Starting phenix.real_space_refine on Sat May 10 19:03:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8afe_15395/05_2025/8afe_15395.cif Found real_map, /net/cci-nas-00/data/ceres_data/8afe_15395/05_2025/8afe_15395.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8afe_15395/05_2025/8afe_15395.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8afe_15395/05_2025/8afe_15395.map" model { file = "/net/cci-nas-00/data/ceres_data/8afe_15395/05_2025/8afe_15395.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8afe_15395/05_2025/8afe_15395.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 23 5.16 5 C 4124 2.51 5 N 1282 2.21 5 O 1356 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 6785 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 739 Classifications: {'peptide': 96} Link IDs: {'TRANS': 95} Chain: "B" Number of atoms: 747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 747 Classifications: {'peptide': 97} Link IDs: {'TRANS': 96} Chain: "D" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 869 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 2, 'TRANS': 109} Chain breaks: 1 Chain: "C" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 869 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 2, 'TRANS': 109} Chain breaks: 1 Chain: "E" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 600 Classifications: {'peptide': 79} Link IDs: {'TRANS': 78} Chain: "F" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 600 Classifications: {'peptide': 79} Link IDs: {'TRANS': 78} Chain: "G" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 333 Classifications: {'peptide': 43} Link IDs: {'TRANS': 42} Chain: "H" Number of atoms: 299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 299 Classifications: {'peptide': 39} Link IDs: {'TRANS': 38} Chain: "I" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 860 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 2, 'TRANS': 108} Chain breaks: 1 Chain: "J" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 869 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 2, 'TRANS': 109} Chain breaks: 1 Time building chain proxies: 4.49, per 1000 atoms: 0.66 Number of scatterers: 6785 At special positions: 0 Unit cell: (63.6, 242.475, 88.775, 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 23 16.00 O 1356 8.00 N 1282 7.00 C 4124 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS D 795 " - pdb=" SG CYS D 868 " distance=2.03 Simple disulfide: pdb=" SG CYS C 795 " - pdb=" SG CYS C 868 " distance=2.03 Simple disulfide: pdb=" SG CYS I 795 " - pdb=" SG CYS I 868 " distance=2.03 Simple disulfide: pdb=" SG CYS J 795 " - pdb=" SG CYS J 868 " distance=2.03 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 Time building additional restraints: 1.43 Conformation dependent library (CDL) restraints added in 895.8 milliseconds 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1648 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 13 sheets defined 50.3% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 350 through 357 removed outlier: 3.961A pdb=" N ASP A 354 " --> pdb=" O HIS A 350 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR A 355 " --> pdb=" O ALA A 351 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG A 357 " --> pdb=" O VAL A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 441 removed outlier: 3.647A pdb=" N GLU A 362 " --> pdb=" O ALA A 358 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ARG A 363 " --> pdb=" O THR A 359 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA A 368 " --> pdb=" O ALA A 364 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS A 369 " --> pdb=" O ASP A 365 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL A 372 " --> pdb=" O ALA A 368 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER A 425 " --> pdb=" O GLU A 421 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N GLU A 426 " --> pdb=" O ARG A 422 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG A 441 " --> pdb=" O ALA A 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 432 removed outlier: 3.877A pdb=" N ALA B 356 " --> pdb=" O GLY B 352 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU B 362 " --> pdb=" O ALA B 358 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU B 367 " --> pdb=" O ARG B 363 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA B 371 " --> pdb=" O LEU B 367 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL B 372 " --> pdb=" O ALA B 368 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU B 383 " --> pdb=" O LYS B 379 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG B 404 " --> pdb=" O ASP B 400 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE B 420 " --> pdb=" O LEU B 416 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU B 429 " --> pdb=" O SER B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 442 Processing helix chain 'B' and resid 443 through 446 Processing helix chain 'D' and resid 859 through 863 removed outlier: 3.554A pdb=" N THR D 863 " --> pdb=" O PRO D 860 " (cutoff:3.500A) Processing helix chain 'C' and resid 859 through 863 removed outlier: 3.892A pdb=" N THR C 863 " --> pdb=" O PRO C 860 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 163 removed outlier: 3.828A pdb=" N LEU E 115 " --> pdb=" O VAL E 111 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ALA E 116 " --> pdb=" O SER E 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 163 removed outlier: 3.591A pdb=" N ALA F 92 " --> pdb=" O ILE F 88 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ASN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 