Starting phenix.real_space_refine on Wed Jul 30 09:22:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ds9_27686/07_2025/8ds9_27686.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ds9_27686/07_2025/8ds9_27686.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ds9_27686/07_2025/8ds9_27686.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ds9_27686/07_2025/8ds9_27686.map" model { file = "/net/cci-nas-00/data/ceres_data/8ds9_27686/07_2025/8ds9_27686.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ds9_27686/07_2025/8ds9_27686.cif" } resolution = 3.17 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.064 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 97 5.16 5 C 8030 2.51 5 N 1877 2.21 5 O 2033 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 67 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12039 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1662 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 5, 'TRANS': 191} Chain breaks: 2 Chain: "B" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1662 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 5, 'TRANS': 191} Chain breaks: 2 Chain: "C" Number of atoms: 2685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2685 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 9, 'TRANS': 310} Chain breaks: 2 Chain: "D" Number of atoms: 2646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2646 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Chain breaks: 2 Chain: "E" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1662 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 5, 'TRANS': 191} Chain breaks: 2 Chain: "F" Number of atoms: 1599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1599 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 3, 'TRANS': 187} Chain breaks: 2 Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'PEE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 95 Unusual residues: {'PEE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 7.99, per 1000 atoms: 0.66 Number of scatterers: 12039 At special positions: 0 Unit cell: (105.848, 98.512, 137.288, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 97 16.00 P 2 15.00 O 2033 8.00 N 1877 7.00 C 8030 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 310 " distance=2.02 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 65 " distance=2.03 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 295 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 310 " distance=2.03 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 65 " distance=2.03 Simple disulfide: pdb=" SG CYS B 113 " - pdb=" SG CYS B 295 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 310 " distance=2.03 Simple disulfide: pdb=" SG CYS C 57 " - pdb=" SG CYS C 65 " distance=2.03 Simple disulfide: pdb=" SG CYS C 113 " - pdb=" SG CYS C 295 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 310 " distance=2.02 Simple disulfide: pdb=" SG CYS D 57 " - pdb=" SG CYS D 65 " distance=2.03 Simple disulfide: pdb=" SG CYS D 113 " - pdb=" SG CYS D 295 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 310 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 65 " distance=2.03 Simple disulfide: pdb=" SG CYS E 113 " - pdb=" SG CYS E 295 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 308 " distance=2.03 Simple disulfide: pdb=" SG CYS F 115 " - pdb=" SG CYS F 293 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.43 Conformation dependent library (CDL) restraints added in 2.0 seconds 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2754 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 6 sheets defined 73.0% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 22 through 49 Processing helix chain 'A' and resid 102 through 117 Processing helix chain 'A' and resid 119 through 141 removed outlier: 3.538A pdb=" N LYS A 123 " --> pdb=" O HIS A 119 " (cutoff:3.500A) Proline residue: A 126 - end of helix Processing helix chain 'A' and resid 259 through 287 removed outlier: 4.844A pdb=" N HIS A 287 " --> pdb=" O VAL A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 345 Processing helix chain 'B' and resid 15 through 21 removed outlier: 4.205A pdb=" N ARG B 18 " --> pdb=" O PRO B 15 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ILE B 19 " --> pdb=" O ALA B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 50 removed outlier: 3.793A pdb=" N ASP B 50 " --> pdb=" O GLN B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 116 Processing helix chain 'B' and resid 119 through 141 Proline residue: B 126 - end of helix Processing helix chain 'B' and resid 141 through 146 removed outlier: 3.781A pdb=" N LYS B 145 " --> pdb=" O ASN B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 286 removed outlier: 3.849A pdb=" N TYR B 285 " --> pdb=" O TYR B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 289 No H-bonds generated for 'chain 'B' and resid 287 through 289' Processing helix chain 'B' and resid 314 through 345 removed outlier: 3.632A pdb=" N PHE B 324 " --> pdb=" O ILE B 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 removed outlier: 3.985A pdb=" N ILE C 19 " --> pdb=" O ALA C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 49 Processing helix chain 'C' and resid 102 through 117 removed outlier: 3.519A pdb=" N ARG C 117 " --> pdb=" O CYS C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 141 Proline residue: C 126 - end of helix Processing helix chain 'C' and resid 141 through 146 removed outlier: 3.635A pdb=" N LYS C 145 " --> pdb=" O ASN C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 166 removed outlier: 3.928A pdb=" N LYS C 152 " --> pdb=" O ARG C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 175 removed outlier: 4.417A pdb=" N THR C 170 " --> pdb=" O SER C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 256 removed outlier: 4.104A pdb=" N GLU C 256 " --> pdb=" O THR C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 286 Processing helix chain 'C' and resid 287 through 289 No H-bonds generated for 'chain 'C' and resid 287 through 289' Processing helix chain 'C' and resid 315 through 346 removed outlier: 3.542A pdb=" N ALA C 322 " --> pdb=" O PHE C 318 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ARG C 346 " --> pdb=" O TRP C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 360 Processing helix chain 'C' and resid 369 through 383 Processing helix chain 'C' and resid 383 through 395 removed outlier: 4.494A pdb=" N SER C 387 " --> pdb=" O ASP C 383 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N VAL C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N PHE C 393 " --> pdb=" O ARG C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 411 Processing helix chain 'D' and resid 17 through 21 Processing helix chain 'D' and resid 22 through 49 Processing helix chain 'D' and resid 102 through 116 removed outlier: 3.548A pdb=" N ASN D 107 " --> pdb=" O ARG D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 146 removed outlier: 3.547A pdb=" N LYS D 123 " --> pdb=" O HIS D 119 " (cutoff:3.500A) Proline residue: D 126 - end of helix removed