Starting phenix.real_space_refine on Thu Nov 14 14:41:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gau_29908/11_2024/8gau_29908.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gau_29908/11_2024/8gau_29908.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gau_29908/11_2024/8gau_29908.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gau_29908/11_2024/8gau_29908.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gau_29908/11_2024/8gau_29908.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gau_29908/11_2024/8gau_29908.cif" } resolution = 3.6 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= 0.002 sd= 0.035 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 34 5.16 5 C 4163 2.51 5 N 1133 2.21 5 O 1274 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 6604 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 2987 Classifications: {'peptide': 386} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 372} Chain: "H" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 974 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 7, 'TRANS': 117} Chain: "L" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 798 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 98} Chain: "M" Number of atoms: 998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 998 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 6, 'TRANS': 120} Chain: "N" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 833 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} 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: 4.44, per 1000 atoms: 0.67 Number of scatterers: 6604 At special positions: 0 Unit cell: (105.45, 93.24, 113.22, 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 34 16.00 O 1274 8.00 N 1133 7.00 C 4163 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS A 124 " - pdb=" SG CYS A 129 " distance=2.03 Simple disulfide: pdb=" SG CYS A 175 " - pdb=" SG CYS A 193 " distance=2.03 Simple disulfide: pdb=" SG CYS A 183 " - pdb=" SG CYS A 230 " distance=2.00 Simple disulfide: pdb=" SG CYS A 232 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 280 " - pdb=" SG CYS A 289 " distance=2.03 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 337 " distance=2.03 Simple disulfide: pdb=" SG CYS A 421 " - pdb=" SG CYS A 447 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.04 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " 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 NAG-ASN " NAG A 501 " - " ASN A 200 " Time building additional restraints: 1.65 Conformation dependent library (CDL) restraints added in 1.2 seconds 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1530 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 20 sheets defined 2.9% alpha, 33.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 104 through 109 Processing helix chain 'A' and resid 142 through 146 removed outlier: 3.674A pdb=" N SER A 145 " --> pdb=" O ASN A 142 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASN A 146 " --> pdb=" O GLY A 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 142 through 146' Processing helix chain 'H' and resid 99 through 100C removed outlier: 3.757A pdb=" N VAL H 100B" --> pdb=" O TYR H 99 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N HIS H 100C" --> pdb=" O ASP H 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 99 through 100C' Processing helix chain 'M' and resid 28 through 32 removed outlier: 3.717A pdb=" N ASP M 31 " --> pdb=" O LYS M 28 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N TYR M 32 " --> pdb=" O PHE M 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 28 through 32' Processing helix chain 'M' and resid 61 through 64 removed outlier: 3.715A pdb=" N LYS M 64 " --> pdb=" O ASP M 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 61 through 64' Processing sheet with id=AA1, first strand: chain 'A' and resid 97 through 102 removed outlier: 6.828A pdb=" N VAL A 445 " --> pdb=" O PHE A 100 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N LYS A 102 " --> pdb=" O ILE A 443 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N ILE A 443 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ARG A 420 " --> pdb=" O GLY A 448 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 121 removed outlier: 5.372A pdb=" N GLU A 119 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU A 134 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA A 133 " --> pdb=" O LEU A 159 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 179 through 184 removed outlier: 3.659A pdb=" N SER A 179 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ALA A 203 " --> pdb=" O SER A 214 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N SER A 214 " --> pdb=" O ALA A 203 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N PHE A 205 " --> pdb=" O VAL A 212 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 231 through 233 removed outlier: 3.969A pdb=" N VAL A 231 " --> pdb=" O THR A 238 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N HIS A 264 " --> pdb=" O PHE A 256 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N GLU A 258 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N ILE A 262 " --> pdb=" O GLU A 258 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 280 through 283 removed outlier: 3.715A pdb=" N SER A 311 " --> pdb=" O ASN A 306 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 352 through 356 removed outlier: 4.834A pdb=" N TRP A 352 " --> pdb=" O GLY A 363 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY A 363 " --> pdb=" O TRP A 352 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP A 356 " --> pdb=" O ASP A 359 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP A 359 " --> pdb=" O ASP A 356 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET A 362 " --> pdb=" O PHE A 377 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE A 377 " --> pdb=" O MET A 362 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N LEU A 372 " --> pdb=" O GLU A 399 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N GLU A 399 " --> pdb=" O LEU A 372 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N TYR A 374 " --> pdb=" O ILE A 397 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LYS A 378 " --> pdb=" O ASN A 393 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N ASN A 393 " --> pdb=" O LYS A 378 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 17 through 22 removed outlier: 3.542A pdb=" N SER H 79 " --> pdb=" O SER H 70 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER H 70 " --> pdb=" O SER H 79 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 58 through 59 removed outlier: 3.505A pdb=" N GLU H 50 " --> pdb=" O THR H 58 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR H 107 " --> pdb=" O TYR H 90 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AB1, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.827A pdb=" N GLU L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 34 through 37 removed outlier: 3.802A pdb=" N ILE L 48 " --> pdb=" O TRP L 35 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 62 through 63 Processing sheet with id=AB4, first strand: chain 'L' and resid 66 through 67 removed outlier: 3.853A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'M' and resid 3 through 5 removed outlier: 3.762A pdb=" N GLN M 3 " --> pdb=" O SER M 25 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER M 25 " --> pdb=" O GLN M 3 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 18 through 21 removed outlier: 3.645A pdb=" N LEU M 18 " --> pdb=" O ILE M 82 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE M 82 " --> pdb=" O