Starting phenix.real_space_refine on Thu Sep 18 05:11:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z27_39743/09_2025/8z27_39743.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z27_39743/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8z27_39743/09_2025/8z27_39743.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z27_39743/09_2025/8z27_39743.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8z27_39743/09_2025/8z27_39743.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z27_39743/09_2025/8z27_39743.map" } resolution = 2.86 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 2.07, per 1000 atoms: 0.24 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: 0.93 Conformation dependent library (CDL) restraints added in 347.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.45 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: 1.50 Time building geometry restraints manager: 1.18 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: 4.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.680 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.250 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.16 (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 ARG 0.005 0.001 ARG b 142 TYR 0.022 0.002 TYR b 368 PHE 0.032 0.003 PHE b 496 TRP 0.020 0.002 TRP b 969 HIS 0.005 0.001 HIS b 394 Details of bonding type rmsd covalent geometry : bond 0.00732 ( 8811) covalent geometry : angle 1.41071 (12008) SS BOND : bond 0.00452 ( 5) SS BOND : angle 0.79232 ( 10) hydrogen bonds : bond 0.21957 ( 379) hydrogen bonds : angle 7.64993 ( 1101) link_BETA1-4 : bond 0.00293 ( 7) link_BETA1-4 : angle 1.19858 ( 21) link_BETA1-6 : bond 0.00104 ( 1) link_BETA1-6 : angle 0.82342 ( 3) link_NAG-ASN : bond 0.00501 ( 6) link_NAG-ASN : angle 2.80140 ( 18) *********************** 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 : 0.385 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: 0.5301 (p0) outliers start: 306 outliers final: 44 residues processed: 415 average time/residue: 0.5146 time to fit residues: 229.5182 Evaluate side-chains 122 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 77 time to evaluate : 0.363 ------------------------------------------------------------------------------- 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 142 ARG 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 49 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 0.2980 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 0.3980 chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 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 = 0.4478 r_free = 0.4478 target = 0.105701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.080639 restraints weight = 34239.222| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 4.60 r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.4256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 8830 Z= 0.208 Angle : 0.854 12.250 12060 Z= 0.445 Chirality : 0.051 0.245 1379 Planarity : 0.006 0.054 1515 Dihedral : 11.983 66.710 1503 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.21 % Favored : 97.69 % Rotamer: Outliers : 10.58 % Allowed : 29.17 % Favored : 60.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.34 (0.25), residues: 1039 helix: 2.01 (0.23), residues: 441 sheet: 0.42 (0.36), residues: 195 loop : -0.05 (0.29), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG b 549 TYR 0.028 0.002 TYR a 71 PHE 0.028 0.003 PHE b 784 TRP 0.020 0.002 TRP b 892 HIS 0.010 0.002 HIS a 83 Details of bonding type rmsd covalent geometry : bond 0.00449 ( 8811) covalent geometry : angle 0.84649 (12008) SS BOND : bond 0.00415 ( 5) SS BOND : angle 1.10749 ( 10) hydrogen bonds : bond 0.07230 ( 379) hydrogen bonds : angle 6.41209 ( 1101) link_BETA1-4 : bond 0.00324 ( 7) link_BETA1-4 : angle 1.75988 ( 21) link_BETA1-6 : bond 0.00333 ( 1) link_BETA1-6 : angle 1.35598 ( 3) link_NAG-ASN : bond 0.00375 ( 6) link_NAG-ASN : angle 2.47729 ( 18) *********************** 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 193 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 94 time to evaluate : 0.297 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: a 43 MET cc_start: 0.5861 (OUTLIER) cc_final: 0.5605 (mtp) REVERT: a 118 PHE cc_start: 0.8663 (m-80) cc_final: 0.8388 (m-80) REVERT: a 128 ASN cc_start: 0.9382 (t0) cc_final: 0.9121 (m-40) REVERT: b 449 VAL cc_start: 0.9600 (t) cc_final: 0.9382 (p) REVERT: b 675 ASP cc_start: 0.8587 (m-30) cc_final: 0.8072 (t0) REVERT: b 916 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.8198 (mtm-85) outliers start: 99 outliers