Starting phenix.real_space_refine on Mon Dec 30 23:39:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z27_39743/12_2024/8z27_39743.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z27_39743/12_2024/8z27_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_39743/12_2024/8z27_39743.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z27_39743/12_2024/8z27_39743.map" model { file = "/net/cci-nas-00/data/ceres_data/8z27_39743/12_2024/8z27_39743.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z27_39743/12_2024/8z27_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 6.07, per 1000 atoms: 0.71 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: 2.49 Conformation dependent library (CDL) restraints added in 993.6 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: 0.99 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: 2.82 Time building geometry restraints manager: 2.79 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.580 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: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.280 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.010 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:11.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.600 ------------------------------------------------------------------------------- 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 8811 Z= 0.478 Angle : 1.411 12.443 12008 Z= 0.943 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 *********************** 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 : 0.990 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: 0.9609 time to fit residues: 430.0772 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 : 0.986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5123 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 8811 Z= 0.371 Angle : 0.869 13.137 12008 Z= 0.461 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 *********************** 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 : 0.939 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 77 GLN cc_start: -0.0863 (OUTLIER) cc_final: -0.1440 (pp30) REVERT: b 916 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.8116 (ttp-170) REVERT: b 958 TRP cc_start: 0.3907 (OUTLIER) cc_final: 0.2585 (t-100) outliers start: 103 outliers final: 40 residues processed: 171 average time/residue: 0.9000 time to fit residues: 168.3816 Evaluate side-chains 107 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 64 time to evaluate : 0.750 ------------------------------------------------------------------------------- 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 77 GLN 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 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 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 52 optimal weight: 10.0000 chunk 29 optimal weight: 20.0000 chunk 78 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 94 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 646 ASN ** b 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 740 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 758 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5200 moved from start: 0.5273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 8811 Z= 0.330 Angle : 0.770 9.608 12008 Z= 0.408 Chirality : 0.048 0.211 1379 Planarity : 0.006 0.050 1515 Dihedral : 8.991 59.033 1452 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 18.72 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.79 % Favored : 97.11 % Rotamer: Outliers : 8.23 % Allowed : 29.27 % Favored : 62.50 % 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: 0.59 (0.25), residues: 1039 helix: 1.22 (0.23), residues: 441 sheet: 0.17 (0.36), residues: 202 loop : -0.30 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP b 892 HIS 0.008 0.002 HIS a 83 PHE 0.025 0.003 PHE a 118 TYR 0.027 0.002 TYR b 200 ARG 0.008 0.001 ARG a 148 *********************** 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 147 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 70 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 479 ASP cc_start: 0.6012 (OUTLIER) cc_final: 0.5249 (p0) outliers start: 77 outliers final: 40 residues processed: 134 average time/residue: 0.8215 time to fit residues: 121.6222 Evaluate side-chains 95 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 54 time to evaluate : 1.010 ------------------------------------------------------------------------------- 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 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 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 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 421 SER 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 591 TRP Chi-restraints excluded: chain b residue 649 LYS 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 907 SER Chi-restraints excluded: chain b residue 913 VAL Chi-restraints excluded: chain b residue 926 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 49 optimal weight: 20.0000 chunk 10 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 100 optimal weight: 20.0000 chunk 89 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 740 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 793 ASN b 823 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5163 moved from start: 0.5711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8811 Z= 0.254 Angle : 0.708 9.638 12008 Z= 0.371 Chirality : 0.045 0.214 1379 Planarity : 0.005 0.043 1515 Dihedral : 7.372 57.759 1434 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 16.95 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.98 % Favored : 96.92 % Rotamer: Outliers : 6.94 % Allowed : 30.45 % Favored : 62.