LEU M 18 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU M 80 " --> pdb=" O LEU M 20 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR M 79 " --> pdb=" O SER M 70 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER M 70 " --> pdb=" O TYR M 79 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 57 through 59 removed outlier: 6.890A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N GLY M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N MET M 34 " --> pdb=" O GLY M 50 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU M 89 " --> pdb=" O GLN M 39 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N CYS M 92 " --> pdb=" O TRP M 103 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N TRP M 103 " --> pdb=" O CYS M 92 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ARG M 94 " --> pdb=" O ASP M 101 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'M' and resid 57 through 59 removed outlier: 6.890A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N GLY M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N MET M 34 " --> pdb=" O GLY M 50 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU M 89 " --> pdb=" O GLN M 39 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 5 through 7 removed outlier: 3.592A pdb=" N SER N 63 " --> pdb=" O THR N 74 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 10 through 13 removed outlier: 3.599A pdb=" N ASP N 105 " --> pdb=" O LEU N 11 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 53 through 54 removed outlier: 6.694A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N TYR N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N LEU N 33 " --> pdb=" O TYR N 49 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR N 87 " --> pdb=" O TYR N 36 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN N 38 " --> pdb=" O THR N 85 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR N 85 " --> pdb=" O GLN N 38 " (cutoff:3.500A) 163 hydrogen bonds defined for protein. 423 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.29 Time building geometry restraints manager: 1.91 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: 1971 1.33 - 1.46: 1709 1.46 - 1.58: 3047 1.58 - 1.71: 0 1.71 - 1.83: 42 Bond restraints: 6769 Sorted by residual: bond pdb=" N CYS A 183 " pdb=" CA CYS A 183 " ideal model delta sigma weight residual 1.455 1.494 -0.040 1.32e-02 5.74e+03 8.98e+00 bond pdb=" N HIS A 184 " pdb=" CA HIS A 184 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.23e-02 6.61e+03 7.49e+00 bond pdb=" N ARG A 327 " pdb=" CA ARG A 327 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.16e-02 7.43e+03 7.40e+00 bond pdb=" N ASN A 367 " pdb=" CA ASN A 367 " ideal model delta sigma weight residual 1.453 1.488 -0.035 1.31e-02 5.83e+03 7.28e+00 bond pdb=" N ASP A 359 " pdb=" CA ASP A 359 " ideal model delta sigma weight residual 1.455 1.490 -0.036 1.36e-02 5.41e+03 6.93e+00 ... (remaining 6764 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 8703 2.13 - 4.27: 418 4.27 - 6.40: 59 6.40 - 8.53: 14 8.53 - 10.67: 3 Bond angle restraints: 9197 Sorted by residual: angle pdb=" CA PHE H 31 " pdb=" C PHE H 31 " pdb=" O PHE H 31 " ideal model delta sigma weight residual 120.43 113.36 7.07 1.12e+00 7.97e-01 3.99e+01 angle pdb=" N ARG H 66 " pdb=" CA ARG H 66 " pdb=" C ARG H 66 " ideal model delta sigma weight residual 114.39 105.95 8.44 1.45e+00 4.76e-01 3.39e+01 angle pdb=" C PRO A 326 " pdb=" CA PRO A 326 " pdb=" CB PRO A 326 " ideal model delta sigma weight residual 111.40 116.04 -4.64 9.10e-01 1.21e+00 2.60e+01 angle pdb=" CA ARG A 430 " pdb=" C ARG A 430 " pdb=" O ARG A 430 " ideal model delta sigma weight residual 122.01 116.67 5.34 1.05e+00 9.07e-01 2.58e+01 angle pdb=" C VAL H 100B" pdb=" N HIS H 100C" pdb=" CA HIS H 100C" ideal model delta sigma weight residual 120.54 127.19 -6.65 1.35e+00 5.49e-01 2.42e+01 ... (remaining 9192 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.99: 3746 14.99 - 29.99: 170 29.99 - 44.98: 58 44.98 - 59.97: 16 59.97 - 74.96: 5 Dihedral angle restraints: 3995 sinusoidal: 1579 harmonic: 2416 Sorted by residual: dihedral pdb=" CA ARG M 13 " pdb=" C ARG M 13 " pdb=" N PRO M 14 " pdb=" CA PRO M 14 " ideal model delta harmonic sigma weight residual -180.00 -145.43 -34.57 0 5.00e+00 4.00e-02 4.78e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual 93.00 152.36 -59.36 1 1.00e+01 1.00e-02 4.71e+01 dihedral pdb=" CD ARG A 430 " pdb=" NE ARG A 430 " pdb=" CZ ARG A 430 " pdb=" NH1 ARG A 430 " ideal model delta sinusoidal sigma weight residual 0.00 -58.81 58.81 1 1.00e+01 1.00e-02 4.63e+01 ... (remaining 3992 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 752 0.064 - 0.129: 200 0.129 - 0.193: 42 0.193 - 0.257: 2 0.257 - 0.322: 1 Chirality restraints: 997 Sorted by residual: chirality pdb=" CA PHE H 33 " pdb=" N PHE H 33 " pdb=" C PHE H 33 " pdb=" CB PHE H 33 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" CB ILE H 60 " pdb=" CA ILE H 60 " pdb=" CG1 ILE H 60 " pdb=" CG2 ILE H 60 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CA PHE H 31 " pdb=" N PHE H 31 " pdb=" C PHE H 31 " pdb=" CB PHE H 31 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 994 not shown) Planarity restraints: 1180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 430 " -0.933 9.50e-02 1.11e+02 4.18e-01 1.06e+02 pdb=" NE ARG A 430 " 0.056 2.00e-02 2.50e+03 pdb=" CZ ARG A 430 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG A 430 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 430 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 327 " -0.321 9.50e-02 1.11e+02 1.44e-01 1.27e+01 pdb=" NE ARG A 327 " 0.019 2.00e-02 2.50e+03 pdb=" CZ ARG A 327 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 327 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 327 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER H 28 " -0.015 2.00e-02 2.50e+03 2.96e-02 8.78e+00 pdb=" C SER H 28 " 0.051 2.00e-02 2.50e+03 pdb=" O SER H 28 " -0.019 2.00e-02 2.50e+03 pdb=" N PHE H 29 " -0.017 2.00e-02 2.50e+03 ... (remaining 1177 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1820 2.81 - 3.33: 5138 3.33 - 3.85: 10435 3.85 - 4.38: 11342 4.38 - 4.90: 20836 Nonbonded interactions: 49571 Sorted by model distance: nonbonded pdb=" OG SER A 217 " pdb=" OD2 ASP A 243 " model vdw 2.285 3.040 nonbonded pdb=" OE1 GLN A 136 " pdb=" NH1 ARG A 156 " model vdw 2.303 3.120 nonbonded pdb=" OE2 GLU A 277 " pdb=" OH TYR M 100A" model vdw 2.310 3.040 nonbonded pdb=" OG SER M 17 " pdb=" OD1 ASN M 82A" model vdw 2.353 3.040 nonbonded pdb=" OH TYR H 32 " pdb=" O PRO H 100H" model vdw 2.365 3.040 ... (remaining 49566 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue 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: 0.