final: 40 residues processed: 175 average time/residue: 0.4652 time to fit residues: 88.5679 Evaluate side-chains 109 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 67 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 31 THR Chi-restraints excluded: chain a residue 43 MET Chi-restraints excluded: chain a residue 55 THR Chi-restraints excluded: chain a residue 77 GLN 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 141 CYS 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 143 VAL 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 250 VAL Chi-restraints excluded: chain b residue 326 VAL Chi-restraints excluded: chain b residue 479 ASP Chi-restraints excluded: chain b residue 542 THR 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 682 VAL Chi-restraints excluded: chain b residue 685 THR 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 864 LYS Chi-restraints excluded: chain b residue 907 SER 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 10 optimal weight: 0.9990 chunk 64 optimal weight: 0.2980 chunk 66 optimal weight: 7.9990 chunk 32 optimal weight: 20.0000 chunk 102 optimal weight: 3.9990 chunk 16 optimal weight: 30.0000 chunk 33 optimal weight: 0.5980 chunk 42 optimal weight: 8.9990 chunk 54 optimal weight: 0.9990 chunk 15 optimal weight: 30.0000 chunk 94 optimal weight: 0.9980 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 137 ASN ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.106001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.080851 restraints weight = 34669.534| |-----------------------------------------------------------------------------| r_work (start): 0.3910 rms_B_bonded: 4.81 r_work (final): 0.3910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.4970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8830 Z= 0.157 Angle : 0.742 9.398 12060 Z= 0.382 Chirality : 0.047 0.332 1379 Planarity : 0.005 0.045 1515 Dihedral : 8.976 57.382 1452 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.60 % Favored : 97.31 % Rotamer: Outliers : 7.37 % Allowed : 31.41 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.25), residues: 1039 helix: 1.71 (0.23), residues: 438 sheet: 0.11 (0.35), residues: 203 loop : -0.33 (0.29), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG a 148 TYR 0.024 0.002 TYR a 81 PHE 0.021 0.002 PHE b 929 TRP 0.013 0.001 TRP b 591 HIS 0.007 0.001 HIS a 83 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 8811) covalent geometry : angle 0.73568 (12008) SS BOND : bond 0.00340 ( 5) SS BOND : angle 1.31375 ( 10) hydrogen bonds : bond 0.05751 ( 379) hydrogen bonds : angle 6.02744 ( 1101) link_BETA1-4 : bond 0.00342 ( 7) link_BETA1-4 : angle 1.69483 ( 21) link_BETA1-6 : bond 0.00472 ( 1) link_BETA1-6 : angle 0.87205 ( 3) link_NAG-ASN : bond 0.00217 ( 6) link_NAG-ASN : angle 1.96488 ( 18) *********************** 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 144 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 75 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 118 PHE cc_start: 0.8654 (m-80) cc_final: 0.8286 (m-80) REVERT: a 128 ASN cc_start: 0.9372 (t0) cc_final: 0.9043 (m-40) REVERT: b 200 TYR cc_start: 0.8273 (p90) cc_final: 0.8015 (p90) REVERT: b 281 MET cc_start: 0.6104 (ptp) cc_final: 0.5660 (tmm) REVERT: b 315 MET cc_start: 0.7209 (mmp) cc_final: 0.6940 (mmp) REVERT: b 449 VAL cc_start: 0.9600 (t) cc_final: 0.9373 (p) REVERT: b 490 LEU cc_start: 0.8762 (tp) cc_final: 0.8465 (mp) REVERT: b 621 LYS cc_start: 0.6726 (OUTLIER) cc_final: 0.6386 (tmtt) REVERT: b 675 ASP cc_start: 0.8617 (m-30) cc_final: 0.8129 (t0) REVERT: b 916 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.8299 (mtm-85) outliers start: 69 outliers final: 34 residues processed: 131 average time/residue: 0.4261 time to fit residues: 61.2897 Evaluate side-chains 100 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 64 time to evaluate : 0.350 ------------------------------------------------------------------------------- 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 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 143 VAL 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 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 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 621 LYS Chi-restraints excluded: chain b residue 649 LYS 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 53 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 25 optimal weight: 30.0000 chunk 65 optimal weight: 0.5980 chunk 57 optimal weight: 30.0000 chunk 13 optimal weight: 10.0000 chunk 11 optimal weight: 7.9990 chunk 82 optimal