outlier: 4.828A pdb=" N TRP D 143 " --> pdb=" O CYS D 139 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N PHE D 144 " --> pdb=" O SER D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 166 removed outlier: 4.149A pdb=" N LYS D 152 " --> pdb=" O ARG D 148 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP D 165 " --> pdb=" O LEU D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 175 removed outlier: 4.161A pdb=" N THR D 170 " --> pdb=" O SER D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 256 removed outlier: 4.063A pdb=" N GLU D 256 " --> pdb=" O THR D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 287 removed outlier: 4.804A pdb=" N HIS D 287 " --> pdb=" O VAL D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 346 removed outlier: 3.905A pdb=" N ARG D 346 " --> pdb=" O TRP D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 360 Processing helix chain 'D' and resid 369 through 383 Processing helix chain 'D' and resid 383 through 391 removed outlier: 4.095A pdb=" N SER D 387 " --> pdb=" O ASP D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 394 No H-bonds generated for 'chain 'D' and resid 392 through 394' Processing helix chain 'D' and resid 395 through 407 Processing helix chain 'E' and resid 22 through 50 removed outlier: 3.791A pdb=" N ASP E 50 " --> pdb=" O GLN E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 117 Processing helix chain 'E' and resid 119 through 124 Processing helix chain 'E' and resid 124 through 141 Processing helix chain 'E' and resid 141 through 146 removed outlier: 3.742A pdb=" N LYS E 145 " --> pdb=" O ASN E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 286 Processing helix chain 'E' and resid 287 through 289 No H-bonds generated for 'chain 'E' and resid 287 through 289' Processing helix chain 'E' and resid 299 through 304 Processing helix chain 'E' and resid 315 through 344 Processing helix chain 'F' and resid 22 through 48 removed outlier: 3.551A pdb=" N VAL F 26 " --> pdb=" O PRO F 22 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N MET F 48 " --> pdb=" O THR F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 119 Processing helix chain 'F' and resid 121 through 143 Proline residue: F 128 - end of helix removed outlier: 4.163A pdb=" N ASN F 143 " --> pdb=" O MET F 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 257 through 284 Processing helix chain 'F' and resid 285 through 287 No H-bonds generated for 'chain 'F' and resid 285 through 287' Processing helix chain 'F' and resid 312 through 344 removed outlier: 4.263A pdb=" N ARG F 344 " --> pdb=" O TRP F 340 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 56 removed outlier: 3.879A pdb=" N LEU A 55 " --> pdb=" O ARG A 309 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 53 through 56 removed outlier: 3.701A pdb=" N LEU B 55 " --> pdb=" O ARG B 309 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 53 through 56 Processing sheet with id=AA4, first strand: chain 'D' and resid 53 through 56 Processing sheet with id=AA5, first strand: chain 'E' and resid 292 through 296 Processing sheet with id=AA6, first strand: chain 'F' and resid 52 through 56 806 hydrogen bonds defined for protein. 2379 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: 3.54 Time building geometry restraints manager: 3.53 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: 2565 1.33 - 1.46: 3178 1.46 - 1.58: 6500 1.58 - 1.70: 2 1.70 - 1.82: 140 Bond restraints: 12385 Sorted by residual: bond pdb=" C10 PEE C 902 " pdb=" O4 PEE C 902 " ideal model delta sigma weight residual 1.206 1.357 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" C10 PEE C 901 " pdb=" O4 PEE C 901 " ideal model delta sigma weight residual 1.206 1.357 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" O4P PEE D 902 " pdb=" P PEE D 902 " ideal model delta sigma weight residual 1.653 1.777 -0.124 2.00e-02 2.50e+03 3.82e+01 bond pdb=" O4P PEE D 901 " pdb=" P PEE D 901 " ideal model delta sigma weight residual 1.653 1.776 -0.123 2.00e-02 2.50e+03 3.79e+01 bond pdb=" C10 PEE C 902 " pdb=" O2 PEE C 902 " ideal model delta sigma weight residual 1.332 1.215 0.117 2.00e-02 2.50e+03 3.41e+01 ... (remaining 12380 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.77: 16543 2.77 - 5.54: 189 5.54 - 8.31: 32 8.31 - 11.08: 5 11.08 - 13.85: 4 Bond angle restraints: 16773 Sorted by residual: angle pdb=" O1P PEE D 902 " pdb=" P PEE D 902 " pdb=" O2P PEE D 902 " ideal model delta sigma weight residual 119.43 133.28 -13.85 3.00e+00 1.11e-01 2.13e+01 angle pdb=" O1P PEE D 901 " pdb=" P PEE D 901 " pdb=" O2P PEE D 901 " ideal model delta sigma weight residual 119.43 133.19 -13.76 3.00e+00 1.11e-01 2.10e+01 angle pdb=" C11 PEE C 901 " pdb=" C10 PEE C 901 " pdb=" O2 PEE C 901 " ideal model delta sigma weight residual 111.70 124.69 -12.99 3.00e+00 1.11e-01 1.87e+01 angle pdb=" C11 PEE C 902 " pdb=" C10 PEE C 902 " pdb=" O2 PEE C 902 " ideal model delta sigma weight residual 111.70 124.67 -12.97 3.00e+00 1.11e-01 1.87e+01 angle pdb=" CA GLU C 245 " pdb=" CB GLU C 245 " pdb=" CG GLU C 245 " ideal model delta sigma weight residual 114.10 121.71 -7.61 2.00e+00 2.50e-01 1.45e+01 ... (remaining 16768 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.75: 6964 34.75 - 69.50: 257 69.50 - 104.25: 13 104.25 - 139.00: 2 139.00 - 173.75: 2 Dihedral angle restraints: 7238 sinusoidal: 2971 harmonic: 4267 Sorted by residual: dihedral pdb=" CB CYS D 113 " pdb=" SG CYS D 113 " pdb=" SG CYS D 295 " pdb=" CB CYS D 295 " ideal model delta sinusoidal sigma weight residual 93.00 37.93 55.07 1 1.00e+01 1.00e-02 4.10e+01 dihedral pdb=" CA GLU A 115 " pdb=" C GLU A 115 " pdb=" N ASN A 116 " pdb=" CA ASN A 116 " ideal model delta harmonic sigma weight residual -180.00 -156.01 -23.99 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" N PEE D 902 " pdb=" C4 PEE D 902 " pdb=" C5 PEE D 902 " pdb=" O4P PEE D 902 " ideal model delta sinusoidal sigma weight residual -56.97 116.78 -173.75 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 7235 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 1724 0.085 - 0.171: 117 0.171 - 0.256: 3 0.256 - 0.341: 0 0.341 - 0.426: 2 Chirality restraints: 1846 Sorted by residual: chirality pdb=" C2 PEE D 902 " pdb=" C1 PEE D 902 " pdb=" C3 PEE D 902 " pdb=" O2 PEE D 902 " both_signs ideal model delta sigma weight residual False -2.33 -2.75 0.43 2.00e-01 2.50e+01 4.55e+00 chirality pdb=" C2 PEE D 901 " pdb=" C1 PEE D 901 " pdb=" C3 PEE D 901 " pdb=" O2 PEE D 901 " both_signs ideal model delta sigma weight residual False -2.33 -2.73 0.40 2.00e-01 2.50e+01 3.98e+00 chirality pdb=" CB VAL F 263 " pdb=" CA VAL F 263 " pdb=" CG1 VAL F 263 " pdb=" CG2 VAL F 263 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 1843 not shown) Planarity restraints: 1985 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 23 " 0.019 2.00e-02 2.50e+03 2.17e-02 1.18e+01 pdb=" CG TRP A 23 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 TRP A 23 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP A 23 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 23 