond 0.06331 ( 379) hydrogen bonds : angle 5.70002 ( 1101) link_BETA1-6 : bond 0.00654 ( 1) link_BETA1-6 : angle 0.71303 ( 3) SS BOND : bond 0.00285 ( 5) SS BOND : angle 1.70683 ( 10) covalent geometry : bond 0.00478 ( 8811) covalent geometry : angle 0.73463 (12008) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 60 time to evaluate : 0.876 Fit side-chains revert: symmetry clash REVERT: a 81 TYR cc_start: 0.8144 (m-10) cc_final: 0.7927 (m-80) REVERT: a 148 ARG cc_start: 0.7794 (mtp-110) cc_final: 0.7593 (ptm160) REVERT: b 200 TYR cc_start: 0.8104 (p90) cc_final: 0.7884 (p90) REVERT: b 217 GLN cc_start: 0.8745 (tm-30) cc_final: 0.8367 (tm-30) REVERT: b 252 LEU cc_start: 0.7349 (mt) cc_final: 0.6897 (mt) REVERT: b 281 MET cc_start: 0.6827 (ptp) cc_final: 0.6270 (ppp) REVERT: b 479 ASP cc_start: 0.6708 (OUTLIER) cc_final: 0.6439 (p0) REVERT: b 490 LEU cc_start: 0.8853 (tp) cc_final: 0.8556 (mp) REVERT: b 675 ASP cc_start: 0.8611 (m-30) cc_final: 0.8404 (t70) REVERT: b 681 ILE cc_start: 0.8941 (OUTLIER) cc_final: 0.8732 (tp) outliers start: 38 outliers final: 30 residues processed: 95 average time/residue: 0.7074 time to fit residues: 75.0619 Evaluate side-chains 90 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 58 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 55 THR Chi-restraints excluded: chain a residue 70 VAL Chi-restraints excluded: chain a residue 78 PHE Chi-restraints excluded: chain a residue 79 SER Chi-restraints excluded: chain a residue 113 THR Chi-restraints excluded: chain a residue 121 LEU Chi-restraints excluded: chain a residue 141 CYS Chi-restraints excluded: chain a residue 149 THR Chi-restraints excluded: chain b residue 130 SER Chi-restraints excluded: chain b residue 164 VAL Chi-restraints excluded: chain b residue 168 LEU Chi-restraints excluded: chain b residue 169 VAL Chi-restraints excluded: chain b residue 187 LYS Chi-restraints excluded: chain b residue 205 THR Chi-restraints excluded: chain b residue 213 LEU Chi-restraints excluded: chain b residue 215 THR Chi-restraints excluded: chain b residue 242 THR Chi-restraints excluded: chain b residue 308 ILE Chi-restraints excluded: chain b residue 326 VAL Chi-restraints excluded: chain b residue 446 VAL Chi-restraints excluded: chain b residue 479 ASP Chi-restraints excluded: chain b residue 561 VAL Chi-restraints excluded: chain b residue 575 LEU Chi-restraints excluded: chain b residue 591 TRP Chi-restraints excluded: chain b residue 628 VAL Chi-restraints excluded: chain b residue 681 ILE Chi-restraints excluded: chain b residue 682 VAL Chi-restraints excluded: chain b residue 831 ASN Chi-restraints excluded: chain b residue 844 THR Chi-restraints excluded: chain b residue 869 SER Chi-restraints excluded: chain b residue 876 SER Chi-restraints excluded: chain b residue 895 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 64 optimal weight: 0.5980 chunk 84 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 59 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 181 GLN ** b 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 740 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.100590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.075210 restraints weight = 36650.060| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 4.85 r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.7286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8830 Z= 0.135 Angle : 0.707 12.641 12060 Z= 0.358 Chirality : 0.044 0.219 1379 Planarity : 0.005 0.054 1515 Dihedral : 5.689 49.062 1426 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.04 % Favored : 95.77 % Rotamer: Outliers : 3.85 % Allowed : 34.62 % Favored : 61.54 % 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: 0.11 (0.25), residues: 1039 helix: 1.17 (0.24), residues: 440 sheet: -0.19 (0.37), residues: 194 loop : -0.95 (0.29), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP b 77 HIS 0.011 0.001 HIS b 740 PHE 0.019 0.002 PHE a 130 TYR 0.022 0.001 TYR a 163 ARG 0.012 0.001 ARG a 148 Details of bonding type rmsd link_NAG-ASN : bond 0.00249 ( 6) link_NAG-ASN : angle 1.26589 ( 18) link_BETA1-4 : bond 0.00385 ( 7) link_BETA1-4 : angle 1.34443 ( 21) hydrogen bonds : bond 0.04887 ( 379) hydrogen bonds : angle 5.43443 ( 1101) link_BETA1-6 : bond 0.00564 ( 1) link_BETA1-6 : angle 0.80817 ( 3) SS BOND : bond 0.00252 ( 5) SS BOND : angle 1.45767 ( 10) covalent geometry : bond 0.00295 ( 8811) covalent geometry : angle 0.70355 (12008) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6225.04 seconds wall clock time: 108 minutes 1.55 seconds (6481.55 seconds total)