404 through 439 removed outlier: 3.796A pdb=" N ALA G 411 " --> pdb=" O ALA G 407 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS G 412 " --> pdb=" O THR G 408 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA G 418 " --> pdb=" O ALA G 414 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLU G 426 " --> pdb=" O ARG G 422 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA G 427 " --> pdb=" O LEU G 423 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU G 429 " --> pdb=" O SER G 425 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA G 433 " --> pdb=" O LEU G 429 " (cutoff:3.500A) Processing helix chain 'G' and resid 440 through 444 Processing helix chain 'H' and resid 405 through 431 removed outlier: 3.648A pdb=" N HIS H 409 " --> pdb=" O ASP H 405 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU H 410 " --> pdb=" O SER H 406 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE H 420 " --> pdb=" O LEU H 416 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU H 421 " --> pdb=" O GLN H 417 " (cutoff:3.500A) Processing helix chain 'H' and resid 432 through 441 removed outlier: 3.589A pdb=" N ASP H 440 " --> pdb=" O ALA H 436 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG H 441 " --> pdb=" O ALA H 437 " (cutoff:3.500A) Processing helix chain 'I' and resid 859 through 863 removed outlier: 3.602A pdb=" N THR I 863 " --> pdb=" O PRO I 860 " (cutoff:3.500A) Processing helix chain 'J' and resid 859 through 863 removed outlier: 3.819A pdb=" N THR J 863 " --> pdb=" O PRO J 860 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 6 through 7 removed outlier: 3.711A pdb=" N VAL D 851 " --> pdb=" O CYS D 795 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR D 850 " --> pdb=" O ASP D 845 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.212A pdb=" N GLY D 10 " --> pdb=" O THR D 885 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N MET D 807 " --> pdb=" O VAL D 823 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N VAL D 823 " --> pdb=" O MET D 807 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N TRP D 809 " --> pdb=" O VAL D 821 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 870 through 872 Processing sheet with id=AA4, first strand: chain 'C' and resid 5 through 7 Processing sheet with id=AA5, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.550A pdb=" N VAL C 12 " --> pdb=" O THR C 885 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 830 through 832 removed outlier: 7.030A pdb=" N TRP C 809 " --> pdb=" O VAL C 821 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N VAL C 823 " --> pdb=" O MET C 807 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N MET C 807 " --> pdb=" O VAL C 823 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 5 through 6 removed outlier: 3.613A pdb=" N VAL I 851 " --> pdb=" O CYS I 795 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.809A pdb=" N MET I 807 " --> pdb=" O VAL I 823 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N VAL I 823 " --> pdb=" O MET I 807 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N TRP I 809 " --> pdb=" O VAL I 821 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 870 through 872 removed outlier: 3.571A pdb=" N TYR I 872 " --> pdb=" O SER I 875 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 4 through 6 Processing sheet with id=AB2, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.544A pdb=" N GLY J 10 " --> pdb=" O THR J 885 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.544A pdb=" N GLY J 10 " --> pdb=" O THR J 885 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 792 through 793 463 hydrogen bonds defined for protein. 1293 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: 1.83 Time building geometry restraints manager: 1.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2430 1.34 - 1.46: 1083 1.46 - 1.58: 3290 1.58 - 1.70: 0 1.70 - 1.81: 38 Bond restraints: 6841 Sorted by residual: bond pdb=" CB TRP C 827 " pdb=" CG TRP C 827 " ideal model delta sigma weight residual 1.498 1.446 0.052 3.10e-02 1.04e+03 2.78e+00 bond pdb=" CG1 ILE D 806 " pdb=" CD1 ILE D 806 " ideal model delta sigma weight residual 1.513 1.463 0.050 3.90e-02 6.57e+02 1.67e+00 bond pdb=" C TYR J 832 " pdb=" N VAL J 833 " ideal model delta sigma weight residual 1.334 1.317 0.016 1.29e-02 6.01e+03 1.62e+00 bond pdb=" CB ASN I 869 " pdb=" CG ASN I 869 " ideal model delta sigma weight residual 1.516 1.484 0.032 2.50e-02 1.60e+03 1.59e+00 bond pdb=" C LYS D 859 " pdb=" N PRO D 860 " ideal model delta sigma weight residual 1.337 1.323 0.014 1.11e-02 8.12e+03 1.49e+00 ... (remaining 6836 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.17: 8401 1.17 - 2.34: 683 2.34 - 3.51: 99 3.51 - 4.68: 19 4.68 - 5.85: 7 Bond angle restraints: 9209 Sorted by residual: angle pdb=" N ILE J 806 " pdb=" CA ILE J 806 " pdb=" C ILE J 806 " ideal model delta sigma weight residual 108.93 113.36 -4.43 1.35e+00 5.49e-01 1.08e+01 angle pdb=" N ILE D 806 " pdb=" CA ILE D 806 " pdb=" C ILE D 806 " ideal model delta sigma weight residual 109.30 113.38 -4.08 1.31e+00 5.83e-01 9.70e+00 angle pdb=" C ALA E 118 " pdb=" N GLU E 119 " pdb=" CA GLU E 119 " ideal model delta sigma weight residual 120.68 115.81 4.87 1.70e+00 3.46e-01 8.22e+00 angle pdb=" C SER E 112 " pdb=" N ALA E 113 " pdb=" CA ALA E 113 " ideal model delta sigma weight residual 122.42 118.24 4.18 1.55e+00 4.16e-01 7.29e+00 angle pdb=" CA TRP C 827 " pdb=" CB TRP C 827 " pdb=" CG TRP C 827 " ideal model delta sigma weight residual 113.60 108.52 5.08 1.90e+00 2.77e-01 7.16e+00 ... (remaining 9204 