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 23 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 23 " 0.012 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 23 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 23 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 23 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 120 " 0.021 2.00e-02 2.50e+03 2.00e-02 9.99e+00 pdb=" CG TRP D 120 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 TRP D 120 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP D 120 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 120 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 120 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP D 120 " 0.010 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 120 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 120 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP D 120 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 143 " -0.022 2.00e-02 2.50e+03 1.94e-02 9.44e+00 pdb=" CG TRP A 143 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP A 143 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP A 143 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 143 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 143 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 143 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 143 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 143 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A 143 " 0.001 2.00e-02 2.50e+03 ... (remaining 1982 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 835 2.74 - 3.28: 12354 3.28 - 3.82: 20773 3.82 - 4.36: 23360 4.36 - 4.90: 40918 Nonbonded interactions: 98240 Sorted by model distance: nonbonded pdb=" OD2 ASP A 50 " pdb=" OH TYR A 114 " model vdw 2.201 3.040 nonbonded pdb=" O ILE C 356 " pdb=" OG SER C 360 " model vdw 2.206 3.040 nonbonded pdb=" O THR E 44 " pdb=" OG1 THR E 48 " model vdw 2.221 3.040 nonbonded pdb=" OD2 ASP E 110 " pdb=" NE2 GLN F 106 " model vdw 2.251 3.120 nonbonded pdb=" OG1 THR C 316 " pdb=" OE2 GLU D 115 " model vdw 2.265 3.040 ... (remaining 98235 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'E' } ncs_group { reference = (chain 'C' and (resid 15 through 407 or resid 901 through 902)) selection = (chain 'D' and (resid 15 through 407 or (resid 901 and (name C10 or name C11 or \ name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name O2 \ or name O4 )) or (resid 902 and (name C10 or name C11 or name C12 or name C13 or \ name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name O2 \ or name O4 )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.230 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: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 29.200 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5913 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 : 0.005 0.151 12402 Z= 0.266 Angle : 0.807 13.851 16807 Z= 0.440 Chirality : 0.047 0.426 1846 Planarity : 0.006 0.054 1985 Dihedral : 17.316 173.749 4433 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.53 % Allowed : 23.59 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.22), residues: 1382 helix: 0.52 (0.16), residues: 962 sheet: 0.25 (0.54), residues: 102 loop : -1.23 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP A 23 HIS 0.023 0.002 HIS E 119 PHE 0.039 0.002 PHE C 390 TYR 0.031 0.002 TYR E 325 ARG 0.014 0.001 ARG B 345 Details of bonding type rmsd hydrogen bonds : bond 0.13389 ( 806) hydrogen bonds : angle 6.19165 ( 2379) SS BOND : bond 0.00319 ( 17) SS BOND : angle 1.25539 ( 34) covalent geometry : bond 0.00527 (12385) covalent geometry : angle 0.80545 (16773) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 225 time to evaluate : 1.380 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 231 average time/residue: 0.2517 time to fit residues: 82.6538 Evaluate side-chains 212 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 207 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLN Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain B residue 23 TRP Chi-restraints excluded: chain C residue 253 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 117 optimal weight: 0.5980 chunk 105 optimal weight: 0.2980 chunk 58 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 71 optimal weight: 0.5980 chunk 56 optimal weight: 0.6980 chunk 108 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 66 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 126 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 GLN C 404 GLN D 105 GLN ** D 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 46 GLN ** F 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4726 r_free = 0.4726 target = 0.228708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.186924 restraints weight = 15681.157| |-----------------------------------------------------------------------------| r_work (start): 0.4310 rms_B_bonded: 2.83 r_work: 0.4131 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.4131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6470 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12402 Z= 0.137 Angle : 0.517 7.087 16807 Z= 0.280 Chirality : 0.040 0.167 1846 Planarity : 0.004 0.046 1985 Dihedral : 9.681 178.498 1680 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 4.19 % Allowed : 20.40 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.22), residues: 1382 helix: 1.46 (0.16), residues: 970 sheet: 0.44 (0.53), residues: 107 loop : -1.41 (0.32), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 23 HIS 0.008 0.001 HIS E 119 PHE 0.024 0.002 PHE D 390 TYR 0.024 0.001 TYR D 284 ARG 0.006 0.000 ARG D 389 Details of bonding type rmsd hydrogen bonds : bond 0.04070 ( 806) hydrogen bonds : angle 4.36390 ( 2379) SS BOND : bond 0.00288 ( 17) SS BOND : angle 0.83617 ( 34) covalent geometry : bond 0.00301 (12385) covalent geometry : angle 0.51631 (16773) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 235 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 319 LYS cc_start: 0.3859 (mtmt) cc_final: 0.3259 (tppp) REVERT: B 46 GLN cc_start: 0.7373 (tm-30) cc_final: 0.7140 (tm-30) REVERT: B 98 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7897 (mmmt) REVERT: B 117 ARG cc_start: 0.7418 (mmm160) cc_final: 0.6737 (tpt90) REVERT: B 275 PHE cc_start: 0.6126 (OUTLIER) cc_final: 0.5461 (t80) REVERT: B 336 CYS cc_start: 0.6041 (m) cc_final: 0.5445 (t) REVERT: C 46 GLN cc_start: 0.7604 (tm-30) cc_final: 0.7315 (tm-30) REVERT: C 47 VAL cc_start: 0.8801 (t) cc_final: 0.8348 (t) REVERT: C 49 GLN cc_start: 0.8267 (mm-40) cc_final: 0.7889 (mm110) REVERT: C 108 TYR cc_start: 0.7257 (t80) cc_final: 0.6926 (t80) REVERT: C 275 PHE cc_start: 0.7950 (OUTLIER) cc_final: 0.7459 (t80) REVERT: C 404 GLN cc_start: 0.7658 (tp-100) cc_final: 0.7447 (tp40) REVERT: D 305 TYR cc_start: 0.8482 (m-80) cc_final: 0.7995 (m-80) REVERT: D 324 PHE cc_start: 0.6699 (t80) cc_final: 0.6492 (t80) REVERT: E 299 ILE cc_start: 0.3695 (OUTLIER) cc_final: 0.2422 (pt) REVERT: E 314 LEU cc_start: 0.6684 (OUTLIER) cc_final: 0.6449 (pp) REVERT: E 343 MET cc_start: 0.2363 (OUTLIER) cc_final: 0.2083 (mtt) REVERT: F 288 GLN cc_start: 0.7096 (mm110) cc_final: 0.6832 (mm110) outliers start: 55 outliers final: 28 residues processed: 275 average time/residue: 0.2306 time to fit residues: 91.5122 Evaluate side-chains 243 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 209 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain B residue 23 TRP Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 98 LYS Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 331 PHE Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 250 PHE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 400 ASN Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 310 CYS Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 343 MET Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 46 GLN Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 293 CYS Chi-restraints excluded: chain F residue 343 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 40 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 113 optimal weight: 7.9990 chunk 28 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 111 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 108 optimal weight: 0.5980 chunk 121 optimal weight: 5.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 155 HIS D 104 HIS ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 288 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4695 r_free = 0.4695 target = 0.225250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.183691 restraints weight = 15979.589| |-----------------------------------------------------------------------------| r_work (start): 0.4282 rms_B_bonded: 2.87 r_work: 0.4087 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.4087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6550 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12402 Z= 0.155 Angle : 0.529 6.146 16807 Z= 0.286 Chirality : 0.040 0.142 1846 Planarity : 0.004 0.043 1985 Dihedral : 9.214 178.290 1676 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 4.79 % Allowed : 21.08 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.22), residues: 1382 helix: 1.62 (0.16), residues: 965 sheet: 0.41 (0.53), residues: 107 loop : -1.46 (0.32), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 120 HIS 0.007 0.001 HIS D 104 PHE 0.019 0.002 PHE B 27 TYR 0.028 0.002 TYR D 284 ARG 0.009 0.000 ARG E 103 Details of bonding type rmsd hydrogen bonds : bond 0.04034 ( 806) hydrogen bonds : angle 4.30272 ( 2379) SS BOND : bond 0.00356 ( 17) SS BOND : angle 0.99470 ( 34) covalent geometry : bond 0.00351 (12385) covalent geometry : angle 0.52760 (16773) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 220 time to evaluate : 1.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 PHE cc_start: 0.5139 (OUTLIER) cc_final: 0.4820 (m-10) REVERT: A 319 LYS cc_start: 0.4090 (mtmt) cc_final: 0.3335 (tppp) REVERT: B 46 GLN cc_start: 0.7359 (tm-30) cc_final: 0.7067 (tm-30) REVERT: B 98 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7935 (mmmt) REVERT: B 130 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7103 (tp) REVERT: B 275 PHE cc_start: 0.6151 (OUTLIER) cc_final: 0.5440 (t80) REVERT: B 336 CYS cc_start: 0.6258 (m) cc_final: 0.5573 (t) REVERT: C 47 VAL cc_start: 0.8768 (t) cc_final: 0.8545 (t) REVERT: C 49 GLN cc_start: 0.8352 (mm-40) cc_final: 0.7978 (mm110) REVERT: C 104 HIS cc_start: 0.7559 (OUTLIER) cc_final: 0.6780 (t70) REVERT: C 275 PHE cc_start: 0.8058 (OUTLIER) cc_final: 0.7546 (t80) REVERT: D 148 ARG cc_start: 0.7203 (mtp180) cc_final: 0.6915 (mmt-90) REVERT: D 305 TYR cc_start: 0.8545 (m-80) cc_final: 0.8113 (m-80) REVERT: E 299 ILE cc_start: 0.3766 (OUTLIER) cc_final: 0.2551 (pt) REVERT: E 314 LEU cc_start: 0.6724 (OUTLIER) cc_final: 0.6368 (pp) REVERT: E 343 MET cc_start: 0.2838 (OUTLIER) cc_final: 0.2558 (mtt) REVERT: F 126 TYR cc_start: 0.6248 (m-80) cc_final: 0.6012 (m-80) REVERT: F 288 GLN cc_start: 0.7143 (mm110) cc_final: 0.6865 (mm110) outliers start: 63 outliers final: 37 residues processed: 269 average time/residue: 0.2414 time to fit residues: 93.0757 Evaluate side-chains 249 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 203 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 59 TRP Chi-restraints excluded: chain A residue 136 PHE Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain B residue 23 TRP Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 98 LYS Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 294 ASP Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 400 ASN Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 343 MET Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 293 CYS Chi-restraints excluded: chain F residue 315 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 44 optimal weight: 0.8980 chunk 75 optimal weight: 9.9990 chunk 57 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 111 optimal weight: 5.9990 chunk 110 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 42 optimal weight: 0.0570 chunk 23 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 46 GLN ** F 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4695 r_free = 0.4695 target = 0.225431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.185287 restraints weight = 15539.284| |-----------------------------------------------------------------------------| r_work (start): 0.4301 rms_B_bonded: 2.73 r_work: 0.4120 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.4120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6521 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12402 Z= 0.136 Angle : 0.508 5.797 16807 Z= 0.275 Chirality : 0.039 0.127 1846 Planarity : 0.003 0.044 1985 Dihedral : 8.887 179.540 1676 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 5.40 % Allowed : 21.39 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.22), residues: 1382 helix: 1.71 (0.16), residues: 968 sheet: 0.39 (0.52), residues: 107 loop : -1.31 (0.33), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 120 HIS 0.006 0.001 HIS A 132 PHE 0.023 0.001 PHE E 331 TYR 0.026 0.001 TYR D 284 ARG 0.007 0.000 ARG D 389 Details of bonding type rmsd hydrogen bonds : bond 0.03780 ( 806) hydrogen bonds : angle 4.17860 ( 2379) SS BOND : bond 0.00303 ( 17) SS BOND : angle 0.84409 ( 34) covalent geometry : bond 0.00307 (12385) covalent geometry : angle 0.50727 (16773) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 220 time to evaluate : 1.