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 19.830 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 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 0.050 6769 Z= 0.405 Angle : 1.044 10.666 9197 Z= 0.606 Chirality : 0.061 0.322 997 Planarity : 0.015 0.418 1179 Dihedral : 10.366 74.963 2426 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.36 % Allowed : 10.11 % Favored : 89.54 % Rotamer: Outliers : 0.96 % Allowed : 3.17 % Favored : 95.87 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 10.26 % Cis-general : 0.00 % Twisted Proline : 2.56 % 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: -4.38 (0.24), residues: 841 helix: -4.72 (0.38), residues: 6 sheet: -2.42 (0.25), residues: 346 loop : -3.37 (0.22), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.004 TRP M 103 HIS 0.004 0.001 HIS A 264 PHE 0.028 0.003 PHE H 78 TYR 0.036 0.003 TYR M 32 ARG 0.010 0.001 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 301 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 LYS cc_start: 0.8254 (mttt) cc_final: 0.7832 (mmtt) REVERT: A 104 ASN cc_start: 0.8403 (m-40) cc_final: 0.8119 (m110) REVERT: A 105 SER cc_start: 0.8372 (t) cc_final: 0.8012 (m) REVERT: A 108 LEU cc_start: 0.8325 (mt) cc_final: 0.8122 (mt) REVERT: A 119 GLU cc_start: 0.7292 (mp0) cc_final: 0.6890 (mp0) REVERT: A 128 LYS cc_start: 0.8011 (pttm) cc_final: 0.7345 (pttm) REVERT: A 134 LEU cc_start: 0.8389 (mt) cc_final: 0.8108 (mp) REVERT: A 142 ASN cc_start: 0.8227 (t0) cc_final: 0.7856 (t0) REVERT: A 162 GLU cc_start: 0.7760 (mt-10) cc_final: 0.7278 (mt-10) REVERT: A 187 LYS cc_start: 0.8594 (mttt) cc_final: 0.8369 (mtmm) REVERT: A 206 ILE cc_start: 0.8664 (mt) cc_final: 0.8449 (mm) REVERT: A 229 GLU cc_start: 0.7510 (pt0) cc_final: 0.7302 (pt0) REVERT: A 233 ILE cc_start: 0.8602 (mt) cc_final: 0.8250 (mm) REVERT: A 236 THR cc_start: 0.8361 (m) cc_final: 0.8020 (p) REVERT: A 251 ASP cc_start: 0.7459 (m-30) cc_final: 0.7120 (m-30) REVERT: A 258 GLU cc_start: 0.6899 (mt-10) cc_final: 0.6686 (mt-10) REVERT: A 265 ILE cc_start: 0.8888 (mt) cc_final: 0.8684 (mm) REVERT: A 302 ILE cc_start: 0.8671 (mt) cc_final: 0.8109 (mm) REVERT: A 307 VAL cc_start: 0.8665 (m) cc_final: 0.8398 (t) REVERT: A 309 ASN cc_start: 0.7478 (p0) cc_final: 0.7223 (t0) REVERT: A 319 SER cc_start: 0.8539 (t) cc_final: 0.8292 (p) REVERT: A 328 LYS cc_start: 0.8118 (mttt) cc_final: 0.7640 (mttt) REVERT: A 343 GLU cc_start: 0.7239 (mp0) cc_final: 0.6948 (mp0) REVERT: A 370 LEU cc_start: 0.8673 (mt) cc_final: 0.8470 (mm) REVERT: A 375 GLU cc_start: 0.7634 (pt0) cc_final: 0.7152 (pt0) REVERT: A 378 LYS cc_start: 0.8107 (ttpt) cc_final: 0.7860 (ttpp) REVERT: A 380 ILE cc_start: 0.8127 (mt) cc_final: 0.7916 (mm) REVERT: A 385 LYS cc_start: 0.8426 (mmmt) cc_final: 0.8064 (mtpp) REVERT: A 413 GLU cc_start: 0.7438 (tt0) cc_final: 0.7135 (tt0) REVERT: A 416 SER cc_start: 0.8892 (m) cc_final: 0.8404 (p) REVERT: A 427 ILE cc_start: 0.8161 (mt) cc_final: 0.7731 (tp) REVERT: A 433 GLU cc_start: 0.7590 (mp0) cc_final: 0.6787 (mp0) REVERT: A 437 TRP cc_start: 0.8286 (m100) cc_final: 0.7705 (m-10) REVERT: A 440 SER cc_start: 0.8643 (t) cc_final: 0.8296 (p) REVERT: A 445 VAL cc_start: 0.8368 (t) cc_final: 0.8029 (p) REVERT: H 13 LYS cc_start: 0.7752 (mtmm) cc_final: 0.7362 (mtmm) REVERT: H 16 GLU cc_start: 0.7761 (mt-10) cc_final: 0.7438 (mt-10) REVERT: H 22 CYS cc_start: 0.6132 (t) cc_final: 0.5752 (t) REVERT: H 29 PHE cc_start: 0.7984 (t80) cc_final: 0.7627 (t80) REVERT: H 31 PHE cc_start: 0.7832 (OUTLIER) cc_final: 0.7291 (p90) REVERT: H 60 ILE cc_start: 0.8172 (tp) cc_final: 0.7957 (tp) REVERT: H 100 HIS cc_start: 0.7566 (t-90) cc_final: 0.7196 (t-90) REVERT: H 100 LEU cc_start: 0.8159 (mt) cc_final: 0.7783 (mt) REVERT: L 7 SER cc_start: 0.8699 (m) cc_final: 0.8351 (p) REVERT: L 58 VAL cc_start: 0.8839 (t) cc_final: 0.8540 (p) REVERT: L 103 LYS cc_start: 0.8068 (tttt) cc_final: 0.7431 (tttt) REVERT: L 104 VAL cc_start: 0.8152 (t) cc_final: 0.7911 (m) REVERT: M 32 TYR cc_start: 0.7842 (m-10) cc_final: 0.7384 (m-10) REVERT: N 26 SER cc_start: 0.8338 (p) cc_final: 0.8058 (m) REVERT: N 82 ASP cc_start: 0.8080 (m-30) cc_final: 0.7804 (m-30) REVERT: N 86 TYR cc_start: 0.8093 (m-10) cc_final: 0.7562 (m-80) REVERT: N 89 GLN cc_start: 0.7883 (tm130) cc_final: 0.7528 (tm130) REVERT: N 103 LYS cc_start: 0.7924 (tptt) cc_final: 0.7648 (tptt) outliers start: 7 outliers final: 3 residues processed: 303 average time/residue: 0.2074 time to fit residues: 81.1415 Evaluate side-chains 283 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 279 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain H residue 31 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 69 optimal weight: 2.9990 chunk 62 optimal weight: 0.0020 chunk 34 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 64 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN A 93 ASN A 147 ASN A 273 GLN A 347 HIS ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN H 105 GLN L 55 GLN L 89 GLN M 81 HIS N 89 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6769 Z= 0.190 Angle : 0.645 8.266 9197 Z= 0.338 Chirality : 0.047 0.156 997 Planarity : 0.006 0.052 1179 Dihedral : 6.403 58.873 959 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 3.44 % Allowed : 11.98 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.53 (0.26), residues: 841 helix: -4.23 (0.54), residues: 6 sheet: -1.60 (0.29), residues: 323 loop : -2.97 (0.23), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 7 HIS 0.002 0.001 HIS H 100C PHE 0.012 0.002 PHE H 78 TYR 0.020 0.002 TYR M 100A ARG 0.004 0.001 ARG M 94 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 254 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 LYS cc_start: 0.8262 (mttt) cc_final: 0.7887 (mmtt) REVERT: A 104 ASN cc_start: 0.8311 (m-40) cc_final: 0.7975 (m110) REVERT: A 128 LYS cc_start: 0.7978 (pttm) cc_final: 0.7311 (pttm) REVERT: A 142 ASN cc_start: 0.8024 (t0) cc_final: 0.7771 (t0) REVERT: A 162 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7333 (mt-10) REVERT: A 245 SER cc_start: 0.8504 (t) cc_final: 0.7942 (p) REVERT: A 249 LYS cc_start: 0.8407 (mttt) cc_final: 0.7524 (mtpp) REVERT: A 251 ASP cc_start: 0.7446 (m-30) cc_final: 0.7097 (m-30) REVERT: A 261 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7569 (tmmm) REVERT: A 276 GLU cc_start: 0.6907 (mm-30) cc_final: 0.6667 (mm-30) REVERT: A 292 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7294 (ptt180) REVERT: A 302 ILE cc_start: 0.8578 (mt) cc_final: 0.8109 (mm) REVERT: A 309 ASN cc_start: 0.7404 (p0) cc_final: 0.7159 (t0) REVERT: A 327 ARG cc_start: 0.8301 (ptt-90) cc_final: 0.8089 (ptt-90) REVERT: A 343 GLU cc_start: 0.7368 (mp0) cc_final: 0.6867 (mp0) REVERT: A 356 ASP cc_start: 0.8223 (t0) cc_final: 0.8009 (t0) REVERT: A 370 LEU cc_start: 0.8700 (mt) cc_final: 0.8482 (mm) REVERT: A 375 GLU cc_start: 0.7657 (pt0) cc_final: 0.7089 (pt0) REVERT: A 378 LYS cc_start: 0.8151 (ttpt) cc_final: 0.7925 (ttpt) REVERT: A 381 GLU cc_start: 0.7254 (mt-10) cc_final: 0.7025 (mm-30) REVERT: A 385 LYS cc_start: 0.8379 (mmmt) cc_final: 0.8046 (mtpp) REVERT: A 388 SER cc_start: 0.8402 (t) cc_final: 0.7976 (p) REVERT: A 399 GLU cc_start: 0.7155 (mt-10) cc_final: 0.6721 (mt-10) REVERT: A 413 GLU cc_start: 0.7310 (tt0) cc_final: 0.7079 (tt0) REVERT: A 416 SER cc_start: 0.8912 (m) cc_final: 0.8409 (p) REVERT: A 427 ILE cc_start: 0.8174 (mt) cc_final: 0.7760 (tp) REVERT: A 433 GLU cc_start: 0.7669 (mp0) cc_final: 0.7013 (mp0) REVERT: A 437 TRP cc_start: 0.8342 (m100) cc_final: 0.7572 (m-10) REVERT: A 453 TYR cc_start: 0.7846 (p90) cc_final: 0.7644 (p90) REVERT: A 463 ASP cc_start: 0.7990 (t0) cc_final: 0.7773 (t0) REVERT: H 7 TRP cc_start: 0.7547 (p-90) cc_final: 0.7328 (p-90) REVERT: H 13 LYS cc_start: 0.7705 (mtmm) cc_final: 0.7423 (mtmm) REVERT: H 25 TYR cc_start: 0.7906 (m-80) cc_final: 0.7687 (m-10) REVERT: H 31 PHE cc_start: 0.7510 (OUTLIER) cc_final: 0.6815 (p90) REVERT: H 100 HIS cc_start: 0.7377 (t-90) cc_final: 0.6940 (t-90) REVERT: H 100 LEU cc_start: 0.8075 (mt) cc_final: 0.7374 (mt) REVERT: L 4 MET cc_start: 0.5636 (mpp) cc_final: 0.5410 (mpp) REVERT: L 7 SER cc_start: 0.8638 (m) cc_final: 0.8228 (p) REVERT: L 58 VAL cc_start: 0.8807 (t) cc_final: 0.8520 (p) REVERT: L 103 LYS cc_start: 0.7754 (tttt) cc_final: 0.7269 (tttt) REVERT: L 107 LYS cc_start: 0.7662 (pttp) cc_final: 0.7250 (tppt) REVERT: M 32 TYR cc_start: 0.7702 (m-80) cc_final: 0.7435 (m-10) REVERT: M 59 TYR cc_start: 0.8224 (m-10) cc_final: 0.7839 (m-80) REVERT: M 96 SER cc_start: 0.8380 (m) cc_final: 0.8021 (p) REVERT: N 56 SER cc_start: 0.8637 (t) cc_final: 0.8266 (p) REVERT: N 82 ASP cc_start: 0.8205 (m-30) cc_final: 0.7741 (m-30) REVERT: N 86 TYR cc_start: 0.8103 (m-10) cc_final: 0.7896 (m-80) outliers start: 25 outliers final: 12 residues processed: 265 average time/residue: 0.2095 time to fit residues: 72.1018 Evaluate side-chains 255 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 240 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 467 MET Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 31 PHE Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain N residue 97 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 41 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 61 optimal weight: 0.0870 chunk 50 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 chunk 66 optimal weight: 0.0040 chunk 73 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 overall best weight: 0.4970 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN A 273 GLN ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 53 HIS M 73 ASN N 90 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6769 Z= 0.158 Angle : 0.610 7.724 9197 Z= 0.312 Chirality : 0.045 0.153 997 Planarity : 0.005 0.044 1179 Dihedral : 5.645 52.671 958 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 3.31 % Allowed : 15.98 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.14 (0.26), residues: 841 helix: -3.40 (1.40), residues: 6 sheet: -1.22 (0.29), residues: 320 loop : -2.79 (0.23), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 7 HIS 0.002 0.001 HIS A 264 PHE 0.015 0.001 PHE H 78 TYR 0.025 0.002 TYR M 100A ARG 0.003 0.000 ARG A 292 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 245 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 LYS cc_start: 0.8276 (mttt) cc_final: 0.7857 (mmtt) REVERT: A 104 ASN cc_start: 0.8286 (m-40) cc_final: 0.7989 (m110) REVERT: A 128 LYS cc_start: 0.7985 (pttm) cc_final: 0.7453 (pttm) REVERT: A 142 ASN cc_start: 0.7997 (t0) cc_final: 0.7708 (t0) REVERT: A 162 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7345 (mt-10) REVERT: A 245 SER cc_start: 0.8511 (t) cc_final: 0.7980 (p) REVERT: A 249 LYS cc_start: 0.8364 (mttt) cc_final: 0.7673 (mtpp) REVERT: A 251 ASP cc_start: 0.7453 (m-30) cc_final: 0.7203 (m-30) REVERT: A 258 GLU cc_start: 0.7160 (mt-10) cc_final: 0.6905 (mt-10) REVERT: A 261 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.7702 (tmmm) REVERT: A 292 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7380 (ptt180) REVERT: A 302 ILE cc_start: 0.8652 (mt) cc_final: 0.8157 (mm) REVERT: A 327 ARG cc_start: 0.8301 (ptt-90) cc_final: 0.8063 (ptt-90) REVERT: A 343 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.6819 (mp0) REVERT: A 356 ASP cc_start: 0.8187 (t0) cc_final: 0.7915 (t0) REVERT: A 370 LEU cc_start: 0.8719 (mt) cc_final: 0.8393 (mm) REVERT: A 375 GLU cc_start: 0.7639 (pt0) cc_final: 0.7105 (pt0) REVERT: A 378 LYS cc_start: 0.8236 (ttpt) cc_final: 0.7871 (ttpp) REVERT: A 385 LYS cc_start: 0.8411 (mmmt) cc_final: 0.8017 (mtpp) REVERT: A 388 SER cc_start: 0.8460 (t) cc_final: 0.7984 (p) REVERT: A 399 GLU cc_start: 0.7151 (mt-10) cc_final: 0.6812 (mt-10) REVERT: A 403 ARG cc_start: 0.7868 (mtp180) cc_final: 0.6306 (mtm180) REVERT: A 413 GLU cc_start: 0.7312 (tt0) cc_final: 0.7058 (tt0) REVERT: A 427 ILE cc_start: 0.8122 (mt) cc_final: 0.7502 (tt) REVERT: A 430 ARG cc_start: 0.8066 (tpt170) cc_final: 0.7865 (tpt170) REVERT: A 432 GLU cc_start: 0.7234 (mp0) cc_final: 0.6709 (mp0) REVERT: A 433 GLU cc_start: 0.7807 (mp0) cc_final: 0.6853 (mp0) REVERT: A 437 TRP cc_start: 0.8453 (m100) cc_final: 0.7600 (m-10) REVERT: A 440 SER cc_start: 0.8501 (t) cc_final: 0.8287 (t) REVERT: A 453 TYR cc_start: 0.7953 (p90) cc_final: 0.7700 (p90) REVERT: H 13 LYS cc_start: 0.7610 (mtmm) cc_final: 0.7376 (mtmm) REVERT: H 99 TYR cc_start: 0.7948 (m-80) cc_final: 0.7588 (m-80) REVERT: H 100 HIS cc_start: 0.7244 (t-90) cc_final: 0.6847 (t-90) REVERT: H 100 LEU cc_start: 0.8053 (mt) cc_final: 0.7302 (mt) REVERT: L 7 SER cc_start: 0.8588 (m) cc_final: 0.8178 (p) REVERT: L 33 LEU cc_start: 0.5805 (OUTLIER) cc_final: 0.5577 (tm) REVERT: L 58 VAL cc_start: 0.8793 (t) cc_final: 0.8513 (p) REVERT: L 103 LYS cc_start: 0.7772 (tttt) cc_final: 0.7225 (tttt) REVERT: L 107 LYS cc_start: 0.7407 (pttp) cc_final: 0.7151 (tppt) REVERT: M 32 TYR cc_start: 0.7738 (m-80) cc_final: 0.7426 (m-10) REVERT: M 59 TYR cc_start: 0.8278 (m-10) cc_final: 0.8016 (m-80) REVERT: M 83 LYS cc_start: 0.8447 (mttt) cc_final: 0.8076 (ttmm) REVERT: M 96 SER cc_start: 0.8223 (m) cc_final: 0.7978 (p) REVERT: N 56 SER cc_start: 0.8670 (t) cc_final: 0.8314 (p) REVERT: N 82 ASP cc_start: 0.8190 (m-30) cc_final: 0.7943 (m-30) outliers start: 24 outliers final: 13 residues processed: 254 average time/residue: 0.1984 time to fit residues: 65.0844 Evaluate side-chains 253 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 236 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 31 PHE Chi-restraints excluded: chain H residue 53 HIS Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 100 PHE Chi-restraints excluded: chain N residue 97 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 73 optimal weight: 7.9990 chunk 56 optimal weight: 6.9990 chunk 38 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN A 93 ASN ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 90 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 6769 Z= 0.481 Angle : 0.779 9.308 9197 Z= 0.410 Chirality : 0.051 0.163 997 Planarity : 0.007 0.069 1179 Dihedral : 6.428 47.637 958 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.30 % Favored : 88.70 % Rotamer: Outliers : 6.06 % Allowed : 15.29 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.32 (0.26), residues: 841 helix: -3.08 (2.01), residues: 6 sheet: -1.32 (0.28), residues: 334 loop : -2.96 (0.23), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP H 7 HIS 0.015 0.002 HIS H 53 PHE 0.033 0.003 PHE H 78 TYR 0.038 0.003 TYR N 94 ARG 0.006 0.001 ARG M 13 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 255 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 LYS cc_start: 0.8377 (mttt) cc_final: 0.7996 (mmtt) REVERT: A 102 LYS cc_start: 0.8446 (tttp) cc_final: 0.8245 (tttt) REVERT: A 104 ASN cc_start: 0.8281 (m-40) cc_final: 0.8077 (m-40) REVERT: A 128 LYS cc_start: 0.8051 (pttm) cc_final: 0.7690 (pttm) REVERT: A 245 SER cc_start: 0.8530 (t) cc_final: 0.8000 (p) REVERT: A 251 ASP cc_start: 0.7639 (m-30) cc_final: 0.7268 (m-30) REVERT: A 261 LYS cc_start: 0.8379 (OUTLIER) cc_final: 0.8135 (tptm) REVERT: A 271 SER cc_start: 0.8815 (OUTLIER) cc_final: 0.8582 (p) REVERT: A 276 GLU cc_start: 0.7009 (mm-30) cc_final: 0.6779 (mm-30) REVERT: A 292 ARG cc_start: 0.8138 (OUTLIER) cc_final: 0.7089 (ptt180) REVERT: A 302 ILE cc_start: 0.8733 (mt) cc_final: 0.8298 (mm) REVERT: A 307 VAL cc_start: 0.8739 (m) cc_final: 0.8449 (t) REVERT: A 309 ASN cc_start: 0.7521 (t0) cc_final: 0.7138 (t0) REVERT: A 343 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.6865 (mp0) REVERT: A 356 ASP cc_start: 0.8337 (t0) cc_final: 0.8110 (t0) REVERT: A 375 GLU cc_start: 0.7648 (pt0) cc_final: 0.7118 (pt0) REVERT: A 378 LYS cc_start: 0.8250 (ttpt) cc_final: 0.8037 (ttpt) REVERT: A 385 LYS cc_start: 0.8315 (mmmt) cc_final: 0.7974 (mtpp) REVERT: A 389 LYS cc_start: 0.8892 (mtpp) cc_final: 0.8657 (mtpp) REVERT: A 399 GLU cc_start: 0.7208 (mt-10) cc_final: 0.6713 (mt-10) REVERT: A 413 GLU cc_start: 0.7349 (tt0) cc_final: 0.7079 (tt0) REVERT: A 427 ILE cc_start: 0.8255 (mt) cc_final: 0.7943 (tt) REVERT: A 430 ARG cc_start: 0.8185 (tpt170) cc_final: 0.7951 (tpt170) REVERT: A 