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.25: 3786 17.25 - 34.51: 381 34.51 - 51.76: 46 51.76 - 69.02: 6 69.02 - 86.27: 14 Dihedral angle restraints: 4233 sinusoidal: 1691 harmonic: 2542 Sorted by residual: dihedral pdb=" CB CYS C 795 " pdb=" SG CYS C 795 " pdb=" SG CYS C 868 " pdb=" CB CYS C 868 " ideal model delta sinusoidal sigma weight residual 93.00 43.73 49.27 1 1.00e+01 1.00e-02 3.34e+01 dihedral pdb=" CB CYS I 795 " pdb=" SG CYS I 795 " pdb=" SG CYS I 868 " pdb=" CB CYS I 868 " ideal model delta sinusoidal sigma weight residual 93.00 44.90 48.10 1 1.00e+01 1.00e-02 3.19e+01 dihedral pdb=" CA HIS A 350 " pdb=" C HIS A 350 " pdb=" N ALA A 351 " pdb=" CA ALA A 351 " ideal model delta harmonic sigma weight residual 180.00 -154.67 -25.33 0 5.00e+00 4.00e-02 2.57e+01 ... (remaining 4230 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 711 0.039 - 0.079: 242 0.079 - 0.118: 79 0.118 - 0.158: 4 0.158 - 0.197: 5 Chirality restraints: 1041 Sorted by residual: chirality pdb=" CB ILE J 842 " pdb=" CA ILE J 842 " pdb=" CG1 ILE J 842 " pdb=" CG2 ILE J 842 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.72e-01 chirality pdb=" CB ILE I 842 " pdb=" CA ILE I 842 " pdb=" CG1 ILE I 842 " pdb=" CG2 ILE I 842 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.14e-01 chirality pdb=" CB VAL J 823 " pdb=" CA VAL J 823 " pdb=" CG1 VAL J 823 " pdb=" CG2 VAL J 823 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.18 2.00e-01 2.50e+01 8.50e-01 ... (remaining 1038 not shown) Planarity restraints: 1219 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 859 " 0.057 5.00e-02 4.00e+02 8.65e-02 1.20e+01 pdb=" N PRO C 860 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO C 860 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO C 860 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 417 " -0.011 2.00e-02 2.50e+03 2.26e-02 5.12e+00 pdb=" CD GLN B 417 " 0.039 2.00e-02 2.50e+03 pdb=" OE1 GLN B 417 " -0.015 2.00e-02 2.50e+03 pdb=" NE2 GLN B 417 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS J 859 " 0.024 5.00e-02 4.00e+02 3.70e-02 2.19e+00 pdb=" N PRO J 860 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO J 860 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO J 860 " 0.021 5.00e-02 4.00e+02 ... (remaining 1216 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 272 2.71 - 3.26: 6877 3.26 - 3.80: 10416 3.80 - 4.35: 13277 4.35 - 4.90: 22214 Nonbonded interactions: 53056 Sorted by model distance: nonbonded pdb=" O THR B 424 " pdb=" ND2 ASN C 831 " model vdw 2.161 3.120 nonbonded pdb=" NH1 ARG D 799 " pdb=" OG SER D 800 " model vdw 2.201 3.120 nonbonded pdb=" OD1 ASP I 802 " pdb=" NH2 ARG I 844 " model vdw 2.245 3.120 nonbonded pdb=" NH1 ARG I 808 " pdb=" OH TYR I 810 " model vdw 2.245 3.120 nonbonded pdb=" O ASP C 862 " pdb=" OH TYR C 866 " model vdw 2.255 3.040 ... (remaining 53051 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 350 through 445) } ncs_group { reference = (chain 'C' and resid 2 through 887) selection = (chain 'D' and resid 2 through 887) selection = chain 'I' selection = (chain 'J' and resid 2 through 887) } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = (chain 'G' and resid 403 through 441) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 18.070 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6057 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 : 0.006 0.052 6845 Z= 0.272 Angle : 0.700 5.850 9217 Z= 0.430 Chirality : 0.044 0.197 1041 Planarity : 0.004 0.086 1219 Dihedral : 14.166 86.270 2573 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.28), residues: 852 helix: -0.24 (0.25), residues: 379 sheet: -2.06 (0.31), residues: 239 loop : 0.03 (0.44), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP C 827 HIS 0.005 0.002 HIS A 350 PHE 0.005 0.001 PHE I 840 TYR 0.018 0.002 TYR J 13 ARG 0.013 0.001 ARG B 404 Details of bonding type rmsd hydrogen bonds : bond 0.21907 ( 459) hydrogen bonds : angle 9.24475 ( 1293) SS BOND : bond 0.00226 ( 4) SS BOND : angle 1.61102 ( 8) covalent geometry : bond 0.00580 ( 6841) covalent geometry : angle 0.69894 ( 9209) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.674 Fit side-chains revert: symmetry clash REVERT: C 865 VAL cc_start: 0.7852 (m) cc_final: 0.7637 (p) REVERT: I 862 ASP cc_start: 0.7207 (m-30) cc_final: 0.6998 (m-30) REVERT: J 807 MET cc_start: 0.6494 (mmm) cc_final: 0.5574 (mmm) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.2121 time to fit residues: 33.6931 Evaluate side-chains 116 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 70 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 21 optimal weight: 0.4980 chunk 42 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 831 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 854 GLN E 139 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.176246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.165916 restraints weight = 9385.627| |-----------------------------------------------------------------------------| r_work (start): 0.4128 rms_B_bonded: 1.56 r_work: 0.4042 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3915 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6630 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 6845 Z= 0.263 Angle : 0.671 8.547 9217 Z= 0.365 Chirality : 0.044 0.181 1041 Planarity : 0.005 0.067 1219 Dihedral : 5.500 27.507 981 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.44 % Allowed : 9.17 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.29), residues: 852 helix: 0.86 (0.26), residues: 381 sheet: -2.10 (0.31), residues: 226 loop : 0.01 (0.43), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 827 HIS 0.006 0.002 HIS B 350 PHE 0.006 0.001 PHE D 840 TYR 0.015 0.002 TYR C 13 ARG 0.007 0.001 ARG E 129 Details of bonding type rmsd hydrogen bonds : bond 0.05404 ( 459) hydrogen bonds : angle 5.95727 ( 1293) SS BOND : bond 0.00323 ( 4) SS BOND : angle 1.42459 ( 8) covalent geometry : bond 0.00574 ( 6841) covalent geometry : angle 0.67020 ( 9209) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.726 Fit side-chains REVERT: D 839 ARG cc_start: 0.7979 (ttp-110) cc_final: 0.7728 (ttp-110) REVERT: C 865 VAL cc_start: 0.8131 (m) cc_final: 0.7898 (p) REVERT: F 143 ILE cc_start: 0.7701 (OUTLIER) cc_final: 0.7155 (mt) REVERT: H 426 GLU cc_start: 0.7252 (mt-10) cc_final: 0.6971 (mt-10) REVERT: I 817 GLN cc_start: 0.7025 (mp10) cc_final: 0.6633 (mp10) REVERT: I 862 ASP cc_start: 0.7513 (m-30) cc_final: 0.7103 (m-30) REVERT: J 807 MET cc_start: 0.7833 (mmm) cc_final: 0.7526 (mmp) outliers start: 17 outliers final: 9 residues processed: 114 average time/residue: 0.2058 time to fit residues: 31.0246 Evaluate side-chains 120 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 110 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain D residue 834 ASP Chi-restraints excluded: chain C residue 798 SER Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 827 TRP Chi-restraints excluded: chain C residue 836 VAL Chi-restraints excluded: chain C residue 846 SER Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain I residue 821 VAL Chi-restraints excluded: chain J residue 833 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 67 optimal weight: 1.9990 chunk 54 optimal weight: 0.4980 chunk 28 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 chunk 31 optimal weight: 0.1980 chunk 49 optimal weight: 0.7980 chunk 64 optimal weight: 0.5980 chunk 59 optimal weight: 0.5980 chunk 48 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 854 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.178416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.167928 restraints weight = 9422.548| |-----------------------------------------------------------------------------| r_work (start): 0.4152 rms_B_bonded: 1.58 r_work: 0.4066 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3939 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6592 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6845 Z= 0.182 Angle : 0.552 5.751 9217 Z= 0.304 Chirality : 0.040 0.155 1041 Planarity : 0.004 0.059 1219 Dihedral : 5.066 22.012 981 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.58 % Allowed : 13.04 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.30), residues: 852 helix: 1.46 (0.26), residues: 385 sheet: -1.88 (0.31), residues: 244 loop : 0.24 (0.46), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 878 HIS 0.003 0.001 HIS B 350 PHE 0.004 0.001 PHE I 840 TYR 0.014 0.002 TYR C 13 ARG 0.008 0.001 ARG F 129 Details of bonding type rmsd hydrogen bonds : bond 0.04699 ( 459) hydrogen bonds : angle 5.42101 ( 1293) SS BOND : bond 0.00237 ( 4) SS BOND : angle 0.99625 ( 8) covalent geometry : bond 0.00392 ( 6841) covalent geometry : angle 0.55102 ( 9209) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 0.756 Fit side-chains REVERT: A 350 HIS cc_start: 0.3764 (OUTLIER) cc_final: 0.3281 (m-70) REVERT: A 423 LEU cc_start: 0.8235 (tp) cc_final: 0.8033 (tt) REVERT: B 397 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7439 (tp30) REVERT: E 139 ASN cc_start: 0.6234 (t0) cc_final: 0.5712 (t0) REVERT: F 143 ILE cc_start: 0.7625 (OUTLIER) cc_final: 0.7093 (mt) REVERT: H 426 GLU cc_start: 0.7195 (mt-10) cc_final: 0.6875 (mt-10) REVERT: I 817 GLN cc_start: 0.6949 (mp10) cc_final: 0.6562 (mp10) REVERT: I 862 ASP cc_start: 0.7381 (m-30) cc_final: 0.7015 (m-30) REVERT: J 807 MET cc_start: 0.7919 (mmm) cc_final: 0.7496 (mmm) REVERT: J 810 TYR cc_start: 0.6559 (m-80) cc_final: 0.6238 (m-80) REVERT: J 859 LYS cc_start: 0.7128 (mtmm) cc_final: 0.6864 (mtmm) outliers start: 18 outliers final: 7 residues processed: 118 average time/residue: 0.2045 time to fit residues: 31.8887 Evaluate side-chains 120 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 110 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 HIS Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain C residue 798 SER Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 827 TRP Chi-restraints excluded: chain C residue 836 VAL Chi-restraints excluded: chain C residue 846 SER Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain I residue 821 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 56 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 5 GLN C 854 GLN I 883 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.181104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.170183 restraints weight = 9310.801| |-----------------------------------------------------------------------------| r_work (start): 0.4183 rms_B_bonded: 1.75 r_work: 0.4083 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3941 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6679 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 6845 Z= 0.268 Angle : 0.632 7.620 9217 Z= 0.346 Chirality : 0.043 0.163 1041 Planarity : 0.004 0.057 1219 Dihedral : 5.411 26.491 981 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.72 % Allowed : 13.90 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.30), residues: 852 helix: 1.44 (0.25), residues: 384 sheet: -2.02 (0.31), residues: 244 loop : 0.34 (0.46), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP J 878 HIS 0.006 0.002 HIS B 350 PHE 0.004 