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 PHE cc_start: 0.5420 (OUTLIER) cc_final: 0.5191 (m-10) REVERT: A 319 LYS cc_start: 0.4370 (mtmt) cc_final: 0.3508 (tppp) REVERT: B 33 ILE cc_start: 0.7052 (mp) cc_final: 0.6730 (tp) REVERT: B 46 GLN cc_start: 0.7349 (tm-30) cc_final: 0.7069 (tm-30) REVERT: B 130 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7032 (tp) REVERT: B 275 PHE cc_start: 0.6155 (OUTLIER) cc_final: 0.5308 (t80) REVERT: B 336 CYS cc_start: 0.6311 (m) cc_final: 0.5572 (t) REVERT: C 104 HIS cc_start: 0.7549 (OUTLIER) cc_final: 0.6674 (t70) REVERT: C 275 PHE cc_start: 0.7970 (OUTLIER) cc_final: 0.7459 (t80) REVERT: D 148 ARG cc_start: 0.7234 (mtp180) cc_final: 0.6941 (mmt-90) REVERT: D 305 TYR cc_start: 0.8515 (m-80) cc_final: 0.8146 (m-80) REVERT: E 17 TYR cc_start: 0.4464 (OUTLIER) cc_final: 0.3729 (m-80) REVERT: E 314 LEU cc_start: 0.6659 (OUTLIER) cc_final: 0.6268 (pp) REVERT: E 343 MET cc_start: 0.3770 (OUTLIER) cc_final: 0.3497 (mtt) REVERT: F 126 TYR cc_start: 0.6287 (m-80) cc_final: 0.6026 (m-80) REVERT: F 288 GLN cc_start: 0.7161 (mm110) cc_final: 0.6855 (mm110) outliers start: 71 outliers final: 47 residues processed: 272 average time/residue: 0.2417 time to fit residues: 95.6729 Evaluate side-chains 261 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 206 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 59 TRP Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 136 PHE Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 331 PHE Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 294 ASP Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 400 ASN Chi-restraints excluded: chain E residue 17 TYR Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 310 CYS Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 343 MET Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 46 GLN Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 51 LYS Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 293 CYS Chi-restraints excluded: chain F residue 315 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 105 optimal weight: 0.9980 chunk 128 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 100 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 76 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 11 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN ** A 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4691 r_free = 0.4691 target = 0.224572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.182565 restraints weight = 15674.958| |-----------------------------------------------------------------------------| r_work (start): 0.4265 rms_B_bonded: 2.42 r_work: 0.4113 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.4113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6530 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12402 Z= 0.154 Angle : 0.530 5.950 16807 Z= 0.286 Chirality : 0.040 0.136 1846 Planarity : 0.003 0.042 1985 Dihedral : 8.818 179.940 1674 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 5.33 % Allowed : 22.37 % Favored : 72.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.22), residues: 1382 helix: 1.73 (0.16), residues: 973 sheet: 0.45 (0.53), residues: 107 loop : -1.38 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 120 HIS 0.004 0.001 HIS A 132 PHE 0.025 0.001 PHE E 331 TYR 0.029 0.001 TYR D 284 ARG 0.010 0.000 ARG C 306 Details of bonding type rmsd hydrogen bonds : bond 0.03848 ( 806) hydrogen bonds : angle 4.21081 ( 2379) SS BOND : bond 0.00478 ( 17) SS BOND : angle 1.11541 ( 34) covalent geometry : bond 0.00356 (12385) covalent geometry : angle 0.52775 (16773) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 215 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 TYR cc_start: 0.5310 (m-80) cc_final: 0.5012 (m-80) REVERT: A 136 PHE cc_start: 0.5426 (OUTLIER) cc_final: 0.5137 (m-10) REVERT: A 319 LYS cc_start: 0.4413 (mtmt) cc_final: 0.3487 (tppp) REVERT: B 46 GLN cc_start: 0.7272 (tm-30) cc_final: 0.7023 (tm-30) REVERT: B 130 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.7042 (tp) REVERT: B 275 PHE cc_start: 0.6140 (OUTLIER) cc_final: 0.5223 (t80) REVERT: B 336 CYS cc_start: 0.6339 (m) cc_final: 0.5574 (t) REVERT: C 104 HIS cc_start: 0.7415 (OUTLIER) cc_final: 0.6459 (t70) REVERT: C 275 PHE cc_start: 0.7967 (OUTLIER) cc_final: 0.7426 (t80) REVERT: C 392 VAL cc_start: 0.8169 (p) cc_final: 0.7912 (m) REVERT: D 305 TYR cc_start: 0.8534 (m-80) cc_final: 0.8192 (m-80) REVERT: E 17 TYR cc_start: 0.4482 (OUTLIER) cc_final: 0.3741 (m-80) REVERT: E 265 MET cc_start: 0.5780 (tpt) cc_final: 0.5312 (mmt) REVERT: E 290 LYS cc_start: 0.4397 (tptp) cc_final: 0.4131 (tptp) REVERT: E 299 ILE cc_start: 0.3633 (OUTLIER) cc_final: 0.2387 (pt) REVERT: E 314 LEU cc_start: 0.6609 (OUTLIER) cc_final: 0.6225 (pp) REVERT: E 343 MET cc_start: 0.4270 (OUTLIER) cc_final: 0.4032 (mtt) REVERT: F 126 TYR cc_start: 0.6375 (m-80) cc_final: 0.6024 (m-80) REVERT: F 288 GLN cc_start: 0.7135 (mm110) cc_final: 0.6819 (mm110) outliers start: 70 outliers final: 48 residues processed: 269 average time/residue: 0.2199 time to fit residues: 86.9277 Evaluate side-chains 270 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 213 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 59 TRP Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 136 PHE Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 331 PHE Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 400 ASN Chi-restraints excluded: chain E residue 17 TYR Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 310 CYS Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 343 MET Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 51 LYS Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 293 CYS Chi-restraints excluded: chain F residue 315 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 52 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 84 optimal weight: 8.9990 chunk 130 optimal weight: 6.9990 chunk 83 optimal weight: 0.6980 chunk 34 optimal weight: 0.0980 chunk 75 optimal weight: 0.0970 chunk 4 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 101 optimal weight: 20.0000 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 GLN ** D 288 ASN ** 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 = 0.4734 r_free = 0.4734 target = 0.227880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.190538 restraints weight = 15998.828| |-----------------------------------------------------------------------------| r_work (start): 0.4367 rms_B_bonded: 2.49 r_work: 0.4187 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.4187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6496 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12402 Z= 0.123 Angle : 0.498 6.154 16807 Z= 0.270 Chirality : 0.039 0.151 1846 Planarity : 0.003 0.042 1985 Dihedral : 8.557 176.872 1674 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 4.41 % Allowed : 23.90 % Favored : 71.