weight: 0.1980 chunk 68 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 14 optimal weight: 20.0000 overall best weight: 1.7384 ------------------------------------------------------------------------------- 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 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 171 HIS ** b 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 517 ASN ** b 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 740 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 962 ASN ** 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 = 0.4454 r_free = 0.4454 target = 0.103905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.078543 restraints weight = 35475.578| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 4.71 r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.5375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8830 Z= 0.162 Angle : 0.689 10.104 12060 Z= 0.358 Chirality : 0.046 0.244 1379 Planarity : 0.005 0.042 1515 Dihedral : 7.360 59.175 1438 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.69 % Favored : 97.21 % Rotamer: Outliers : 6.41 % Allowed : 31.62 % Favored : 61.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.25), residues: 1039 helix: 1.53 (0.24), residues: 443 sheet: -0.11 (0.35), residues: 212 loop : -0.32 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG b 201 TYR 0.020 0.002 TYR b 712 PHE 0.019 0.002 PHE a 116 TRP 0.021 0.002 TRP b 958 HIS 0.012 0.002 HIS b 171 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 8811) covalent geometry : angle 0.68302 (12008) SS BOND : bond 0.00310 ( 5) SS BOND : angle 1.31037 ( 10) hydrogen bonds : bond 0.05684 ( 379) hydrogen bonds : angle 5.78183 ( 1101) link_BETA1-4 : bond 0.00251 ( 7) link_BETA1-4 : angle 1.40688 ( 21) link_BETA1-6 : bond 0.00901 ( 1) link_BETA1-6 : angle 0.82282 ( 3) link_NAG-ASN : bond 0.00250 ( 6) link_NAG-ASN : angle 1.87186 ( 18) *********************** 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 129 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 69 time to evaluate : 0.389 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: a 37 ILE cc_start: 0.8335 (mm) cc_final: 0.7416 (tp) REVERT: a 128 ASN cc_start: 0.9339 (t0) cc_final: 0.8970 (m-40) REVERT: b 200 TYR cc_start: 0.8193 (p90) cc_final: 0.7920 (p90) REVERT: b 315 MET cc_start: 0.7356 (mmp) cc_final: 0.7091 (mmp) REVERT: b 490 LEU cc_start: 0.8745 (tp) cc_final: 0.8457 (mp) REVERT: b 675 ASP cc_start: 0.8614 (m-30) cc_final: 0.8146 (t0) outliers start: 60 outliers final: 37 residues processed: 124 average time/residue: 0.4214 time to fit residues: 57.3690 Evaluate side-chains 94 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 57 time to evaluate : 0.359 ------------------------------------------------------------------------------- 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 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 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 85 THR Chi-restraints excluded: chain b residue 130 SER Chi-restraints excluded: chain b residue 143 VAL Chi-restraints excluded: chain b residue 164 VAL Chi-restraints excluded: chain b residue 169 VAL 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 494 SER Chi-restraints excluded: chain b residue 497 LEU Chi-restraints excluded: chain b residue 542 THR 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 649 LYS Chi-restraints excluded: chain b residue 682 VAL Chi-restraints excluded: chain b residue 803 THR 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 96 optimal weight: 6.9990 chunk 60 optimal weight: 20.0000 chunk 67 optimal weight: 6.9990 chunk 89 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 chunk 32 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 34 optimal weight: 30.0000 chunk 51 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 207 ASN ** b 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 644 GLN ** b 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 680 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.098323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.072597 restraints weight = 36881.972| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 4.57 r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.5955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 8830 Z= 0.311 Angle : 0.799 10.508 12060 Z= 0.430 Chirality : 0.050 0.293 1379 Planarity : 0.006 0.057 1515 Dihedral : 7.522 59.499 1433 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 19.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.46 % Favored : 96.44 % Rotamer: Outliers : 8.01 % Allowed : 29.17 % Favored : 62.