433 GLU cc_start: 0.7760 (mp0) cc_final: 0.7031 (mp0) REVERT: A 437 TRP cc_start: 0.8405 (m100) cc_final: 0.7305 (m-10) REVERT: A 440 SER cc_start: 0.8648 (t) cc_final: 0.8378 (t) REVERT: A 453 TYR cc_start: 0.8068 (p90) cc_final: 0.7678 (p90) REVERT: H 13 LYS cc_start: 0.7821 (mtmm) cc_final: 0.7478 (mtmm) REVERT: H 16 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7562 (mt-10) REVERT: H 22 CYS cc_start: 0.6009 (t) cc_final: 0.5780 (t) REVERT: H 81 LYS cc_start: 0.8157 (mttt) cc_final: 0.7862 (mptt) REVERT: H 99 TYR cc_start: 0.7889 (m-80) cc_final: 0.7357 (m-80) REVERT: H 100 LEU cc_start: 0.8305 (mt) cc_final: 0.8035 (mp) REVERT: L 7 SER cc_start: 0.8852 (m) cc_final: 0.8350 (p) REVERT: L 10 SER cc_start: 0.8176 (t) cc_final: 0.7807 (m) REVERT: L 22 THR cc_start: 0.7824 (p) cc_final: 0.7481 (p) REVERT: L 45 LYS cc_start: 0.8326 (tttt) cc_final: 0.8115 (tttt) REVERT: L 58 VAL cc_start: 0.8893 (t) cc_final: 0.8584 (p) REVERT: L 103 LYS cc_start: 0.7887 (tttt) cc_final: 0.7418 (tttt) REVERT: M 83 LYS cc_start: 0.8498 (mttm) cc_final: 0.8068 (ttmm) REVERT: N 9 SER cc_start: 0.8740 (m) cc_final: 0.8379 (t) REVERT: N 24 ARG cc_start: 0.7251 (ttm170) cc_final: 0.7027 (ttm170) REVERT: N 56 SER cc_start: 0.8591 (t) cc_final: 0.8272 (p) REVERT: N 67 TYR cc_start: 0.8396 (t80) cc_final: 0.8110 (t80) outliers start: 44 outliers final: 31 residues processed: 271 average time/residue: 0.2041 time to fit residues: 70.9766 Evaluate side-chains 283 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 248 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 467 MET Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 31 PHE Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain L residue 83 ILE Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 94 ARG Chi-restraints excluded: chain M residue 100 PHE Chi-restraints excluded: chain N residue 17 ASP Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 95 LEU Chi-restraints excluded: chain N residue 97 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 66 optimal weight: 0.8980 chunk 44 optimal weight: 0.4980 chunk 1 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN A 147 ASN A 299 ASN ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 53 HIS N 90 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6769 Z= 0.182 Angle : 0.633 9.120 9197 Z= 0.325 Chirality : 0.047 0.192 997 Planarity : 0.005 0.057 1179 Dihedral : 5.638 46.955 958 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 4.55 % Allowed : 18.32 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.27), residues: 841 helix: -2.85 (2.12), residues: 6 sheet: -1.09 (0.29), residues: 334 loop : -2.63 (0.24), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP H 7 HIS 0.005 0.001 HIS H 53 PHE 0.018 0.002 PHE A 410 TYR 0.029 0.002 TYR N 49 ARG 0.005 0.000 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 241 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 LYS cc_start: 0.8327 (mttt) cc_final: 0.7910 (mmtt) REVERT: A 102 LYS cc_start: 0.8292 (tttp) cc_final: 0.8075 (tttt) REVERT: A 104 ASN cc_start: 0.8180 (m-40) cc_final: 0.7946 (m-40) REVERT: A 128 LYS cc_start: 0.8054 (pttm) cc_final: 0.7769 (pttm) REVERT: A 251 ASP cc_start: 0.7620 (m-30) cc_final: 0.7330 (m-30) REVERT: A 252 THR cc_start: 0.8619 (m) cc_final: 0.8346 (t) REVERT: A 261 LYS cc_start: 0.8370 (OUTLIER) cc_final: 0.7793 (tmmm) REVERT: A 271 SER cc_start: 0.8781 (OUTLIER) cc_final: 0.8567 (p) REVERT: A 276 GLU cc_start: 0.6959 (mm-30) cc_final: 0.6755 (mm-30) REVERT: A 292 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.7346 (ptt180) REVERT: A 302 ILE cc_start: 0.8778 (mt) cc_final: 0.8285 (mm) REVERT: A 306 ASN cc_start: 0.7868 (t0) cc_final: 0.7587 (t0) REVERT: A 307 VAL cc_start: 0.8581 (m) cc_final: 0.8112 (t) REVERT: A 309 ASN cc_start: 0.7534 (t0) cc_final: 0.7103 (t0) REVERT: A 343 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.6772 (mp0) REVERT: A 356 ASP cc_start: 0.8199 (t0) cc_final: 0.7991 (t0) REVERT: A 370 LEU cc_start: 0.8728 (mt) cc_final: 0.8487 (mm) REVERT: A 375 GLU cc_start: 0.7594 (pt0) cc_final: 0.7068 (pt0) REVERT: A 378 LYS cc_start: 0.8235 (ttpt) cc_final: 0.8000 (ttpt) REVERT: A 385 LYS cc_start: 0.8471 (mmmt) cc_final: 0.8117 (mtpp) REVERT: A 388 SER cc_start: 0.8562 (t) cc_final: 0.8035 (p) REVERT: A 389 LYS cc_start: 0.8899 (mtpp) cc_final: 0.8553 (mtpp) REVERT: A 403 ARG cc_start: 0.7981 (mtp180) cc_final: 0.7698 (mtp180) REVERT: A 413 GLU cc_start: 0.7274 (tt0) cc_final: 0.7007 (tt0) REVERT: A 416 SER cc_start: 0.8953 (m) cc_final: 0.8476 (p) REVERT: A 427 ILE cc_start: 0.8227 (mt) cc_final: 0.7977 (tt) REVERT: A 430 ARG cc_start: 0.8155 (tpt170) cc_final: 0.7898 (tpt170) REVERT: A 433 GLU cc_start: 0.7770 (mp0) cc_final: 0.7105 (mp0) REVERT: A 437 TRP cc_start: 0.8335 (m100) cc_final: 0.7385 (m-10) REVERT: A 440 SER cc_start: 0.8470 (t) cc_final: 0.8243 (t) REVERT: A 453 TYR cc_start: 0.8073 (p90) cc_final: 0.7659 (p90) REVERT: H 13 LYS cc_start: 0.7707 (mtmm) cc_final: 0.7376 (mtmm) REVERT: H 16 GLU cc_start: 0.7593 (mt-10) cc_final: 0.7281 (mt-10) REVERT: H 81 LYS cc_start: 0.8149 (mttt) cc_final: 0.7903 (mptt) REVERT: H 99 TYR cc_start: 0.7885 (m-80) cc_final: 0.7517 (m-80) REVERT: H 100 LEU cc_start: 0.8148 (mt) cc_final: 0.7928 (mp) REVERT: L 7 SER cc_start: 0.8730 (m) cc_final: 0.8277 (p) REVERT: L 45 LYS cc_start: 0.8323 (tttt) cc_final: 0.8105 (tttt) REVERT: L 58 VAL cc_start: 0.8874 (t) cc_final: 0.8577 (p) REVERT: L 103 LYS cc_start: 0.7798 (tttt) cc_final: 0.7250 (tttt) REVERT: M 32 TYR cc_start: 0.7478 (m-10) cc_final: 0.7257 (m-10) REVERT: M 59 TYR cc_start: 0.8546 (m-80) cc_final: 0.8148 (m-80) REVERT: M 83 LYS cc_start: 0.8401 (mttt) cc_final: 0.8061 (ttmm) REVERT: M 96 SER cc_start: 0.8264 (m) cc_final: 0.8038 (p) REVERT: M 100 TYR cc_start: 0.7696 (t80) cc_final: 0.7434 (t80) REVERT: N 56 SER cc_start: 0.8607 (t) cc_final: 0.8323 (p) REVERT: N 67 TYR cc_start: 0.8437 (t80) cc_final: 0.7861 (t80) REVERT: N 89 GLN cc_start: 0.8003 (tm-30) cc_final: 0.7218 (tt0) outliers start: 33 outliers final: 23 residues processed: 255 average time/residue: 0.2095 time to fit residues: 69.0799 Evaluate side-chains 263 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 236 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 467 MET Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 31 PHE Chi-restraints excluded: chain H residue 53 HIS Chi-restraints excluded: chain H residue 60 ILE Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 83 ILE Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 100 PHE Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 97 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 26 optimal weight: 4.9990 chunk 71 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 79 optimal weight: 4.9990 chunk 65 optimal weight: 0.1980 chunk 36 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN A 184 HIS A 226 GLN ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 53 HIS ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6769 Z= 0.173 Angle : 0.613 8.539 9197 Z= 0.313 Chirality : 0.046 0.167 997 Planarity : 0.005 0.044 1179 Dihedral : 5.427 47.391 958 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 4.55 % Allowed : 19.42 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.27), residues: 841 helix: -2.70 (2.23), residues: 6 sheet: -0.92 (0.29), residues: 336 loop : -2.53 (0.25), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP H 7 HIS 0.007 0.001 HIS H 53 PHE 0.017 0.001 PHE H 78 TYR 0.030 0.002 TYR N 49 ARG 0.006 0.000 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 241 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 