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.23), residues: 1382 helix: 1.85 (0.16), residues: 973 sheet: 0.53 (0.52), residues: 107 loop : -1.31 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 120 HIS 0.003 0.001 HIS E 104 PHE 0.022 0.001 PHE E 331 TYR 0.024 0.001 TYR D 284 ARG 0.004 0.000 ARG D 117 Details of bonding type rmsd hydrogen bonds : bond 0.03619 ( 806) hydrogen bonds : angle 4.08264 ( 2379) SS BOND : bond 0.00263 ( 17) SS BOND : angle 0.85914 ( 34) covalent geometry : bond 0.00274 (12385) covalent geometry : angle 0.49710 (16773) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 226 time to evaluate : 1.813 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 319 LYS cc_start: 0.4290 (mtmt) cc_final: 0.3531 (tppp) REVERT: B 117 ARG cc_start: 0.7378 (mmm160) cc_final: 0.6693 (mmm160) REVERT: B 130 LEU cc_start: 0.7801 (OUTLIER) cc_final: 0.7092 (tp) REVERT: B 275 PHE cc_start: 0.6074 (OUTLIER) cc_final: 0.5083 (t80) REVERT: B 336 CYS cc_start: 0.6284 (m) cc_final: 0.5554 (t) REVERT: C 104 HIS cc_start: 0.7411 (OUTLIER) cc_final: 0.6430 (t70) REVERT: C 153 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7675 (mm) REVERT: C 275 PHE cc_start: 0.7980 (OUTLIER) cc_final: 0.7473 (t80) REVERT: C 371 ASP cc_start: 0.7354 (m-30) cc_final: 0.7088 (m-30) REVERT: C 392 VAL cc_start: 0.8072 (p) cc_final: 0.7859 (m) REVERT: D 274 LYS cc_start: 0.8042 (OUTLIER) cc_final: 0.7835 (tptm) REVERT: D 305 TYR cc_start: 0.8510 (m-80) cc_final: 0.8245 (m-80) REVERT: E 17 TYR cc_start: 0.4366 (OUTLIER) cc_final: 0.3688 (m-80) REVERT: E 265 MET cc_start: 0.5718 (tpt) cc_final: 0.5430 (mmt) REVERT: E 299 ILE cc_start: 0.3632 (OUTLIER) cc_final: 0.2557 (pt) REVERT: E 314 LEU cc_start: 0.6514 (OUTLIER) cc_final: 0.6105 (pp) REVERT: E 343 MET cc_start: 0.4379 (OUTLIER) cc_final: 0.4169 (mtt) REVERT: F 126 TYR cc_start: 0.6352 (m-80) cc_final: 0.6089 (m-80) REVERT: F 288 GLN cc_start: 0.7055 (mm110) cc_final: 0.6773 (mm110) outliers start: 58 outliers final: 41 residues processed: 271 average time/residue: 0.2808 time to fit residues: 111.9691 Evaluate side-chains 264 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 213 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 59 TRP Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 274 LYS Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 400 ASN Chi-restraints excluded: chain E residue 17 TYR Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 310 CYS Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 343 MET Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 51 LYS Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 293 CYS Chi-restraints excluded: chain F residue 315 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 3 optimal weight: 0.0050 chunk 108 optimal weight: 0.3980 chunk 64 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 72 optimal weight: 0.9990 chunk 32 optimal weight: 0.3980 chunk 10 optimal weight: 6.9990 chunk 124 optimal weight: 0.9990 chunk 86 optimal weight: 0.6980 chunk 126 optimal weight: 0.7980 chunk 107 optimal weight: 0.8980 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 312 HIS F 46 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4742 r_free = 0.4742 target = 0.228953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.189786 restraints weight = 15957.852| |-----------------------------------------------------------------------------| r_work (start): 0.4359 rms_B_bonded: 2.66 r_work: 0.4152 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.4152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6530 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12402 Z= 0.119 Angle : 0.501 7.964 16807 Z= 0.272 Chirality : 0.039 0.138 1846 Planarity : 0.003 0.042 1985 Dihedral : 8.326 173.340 1674 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 4.57 % Allowed : 24.20 % Favored : 71.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.23), residues: 1382 helix: 1.89 (0.16), residues: 974 sheet: 0.61 (0.52), residues: 107 loop : -1.21 (0.34), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP D 120 HIS 0.003 0.001 HIS E 104 PHE 0.031 0.001 PHE C 390 TYR 0.024 0.001 TYR D 284 ARG 0.003 0.000 ARG D 117 Details of bonding type rmsd hydrogen bonds : bond 0.03550 ( 806) hydrogen bonds : angle 4.05297 ( 2379) SS BOND : bond 0.00399 ( 17) SS BOND : angle 1.00915 ( 34) covalent geometry : bond 0.00261 (12385) covalent geometry : angle 0.49956 (16773) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 237 time to evaluate : 1.569 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 ILE cc_start: 0.6825 (mt) cc_final: 0.6544 (mp) REVERT: A 51 LYS cc_start: 0.7803 (ptpp) cc_final: 0.7506 (pttp) REVERT: A 319 LYS cc_start: 0.4316 (mtmt) cc_final: 0.3533 (tppp) REVERT: B 27 PHE cc_start: 0.4382 (m-10) cc_final: 0.4046 (m-10) REVERT: B 117 ARG cc_start: 0.7456 (mmm160) cc_final: 0.6985 (mmm160) REVERT: B 130 LEU cc_start: 0.7805 (OUTLIER) cc_final: 0.7093 (tp) REVERT: B 275 PHE cc_start: 0.6087 (OUTLIER) cc_final: 0.5003 (t80) REVERT: B 336 CYS cc_start: 0.6286 (m) cc_final: 0.5543 (t) REVERT: C 46 GLN cc_start: 0.7539 (tm-30) cc_final: 0.7332 (tm-30) REVERT: C 104 HIS cc_start: 0.7477 (OUTLIER) cc_final: 0.6456 (t70) REVERT: C 153 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7627 (mm) REVERT: C 275 PHE cc_start: 0.8057 (OUTLIER) cc_final: 0.7562 (t80) REVERT: C 293 VAL cc_start: 0.8603 (t) cc_final: 0.8292 (t) REVERT: C 371 ASP cc_start: 0.7362 (m-30) cc_final: 0.7139 (m-30) REVERT: C 392 VAL cc_start: 0.8105 (p) cc_final: 0.7864 (m) REVERT: D 274 LYS cc_start: 0.8079 (OUTLIER) cc_final: 0.7861 (tptm) REVERT: D 305 TYR cc_start: 0.8490 (m-80) cc_final: 0.8229 (m-80) REVERT: E 17 TYR cc_start: 0.4383 (OUTLIER) cc_final: 0.3663 (m-80) REVERT: E 127 TYR cc_start: 0.4937 (m-10) cc_final: 0.4551 (m-10) REVERT: E 265 MET cc_start: 0.5681 (tpt) cc_final: 0.5462 (mmt) REVERT: E 290 LYS cc_start: 0.4212 (tptp) cc_final: 0.3972 (tptp) REVERT: E 299 ILE cc_start: 0.3679 (OUTLIER) cc_final: 0.2532 (pt) REVERT: E 314 LEU cc_start: 0.6511 (OUTLIER) cc_final: 0.6108 (pp) REVERT: E 343 MET cc_start: 0.4226 (OUTLIER) cc_final: 0.4025 (mtt) REVERT: F 126 TYR cc_start: 0.6264 (m-80) cc_final: 0.5877 (m-80) REVERT: F 288 GLN cc_start: 0.6903 (mm110) cc_final: 0.6634 (mm110) outliers start: 60 outliers final: 40 residues processed: 283 average time/residue: 0.3130 time to fit residues: 133.8969 Evaluate side-chains 274 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 224 time to evaluate : 1.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 331 PHE Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 274 LYS Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 400 ASN Chi-restraints excluded: chain E residue 17 TYR Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 310 CYS Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 343 MET Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 46 GLN Chi-restraints excluded: chain F residue 51 LYS Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 293 CYS Chi-restraints excluded: chain F residue 315 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 47 optimal weight: 1.9990 chunk 124 optimal weight: 0.0870 chunk 19 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 2 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 23 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 HIS ** D 288 ASN ** 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 = 0.4732 r_free = 0.4732 target = 0.227826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.188584 restraints weight = 15990.179| |-----------------------------------------------------------------------------| r_work (start): 0.4345 rms_B_bonded: 2.61 r_work: 0.4141 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.4141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6560 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12402 Z= 0.138 Angle : 0.527 8.922 16807 Z= 0.285 Chirality : 0.040 0.217 1846 Planarity : 0.003 0.042 1985 Dihedral : 8.245 170.256 1674 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 4.41 % Allowed : 24.58 % Favored : 71.