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.25), residues: 1039 helix: 0.79 (0.24), residues: 435 sheet: -0.14 (0.36), residues: 208 loop : -0.66 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG b 719 TYR 0.021 0.003 TYR b 589 PHE 0.025 0.004 PHE b 970 TRP 0.021 0.003 TRP b 787 HIS 0.010 0.002 HIS b 671 Details of bonding type rmsd covalent geometry : bond 0.00702 ( 8811) covalent geometry : angle 0.79240 (12008) SS BOND : bond 0.00445 ( 5) SS BOND : angle 1.84385 ( 10) hydrogen bonds : bond 0.08164 ( 379) hydrogen bonds : angle 6.16537 ( 1101) link_BETA1-4 : bond 0.00282 ( 7) link_BETA1-4 : angle 1.35534 ( 21) link_BETA1-6 : bond 0.00864 ( 1) link_BETA1-6 : angle 0.91096 ( 3) link_NAG-ASN : bond 0.00772 ( 6) link_NAG-ASN : angle 2.19195 ( 18) *********************** 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 137 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 62 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 76 ASP cc_start: 0.3163 (OUTLIER) cc_final: 0.1915 (p0) REVERT: a 81 TYR cc_start: 0.7689 (m-10) cc_final: 0.7345 (m-80) REVERT: b 119 CYS cc_start: 0.6334 (OUTLIER) cc_final: 0.6042 (t) REVERT: b 200 TYR cc_start: 0.8124 (p90) cc_final: 0.7907 (p90) REVERT: b 281 MET cc_start: 0.6898 (ptp) cc_final: 0.6200 (ppp) REVERT: b 370 GLU cc_start: 0.6811 (OUTLIER) cc_final: 0.6547 (mt-10) REVERT: b 479 ASP cc_start: 0.6758 (OUTLIER) cc_final: 0.6145 (p0) REVERT: b 490 LEU cc_start: 0.8839 (tp) cc_final: 0.8478 (mp) REVERT: b 675 ASP cc_start: 0.8645 (m-30) cc_final: 0.8259 (t0) REVERT: b 681 ILE cc_start: 0.8959 (OUTLIER) cc_final: 0.8697 (tp) outliers start: 75 outliers final: 39 residues processed: 126 average time/residue: 0.3996 time to fit residues: 55.5611 Evaluate side-chains 102 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 58 time to evaluate : 0.353 ------------------------------------------------------------------------------- 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 59 ILE Chi-restraints excluded: chain a residue 70 VAL Chi-restraints excluded: chain a residue 76 ASP 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 97 ARG 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 119 CYS Chi-restraints excluded: chain b residue 130 SER Chi-restraints excluded: chain b residue 142 ARG Chi-restraints excluded: chain b residue 143 VAL 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 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 370 GLU 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 497 LEU 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 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 844 THR 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 61 optimal weight: 4.9990 chunk 48 optimal weight: 10.0000 chunk 63 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 89 optimal weight: 0.9980 chunk 92 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 181 GLN ** b 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 297 GLN ** b 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4421 r_free = 0.4421 target = 0.101844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.076435 restraints weight = 35728.249| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 4.78 r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.6247 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= 0.145 Angle : 0.693 10.604 12060 Z= 0.359 Chirality : 0.045 0.253 1379 Planarity : 0.005 0.063 1515 Dihedral : 6.734 57.956 1432 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.27 % Favored : 96.63 % Rotamer: Outliers : 5.77 % Allowed : 32.80 % Favored : 61.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.25), residues: 1039 helix: 1.15 (0.24), residues: 441 sheet: -0.10 (0.36), residues: 205 loop : -0.66 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG a 148 TYR 0.020 0.001 TYR a 163 PHE 0.022 0.002 PHE a 118 TRP 0.043 0.002 TRP b 77 HIS 0.005 0.001 HIS a 83 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 8811) covalent geometry : angle 0.68889 (12008) SS BOND : bond 0.00261 ( 5) SS BOND : angle 1.46950 ( 10) hydrogen bonds : bond 0.05312 ( 379) hydrogen bonds : angle 5.66392 ( 1101) link_BETA1-4 : bond 0.00360 ( 7) link_BETA1-4 : angle 1.20442 ( 21) link_BETA1-6 : bond 0.00739 ( 1) link_BETA1-6 : angle 0.80580 ( 3) link_NAG-ASN : bond 0.00256 ( 6) link_NAG-ASN : angle 1.47996 ( 18) *********************** 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 117 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 63 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 