Starting phenix.real_space_refine on Mon Dec 30 04:40:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ds9_27686/12_2024/8ds9_27686.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ds9_27686/12_2024/8ds9_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_27686/12_2024/8ds9_27686.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ds9_27686/12_2024/8ds9_27686.map" model { file = "/net/cci-nas-00/data/ceres_data/8ds9_27686/12_2024/8ds9_27686.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ds9_27686/12_2024/8ds9_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-5532/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: 8.34, per 1000 atoms: 0.69 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: 3.13 Conformation dependent library (CDL) restraints added in 1.6 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: 1.16 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: 3.56 Time building geometry restraints manager: 3.54 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: 4.840 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: 0.090 Set scattering table: 0.100 Process input model: 29.290 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.270 ------------------------------------------------------------------------------- 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 12385 Z= 0.320 Angle : 0.805 13.851 16773 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 *********************** 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 : 1.398 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 231 average time/residue: 0.2539 time to fit residues: 83.1045 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 : 1.427 ------------------------------------------------------------------------------- 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: 0.9990 chunk 105 optimal weight: 0.8980 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: 0.9990 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: 0.6580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5974 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12385 Z= 0.215 Angle : 0.529 7.004 16773 Z= 0.287 Chirality : 0.040 0.165 1846 Planarity : 0.004 0.046 1985 Dihedral : 9.778 177.221 1680 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 4.49 % Allowed : 20.55 % Favored : 74.96 % 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: 1.06 (0.22), residues: 1382 helix: 1.42 (0.16), residues: 970 sheet: 0.41 (0.53), residues: 107 loop : -1.45 (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 0.025 0.001 TYR D 284 ARG 0.006 0.000 ARG D 389 *********************** 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 288 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 229 time to evaluate : 1.462 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 117 ARG cc_start: 0.7005 (mmm160) cc_final: 0.6760 (tpt90) REVERT: B 275 PHE cc_start: 0.6596 (OUTLIER) cc_final: 0.6094 (t80) REVERT: C 275 PHE cc_start: 0.7691 (OUTLIER) cc_final: 0.7278 (t80) REVERT: D 305 TYR cc_start: 0.8030 (m-80) cc_final: 0.7744 (m-80) REVERT: D 324 PHE cc_start: 0.6422 (t80) cc_final: 0.6195 (t80) REVERT: D 390 PHE cc_start: 0.7379 (t80) cc_final: 0.7140 (t80) REVERT: E 299 ILE cc_start: 0.3976 (OUTLIER) cc_final: 0.2883 (pt) REVERT: E 343 MET cc_start: 0.1884 (OUTLIER) cc_final: 0.1501 (mtt) outliers start: 59 outliers final: 30 residues processed: 273 average time/residue: 0.2509 time to fit residues: 99.3082 Evaluate side-chains 240 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 206 time to evaluate : 1.413 ------------------------------------------------------------------------------- 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 280 CYS 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 44 THR Chi-restraints excluded: chain B residue 275 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 286 VAL Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 310 CYS 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 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 70 optimal weight: 5.9990 chunk 39 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 126 optimal weight: 0.5980 chunk 136 optimal weight: 3.9990 chunk 112 optimal weight: 7.9990 chunk 125 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 101 optimal weight: 20.0000 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 49 GLN C 155 HIS C 404 GLN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6068 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12385 Z= 0.275 Angle : 0.562 6.307 16773 Z= 0.303 Chirality : 0.042 0.147 1846 Planarity : 0.004 0.046 1985 Dihedral : 9.391 175.873 1676 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 5.10 % Allowed : 21.31 % Favored : 73.59 % 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: 1.07 (0.22), residues: 1382 helix: 1.48 (0.16), residues: 965 sheet: 0.24 (0.52), residues: 107 loop : -1.55 (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 0.023 0.002 PHE D 390 TYR 0.029 0.002 TYR D 284 ARG 0.005 0.000 ARG D 389 *********************** 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: 67 poor density : 216 time to evaluate : 1.