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.26), residues: 1039 helix: 1.23 (0.24), residues: 441 sheet: -0.07 (0.36), residues: 209 loop : -0.36 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP b 958 HIS 0.008 0.001 HIS b 171 PHE 0.018 0.002 PHE b 496 TYR 0.019 0.002 TYR b 712 ARG 0.005 0.001 ARG a 157 *********************** 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 130 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 65 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 479 ASP cc_start: 0.5961 (OUTLIER) cc_final: 0.5199 (p0) outliers start: 65 outliers final: 34 residues processed: 123 average time/residue: 0.8228 time to fit residues: 111.5664 Evaluate side-chains 88 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 53 time to evaluate : 0.958 ------------------------------------------------------------------------------- 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 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 111 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 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 186 SER 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 308 ILE Chi-restraints excluded: chain b residue 326 VAL Chi-restraints excluded: chain b residue 421 SER 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 591 TRP Chi-restraints excluded: chain b residue 649 LYS Chi-restraints excluded: chain b residue 682 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 20.0000 chunk 1 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 41 optimal weight: 20.0000 chunk 85 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 51 optimal weight: 10.0000 chunk 90 optimal weight: 0.2980 chunk 25 optimal weight: 40.0000 chunk 33 optimal weight: 40.0000 overall best weight: 3.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 207 ASN b 572 HIS b 644 GLN ** b 740 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5259 moved from start: 0.6119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 8811 Z= 0.328 Angle : 0.731 10.728 12008 Z= 0.385 Chirality : 0.046 0.207 1379 Planarity : 0.005 0.047 1515 Dihedral : 7.012 59.749 1433 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 18.48 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.37 % Favored : 96.54 % Rotamer: Outliers : 7.05 % Allowed : 30.88 % 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: 0.27 (0.26), residues: 1039 helix: 1.01 (0.24), residues: 441 sheet: -0.07 (0.37), residues: 199 loop : -0.52 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP b 77 HIS 0.006 0.001 HIS b 671 PHE 0.020 0.002 PHE a 143 TYR 0.019 0.002 TYR a 163 ARG 0.009 0.001 ARG a 148 *********************** 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 128 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 62 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 479 ASP cc_start: 0.6120 (OUTLIER) cc_final: 0.5436 (p0) outliers start: 66 outliers final: 40 residues processed: 121 average time/residue: 0.8267 time to fit residues: 110.4363 Evaluate side-chains 94 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 53 time to evaluate : 1.044 ------------------------------------------------------------------------------- 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 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 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 108 THR Chi-restraints excluded: chain b residue 130 SER Chi-restraints excluded: chain b residue 164 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 308 ILE Chi-restraints excluded: chain b residue 326 VAL Chi-restraints excluded: chain b residue 421 SER Chi-restraints excluded: chain b residue 479 ASP Chi-restraints excluded: chain b residue 490 LEU 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 591 TRP Chi-restraints excluded: chain b residue 628 VAL Chi-restraints excluded: chain b residue 682 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 7.9990 chunk 19 optimal weight: 30.0000 chunk 59 optimal weight: 5.9990 chunk 24 optimal weight: 0.1980 chunk 100 optimal weight: 8.9990 chunk 83 optimal weight: 1.9990 chunk 46 optimal weight: 8.9990 chunk 8 optimal weight: 3.9990 chunk 33 optimal weight: 30.0000 chunk 52 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 overall best weight: 4.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 181 GLN ** b 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 399 GLN ** b 646 ASN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5313 moved from start: 0.6584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 8811 Z= 0.360 Angle : 0.760 10.966 12008 Z= 0.402 Chirality : 0.047 0.213 1379 Planarity : 0.006 0.067 1515 Dihedral : 7.001 55.980 1432 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 19.37 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.04 % Favored : 95.86 % Rotamer: Outliers : 6.84 % Allowed : 31.94 % Favored : 61.22 % 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: -0.07 (0.25), residues: 1039 helix: 0.78 (0.24), residues: 439 sheet: -0.16 (0.36), residues: 199 loop : -0.80 (0.30), residues: 401 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 0.031 0.003 PHE a 118 TYR 0.015 0.002 TYR b 204 ARG 0.010 0.001 ARG a 148 *********************** 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 123 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 59 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 479 ASP cc_start: 0.6401 (OUTLIER) cc_final: 0.5981 (p0) REVERT: b 592 ILE cc_start: 0.7139 (OUTLIER) cc_final: 0.6736 (pp) outliers start: 64 outliers final: 44 residues processed: 115 average time/residue: 0.7106 time to fit residues: 91.8129 Evaluate side-chains 96 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 50 time to evaluate : 1.166 ------------------------------------------------------------------------------- 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 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 116 PHE 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 a residue 170 VAL 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 181 GLN 