81 TYR cc_start: 0.7773 (m-10) cc_final: 0.7438 (m-80) REVERT: a 130 PHE cc_start: 0.4964 (m-80) cc_final: 0.4459 (m-80) REVERT: b 200 TYR cc_start: 0.8273 (p90) cc_final: 0.7997 (p90) REVERT: b 217 GLN cc_start: 0.8821 (tm-30) cc_final: 0.8369 (tm-30) REVERT: b 281 MET cc_start: 0.6502 (ptp) cc_final: 0.6100 (tmm) REVERT: b 479 ASP cc_start: 0.6524 (OUTLIER) cc_final: 0.5915 (p0) REVERT: b 490 LEU cc_start: 0.8804 (tp) cc_final: 0.8549 (OUTLIER) REVERT: b 675 ASP cc_start: 0.8587 (m-30) cc_final: 0.8206 (t0) outliers start: 54 outliers final: 35 residues processed: 112 average time/residue: 0.3759 time to fit residues: 46.9503 Evaluate side-chains 91 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 56 time to evaluate : 0.440 ------------------------------------------------------------------------------- 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 79 SER Chi-restraints excluded: chain a residue 89 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 119 CYS Chi-restraints excluded: chain b residue 130 SER Chi-restraints excluded: chain b residue 143 VAL 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 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 3 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 chunk 42 optimal weight: 9.9990 chunk 64 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 28 optimal weight: 30.0000 chunk 74 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 46 optimal weight: 9.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 181 GLN ** b 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 680 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 = 0.4398 r_free = 0.4398 target = 0.100477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.074988 restraints weight = 36737.282| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 4.84 r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.6473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8830 Z= 0.173 Angle : 0.692 11.254 12060 Z= 0.360 Chirality : 0.046 0.330 1379 Planarity : 0.005 0.058 1515 Dihedral : 6.567 56.828 1432 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.75 % Favored : 96.15 % Rotamer: Outliers : 5.56 % Allowed : 32.91 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.26), residues: 1039 helix: 1.13 (0.25), residues: 441 sheet: -0.15 (0.36), residues: 205 loop : -0.71 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG a 148 TYR 0.014 0.002 TYR b 284 PHE 0.021 0.002 PHE b 496 TRP 0.044 0.002 TRP b 77 HIS 0.015 0.002 HIS b 740 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 8811) covalent geometry : angle 0.68739 (12008) SS BOND : bond 0.00321 ( 5) SS BOND : angle 1.47002 ( 10) hydrogen bonds : bond 0.05832 ( 379) hydrogen bonds : angle 5.63846 ( 1101) link_BETA1-4 : bond 0.00289 ( 7) link_BETA1-4 : angle 1.32287 ( 21) link_BETA1-6 : bond 0.00608 ( 1) link_BETA1-6 : angle 0.79228 ( 3) link_NAG-ASN : bond 0.00292 ( 6) link_NAG-ASN : angle 1.55137 ( 18) *********************** 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 113 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 61 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 81 TYR cc_start: 0.7874 (m-10) cc_final: 0.7493 (m-80) REVERT: a 130 PHE cc_start: 0.4737 (m-80) cc_final: 0.4530 (m-80) REVERT: b 119 CYS cc_start: 0.6193 (OUTLIER) cc_final: 0.5354 (t) REVERT: b 181 GLN cc_start: 0.1515 (OUTLIER) cc_final: 0.1093 (tm-30) REVERT: b 200 TYR cc_start: 0.8261 (p90) cc_final: 0.7970 (p90) REVERT: b 217 GLN cc_start: 0.8806 (tm-30) cc_final: 0.8365 (tm-30) REVERT: b 315 MET cc_start: 0.7829 (tmt) cc_final: 0.7600 (tmm) REVERT: b 479 ASP cc_start: 0.6478 (OUTLIER) cc_final: 0.5862 (p0) REVERT: b 490 LEU cc_start: 0.8801 (tp) cc_final: 0.8544 (OUTLIER) REVERT: b 675 ASP cc_start: 0.8622 (m-30) cc_final: 0.8242 (t0) outliers start: 52 outliers final: 33 residues processed: 108 average time/residue: 0.3912 time to fit residues: 46.8774 Evaluate side-chains 92 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 57 time to evaluate : 0.349 ------------------------------------------------------------------------------- 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 89 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 141 CYS Chi-restraints excluded: chain a residue 149 THR Chi-restraints excluded: chain a residue 165 GLU Chi-restraints excluded: chain b residue 119 CYS 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 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 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 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 876 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 13 optimal weight: 9.9990 chunk 30 optimal weight: 8.9990 chunk 97 optimal weight: 10.0000 chunk 91 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 24 optimal weight: 40.0000 chunk 54 optimal weight: 0.9980 chunk 17 optimal weight: 30.0000 chunk 48 optimal weight: 8.