LYS cc_start: 0.8313 (mttt) cc_final: 0.7909 (mmtt) REVERT: A 102 LYS cc_start: 0.8332 (tttp) cc_final: 0.8079 (tttt) REVERT: A 104 ASN cc_start: 0.8186 (m-40) cc_final: 0.7917 (m-40) REVERT: A 128 LYS cc_start: 0.8058 (pttm) cc_final: 0.7772 (pttm) REVERT: A 251 ASP cc_start: 0.7639 (m-30) cc_final: 0.7331 (m-30) REVERT: A 261 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.7822 (tmmm) REVERT: A 271 SER cc_start: 0.8776 (p) cc_final: 0.8561 (p) REVERT: A 292 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7369 (ptt180) REVERT: A 302 ILE cc_start: 0.8768 (mt) cc_final: 0.8276 (mm) REVERT: A 307 VAL cc_start: 0.8554 (m) cc_final: 0.8186 (t) REVERT: A 309 ASN cc_start: 0.7621 (t0) cc_final: 0.7121 (t0) REVERT: A 343 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.6770 (mp0) REVERT: A 370 LEU cc_start: 0.8733 (mt) cc_final: 0.8495 (mm) REVERT: A 375 GLU cc_start: 0.7594 (pt0) cc_final: 0.7067 (pt0) REVERT: A 378 LYS cc_start: 0.8163 (ttpt) cc_final: 0.7904 (ttpt) REVERT: A 385 LYS cc_start: 0.8384 (mmmt) cc_final: 0.7995 (mtpp) REVERT: A 388 SER cc_start: 0.8582 (t) cc_final: 0.8027 (p) REVERT: A 389 LYS cc_start: 0.8890 (mtpp) cc_final: 0.8550 (mtpp) REVERT: A 413 GLU cc_start: 0.7318 (tt0) cc_final: 0.7069 (tt0) REVERT: A 416 SER cc_start: 0.8945 (m) cc_final: 0.8464 (p) REVERT: A 427 ILE cc_start: 0.8178 (mt) cc_final: 0.7750 (tt) REVERT: A 430 ARG cc_start: 0.8137 (tpt170) cc_final: 0.7890 (tpt170) REVERT: A 433 GLU cc_start: 0.7767 (mp0) cc_final: 0.7212 (mp0) REVERT: A 437 TRP cc_start: 0.8315 (m100) cc_final: 0.7361 (m-10) REVERT: A 440 SER cc_start: 0.8461 (t) cc_final: 0.8186 (t) REVERT: A 453 TYR cc_start: 0.8065 (p90) cc_final: 0.7679 (p90) REVERT: H 13 LYS cc_start: 0.7670 (mtmm) cc_final: 0.7343 (mtmm) REVERT: H 16 GLU cc_start: 0.7445 (mt-10) cc_final: 0.7114 (mt-10) REVERT: H 99 TYR cc_start: 0.7902 (m-80) cc_final: 0.7536 (m-80) REVERT: L 7 SER cc_start: 0.8663 (m) cc_final: 0.8223 (p) REVERT: L 42 LYS cc_start: 0.8396 (mmmt) cc_final: 0.8117 (mmmt) REVERT: L 58 VAL cc_start: 0.8845 (t) cc_final: 0.8556 (p) REVERT: L 103 LYS cc_start: 0.7777 (tttt) cc_final: 0.7237 (tttt) REVERT: M 43 LYS cc_start: 0.7965 (mtmm) cc_final: 0.7677 (mtmm) REVERT: M 59 TYR cc_start: 0.8519 (m-80) cc_final: 0.8075 (m-80) REVERT: M 83 LYS cc_start: 0.8385 (mttt) cc_final: 0.8073 (ttmm) REVERT: M 100 TYR cc_start: 0.7748 (t80) cc_final: 0.7513 (t80) REVERT: N 27 GLN cc_start: 0.7388 (OUTLIER) cc_final: 0.7181 (pt0) REVERT: N 56 SER cc_start: 0.8639 (t) cc_final: 0.8368 (p) REVERT: N 89 GLN cc_start: 0.7963 (tm-30) cc_final: 0.7233 (tt0) outliers start: 33 outliers final: 25 residues processed: 254 average time/residue: 0.2059 time to fit residues: 67.4426 Evaluate side-chains 267 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 238 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 467 MET Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 31 PHE Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain L residue 83 ILE Chi-restraints excluded: chain M residue 100 PHE Chi-restraints excluded: chain N residue 27 GLN Chi-restraints excluded: chain N residue 37 GLN Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 97 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 8 optimal weight: 0.0000 chunk 45 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 31 optimal weight: 0.0270 chunk 47 optimal weight: 5.9990 overall best weight: 1.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN A 342 ASN ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6769 Z= 0.280 Angle : 0.665 8.861 9197 Z= 0.344 Chirality : 0.048 0.173 997 Planarity : 0.005 0.052 1179 Dihedral : 5.662 48.430 958 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.51 % Favored : 90.49 % Rotamer: Outliers : 6.06 % Allowed : 19.42 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.80 (0.27), residues: 841 helix: -2.62 (2.39), residues: 6 sheet: -0.99 (0.29), residues: 337 loop : -2.59 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP H 7 HIS 0.004 0.001 HIS N 90 PHE 0.024 0.002 PHE H 78 TYR 0.033 0.002 TYR N 94 ARG 0.005 0.001 ARG A 327 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 245 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 LYS cc_start: 0.8352 (mttt) cc_final: 0.7948 (mmtt) REVERT: A 102 LYS cc_start: 0.8336 (tttp) cc_final: 0.8112 (tttt) REVERT: A 104 ASN cc_start: 0.8229 (m-40) cc_final: 0.8014 (m-40) REVERT: A 128 LYS cc_start: 0.8117 (pttm) cc_final: 0.7790 (pttm) REVERT: A 251 ASP cc_start: 0.7624 (m-30) cc_final: 0.7314 (m-30) REVERT: A 252 THR cc_start: 0.8594 (m) cc_final: 0.8368 (t) REVERT: A 261 LYS cc_start: 0.8442 (OUTLIER) cc_final: 0.7824 (tmmm) REVERT: A 271 SER cc_start: 0.8764 (OUTLIER) cc_final: 0.8531 (p) REVERT: A 292 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7121 (ptt180) REVERT: A 302 ILE cc_start: 0.8744 (mt) cc_final: 0.8310 (mm) REVERT: A 307 VAL cc_start: 0.8594 (m) cc_final: 0.8277 (t) REVERT: A 309 ASN cc_start: 0.7595 (t0) cc_final: 0.7077 (t0) REVERT: A 327 ARG cc_start: 0.8384 (ptt-90) cc_final: 0.8176 (ptt-90) REVERT: A 343 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.6781 (mp0) REVERT: A 375 GLU cc_start: 0.7606 (pt0) cc_final: 0.7087 (pt0) REVERT: A 378 LYS cc_start: 0.8165 (ttpt) cc_final: 0.7883 (ttpt) REVERT: A 385 LYS cc_start: 0.8394 (mmmt) cc_final: 0.8026 (mtpp) REVERT: A 388 SER cc_start: 0.8515 (t) cc_final: 0.7960 (p) REVERT: A 389 LYS cc_start: 0.8883 (mtpp) cc_final: 0.8496 (mtpp) REVERT: A 413 GLU cc_start: 0.7346 (tt0) cc_final: 0.7124 (tt0) REVERT: A 416 SER cc_start: 0.8956 (m) cc_final: 0.8439 (p) REVERT: A 427 ILE cc_start: 0.8192 (mt) cc_final: 0.7787 (tt) REVERT: A 430 ARG cc_start: 0.8150 (tpt170) cc_final: 0.7933 (tpt170) REVERT: A 433 GLU cc_start: 0.7801 (mp0) cc_final: 0.7177 (mp0) REVERT: A 437 TRP cc_start: 0.8317 (m100) cc_final: 0.7148 (m-10) REVERT: A 440 SER cc_start: 0.8462 (t) cc_final: 0.8175 (t) REVERT: A 453 TYR cc_start: 0.8084 (p90) cc_final: 0.7676 (p90) REVERT: H 13 LYS cc_start: 0.7732 (mtmm) cc_final: 0.7358 (mtmm) REVERT: H 16 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7263 (mt-10) REVERT: H 81 LYS cc_start: 0.8177 (mttt) cc_final: 0.7933 (mptt) REVERT: H 99 TYR cc_start: 0.7918 (m-80) cc_final: 0.7430 (m-80) REVERT: L 7 SER cc_start: 0.8720 (m) cc_final: 0.8286 (p) REVERT: L 10 SER cc_start: 0.8075 (t) cc_final: 0.7787 (m) REVERT: L 42 LYS cc_start: 0.8436 (mmmt) cc_final: 0.8142 (mmmt) REVERT: L 58 VAL cc_start: 0.8878 (t) cc_final: 0.8576 (p) REVERT: L 103 LYS cc_start: 0.7821 (tttt) cc_final: 0.7357 (tttt) REVERT: M 43 LYS cc_start: 0.8186 (mtmm) cc_final: 0.7955 (mtmm) REVERT: M 59 TYR cc_start: 0.8565 (m-80) cc_final: 0.7930 (m-80) REVERT: M 83 LYS cc_start: 0.8406 (mttt) cc_final: 0.8097 (ttmm) REVERT: N 56 SER cc_start: 0.8625 (t) cc_final: 0.8348 (p) REVERT: N 61 ARG cc_start: 0.7819 (OUTLIER) cc_final: 0.7614 (ptt180) REVERT: N 89 GLN cc_start: 0.7984 (tm-30) cc_final: 0.7280 (tt0) outliers start: 44 outliers final: 30 residues processed: 256 average time/residue: 0.2311 time to fit residues: 76.4929 Evaluate side-chains 280 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 245 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 467 MET Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 31 PHE Chi-restraints excluded: chain H residue 53 HIS Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain L residue 83 ILE Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 100 PHE Chi-restraints excluded: chain N residue 17 ASP Chi-restraints excluded: chain N residue 37 GLN Chi-restraints excluded: chain N residue 38 GLN Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 61 ARG Chi-restraints excluded: chain N residue 97 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 23 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 50 optimal weight: 0.3980 chunk 53 optimal weight: 0.9990 chunk 39 optimal weight: 0.0050 chunk 7 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 73 optimal weight: 0.3980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 GLN ** M 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.3820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 6769 Z= 0.168 Angle : 0.613 8.619 9197 Z= 0.313 Chirality : 0.046 0.177 997 Planarity : 0.005 0.041 1179 Dihedral : 5.275 45.396 958 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 4.13 % Allowed : 22.73 % Favored : 73.