0.002 PHE I 840 TYR 0.015 0.002 TYR C 13 ARG 0.009 0.001 ARG B 404 Details of bonding type rmsd hydrogen bonds : bond 0.05025 ( 459) hydrogen bonds : angle 5.61662 ( 1293) SS BOND : bond 0.00301 ( 4) SS BOND : angle 1.26025 ( 8) covalent geometry : bond 0.00585 ( 6841) covalent geometry : angle 0.63164 ( 9209) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 111 time to evaluate : 0.754 Fit side-chains REVERT: A 350 HIS cc_start: 0.4256 (OUTLIER) cc_final: 0.3463 (m-70) REVERT: B 397 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7601 (tp30) REVERT: F 143 ILE cc_start: 0.7679 (OUTLIER) cc_final: 0.7026 (mt) REVERT: H 426 GLU cc_start: 0.7203 (mt-10) cc_final: 0.6896 (mt-10) REVERT: J 807 MET cc_start: 0.8042 (mmm) cc_final: 0.7783 (mmm) REVERT: J 810 TYR cc_start: 0.6825 (m-80) cc_final: 0.6545 (m-80) outliers start: 26 outliers final: 15 residues processed: 124 average time/residue: 0.2114 time to fit residues: 34.9730 Evaluate side-chains 129 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 HIS Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain B residue 383 GLU Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain D residue 834 ASP Chi-restraints excluded: chain D residue 868 CYS Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 798 SER Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 827 TRP Chi-restraints excluded: chain C residue 835 SER Chi-restraints excluded: chain C residue 836 VAL Chi-restraints excluded: chain C residue 846 SER Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain I residue 821 VAL Chi-restraints excluded: chain J residue 798 SER Chi-restraints excluded: chain J residue 823 VAL Chi-restraints excluded: chain J residue 833 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 46 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 chunk 58 optimal weight: 0.4980 chunk 13 optimal weight: 0.3980 chunk 17 optimal weight: 1.9990 chunk 16 optimal weight: 0.3980 chunk 66 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 831 ASN C 854 GLN H 417 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.182753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.171667 restraints weight = 9203.244| |-----------------------------------------------------------------------------| r_work (start): 0.4195 rms_B_bonded: 1.75 r_work: 0.4099 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3960 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6646 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6845 Z= 0.185 Angle : 0.550 8.230 9217 Z= 0.302 Chirality : 0.040 0.145 1041 Planarity : 0.004 0.053 1219 Dihedral : 5.022 22.176 981 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.30 % Allowed : 16.76 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.30), residues: 852 helix: 1.78 (0.25), residues: 381 sheet: -1.86 (0.30), residues: 251 loop : 0.28 (0.46), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 878 HIS 0.003 0.001 HIS A 350 PHE 0.005 0.001 PHE I 840 TYR 0.013 0.002 TYR C 13 ARG 0.005 0.000 ARG E 129 Details of bonding type rmsd hydrogen bonds : bond 0.04506 ( 459) hydrogen bonds : angle 5.22917 ( 1293) SS BOND : bond 0.00207 ( 4) SS BOND : angle 0.95720 ( 8) covalent geometry : bond 0.00399 ( 6841) covalent geometry : angle 0.54972 ( 9209) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 113 time to evaluate : 0.717 Fit side-chains revert: symmetry clash REVERT: A 350 HIS cc_start: 0.4170 (OUTLIER) cc_final: 0.3476 (m-70) REVERT: B 397 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7548 (tp30) REVERT: D 2 VAL cc_start: 0.8096 (p) cc_final: 0.7863 (p) REVERT: E 128 ARG cc_start: 0.5982 (ttm110) cc_final: 0.5760 (ttm170) REVERT: E 139 ASN cc_start: 0.6073 (t0) cc_final: 0.5763 (t0) REVERT: F 143 ILE cc_start: 0.7868 (OUTLIER) cc_final: 0.7261 (mt) REVERT: H 426 GLU cc_start: 0.7260 (mt-10) cc_final: 0.6909 (mt-10) REVERT: J 13 TYR cc_start: 0.4768 (OUTLIER) cc_final: 0.3576 (t80) REVERT: J 807 MET cc_start: 0.7967 (mmm) cc_final: 0.7745 (mmm) REVERT: J 810 TYR cc_start: 0.6809 (m-80) cc_final: 0.6485 (m-80) REVERT: J 859 LYS cc_start: 0.7234 (mtmm) cc_final: 0.6967 (mtmm) outliers start: 23 outliers final: 13 residues processed: 126 average time/residue: 0.1828 time to fit residues: 30.6474 Evaluate side-chains 129 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 HIS Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 798 SER Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 827 TRP Chi-restraints excluded: chain C residue 835 SER Chi-restraints excluded: chain C residue 836 VAL Chi-restraints excluded: chain C residue 846 SER Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain H residue 417 GLN Chi-restraints excluded: chain I residue 821 VAL Chi-restraints excluded: chain J residue 13 TYR Chi-restraints excluded: chain J residue 833 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 17 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 61 optimal weight: 0.3980 chunk 6 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 9 optimal weight: 0.3980 chunk 58 optimal weight: 0.0060 chunk 77 optimal weight: 0.0770 chunk 36 optimal weight: 0.4980 chunk 63 optimal weight: 0.2980 overall best weight: 0.2354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 854 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.185145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.173820 restraints weight = 9253.815| |-----------------------------------------------------------------------------| r_work (start): 0.4220 rms_B_bonded: 1.78 r_work: 0.4124 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3985 