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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 399 GLN ** b 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 680 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4376 r_free = 0.4376 target = 0.099257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.073525 restraints weight = 36356.329| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 4.64 r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.6703 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= 0.213 Angle : 0.722 11.706 12060 Z= 0.377 Chirality : 0.047 0.312 1379 Planarity : 0.006 0.059 1515 Dihedral : 6.424 50.925 1430 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 17.19 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.14 % Favored : 95.77 % Rotamer: Outliers : 5.34 % Allowed : 33.65 % Favored : 61.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.26), residues: 1039 helix: 1.00 (0.24), residues: 440 sheet: -0.09 (0.37), residues: 204 loop : -0.92 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG a 148 TYR 0.021 0.002 TYR a 163 PHE 0.026 0.002 PHE a 118 TRP 0.045 0.002 TRP b 77 HIS 0.011 0.002 HIS b 740 Details of bonding type rmsd covalent geometry : bond 0.00482 ( 8811) covalent geometry : angle 0.71752 (12008) SS BOND : bond 0.00376 ( 5) SS BOND : angle 1.54571 ( 10) hydrogen bonds : bond 0.06313 ( 379) hydrogen bonds : angle 5.68063 ( 1101) link_BETA1-4 : bond 0.00286 ( 7) link_BETA1-4 : angle 1.34087 ( 21) link_BETA1-6 : bond 0.00614 ( 1) link_BETA1-6 : angle 0.77238 ( 3) link_NAG-ASN : bond 0.00335 ( 6) link_NAG-ASN : angle 1.64983 ( 18) *********************** 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 109 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 59 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 81 TYR cc_start: 0.7862 (m-10) cc_final: 0.7470 (m-80) REVERT: a 130 PHE cc_start: 0.5203 (m-80) cc_final: 0.4959 (m-80) REVERT: b 119 CYS cc_start: 0.6377 (OUTLIER) cc_final: 0.5500 (t) REVERT: b 200 TYR cc_start: 0.8233 (p90) cc_final: 0.8010 (p90) REVERT: b 217 GLN cc_start: 0.8878 (tm-30) cc_final: 0.8408 (tm-30) REVERT: b 281 MET cc_start: 0.6730 (ptp) cc_final: 0.5868 (tmm) REVERT: b 315 MET cc_start: 0.7835 (tmt) cc_final: 0.7578 (tmm) REVERT: b 360 MET cc_start: 0.6744 (mmm) cc_final: 0.6501 (mmm) REVERT: b 479 ASP cc_start: 0.6650 (OUTLIER) cc_final: 0.6153 (p0) REVERT: b 490 LEU cc_start: 0.8840 (tp) cc_final: 0.8559 (OUTLIER) REVERT: b 675 ASP cc_start: 0.8633 (m-30) cc_final: 0.8280 (t0) outliers start: 50 outliers final: 36 residues processed: 104 average time/residue: 0.3876 time to fit residues: 44.8636 Evaluate side-chains 91 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 54 time to evaluate : 0.372 ------------------------------------------------------------------------------- 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 141 CYS Chi-restraints excluded: chain a residue 149 THR Chi-restraints excluded: chain a residue 165 GLU Chi-restraints excluded: chain a residue 170 VAL Chi-restraints excluded: chain b residue 119 CYS 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 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 479 ASP 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 649 LYS 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 876 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 21 optimal weight: 30.0000 chunk 32 optimal weight: 7.9990 chunk 24 optimal weight: 7.9990 chunk 97 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 16 optimal weight: 30.0000 chunk 44 optimal weight: 0.5980 chunk 89 optimal weight: 2.9990 chunk 11 optimal weight: 8.9990 chunk 55 optimal weight: 0.9980 chunk 41 optimal weight: 20.0000 overall best weight: 2.9186 ------------------------------------------------------------------------------- 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 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 680 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 = 0.4382 r_free = 0.4382 target = 0.099213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.073475 restraints weight = 36037.503| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 4.56 r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.6897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8830 