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.23), residues: 1382 helix: 1.89 (0.16), residues: 974 sheet: 0.54 (0.51), residues: 107 loop : -1.21 (0.35), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP D 120 HIS 0.003 0.001 HIS E 104 PHE 0.029 0.001 PHE C 390 TYR 0.026 0.001 TYR D 284 ARG 0.004 0.000 ARG B 306 Details of bonding type rmsd hydrogen bonds : bond 0.03634 ( 806) hydrogen bonds : angle 4.09114 ( 2379) SS BOND : bond 0.00327 ( 17) SS BOND : angle 1.10143 ( 34) covalent geometry : bond 0.00313 (12385) covalent geometry : angle 0.52483 (16773) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 214 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 LYS cc_start: 0.7605 (ptpp) cc_final: 0.7361 (pttp) REVERT: A 98 LYS cc_start: 0.7210 (mmtt) cc_final: 0.6940 (mtpp) REVERT: A 319 LYS cc_start: 0.4399 (mtmt) cc_final: 0.3559 (tppt) REVERT: B 27 PHE cc_start: 0.4435 (m-10) cc_final: 0.4136 (m-10) REVERT: B 117 ARG cc_start: 0.7441 (mmm160) cc_final: 0.7044 (mmm160) REVERT: B 130 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7106 (tp) REVERT: B 275 PHE cc_start: 0.6099 (OUTLIER) cc_final: 0.5031 (t80) REVERT: B 336 CYS cc_start: 0.6311 (m) cc_final: 0.5559 (t) REVERT: C 46 GLN cc_start: 0.7530 (tm-30) cc_final: 0.7329 (tm-30) REVERT: C 104 HIS cc_start: 0.7471 (OUTLIER) cc_final: 0.6410 (t70) REVERT: C 153 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7575 (mm) REVERT: C 275 PHE cc_start: 0.8048 (OUTLIER) cc_final: 0.7525 (t80) REVERT: C 293 VAL cc_start: 0.8602 (t) cc_final: 0.8309 (t) REVERT: C 392 VAL cc_start: 0.8129 (p) cc_final: 0.7879 (m) REVERT: D 274 LYS cc_start: 0.8070 (OUTLIER) cc_final: 0.7841 (tptm) REVERT: D 305 TYR cc_start: 0.8526 (m-80) cc_final: 0.8294 (m-80) REVERT: E 17 TYR cc_start: 0.4465 (OUTLIER) cc_final: 0.3706 (m-80) REVERT: E 127 TYR cc_start: 0.5310 (m-10) cc_final: 0.4856 (m-10) REVERT: E 144 PHE cc_start: 0.6246 (m-10) cc_final: 0.6030 (m-10) REVERT: E 265 MET cc_start: 0.5616 (tpt) cc_final: 0.5409 (mmt) REVERT: E 290 LYS cc_start: 0.4294 (tptp) cc_final: 0.4048 (tptp) REVERT: E 299 ILE cc_start: 0.3770 (OUTLIER) cc_final: 0.2663 (pt) REVERT: E 314 LEU cc_start: 0.6487 (OUTLIER) cc_final: 0.6114 (pp) REVERT: E 343 MET cc_start: 0.4387 (OUTLIER) cc_final: 0.4169 (mtt) REVERT: F 46 GLN cc_start: 0.6089 (mm-40) cc_final: 0.5450 (tm-30) REVERT: F 126 TYR cc_start: 0.6171 (m-80) cc_final: 0.5899 (m-80) outliers start: 58 outliers final: 44 residues processed: 260 average time/residue: 0.2503 time to fit residues: 95.7510 Evaluate side-chains 268 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 214 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 59 TRP Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 331 PHE Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 265 MET Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 274 LYS Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 400 ASN Chi-restraints excluded: chain E residue 17 TYR Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 310 CYS Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 343 MET Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 51 LYS Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 293 CYS Chi-restraints excluded: chain F residue 315 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 61 optimal weight: 0.2980 chunk 109 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 108 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 24 optimal weight: 0.4980 chunk 0 optimal weight: 20.0000 chunk 66 optimal weight: 0.5980 chunk 118 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 chunk 75 optimal weight: 9.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 116 ASN C 49 GLN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 46 GLN ** F 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4738 r_free = 0.4738 target = 0.228468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.188719 restraints weight = 15877.777| |-----------------------------------------------------------------------------| r_work (start): 0.4345 rms_B_bonded: 2.76 r_work: 0.4142 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.4142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6550 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12402 Z= 0.130 Angle : 0.526 9.680 16807 Z= 0.285 Chirality : 0.039 0.202 1846 Planarity : 0.003 0.042 1985 Dihedral : 8.038 160.619 1674 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 4.49 % Allowed : 25.11 % Favored : 70.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.23), residues: 1382 helix: 1.91 (0.16), residues: 974 sheet: 0.64 (0.51), residues: 107 loop : -1.19 (0.35), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP D 120 HIS 0.003 0.001 HIS E 104 PHE 0.027 0.001 PHE C 390 TYR 0.030 0.001 TYR D 284 ARG 0.003 0.000 ARG D 117 Details of bonding type rmsd hydrogen bonds : bond 0.03574 ( 806) hydrogen bonds : angle 4.06151 ( 2379) SS BOND : bond 0.00275 ( 17) SS BOND : angle 1.01568 ( 34) covalent geometry : bond 0.00293 (12385) covalent geometry : angle 0.52418 (16773) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 223 time to evaluate : 2.357 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 ILE cc_start: 0.6815 (mt) cc_final: 0.6549 (mp) REVERT: A 51 LYS cc_start: 0.7609 (ptpp) cc_final: 0.7375 (pttp) REVERT: A 98 LYS cc_start: 0.7216 (mmtt) cc_final: 0.6992 (mtpp) REVERT: A 319 LYS cc_start: 0.4342 (mtmt) cc_final: 0.3495 (tppp) REVERT: B 27 PHE cc_start: 0.4631 (m-10) cc_final: 0.4369 (m-10) REVERT: B 117 ARG cc_start: 0.7453 (mmm160) cc_final: 0.6986 (mmm160) REVERT: B 130 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7101 (tp) REVERT: B 275 PHE cc_start: 0.6112 (OUTLIER) cc_final: 0.5040 (t80) REVERT: C 104 HIS cc_start: 0.7466 (OUTLIER) cc_final: 0.6408 (t70) REVERT: C 153 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7481 (mm) REVERT: C 275 PHE cc_start: 0.8059 (OUTLIER) cc_final: 0.7549 (t80) REVERT: C 293 VAL cc_start: 0.8584 (t) cc_final: 0.8280 (t) REVERT: C 337 MET cc_start: 0.6545 (tmm) cc_final: 0.6319 (tmm) REVERT: C 392 VAL cc_start: 0.8118 (p) cc_final: 0.7867 (m) REVERT: D 274 LYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7863 (tptm) REVERT: D 305 TYR cc_start: 0.8511 (m-80) cc_final: 0.8271 (m-80) REVERT: E 17 TYR cc_start: 0.4452 (OUTLIER) cc_final: 0.3699 (m-80) REVERT: E 127 TYR cc_start: 0.5069 (m-10) cc_final: 0.4647 (m-10) REVERT: E 144 PHE cc_start: 0.6472 (m-10) cc_final: 0.6206 (m-10) REVERT: E 290 LYS cc_start: 0.4306 (tptp) cc_final: 0.4060 (tptp) REVERT: E 299 ILE cc_start: 0.3741 (OUTLIER) cc_final: 0.2618 (pt) REVERT: E 314 LEU cc_start: 0.6372 (OUTLIER) cc_final: 0.6019 (pp) REVERT: E 343 MET cc_start: 0.4468 (OUTLIER) cc_final: 0.4235 (mtt) outliers start: 59 outliers final: 44 residues processed: 268 average time/residue: 0.2875 time to fit residues: 111.9738 Evaluate side-chains 268 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 