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6595 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6845 Z= 0.121 Angle : 0.487 7.212 9217 Z= 0.268 Chirality : 0.038 0.140 1041 Planarity : 0.003 0.049 1219 Dihedral : 4.620 21.036 981 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.01 % Allowed : 17.91 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.30), residues: 852 helix: 2.28 (0.25), residues: 382 sheet: -1.73 (0.30), residues: 253 loop : 0.66 (0.49), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 878 HIS 0.002 0.001 HIS A 350 PHE 0.005 0.001 PHE I 840 TYR 0.009 0.001 TYR C 13 ARG 0.006 0.000 ARG B 404 Details of bonding type rmsd hydrogen bonds : bond 0.04037 ( 459) hydrogen bonds : angle 4.84834 ( 1293) SS BOND : bond 0.00086 ( 4) SS BOND : angle 0.59394 ( 8) covalent geometry : bond 0.00249 ( 6841) covalent geometry : angle 0.48717 ( 9209) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 0.680 Fit side-chains revert: symmetry clash REVERT: A 350 HIS cc_start: 0.3544 (OUTLIER) cc_final: 0.3202 (m-70) REVERT: B 397 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7524 (tp30) REVERT: I 862 ASP cc_start: 0.7474 (m-30) cc_final: 0.7154 (m-30) REVERT: I 872 TYR cc_start: 0.8686 (t80) cc_final: 0.8447 (t80) REVERT: J 807 MET cc_start: 0.7966 (mmm) cc_final: 0.7763 (mmm) REVERT: J 810 TYR cc_start: 0.6761 (m-80) cc_final: 0.6421 (m-80) REVERT: J 859 LYS cc_start: 0.7218 (mtmm) cc_final: 0.6965 (mtmm) outliers start: 21 outliers final: 14 residues processed: 122 average time/residue: 0.1895 time to fit residues: 30.7574 Evaluate side-chains 125 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 HIS Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain B residue 369 LYS Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 868 CYS Chi-restraints excluded: chain C residue 798 SER Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 827 TRP Chi-restraints excluded: chain C residue 846 SER Chi-restraints excluded: chain C residue 886 VAL Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain J residue 823 VAL Chi-restraints excluded: chain J residue 833 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 20 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 41 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 67 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 79 optimal weight: 0.1980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 854 GLN E 139 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.182465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.171270 restraints weight = 9146.383| |-----------------------------------------------------------------------------| r_work (start): 0.4198 rms_B_bonded: 1.76 r_work: 0.4095 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3955 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6652 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6845 Z= 0.191 Angle : 0.548 6.796 9217 Z= 0.300 Chirality : 0.040 0.140 1041 Planarity : 0.004 0.049 1219 Dihedral : 4.863 22.468 981 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.87 % Allowed : 17.91 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.30), residues: 852 helix: 2.14 (0.25), residues: 382 sheet: -1.78 (0.30), residues: 253 loop : 0.60 (0.49), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 878 HIS 0.004 0.001 HIS B 350 PHE 0.006 0.001 PHE I 840 TYR 0.012 0.002 TYR C 13 ARG 0.007 0.000 ARG E 128 Details of bonding type rmsd hydrogen bonds : bond 0.04381 ( 459) hydrogen bonds : angle 5.05607 ( 1293) SS BOND : bond 0.00225 ( 4) SS BOND : angle 0.99031 ( 8) covalent geometry : bond 0.00416 ( 6841) covalent geometry : angle 0.54794 ( 9209) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 107 time to evaluate : 0.660 Fit side-chains revert: symmetry clash REVERT: A 350 HIS cc_start: 0.4246 (OUTLIER) cc_final: 0.3602 (m-70) REVERT: B 397 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7553 (tp30) REVERT: E 139 ASN cc_start: 0.6451 (t0) cc_final: 0.6217 (t0) REVERT: J 810 TYR cc_start: 0.6910 (m-80) cc_final: 0.6488 (m-80) REVERT: J 859 LYS cc_start: 0.7234 (mtmm) cc_final: 0.7001 (mtmm) outliers start: 27 outliers final: 20 residues processed: 119 average time/residue: 0.1853 time to fit residues: 29.3527 Evaluate side-chains 129 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 107 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 HIS Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 868 CYS Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 798 SER Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 827 TRP Chi-restraints excluded: chain C residue 835 SER Chi-restraints excluded: chain C residue 846 SER Chi-restraints excluded: chain C residue 851 VAL Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain I residue 821 VAL Chi-restraints excluded: chain J residue 13 TYR Chi-restraints excluded: chain J residue 798 SER Chi-restraints excluded: chain J residue 823 VAL Chi-restraints excluded: chain J residue 833 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 10 optimal weight: 0.1980 chunk 24 optimal weight: 0.2980 chunk 75 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 79 optimal weight: 0.0270 chunk 2 optimal weight: 0.0980 chunk 25 optimal weight: 0.0070 chunk 29 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 overall best weight: 0.1256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 854 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.186213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.174354 restraints weight = 