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 100 ASP cc_start: 0.7985 (t0) cc_final: 0.7706 (t0) REVERT: B 275 PHE cc_start: 0.6539 (OUTLIER) cc_final: 0.6095 (t80) REVERT: C 104 HIS cc_start: 0.6659 (OUTLIER) cc_final: 0.6022 (t70) REVERT: C 275 PHE cc_start: 0.7710 (OUTLIER) cc_final: 0.7254 (t80) REVERT: D 153 LEU cc_start: 0.7751 (OUTLIER) cc_final: 0.7548 (mp) REVERT: D 305 TYR cc_start: 0.8108 (m-80) cc_final: 0.7837 (m-80) REVERT: D 375 MET cc_start: 0.6812 (mtt) cc_final: 0.6552 (mtm) REVERT: E 299 ILE cc_start: 0.4045 (OUTLIER) cc_final: 0.2862 (pt) REVERT: E 343 MET cc_start: 0.2634 (OUTLIER) cc_final: 0.2264 (mtt) outliers start: 67 outliers final: 38 residues processed: 266 average time/residue: 0.2405 time to fit residues: 92.4379 Evaluate side-chains 250 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 206 time to evaluate : 1.535 ------------------------------------------------------------------------------- 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 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 52 MET Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 102 ASP 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 140 SER 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 60 VAL Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 279 ILE 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 124 optimal weight: 2.9990 chunk 95 optimal weight: 0.0170 chunk 65 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 chunk 84 optimal weight: 0.8980 chunk 126 optimal weight: 0.9990 chunk 134 optimal weight: 0.6980 chunk 66 optimal weight: 0.2980 chunk 120 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 49 GLN D 104 HIS ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 288 ASN F 46 GLN ** F 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6000 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12385 Z= 0.183 Angle : 0.499 5.653 16773 Z= 0.272 Chirality : 0.039 0.134 1846 Planarity : 0.004 0.127 1985 Dihedral : 8.931 178.827 1676 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 4.49 % Allowed : 22.37 % Favored : 73.14 % 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: 1.37 (0.22), residues: 1382 helix: 1.69 (0.16), residues: 964 sheet: 0.38 (0.53), residues: 107 loop : -1.38 (0.33), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 23 HIS 0.006 0.001 HIS D 104 PHE 0.023 0.001 PHE E 331 TYR 0.024 0.001 TYR D 284 ARG 0.006 0.000 ARG D 389 *********************** 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 286 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 227 time to evaluate : 1.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 PHE cc_start: 0.5059 (OUTLIER) cc_final: 0.4497 (m-10) REVERT: A 319 LYS cc_start: 0.5161 (tptm) cc_final: 0.4957 (mtpt) REVERT: B 275 PHE cc_start: 0.6511 (OUTLIER) cc_final: 0.5915 (t80) REVERT: C 104 HIS cc_start: 0.6680 (OUTLIER) cc_final: 0.5862 (t70) REVERT: C 275 PHE cc_start: 0.7685 (OUTLIER) cc_final: 0.7275 (t80) REVERT: E 343 MET cc_start: 0.2703 (OUTLIER) cc_final: 0.2313 (mtt) outliers start: 59 outliers final: 42 residues processed: 271 average time/residue: 0.2345 time to fit residues: 92.3552 Evaluate side-chains 253 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 206 time to evaluate : 1.309 ------------------------------------------------------------------------------- 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 102 ASP 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 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 140 SER 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 160 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 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 104 HIS Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 310 CYS Chi-restraints excluded: chain E residue 343 MET 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 111 optimal weight: 10.0000 chunk 76 optimal weight: 0.6980 chunk 1 optimal weight: 6.9990 chunk 100 optimal weight: 0.5980 chunk 55 optimal weight: 0.9990 chunk 114 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 68 optimal weight: 0.8980 chunk 120 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN A 116 ASN A 312 HIS ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 GLN ** F 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6092 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12385 Z= 0.275 Angle : 0.567 5.824 16773 Z= 0.307 Chirality : 0.042 0.139 1846 Planarity : 0.004 0.101 1985 Dihedral : 8.849 174.400 1674 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 5.56 % Allowed : 22.60 % Favored : 71.84 % 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: 1.19 (0.22), residues: 1382 helix: 1.57 (0.16), residues: 971 sheet: 0.20 (0.52), residues: 107 loop : -1.49 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 120 HIS 0.005 0.001 HIS A 132 PHE 0.024 0.002 PHE E 331 TYR 0.031 0.002 TYR D 284 ARG 0.006 0.000 ARG D 389 *********************** 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 288 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 215 time to evaluate : 1.304 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 PHE cc_start: 0.4911 (OUTLIER) cc_final: 0.4471 (m-80) REVERT: A 319 LYS cc_start: 0.5378 (tptm) cc_final: 0.5021 (mtpt) REVERT: C 104 HIS cc_start: 0.6783 (OUTLIER) cc_final: 0.5975 (t70) REVERT: C 275 