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.28), residues: 841 helix: -2.89 (1.94), residues: 6 sheet: -0.72 (0.29), residues: 331 loop : -2.42 (0.25), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP H 7 HIS 0.003 0.001 HIS A 274 PHE 0.017 0.001 PHE A 410 TYR 0.030 0.001 TYR N 49 ARG 0.004 0.000 ARG A 327 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 244 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 LYS cc_start: 0.8291 (mttt) cc_final: 0.7846 (mmtt) REVERT: A 102 LYS cc_start: 0.8167 (tttp) cc_final: 0.7885 (tttt) REVERT: A 128 LYS cc_start: 0.8050 (pttm) cc_final: 0.7825 (pttm) REVERT: A 132 PHE cc_start: 0.7636 (m-80) cc_final: 0.7349 (m-80) REVERT: A 245 SER cc_start: 0.8475 (t) cc_final: 0.8146 (p) REVERT: A 251 ASP cc_start: 0.7614 (m-30) cc_final: 0.7325 (m-30) REVERT: A 261 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.7907 (tmmm) REVERT: A 271 SER cc_start: 0.8792 (p) cc_final: 0.8532 (p) REVERT: A 292 ARG cc_start: 0.7978 (OUTLIER) cc_final: 0.7368 (ptt180) REVERT: A 302 ILE cc_start: 0.8748 (mt) cc_final: 0.8267 (mm) REVERT: A 307 VAL cc_start: 0.8475 (m) cc_final: 0.8124 (t) REVERT: A 309 ASN cc_start: 0.7632 (t0) cc_final: 0.7141 (t0) REVERT: A 327 ARG cc_start: 0.8376 (ptt-90) cc_final: 0.8165 (ptt-90) REVERT: A 343 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.6754 (mp0) REVERT: A 370 LEU cc_start: 0.8709 (mt) cc_final: 0.8475 (mm) REVERT: A 375 GLU cc_start: 0.7591 (pt0) cc_final: 0.7094 (pt0) REVERT: A 378 LYS cc_start: 0.8155 (ttpt) cc_final: 0.7807 (ttpt) REVERT: A 385 LYS cc_start: 0.8325 (mmmt) cc_final: 0.7977 (mtpp) REVERT: A 388 SER cc_start: 0.8551 (t) cc_final: 0.7990 (p) REVERT: A 389 LYS cc_start: 0.8880 (mtpp) cc_final: 0.8536 (mtpp) REVERT: A 399 GLU cc_start: 0.7078 (mt-10) cc_final: 0.6709 (mt-10) REVERT: A 413 GLU cc_start: 0.7332 (tt0) cc_final: 0.7098 (tt0) REVERT: A 416 SER cc_start: 0.8951 (m) cc_final: 0.8470 (p) REVERT: A 427 ILE cc_start: 0.8089 (mt) cc_final: 0.7669 (tt) REVERT: A 430 ARG cc_start: 0.8120 (tpt170) cc_final: 0.7885 (tpt170) REVERT: A 433 GLU cc_start: 0.7763 (mp0) cc_final: 0.7139 (mp0) REVERT: A 437 TRP cc_start: 0.8358 (m100) cc_final: 0.7368 (m-10) REVERT: A 440 SER cc_start: 0.8397 (t) cc_final: 0.8121 (t) REVERT: A 453 TYR cc_start: 0.8076 (p90) cc_final: 0.7661 (p90) REVERT: H 13 LYS cc_start: 0.7614 (mtmm) cc_final: 0.7238 (mtmm) REVERT: H 16 GLU cc_start: 0.7343 (mt-10) cc_final: 0.7003 (mt-10) REVERT: H 58 THR cc_start: 0.8114 (m) cc_final: 0.7905 (m) REVERT: H 71 VAL cc_start: 0.8636 (p) cc_final: 0.8406 (t) REVERT: H 99 TYR cc_start: 0.7920 (m-80) cc_final: 0.7611 (m-80) REVERT: L 7 SER cc_start: 0.8679 (m) cc_final: 0.8230 (p) REVERT: L 10 SER cc_start: 0.7957 (t) cc_final: 0.7699 (m) REVERT: L 24 ARG cc_start: 0.7143 (mmm160) cc_final: 0.6890 (mmm160) REVERT: L 42 LYS cc_start: 0.8383 (mmmt) cc_final: 0.8026 (mmmt) REVERT: L 58 VAL cc_start: 0.8849 (t) cc_final: 0.8557 (p) REVERT: L 103 LYS cc_start: 0.7808 (tttt) cc_final: 0.7324 (tttt) REVERT: M 59 TYR cc_start: 0.8626 (m-80) cc_final: 0.8016 (m-80) REVERT: M 83 LYS cc_start: 0.8415 (mttt) cc_final: 0.8080 (ttmm) REVERT: N 56 SER cc_start: 0.8629 (t) cc_final: 0.8336 (p) REVERT: N 61 ARG cc_start: 0.7767 (OUTLIER) cc_final: 0.7567 (ptt180) REVERT: N 89 GLN cc_start: 0.7969 (tm-30) cc_final: 0.7246 (tt0) outliers start: 30 outliers final: 22 residues processed: 258 average time/residue: 0.2068 time to fit residues: 69.7456 Evaluate side-chains 269 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 243 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 467 MET Chi-restraints excluded: chain H residue 31 PHE Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain L residue 83 ILE Chi-restraints excluded: chain M residue 100 PHE Chi-restraints excluded: chain N residue 37 GLN Chi-restraints excluded: chain N residue 38 GLN Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 61 ARG Chi-restraints excluded: chain N residue 95 LEU Chi-restraints excluded: chain N residue 97 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 75 optimal weight: 1.9990 chunk 44 optimal weight: 0.0010 chunk 32 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 66 optimal weight: 0.0570 chunk 69 optimal weight: 2.9990 chunk 73 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 overall best weight: 0.5306 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN A 274 HIS ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.3926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 6769 Z= 0.168 Angle : 0.617 8.980 9197 Z= 0.312 Chirality : 0.046 0.178 997 Planarity : 0.005 0.040 1179 Dihedral : 5.186 46.096 958 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 4.55 % Allowed : 23.28 % Favored : 72.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.28), residues: 841 helix: -2.60 (2.27), residues: 6 sheet: -0.59 (0.30), residues: 316 loop : -2.35 (0.25), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP H 7 HIS 0.006 0.001 HIS A 274 PHE 0.017 0.001 PHE A 410 TYR 0.030 0.001 TYR N 49 ARG 0.004 0.000 ARG A 327 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 249 time to evaluate : 0.706 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 89 LYS cc_start: 0.8320 (mttt) cc_final: 0.7938 (mmtt) REVERT: A 132 PHE cc_start: 0.7653 (m-80) cc_final: 0.7333 (m-80) REVERT: A 162 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7493 (mt-10) REVERT: A 189 TRP cc_start: 0.8266 (m100) cc_final: 0.8048 (m100) REVERT: A 245 SER cc_start: 0.8453 (t) cc_final: 0.8163 (p) REVERT: A 251 ASP cc_start: 0.7599 (m-30) cc_final: 0.7325 (m-30) REVERT: A 261 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.7930 (tmmm) REVERT: A 262 ILE cc_start: 0.8397 (mt) cc_final: 0.8179 (tt) REVERT: A 271 SER cc_start: 0.8800 (p) cc_final: 0.8545 (p) REVERT: A 292 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.7162 (ptt180) REVERT: A 302 ILE cc_start: 0.8743 (mt) cc_final: 0.8260 (mm) REVERT: A 307 VAL cc_start: 0.8450 (m) cc_final: 0.8101 (t) REVERT: A 309 ASN cc_start: 0.7604 (t0) cc_final: 0.7105 (t0) REVERT: A 343 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.6761 (mp0) REVERT: A 370 LEU cc_start: 0.8716 (mt) cc_final: 0.8473 (mm) REVERT: A 375 GLU cc_start: 0.7592 (pt0) cc_final: 0.7106 (pt0) REVERT: A 378 LYS cc_start: 0.8143 (ttpt) cc_final: 0.7797 (ttpt) REVERT: A 385 LYS cc_start: 0.8307 (mmmt) cc_final: 0.7973 (mtpp) REVERT: A 388 SER cc_start: 0.8555 (t) cc_final: 0.7995 (p) REVERT: A 389 LYS cc_start: 0.8875 (mtpp) cc_final: 0.8546 (mtpp) REVERT: A 399 GLU cc_start: 0.7047 (mt-10) cc_final: 0.6689 (mt-10) REVERT: A 416 SER cc_start: 0.8944 (m) cc_final: 0.8440 (p) REVERT: A 427 ILE cc_start: 0.8128 (mt) cc_final: 0.7721 (tt) REVERT: A 430 ARG cc_start: 0.8121 (tpt170) cc_final: 0.7872 (tpt170) REVERT: A 433 GLU cc_start: 0.7773 (mp0) cc_final: 0.7146 (mp0) REVERT: A 437 TRP cc_start: 0.8269 (m100) cc_final: 0.7263 (m-10) REVERT: A 440 SER cc_start: 0.8414 (t) cc_final: 0.8110 (t) REVERT: A 453 TYR cc_start: 0.8074 (p90) cc_final: 0.7659 (p90) REVERT: H 13 LYS cc_start: 0.7672 (mtmm) cc_final: 0.7276 (mtmm) REVERT: H 16 GLU cc_start: 0.7273 (mt-10) cc_final: 0.7026 (mt-10) REVERT: H 58 THR cc_start: 0.8112 (m) cc_final: 0.7881 (m) REVERT: H 71 VAL cc_start: 0.8627 (p) cc_final: 0.8382 (t) REVERT: L 7 SER cc_start: 0.8661 (m) cc_final: 0.8208 (p) REVERT: L 10 SER cc_start: 0.7932 (t) cc_final: 0.7677 (m) REVERT: L 24 ARG cc_start: 0.7119 (mmm160) cc_final: 0.6890 (mmm160) REVERT: L 42 LYS cc_start: 0.8351 (mmmt) cc_final: 0.8005 (mmmt) REVERT: L 58 VAL cc_start: 0.8832 (t) cc_final: 0.8551 (p) REVERT: L 103 LYS cc_start: 0.7832 (tttt) cc_final: 0.7346 (tttt) REVERT: M 59 TYR cc_start: 0.8619 (m-80) cc_final: 0.8025 (m-80) REVERT: M 83 LYS cc_start: 0.8398 (mttt) cc_final: 0.8088 (ttmm) REVERT: M 100 LYS cc_start: 0.7683 (ttmm) cc_final: 0.7482 (tttt) REVERT: N 56 SER cc_start: 0.8659 (t) cc_final: 0.8410 (p) outliers start: 33 outliers final: 28 residues processed: 261 average time/residue: 0.2147 time to fit residues: 73.0086 Evaluate side-chains 275 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 244 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 467 MET Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 31 PHE Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain L residue 83 ILE Chi-restraints excluded: chain M residue 100 PHE Chi-restraints excluded: chain N residue 37 GLN Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 95 LEU Chi-restraints excluded: chain N residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 36 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 39 optimal weight: 0.4980 chunk 51 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6769 Z= 0.213 Angle : 0.644 9.096 9197 Z= 0.325 Chirality : 0.047 0.175 997 Planarity : 0.005 0.041 1179 Dihedral : 5.280 45.213 958 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 4.55 % Allowed : 23.69 % Favored : 71.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.28), residues: 841 helix: -2.48 (2.51), residues: 6 sheet: -0.63 (0.29), residues: 336 loop : -2.35 (0.25), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP H 7 HIS 0.004 0.001 HIS A 274 PHE 0.020 0.002 PHE H 78 TYR 0.032 0.002 TYR N 49 ARG 0.002 0.000 ARG M 13 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1682 Ramachandran restraints generated. 841 Oldfield, 0 Emsley, 841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 244 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 LYS cc_start: 0.8249 (mttt) cc_final: 0.7954 (mmtt) REVERT: A 132 PHE cc_start: 0.7660 (m-80) cc_final: 0.7446 (m-80) REVERT: A 165 VAL cc_start: 0.8311 (p) cc_final: 0.7945 (m) REVERT: A 189 TRP cc_start: 0.8282 (m100) cc_final: 0.8059 (m100) REVERT: A 245 SER cc_start: 0.8523 (t) cc_final: 0.8239 (p) REVERT: A 251 ASP cc_start: 0.7570 (m-30) cc_final: 0.7294 (m-30) REVERT: A 261 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.7943 (tmmm) REVERT: A 262 ILE cc_start: 0.8407 (mt) cc_final: 0.8188 (tt) REVERT: A 271 SER cc_start: 0.8796 (p) cc_final: 0.8524 (p) REVERT: A 292 ARG cc_start: 0.7927 (OUTLIER) cc_final: 0.7167 (ptt180) REVERT: A 302 ILE cc_start: 0.8753 (mt) cc_final: 0.8279 (mm) REVERT: A 307 VAL cc_start: 0.8484 (m) cc_final: 0.8150 (t) REVERT: A 309 ASN cc_start: 0.7581 (t0) cc_final: 0.7078 (t0) REVERT: A 343 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.6737 (mp0) REVERT: A 375 GLU cc_start: 0.7602 (pt0) cc_final: 0.7128 (pt0) REVERT: A 378 LYS cc_start: 0.8144 (ttpt) cc_final: 0.7781 (ttpt) REVERT: A 385 LYS cc_start: 0.8354 (mmmt) cc_final: 0.8018 (mtpp) REVERT: A 388 SER cc_start: 0.8530 (t) cc_final: 0.7967 (p) REVERT: A 389 LYS cc_start: 0.8884 (mtpp) cc_final: 0.8539 (mtpp) REVERT: A 399 GLU cc_start: 0.7060 (mt-10) cc_final: 0.6720 (mt-10) REVERT: A 416 SER cc_start: 0.8950 (m) cc_final: 0.8451 (p) REVERT: A 427 ILE cc_start: 0.8170 (mt) cc_final: 0.7760 (tt) REVERT: A 430 ARG cc_start: 0.8141 (tpt170) cc_final: 0.7871 (tpt170) REVERT: A 433 GLU cc_start: 0.7700 (mp0) cc_final: 0.7083 (mp0) REVERT: A 437 TRP cc_start: 0.8297 (m100) cc_final: 0.7139 (m-10) REVERT: A 440 SER cc_start: 0.8450 (t) cc_final: 0.8140 (t) REVERT: A 453 TYR cc_start: 0.8078 (p90) cc_final: 0.7644 (p90) REVERT: H 13 LYS cc_start: 0.7678 (mtmm) cc_final: 0.7290 (mtmm) REVERT: H 16 GLU cc_start: 0.7327 (mt-10) cc_final: 0.7087 (mt-10) REVERT: H 58 THR cc_start: 0.8154 (m) cc_final: 0.7941 (m) REVERT: H 71 VAL cc_start: 0.8663 (p) cc_final: 0.8463 (t) REVERT: H 99 TYR cc_start: 0.7936 (m-80) cc_final: 0.7640 (m-80) REVERT: H 100 MET cc_start: 0.7433 (tpp) cc_final: 0.7216 (tpt) REVERT: L 7 SER cc_start: 0.8675 (m) cc_final: 0.8237 (p) REVERT: L 10 SER cc_start: 0.7952 (t) cc_final: 0.7694 (m) REVERT: L 42 LYS cc_start: 0.8334 (mmmt) cc_final: 0.7994 (mmmt) REVERT: L 58 VAL cc_start: 0.8837 (t) cc_final: 0.8544 (p) REVERT: L 103 LYS cc_start: 0.7876 (tttt) cc_final: 0.7367 (tttt) REVERT: M 59 TYR cc_start: 0.8589 (m-80) cc_final: 0.7983 (m-80) REVERT: M 83 LYS cc_start: 0.8407 (mttt) cc_final: 0.8100 (ttmm) REVERT: N 56 SER cc_start: 0.8642 (t) cc_final: 0.8391 (p) outliers start: 33 outliers final: 29 residues processed: 258 average time/residue: 0.2023 time to fit residues: 68.0958 Evaluate side-chains 274 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 242 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 261 LYS Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 343 GLU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 467 MET Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 19 SER Chi-restraints excluded: chain H residue 31 PHE Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain L residue 83 ILE Chi-restraints excluded: chain M residue 100 PHE Chi-restraints excluded: chain N residue 37 GLN Chi-restraints excluded: chain N residue 38 GLN Chi-restraints excluded: chain N residue 53 LEU Chi-restraints excluded: chain N residue 95 LEU Chi-restraints excluded: chain N residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 59 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 65 optimal weight: 0.0470 chunk 27 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 57 optimal weight: 0.0030 chunk 3 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 overall best weight: 0.7692 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 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 = 0.3342 r_free = 0.3342 target = 0.106237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.094261 restraints weight = 11843.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.097363 restraints weight = 5040.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.099226 restraints weight = 2577.859| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.164 6769 Z= 0.330 Angle : 1.044 59.198 9197 Z= 0.606 Chirality : 0.056 0.873 997 Planarity : 0.005 0.041 1179 Dihedral : 5.289 45.176 958 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 4.55 % Allowed : 23.97 % Favored : 71.49 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 10.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.28), residues: 841 helix: -2.49 (2.51), residues: 6 sheet: -0.65 (0.29), residues: 336 loop : -2.35 (0.25), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP H 7 HIS 0.003 0.001 HIS A 274 PHE 0.020 0.002 PHE H 78 TYR 0.031 0.002 TYR N 49 ARG 0.003 0.000 ARG M 94 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2048.46 seconds wall clock time: 37 minutes 51.48 seconds (2271.48 seconds total)