9447.029| |-----------------------------------------------------------------------------| r_work (start): 0.4225 rms_B_bonded: 1.90 r_work: 0.4123 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3981 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6552 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6845 Z= 0.103 Angle : 0.470 6.048 9217 Z= 0.258 Chirality : 0.037 0.143 1041 Planarity : 0.003 0.046 1219 Dihedral : 4.259 21.115 981 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.29 % Allowed : 19.63 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.31), residues: 852 helix: 2.65 (0.25), residues: 389 sheet: -1.47 (0.31), residues: 253 loop : 0.87 (0.51), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 878 HIS 0.001 0.000 HIS A 350 PHE 0.007 0.001 PHE I 840 TYR 0.007 0.001 TYR C 810 ARG 0.007 0.000 ARG B 404 Details of bonding type rmsd hydrogen bonds : bond 0.03803 ( 459) hydrogen bonds : angle 4.50943 ( 1293) SS BOND : bond 0.00083 ( 4) SS BOND : angle 0.40572 ( 8) covalent geometry : bond 0.00202 ( 6841) covalent geometry : angle 0.46964 ( 9209) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.667 Fit side-chains REVERT: B 397 GLU cc_start: 0.7832 (tp30) cc_final: 0.7124 (tp30) REVERT: E 129 ARG cc_start: 0.7216 (tpp80) cc_final: 0.6757 (ttm-80) REVERT: E 139 ASN cc_start: 0.5969 (t0) cc_final: 0.5683 (t0) REVERT: G 415 GLU cc_start: 0.7179 (tp30) cc_final: 0.6838 (tp30) REVERT: H 429 LEU cc_start: 0.8347 (mm) cc_final: 0.8108 (mp) REVERT: I 872 TYR cc_start: 0.8486 (t80) cc_final: 0.8236 (t80) REVERT: I 878 TRP cc_start: 0.7476 (m100) cc_final: 0.7209 (m100) REVERT: J 798 SER cc_start: 0.8277 (OUTLIER) cc_final: 0.8050 (m) REVERT: J 807 MET cc_start: 0.7815 (mmm) cc_final: 0.7251 (mmp) REVERT: J 810 TYR cc_start: 0.6693 (m-80) cc_final: 0.6017 (m-80) REVERT: J 820 MET cc_start: 0.7956 (OUTLIER) cc_final: 0.7461 (tpt) REVERT: J 859 LYS cc_start: 0.7014 (mtmm) cc_final: 0.6712 (mtmm) outliers start: 16 outliers final: 12 residues processed: 114 average time/residue: 0.1992 time to fit residues: 29.6143 Evaluate side-chains 118 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 868 CYS Chi-restraints excluded: chain C residue 798 SER Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 827 TRP Chi-restraints excluded: chain C residue 846 SER Chi-restraints excluded: chain C residue 886 VAL Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain I residue 6 GLU Chi-restraints excluded: chain I residue 824 VAL Chi-restraints excluded: chain J residue 798 SER Chi-restraints excluded: chain J residue 820 MET Chi-restraints excluded: chain J residue 823 VAL Chi-restraints excluded: chain J residue 833 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 43 optimal weight: 0.5980 chunk 76 optimal weight: 0.3980 chunk 25 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 80 optimal weight: 0.9980 chunk 77 optimal weight: 0.3980 chunk 13 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 9 optimal weight: 0.4980 chunk 52 optimal weight: 0.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 854 GLN H 417 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.184236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.172868 restraints weight = 9343.678| |-----------------------------------------------------------------------------| r_work (start): 0.4214 rms_B_bonded: 1.79 r_work: 0.4110 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3969 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6632 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6845 Z= 0.176 Angle : 0.532 6.313 9217 Z= 0.292 Chirality : 0.040 0.135 1041 Planarity : 0.003 0.047 1219 Dihedral : 4.642 23.439 981 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.01 % Allowed : 19.91 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.30), residues: 852 helix: 2.43 (0.25), residues: 388 sheet: -1.55 (0.31), residues: 253 loop : 0.76 (0.51), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP J 809 HIS 0.004 0.001 HIS B 350 PHE 0.007 0.002 PHE I 840 TYR 0.012 0.002 TYR C 13 ARG 0.003 0.000 ARG E 129 Details of bonding type rmsd hydrogen bonds : bond 0.04215 ( 459) hydrogen bonds : angle 4.82109 ( 1293) SS BOND : bond 0.00236 ( 4) SS BOND : angle 0.96317 ( 8) covalent geometry : bond 0.00383 ( 6841) covalent geometry : angle 0.53181 ( 9209) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 0.732 Fit side-chains revert: symmetry clash REVERT: E 139 ASN cc_start: 0.6517 (t0) cc_final: 0.6249 (t0) REVERT: H 426 GLU cc_start: 0.7426 (mt-10) cc_final: 0.7095 (mt-10) REVERT: I 872 TYR cc_start: 0.8631 (t80) cc_final: 0.8411 (t80) REVERT: J 807 MET cc_start: 0.7831 (mmm) cc_final: 0.7520 (mmm) REVERT: J 810 TYR cc_start: 0.6887 (m-80) cc_final: 0.6186 (m-80) REVERT: J 820 MET cc_start: 0.7884 (OUTLIER) cc_final: 0.7490 (tpt) REVERT: J 859 LYS cc_start: 0.7198 (mtmm) cc_final: 0.6909 (mtmm) outliers start: 21 outliers final: 20 residues processed: 110 average time/residue: 0.2070 time to fit residues: 29.9610 Evaluate side-chains 122 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 868 CYS Chi-restraints excluded: chain C residue 798 SER Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 827 TRP Chi-restraints excluded: chain C residue 846 SER Chi-restraints excluded: chain C residue 851 VAL Chi-restraints excluded: chain C residue 886 VAL Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain H residue 417 GLN Chi-restraints excluded: chain I residue 6 GLU Chi-restraints excluded: chain I residue 824 VAL Chi-restraints excluded: chain I residue 886 VAL Chi-restraints excluded: chain J residue 13 TYR Chi-restraints