PHE cc_start: 0.7708 (OUTLIER) cc_final: 0.7242 (t80) REVERT: D 305 TYR cc_start: 0.8203 (m-80) cc_final: 0.7971 (m-10) REVERT: E 265 MET cc_start: 0.5306 (tpt) cc_final: 0.4876 (mmt) REVERT: E 299 ILE cc_start: 0.3915 (OUTLIER) cc_final: 0.2736 (pt) REVERT: E 343 MET cc_start: 0.2833 (OUTLIER) cc_final: 0.2461 (mtt) outliers start: 73 outliers final: 51 residues processed: 269 average time/residue: 0.2237 time to fit residues: 88.1320 Evaluate side-chains 265 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 209 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU 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 97 ILE Chi-restraints excluded: chain A residue 116 ASN 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 286 VAL Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 140 SER 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 C residue 371 ASP 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 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 294 ASP Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 317 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 104 HIS Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 299 ILE 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 45 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 78 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 134 optimal weight: 0.3980 chunk 111 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 44 optimal weight: 0.4980 chunk 70 optimal weight: 5.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6038 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12385 Z= 0.203 Angle : 0.520 6.429 16773 Z= 0.283 Chirality : 0.040 0.161 1846 Planarity : 0.003 0.042 1985 Dihedral : 8.658 174.025 1674 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 4.79 % Allowed : 23.82 % Favored : 71.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.22), residues: 1382 helix: 1.64 (0.16), residues: 973 sheet: 0.44 (0.53), residues: 105 loop : -1.40 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 120 HIS 0.004 0.001 HIS A 132 PHE 0.027 0.001 PHE E 331 TYR 0.029 0.001 TYR D 284 ARG 0.005 0.000 ARG D 389 *********************** 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 278 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 215 time to evaluate : 1.455 Fit side-chains revert: symmetry clash REVERT: A 319 LYS cc_start: 0.5226 (tptm) cc_final: 0.4914 (mtpt) REVERT: B 27 PHE cc_start: 0.5227 (m-10) cc_final: 0.4999 (m-10) REVERT: B 275 PHE cc_start: 0.6404 (OUTLIER) cc_final: 0.5616 (t80) REVERT: C 104 HIS cc_start: 0.6827 (OUTLIER) cc_final: 0.6020 (t70) REVERT: C 153 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7572 (mm) REVERT: C 275 PHE cc_start: 0.7696 (OUTLIER) cc_final: 0.7256 (t80) REVERT: D 305 TYR cc_start: 0.8195 (m-80) cc_final: 0.7956 (m-10) REVERT: E 299 ILE cc_start: 0.3966 (OUTLIER) cc_final: 0.2893 (pt) REVERT: E 343 MET cc_start: 0.2884 (OUTLIER) cc_final: 0.2622 (mtt) outliers start: 63 outliers final: 48 residues processed: 261 average time/residue: 0.2230 time to fit residues: 85.4754 Evaluate side-chains 259 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 205 time to evaluate : 1.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU 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 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 136 PHE 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 C residue 104 HIS Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 140 SER 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 C residue 371 ASP 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 129 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 76 optimal weight: 0.0980 chunk 98 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 133 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 81 optimal weight: 0.6980 chunk 61 optimal weight: 0.5980 chunk 82 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN C 49 GLN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6033 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12385 Z= 0.204 Angle : 0.523 6.961 16773 Z= 0.286 Chirality : 0.039 0.147 1846 Planarity : 0.003 0.042 1985 Dihedral : 8.556 171.468 1674 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 4.26 % Allowed : 24.28 % Favored : 71.46 % 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: 1.40 (0.22), residues: 1382 helix: 1.68 (0.16), residues: 973 sheet: 0.54 (0.53), residues: 105 loop : -1.39 (0.34), residues: 304 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 0.032 0.001 PHE C 390 TYR 0.029 0.001 TYR D 284 ARG 0.005 0.000 ARG D 389 *********************** 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 275 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 219 time to evaluate : 1.