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 421 SER Chi-restraints excluded: chain b residue 446 VAL Chi-restraints excluded: chain b residue 479 ASP Chi-restraints excluded: chain b residue 490 LEU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 5.9990 chunk 57 optimal weight: 20.0000 chunk 73 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 100 optimal weight: 20.0000 chunk 62 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 46 optimal weight: 20.0000 chunk 40 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 171 HIS ** b 646 ASN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5261 moved from start: 0.6720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8811 Z= 0.262 Angle : 0.721 11.237 12008 Z= 0.376 Chirality : 0.045 0.327 1379 Planarity : 0.005 0.060 1515 Dihedral : 6.832 53.854 1432 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.85 % Favored : 96.05 % Rotamer: Outliers : 6.09 % Allowed : 33.01 % Favored : 60.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.10 (0.26), residues: 1039 helix: 0.99 (0.24), residues: 440 sheet: -0.10 (0.37), residues: 199 loop : -0.79 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP b 77 HIS 0.014 0.002 HIS b 740 PHE 0.029 0.002 PHE a 118 TYR 0.015 0.002 TYR b 182 ARG 0.012 0.001 ARG a 148 *********************** 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 114 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 57 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b 479 ASP cc_start: 0.6292 (OUTLIER) cc_final: 0.5906 (p0) REVERT: b 649 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.8197 (ttpp) REVERT: b 916 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.8265 (ttp-170) outliers start: 57 outliers final: 37 residues processed: 108 average time/residue: 0.7563 time to fit residues: 90.9246 Evaluate side-chains 89 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 49 time to evaluate : 1.009 ------------------------------------------------------------------------------- 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 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 a residue 170 VAL 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 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 421 SER Chi-restraints excluded: chain b residue 446 VAL Chi-restraints excluded: chain b residue 479 ASP Chi-restraints excluded: chain b residue 490 LEU 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 802 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 916 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 10.0000 chunk 19 optimal weight: 20.0000 chunk 63 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 49 optimal weight: 10.0000 chunk 9 optimal weight: 0.0570 chunk 78 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 96 optimal weight: 0.0270 chunk 87 optimal weight: 0.6980 chunk 93 optimal weight: 0.9980 overall best weight: 0.7558 ------------------------------------------------------------------------------- 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 297 GLN b 646 ASN ** b 740 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 889 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5182 moved from start: 0.6870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 8811 Z= 0.204 Angle : 0.706 11.569 12008 Z= 0.364 Chirality : 0.044 0.346 1379 Planarity : 0.005 0.056 1515 Dihedral : 6.491 52.632 1431 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.75 % Favored : 96.15 % Rotamer: Outliers : 4.81 % Allowed : 34.29 % Favored : 60.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.25 (0.26), residues: 1039 helix: 1.19 (0.24), residues: 440 sheet: -0.06 (0.37), residues: 199 loop : -0.79 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP b 77 HIS 0.011 0.001 HIS b 740 PHE 0.023 0.002 PHE a 118 TYR 0.016 0.001 TYR b 284 ARG 0.011 0.001 ARG a 148 *********************** 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 103 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 58 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b 479 ASP cc_start: 0.5893 (OUTLIER) cc_final: 0.5552 (p0) REVERT: b 916 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.8150 (ttp-170) outliers start: 45 outliers final: 32 residues processed: 98 average time/residue: 0.8548 time to fit residues: 92.6751 Evaluate side-chains 84 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 50 time to evaluate : 0.844 ------------------------------------------------------------------------------- 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 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 163 TYR Chi-restraints excluded: chain a residue 165 GLU Chi-restraints excluded: chain a residue 170 VAL Chi-restraints excluded: chain b residue 130 SER Chi-restraints excluded: chain b residue 164 VAL 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 421 SER Chi-restraints excluded: chain b residue 479 ASP Chi-restraints excluded: chain b residue 490 LEU Chi-restraints excluded: chain b residue 554 MET Chi-restraints excluded: chain b residue 561 VAL Chi-restraints excluded: chain b residue 591 TRP Chi-restraints excluded: chain b residue 682 VAL Chi-restraints excluded: chain b residue 809 ILE Chi-restraints excluded: chain b residue 831 ASN Chi-restraints excluded: chain b residue 869 SER Chi-restraints excluded: chain b residue 916 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 96 optimal weight: 3.9990 chunk 56 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 73 optimal weight: 3.9990 chunk 28 optimal weight: 8.9990 chunk 84 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 98 optimal weight: 0.5980 chunk 60 optimal weight: 6.