Z= 0.192 Angle : 0.720 11.974 12060 Z= 0.371 Chirality : 0.047 0.313 1379 Planarity : 0.006 0.072 1515 Dihedral : 6.384 49.123 1430 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.04 % Favored : 95.86 % Rotamer: Outliers : 4.91 % Allowed : 33.87 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.25), residues: 1039 helix: 0.97 (0.24), residues: 439 sheet: -0.16 (0.37), residues: 204 loop : -1.02 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG a 148 TYR 0.023 0.002 TYR b 182 PHE 0.022 0.002 PHE b 496 TRP 0.042 0.002 TRP b 77 HIS 0.011 0.001 HIS b 740 Details of bonding type rmsd covalent geometry : bond 0.00433 ( 8811) covalent geometry : angle 0.71494 (12008) SS BOND : bond 0.00387 ( 5) SS BOND : angle 1.93350 ( 10) hydrogen bonds : bond 0.06053 ( 379) hydrogen bonds : angle 5.73427 ( 1101) link_BETA1-4 : bond 0.00303 ( 7) link_BETA1-4 : angle 1.34117 ( 21) link_BETA1-6 : bond 0.00588 ( 1) link_BETA1-6 : angle 0.75662 ( 3) link_NAG-ASN : bond 0.00256 ( 6) link_NAG-ASN : angle 1.58777 ( 18) *********************** 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 105 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 59 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 81 TYR cc_start: 0.7823 (m-10) cc_final: 0.7438 (m-10) REVERT: a 130 PHE cc_start: 0.5420 (m-80) cc_final: 0.5145 (m-80) REVERT: a 148 ARG cc_start: 0.7578 (mtp-110) cc_final: 0.7344 (ptm160) REVERT: b 119 CYS cc_start: 0.6549 (OUTLIER) cc_final: 0.5635 (t) REVERT: b 200 TYR cc_start: 0.8211 (p90) cc_final: 0.7987 (p90) REVERT: b 217 GLN cc_start: 0.8903 (tm-30) cc_final: 0.8425 (tm-30) REVERT: b 281 MET cc_start: 0.6948 (ptp) cc_final: 0.6348 (ppp) REVERT: b 288 TYR cc_start: 0.8531 (p90) cc_final: 0.8233 (p90) REVERT: b 289 ILE cc_start: 0.8708 (mm) cc_final: 0.8407 (tp) REVERT: b 315 MET cc_start: 0.7820 (tmt) cc_final: 0.7569 (tmm) REVERT: b 360 MET cc_start: 0.6885 (mmm) cc_final: 0.6670 (mmm) REVERT: b 479 ASP cc_start: 0.6678 (OUTLIER) cc_final: 0.6241 (p0) REVERT: b 490 LEU cc_start: 0.8822 (tp) cc_final: 0.8551 (OUTLIER) REVERT: b 591 TRP cc_start: 0.7831 (OUTLIER) cc_final: 0.5658 (m100) REVERT: b 675 ASP cc_start: 0.8619 (m-30) cc_final: 0.8296 (t0) REVERT: b 957 LYS cc_start: 0.6627 (OUTLIER) cc_final: 0.6390 (mmtm) outliers start: 46 outliers final: 36 residues processed: 101 average time/residue: 0.3807 time to fit residues: 42.7430 Evaluate side-chains 95 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 56 time to evaluate : 0.375 ------------------------------------------------------------------------------- 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 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 165 GLU Chi-restraints excluded: chain a residue 170 VAL Chi-restraints excluded: chain b residue 119 CYS 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 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 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 755 LEU 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 876 SER Chi-restraints excluded: chain b residue 957 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 23 optimal weight: 8.9990 chunk 28 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 18 optimal weight: 20.0000 chunk 31 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 53 optimal weight: 0.8980 chunk 33 optimal weight: 10.0000 overall best weight: 5.1788 ------------------------------------------------------------------------------- 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 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 680 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 = 0.4340 r_free = 0.4340 target = 0.096954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.070940 restraints weight = 36668.957| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 4.62 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.7130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 8830 Z= 0.296 Angle : 0.804 12.298 12060 Z= 0.422 Chirality : 0.050 0.256 1379 Planarity : 0.006 0.075 1515 Dihedral : 6.441 51.060 1429 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 18.96 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.81 % Favored : 95.09 % Rotamer: Outliers : 4.70 % Allowed : 33.87 % Favored : 61.