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 LYS cc_start: 0.5276 (tptm) cc_final: 0.4921 (mtpt) REVERT: B 275 PHE cc_start: 0.6483 (OUTLIER) cc_final: 0.5619 (t80) REVERT: C 104 HIS cc_start: 0.6680 (OUTLIER) cc_final: 0.5766 (t70) REVERT: C 153 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7627 (mm) REVERT: C 275 PHE cc_start: 0.7698 (OUTLIER) cc_final: 0.7262 (t80) REVERT: E 299 ILE cc_start: 0.3963 (OUTLIER) cc_final: 0.2875 (pt) REVERT: E 343 MET cc_start: 0.2367 (OUTLIER) cc_final: 0.2029 (mtt) outliers start: 56 outliers final: 49 residues processed: 263 average time/residue: 0.2225 time to fit residues: 86.2093 Evaluate side-chains 267 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 212 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU 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 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 38 ILE 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 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 140 SER 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 C residue 371 ASP 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 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 317 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 104 HIS 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 343 MET Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 47 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 53 optimal weight: 0.7980 chunk 80 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 91 optimal weight: 0.4980 chunk 66 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 105 optimal weight: 0.6980 chunk 121 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6057 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12385 Z= 0.229 Angle : 0.541 7.461 16773 Z= 0.297 Chirality : 0.040 0.151 1846 Planarity : 0.003 0.042 1985 Dihedral : 8.398 167.417 1674 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 5.02 % Allowed : 24.28 % Favored : 70.70 % 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: 1.40 (0.22), residues: 1382 helix: 1.68 (0.16), residues: 974 sheet: 0.48 (0.52), residues: 105 loop : -1.37 (0.34), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP D 120 HIS 0.004 0.001 HIS C 104 PHE 0.029 0.002 PHE C 390 TYR 0.030 0.001 TYR D 305 ARG 0.005 0.000 ARG D 389 *********************** 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 275 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 209 time to evaluate : 1.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 LYS cc_start: 0.5261 (tptm) cc_final: 0.4917 (mtpt) REVERT: B 27 PHE cc_start: 0.5110 (m-10) cc_final: 0.4534 (m-80) REVERT: B 275 PHE cc_start: 0.6563 (OUTLIER) cc_final: 0.5730 (t80) REVERT: C 104 HIS cc_start: 0.6721 (OUTLIER) cc_final: 0.5830 (t70) REVERT: C 153 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7574 (mm) REVERT: C 275 PHE cc_start: 0.7713 (OUTLIER) cc_final: 0.7279 (t80) REVERT: E 299 ILE cc_start: 0.3975 (OUTLIER) cc_final: 0.2901 (pt) outliers start: 66 outliers final: 53 residues processed: 257 average time/residue: 0.2234 time to fit residues: 84.4513 Evaluate side-chains 267 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 209 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU 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 297 VAL 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 95 THR 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 104 HIS Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 140 SER 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 C residue 371 ASP 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 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 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 104 HIS 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 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 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 128 optimal weight: 0.8980 chunk 117 optimal weight: 0.2980 chunk 124 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 chunk 54 optimal weight: 0.5980 chunk 98 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 112 optimal weight: 6.9990 chunk 118 optimal weight: 0.6980 chunk 81 optimal weight: 0.7980 chunk 132 optimal weight: 6.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 49 GLN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 312 HIS F 46 GLN ** F 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6042 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12385 Z= 0.214 Angle : 0.544 8.569 16773 Z= 0.297 Chirality : 0.040 0.154 1846 Planarity : 0.003 0.042 1985 Dihedral : 8.240 164.425 1674 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 4.72 % Allowed : 24.81 % Favored : 70.47 % 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: 1.70 (0.16), residues: 973 sheet: 0.49 (0.52), residues: 105 loop : -1.35 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP D 120 HIS 0.010 0.001 HIS E 132 PHE 0.027 0.001 PHE C 390 TYR 0.029 0.001 TYR D 284 ARG 0.005 0.000 ARG D 389 *********************** 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 274 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 212 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 LYS cc_start: 0.5239 (tptm) cc_final: 0.4899 (mtpt) REVERT: B 27 PHE cc_start: 0.5107 (m-10) cc_final: 0.4615 (m-10) REVERT: B 275 PHE cc_start: 0.6616 (OUTLIER) cc_final: 0.5780 (t80) REVERT: C 104 HIS cc_start: 0.6792 (OUTLIER) cc_final: 0.5843 (t70) REVERT: C 153 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7633 (mm) REVERT: C 253 HIS cc_start: 0.7831 (OUTLIER) cc_final: 0.7115 (p90) REVERT: C 275 PHE cc_start: 0.7698 (OUTLIER) cc_final: 0.7274 (t80) REVERT: E 127 TYR cc_start: 0.3813 (m-10) cc_final: 0.3345 (m-10) REVERT: E 