excluded: chain J residue 820 MET Chi-restraints excluded: chain J residue 823 VAL Chi-restraints excluded: chain J residue 833 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 68 optimal weight: 0.9990 chunk 45 optimal weight: 0.4980 chunk 24 optimal weight: 0.0770 chunk 32 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 64 optimal weight: 0.1980 chunk 2 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 69 optimal weight: 0.4980 chunk 35 optimal weight: 0.0670 chunk 71 optimal weight: 0.6980 overall best weight: 0.2676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 854 GLN ** F 132 GLN ** 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 = 0.4321 r_free = 0.4321 target = 0.183819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.171896 restraints weight = 9508.332| |-----------------------------------------------------------------------------| r_work (start): 0.4200 rms_B_bonded: 1.94 r_work: 0.4094 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3949 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6600 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6845 Z= 0.125 Angle : 0.497 6.487 9217 Z= 0.272 Chirality : 0.038 0.141 1041 Planarity : 0.003 0.046 1219 Dihedral : 4.454 24.357 981 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.72 % Allowed : 20.49 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.31), residues: 852 helix: 2.60 (0.25), residues: 389 sheet: -1.45 (0.31), residues: 253 loop : 0.84 (0.51), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP J 809 HIS 0.002 0.001 HIS B 350 PHE 0.007 0.001 PHE I 840 TYR 0.010 0.001 TYR C 13 ARG 0.007 0.000 ARG B 404 Details of bonding type rmsd hydrogen bonds : bond 0.03999 ( 459) hydrogen bonds : angle 4.63938 ( 1293) SS BOND : bond 0.00108 ( 4) SS BOND : angle 0.59134 ( 8) covalent geometry : bond 0.00260 ( 6841) covalent geometry : angle 0.49700 ( 9209) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1704 Ramachandran restraints generated. 852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 0.779 Fit side-chains REVERT: A 350 HIS cc_start: 0.3470 (OUTLIER) cc_final: 0.3089 (m-70) REVERT: B 367 LEU cc_start: 0.7889 (mp) cc_final: 0.7618 (mt) REVERT: B 397 GLU cc_start: 0.7828 (tp30) cc_final: 0.7138 (tp30) REVERT: E 139 ASN cc_start: 0.6358 (t0) cc_final: 0.6131 (t0) REVERT: H 426 GLU cc_start: 0.7456 (mt-10) cc_final: 0.7118 (mt-10) REVERT: H 429 LEU cc_start: 0.8349 (mm) cc_final: 0.8066 (mp) REVERT: I 851 VAL cc_start: 0.7586 (OUTLIER) cc_final: 0.7316 (m) REVERT: I 872 TYR cc_start: 0.8581 (t80) cc_final: 0.8339 (t80) REVERT: I 878 TRP cc_start: 0.7532 (m100) cc_final: 0.7281 (m100) REVERT: J 810 TYR cc_start: 0.6803 (m-80) cc_final: 0.6084 (m-80) REVERT: J 820 MET cc_start: 0.7908 (OUTLIER) cc_final: 0.7499 (tpt) REVERT: J 859 LYS cc_start: 0.7213 (mtmm) cc_final: 0.6918 (mtmm) outliers start: 19 outliers final: 14 residues processed: 111 average time/residue: 0.2020 time to fit residues: 29.3363 Evaluate side-chains 117 residues out of total 698 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 HIS Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 868 CYS Chi-restraints excluded: chain C residue 798 SER Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 827 TRP Chi-restraints excluded: chain C residue 846 SER Chi-restraints excluded: chain C residue 851 VAL Chi-restraints excluded: chain C residue 886 VAL Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain I residue 6 GLU Chi-restraints excluded: chain I residue 824 VAL Chi-restraints excluded: chain I residue 851 VAL Chi-restraints excluded: chain J residue 13 TYR Chi-restraints excluded: chain J residue 820 MET Chi-restraints excluded: chain J residue 823 VAL Chi-restraints excluded: chain J residue 833 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 0 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 11 optimal weight: 0.3980 chunk 72 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 36 optimal weight: 0.0470 chunk 73 optimal weight: 0.6980 chunk 30 optimal weight: 0.3980 chunk 5 optimal weight: 0.9990 chunk 42 optimal weight: 0.0970 chunk 10 optimal weight: 0.5980 overall best weight: 0.3076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 854 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.183661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.171782 restraints weight = 9472.084| |-----------------------------------------------------------------------------| r_work (start): 0.4201 rms_B_bonded: 1.89 r_work: 0.4093 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3949 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6607 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6845 Z= 0.135 Angle : 0.508 6.659 9217 Z= 0.277 Chirality : 0.038 0.143 1041 Planarity : 0.004 0.045 1219 Dihedral : 4.460 18.464 981 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.87 % Allowed : 20.20 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.30), residues: 852 helix: 2.60 (0.25), residues: 390 sheet: -1.40 (0.31), residues: 253 loop : 0.84 (0.51), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP J 809 HIS 0.002 0.001 HIS B 350 PHE 0.006 0.001 PHE I 840 TYR 0.010 0.001 TYR C 13 ARG 0.006 0.000 ARG E 128 Details of bonding type rmsd hydrogen bonds : bond 0.03989 ( 459) hydrogen bonds : angle 4.70695 ( 1293) SS BOND : bond 0.00116 ( 4) SS BOND : angle 0.63458 ( 8) covalent geometry : bond 0.00290 ( 6841) covalent geometry : angle 0.50767 ( 9209) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3661.29 seconds wall clock time: 63 minutes 58.00 seconds (3838.00 seconds total)