214 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 59 TRP Chi-restraints excluded: chain A residue 116 ASN Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 331 PHE Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 265 MET Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 274 LYS Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 400 ASN Chi-restraints excluded: chain E residue 17 TYR Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 310 CYS Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 343 MET Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 46 GLN Chi-restraints excluded: chain F residue 51 LYS Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 293 CYS Chi-restraints excluded: chain F residue 315 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 136 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 111 optimal weight: 6.9990 chunk 79 optimal weight: 0.9980 chunk 76 optimal weight: 0.4980 chunk 35 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 42 optimal weight: 0.1980 chunk 135 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 129 optimal weight: 0.0970 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 116 ASN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 46 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4741 r_free = 0.4741 target = 0.229049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.187048 restraints weight = 15796.287| |-----------------------------------------------------------------------------| r_work (start): 0.4320 rms_B_bonded: 2.42 r_work: 0.4170 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.4170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6505 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12402 Z= 0.123 Angle : 0.528 9.364 16807 Z= 0.285 Chirality : 0.039 0.198 1846 Planarity : 0.003 0.042 1985 Dihedral : 7.810 148.529 1674 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 4.11 % Allowed : 25.65 % Favored : 70.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.23), residues: 1382 helix: 1.89 (0.16), residues: 974 sheet: 0.63 (0.51), residues: 107 loop : -1.17 (0.35), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP D 120 HIS 0.003 0.001 HIS E 104 PHE 0.028 0.001 PHE D 393 TYR 0.026 0.001 TYR E 325 ARG 0.004 0.000 ARG D 389 Details of bonding type rmsd hydrogen bonds : bond 0.03532 ( 806) hydrogen bonds : angle 4.05810 ( 2379) SS BOND : bond 0.00296 ( 17) SS BOND : angle 1.00036 ( 34) covalent geometry : bond 0.00275 (12385) covalent geometry : angle 0.52692 (16773) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 214 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 ILE cc_start: 0.6830 (mt) cc_final: 0.6570 (mp) REVERT: A 51 LYS cc_start: 0.7572 (ptpp) cc_final: 0.7314 (pttp) REVERT: A 98 LYS cc_start: 0.7117 (mmtt) cc_final: 0.6906 (mtpp) REVERT: A 319 LYS cc_start: 0.4337 (mtmt) cc_final: 0.3554 (tppt) REVERT: B 27 PHE cc_start: 0.4548 (m-10) cc_final: 0.4334 (m-10) REVERT: B 117 ARG cc_start: 0.7393 (mmm160) cc_final: 0.6924 (mmm160) REVERT: B 275 PHE cc_start: 0.6170 (OUTLIER) cc_final: 0.5063 (t80) REVERT: C 104 HIS cc_start: 0.7487 (OUTLIER) cc_final: 0.6454 (t70) REVERT: C 145 LYS cc_start: 0.8613 (mttt) cc_final: 0.8380 (mmtp) REVERT: C 153 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7617 (mm) REVERT: C 275 PHE cc_start: 0.8024 (OUTLIER) cc_final: 0.7518 (t80) REVERT: C 293 VAL cc_start: 0.8536 (t) cc_final: 0.8214 (t) REVERT: C 392 VAL cc_start: 0.8080 (p) cc_final: 0.7845 (m) REVERT: D 30 TYR cc_start: 0.7052 (m-80) cc_final: 0.6611 (m-80) REVERT: D 274 LYS cc_start: 0.8058 (OUTLIER) cc_final: 0.7835 (tptm) REVERT: D 305 TYR cc_start: 0.8502 (m-80) cc_final: 0.8251 (m-80) REVERT: E 17 TYR cc_start: 0.4378 (OUTLIER) cc_final: 0.3626 (m-80) REVERT: E 127 TYR cc_start: 0.4982 (m-10) cc_final: 0.4739 (m-10) REVERT: E 144 PHE cc_start: 0.6536 (m-10) cc_final: 0.6222 (m-10) REVERT: E 265 MET cc_start: 0.4878 (mmt) cc_final: 0.4440 (mmt) REVERT: E 299 ILE cc_start: 0.3597 (OUTLIER) cc_final: 0.2504 (pt) REVERT: E 314 LEU cc_start: 0.6309 (OUTLIER) cc_final: 0.5979 (pp) REVERT: E 343 MET cc_start: 0.4162 (OUTLIER) cc_final: 0.3917 (mtt) outliers start: 54 outliers final: 44 residues processed: 254 average time/residue: 0.2279 time to fit residues: 85.4644 Evaluate side-chains 262 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 209 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 59 TRP Chi-restraints excluded: chain A residue 116 ASN Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 331 PHE Chi-restraints excluded: chain C residue 25 ASP Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 265 MET Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 300 GLU Chi-restraints excluded: chain C residue 358 GLU Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 274 LYS Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 400 ASN Chi-restraints excluded: chain E residue 17 TYR Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 310 CYS Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain E residue 343 MET Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 46 GLN Chi-restraints excluded: chain F residue 51 LYS Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 293 CYS Chi-restraints excluded: chain F residue 315 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 60 optimal weight: 0.6980 chunk 52 optimal weight: 0.3980 chunk 85 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 48 optimal weight: 0.1980 chunk 35 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 77 optimal weight: 0.5980 chunk 113 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 116 ASN ** D 288 ASN ** 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 = 0.4689 r_free = 0.4689 target = 0.225930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.183625 restraints weight = 15580.086| |-----------------------------------------------------------------------------| r_work (start): 0.4259 rms_B_bonded: 2.56 r_work: 0.4109 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.4109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6442 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12402 Z= 0.132 Angle : 0.536 8.998 16807 Z= 0.290 Chirality : 0.040 0.194 1846 Planarity : 0.003 0.042 1985 Dihedral : 7.541 124.526 1674 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 4.26 % Allowed : 25.49 % Favored : 70.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.22), residues: 1382 helix: 1.87 (0.16), residues: 974 sheet: 0.60 (0.50), residues: 107 loop : -1.17 (0.35), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP D 120 HIS 0.003 0.001 HIS E 104 PHE 0.030 0.001 PHE D 393 TYR 0.027 0.001 TYR E 325 ARG 0.006 0.000 ARG D 389 Details of bonding type rmsd hydrogen bonds : bond 0.03570 ( 806) hydrogen bonds : angle 4.08142 ( 2379) SS BOND : bond 0.00302 ( 17) SS BOND : angle 0.99822 ( 34) covalent geometry : bond 0.00297 (12385) covalent geometry : angle 0.53499 (16773) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7386.28 seconds wall clock time: 132 minutes 38.61 seconds (7958.61 seconds total)