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.25), residues: 1039 helix: 0.63 (0.24), residues: 432 sheet: -0.36 (0.37), residues: 205 loop : -1.22 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG a 148 TYR 0.043 0.003 TYR a 163 PHE 0.025 0.003 PHE b 970 TRP 0.031 0.003 TRP b 77 HIS 0.010 0.002 HIS b 740 Details of bonding type rmsd covalent geometry : bond 0.00672 ( 8811) covalent geometry : angle 0.79781 (12008) SS BOND : bond 0.00505 ( 5) SS BOND : angle 2.12617 ( 10) hydrogen bonds : bond 0.07471 ( 379) hydrogen bonds : angle 5.99552 ( 1101) link_BETA1-4 : bond 0.00285 ( 7) link_BETA1-4 : angle 1.50117 ( 21) link_BETA1-6 : bond 0.00603 ( 1) link_BETA1-6 : angle 0.76639 ( 3) link_NAG-ASN : bond 0.00461 ( 6) link_NAG-ASN : angle 1.93495 ( 18) ********************** 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 104 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 60 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 59 ILE cc_start: 0.9235 (tt) cc_final: 0.8918 (pp) REVERT: a 81 TYR cc_start: 0.7808 (m-10) cc_final: 0.7393 (m-10) REVERT: a 148 ARG cc_start: 0.7852 (mtp-110) cc_final: 0.7644 (ptm160) REVERT: b 119 CYS cc_start: 0.6497 (OUTLIER) cc_final: 0.5670 (t) REVERT: b 217 GLN cc_start: 0.8721 (tm-30) cc_final: 0.8365 (tm-30) REVERT: b 281 MET cc_start: 0.6920 (ptp) cc_final: 0.6354 (ppp) REVERT: b 288 TYR cc_start: 0.8647 (p90) cc_final: 0.8380 (p90) REVERT: b 289 ILE cc_start: 0.8705 (mm) cc_final: 0.8465 (tp) REVERT: b 315 MET cc_start: 0.7871 (tmt) cc_final: 0.7614 (tmm) REVERT: b 479 ASP cc_start: 0.6785 (OUTLIER) cc_final: 0.6361 (p0) REVERT: b 490 LEU cc_start: 0.8849 (tp) cc_final: 0.8532 (OUTLIER) REVERT: b 591 TRP cc_start: 0.7978 (OUTLIER) cc_final: 0.6027 (m100) REVERT: b 675 ASP cc_start: 0.8636 (m-30) cc_final: 0.8352 (t0) REVERT: b 957 LYS cc_start: 0.6721 (OUTLIER) cc_final: 0.6511 (mmtm) outliers start: 44 outliers final: 35 residues processed: 101 average time/residue: 0.3888 time to fit residues: 43.6833 Evaluate side-chains 96 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 58 time to evaluate : 0.358 ------------------------------------------------------------------------------- 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 97 ARG 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 a residue 158 SER Chi-restraints excluded: chain a residue 170 VAL Chi-restraints excluded: chain b residue 119 CYS 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 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 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 803 THR 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 869 SER Chi-restraints excluded: chain b residue 876 SER Chi-restraints excluded: chain b residue 895 LEU Chi-restraints excluded: chain b residue 957 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 13 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 74 optimal weight: 0.3980 chunk 97 optimal weight: 5.9990 chunk 15 optimal weight: 20.0000 chunk 7 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 chunk 94 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 77 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 overall best weight: 1.8784 ------------------------------------------------------------------------------- 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 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 680 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 = 0.4388 r_free = 0.4388 target = 0.099466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.073849 restraints weight = 36495.678| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 4.65 r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.7254 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= 0.156 Angle : 0.719 12.414 12060 Z= 0.367 Chirality : 0.046 0.242 1379 Planarity : 0.005 0.063 1515 Dihedral : 6.039 52.354 1426 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.95 % Favored : 95.96 % Rotamer: Outliers : 4.27 % Allowed : 34.62 % Favored : 61.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.14 (0.26), residues: 1039 helix: 0.91 (0.24), residues: 439 sheet: -0.18 (0.39), residues: 188 loop : -1.08 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG a 148 TYR 0.027 0.002 TYR b 182 PHE 0.020 0.002 PHE b 496 TRP 0.029 0.002 TRP b 524 HIS 0.011 0.001 HIS b 740 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 8811) covalent geometry : angle 0.71437 (12008) SS BOND : bond 0.00325 ( 5) SS BOND : angle 1.62442 ( 10) hydrogen bonds : bond 0.05483 ( 379) hydrogen bonds : angle 5.60790 ( 1101) link_BETA1-4 : bond 0.00334 ( 7) link_BETA1-4 : angle 1.36823 ( 21) link_BETA1-6 : bond 0.00534 ( 1) link_BETA1-6 : angle 0.78579 ( 3) link_NAG-ASN : bond 0.00235 ( 6) link_NAG-ASN : angle 1.46529 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3585.21 seconds wall clock time: 62 minutes 5.82 seconds (3725.82 seconds total)