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 740 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 889 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5182 moved from start: 0.7043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8811 Z= 0.221 Angle : 0.718 11.952 12008 Z= 0.368 Chirality : 0.045 0.350 1379 Planarity : 0.005 0.057 1515 Dihedral : 5.984 44.577 1429 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.56 % Favored : 96.34 % Rotamer: Outliers : 4.38 % Allowed : 35.15 % Favored : 60.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.24 (0.26), residues: 1039 helix: 1.23 (0.24), residues: 439 sheet: -0.07 (0.37), residues: 199 loop : -0.87 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP b 77 HIS 0.011 0.001 HIS b 740 PHE 0.017 0.002 PHE a 130 TYR 0.042 0.002 TYR a 163 ARG 0.013 0.001 ARG a 148 *********************** 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 94 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 53 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b 479 ASP cc_start: 0.5876 (OUTLIER) cc_final: 0.5587 (p0) REVERT: b 916 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.8183 (ttp-170) outliers start: 41 outliers final: 30 residues processed: 90 average time/residue: 0.7992 time to fit residues: 80.1645 Evaluate side-chains 82 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 50 time to evaluate : 0.959 ------------------------------------------------------------------------------- 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 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 170 VAL Chi-restraints excluded: chain b residue 130 SER Chi-restraints excluded: chain b residue 164 VAL 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 421 SER Chi-restraints excluded: chain b residue 479 ASP Chi-restraints excluded: chain b residue 490 LEU Chi-restraints excluded: chain b residue 554 MET Chi-restraints excluded: chain b residue 561 VAL Chi-restraints excluded: chain b residue 591 TRP Chi-restraints excluded: chain b residue 682 VAL Chi-restraints excluded: chain b residue 809 ILE Chi-restraints excluded: chain b residue 831 ASN Chi-restraints excluded: chain b residue 869 SER Chi-restraints excluded: chain b residue 916 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 20.0000 chunk 68 optimal weight: 10.0000 chunk 103 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 25 optimal weight: 20.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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** ** a 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 517 ASN ** b 740 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5258 moved from start: 0.7197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8811 Z= 0.286 Angle : 0.745 12.584 12008 Z= 0.384 Chirality : 0.046 0.323 1379 Planarity : 0.006 0.082 1515 Dihedral : 6.021 42.358 1426 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.43 % Favored : 95.48 % Rotamer: Outliers : 4.17 % Allowed : 35.47 % Favored : 60.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.06 (0.26), residues: 1039 helix: 1.08 (0.24), residues: 439 sheet: -0.24 (0.37), residues: 204 loop : -0.90 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP b 77 HIS 0.010 0.001 HIS b 740 PHE 0.017 0.002 PHE a 127 TYR 0.019 0.002 TYR b 284 ARG 0.016 0.001 ARG a 148 ********************** 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 92 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 53 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b 916 ARG cc_start: 0.8778 (OUTLIER) cc_final: 0.8198 (ttp-170) outliers start: 39 outliers final: 32 residues processed: 89 average time/residue: 0.7163 time to fit residues: 72.5251 Evaluate side-chains 83 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 50 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 31 THR Chi-restraints excluded: chain a residue 35 VAL 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 163 TYR Chi-restraints excluded: chain a residue 170 VAL Chi-restraints excluded: chain b residue 130 SER Chi-restraints excluded: chain b residue 164 VAL 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 421 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 682 VAL Chi-restraints excluded: chain b residue 802 SER Chi-restraints excluded: chain b residue 809 ILE Chi-restraints excluded: chain b residue 831 ASN Chi-restraints excluded: chain b residue 869 SER Chi-restraints excluded: chain b residue 916 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 76 optimal weight: 0.7980 chunk 12 optimal weight: 7.9990 chunk 22 optimal weight: 8.9990 chunk 82 optimal weight: 7.9990 chunk 34 optimal weight: 0.5980 chunk 84 optimal weight: 0.8980 chunk 10 optimal weight: 8.9990 chunk 15 optimal weight: 7.9990 chunk 72 optimal weight: 0.4980 chunk 4 optimal weight: 20.0000 chunk 59 optimal weight: 9.9990 overall best weight: 2.1582 ------------------------------------------------------------------------------- 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** ** a 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 740 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.099563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.073980 restraints weight = 35859.290| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 4.74 r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.7321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8811 Z= 0.260 Angle : 0.749 12.456 12008 Z= 0.382 Chirality : 0.045 0.293 1379 Planarity : 0.006 0.069 1515 Dihedral : 5.815 43.274 1424 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.62 % Favored : 95.28 % Rotamer: Outliers : 3.95 % Allowed : 36.00 % Favored : 60.04 % 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: -0.00 (0.26), residues: 1039 helix: 1.02 (0.24), residues: 440 sheet: -0.24 (0.38), residues: 190 loop : -0.94 (0.29), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP b 524 HIS 0.010 0.001 HIS b 740 PHE 0.013 0.002 PHE b 117 TYR 0.068 0.002 TYR b 509 ARG 0.014 0.001 ARG a 148 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3022.39 seconds wall clock time: 55 minutes 49.46 seconds (3349.46 seconds total)