299 ILE cc_start: 0.3990 (OUTLIER) cc_final: 0.2914 (pt) REVERT: F 261 MET cc_start: 0.0675 (ptt) cc_final: -0.0540 (tmm) outliers start: 62 outliers final: 53 residues processed: 258 average time/residue: 0.2290 time to fit residues: 86.2884 Evaluate side-chains 265 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 206 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU 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 297 VAL Chi-restraints excluded: chain A residue 300 GLU 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 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 104 HIS Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 140 SER 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 358 GLU Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 371 ASP 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 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 317 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 104 HIS Chi-restraints excluded: chain E residue 278 ILE 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 80 optimal weight: 0.9980 chunk 62 optimal weight: 0.5980 chunk 91 optimal weight: 0.8980 chunk 138 optimal weight: 0.9980 chunk 127 optimal weight: 3.9990 chunk 110 optimal weight: 8.9990 chunk 11 optimal weight: 5.9990 chunk 85 optimal weight: 0.9990 chunk 67 optimal weight: 0.5980 chunk 87 optimal weight: 0.5980 chunk 117 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 49 GLN C 253 HIS ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6039 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12385 Z= 0.209 Angle : 0.544 8.249 16773 Z= 0.295 Chirality : 0.040 0.154 1846 Planarity : 0.003 0.042 1985 Dihedral : 8.017 159.213 1674 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 4.49 % Allowed : 25.19 % Favored : 70.32 % 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: 1.44 (0.22), residues: 1382 helix: 1.71 (0.16), residues: 973 sheet: 0.43 (0.52), residues: 105 loop : -1.31 (0.34), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP D 120 HIS 0.012 0.001 HIS E 132 PHE 0.024 0.001 PHE C 390 TYR 0.028 0.001 TYR B 325 ARG 0.004 0.000 ARG D 389 ********************** 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 267 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 208 time to evaluate : 1.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 LYS cc_start: 0.5328 (tptm) cc_final: 0.4960 (mtpt) REVERT: B 27 PHE cc_start: 0.5046 (m-10) cc_final: 0.4641 (m-10) REVERT: B 275 PHE cc_start: 0.6610 (OUTLIER) cc_final: 0.5699 (t80) REVERT: C 104 HIS cc_start: 0.6738 (OUTLIER) cc_final: 0.5913 (t70) REVERT: C 153 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7631 (mm) REVERT: C 253 HIS cc_start: 0.7549 (OUTLIER) cc_final: 0.6778 (p-80) REVERT: C 275 PHE cc_start: 0.7692 (OUTLIER) cc_final: 0.7277 (t80) REVERT: E 127 TYR cc_start: 0.3709 (m-10) cc_final: 0.3423 (m-10) REVERT: E 299 ILE cc_start: 0.3956 (OUTLIER) cc_final: 0.2892 (pt) REVERT: F 261 MET cc_start: 0.0793 (ptt) cc_final: -0.0555 (tmm) outliers start: 59 outliers final: 51 residues processed: 253 average time/residue: 0.2285 time to fit residues: 85.7104 Evaluate side-chains 266 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 209 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU 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 300 GLU 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 140 SER 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 358 GLU Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 371 ASP 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 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 317 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 104 HIS Chi-restraints excluded: chain E residue 278 ILE 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 F residue 26 VAL Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 47 VAL 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 33 optimal weight: 0.5980 chunk 101 optimal weight: 20.0000 chunk 16 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 113 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 96 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 49 GLN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 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 = 0.4666 r_free = 0.4666 target = 0.223068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.182621 restraints weight = 15576.495| |-----------------------------------------------------------------------------| r_work (start): 0.4252 rms_B_bonded: 3.16 r_work: 0.4058 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.4058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6515 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12385 Z= 0.256 Angle : 0.584 9.658 16773 Z= 0.316 Chirality : 0.041 0.150 1846 Planarity : 0.004 0.041 1985 Dihedral : 7.952 151.247 1674 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 4.64 % Allowed : 25.42 % Favored : 69.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.22), residues: 1382 helix: 1.67 (0.16), residues: 971 sheet: 0.37 (0.53), residues: 105 loop : -1.40 (0.34), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP D 120 HIS 0.012 0.001 HIS E 132 PHE 0.023 0.002 PHE C 390 TYR 0.030 0.002 TYR B 325 ARG 0.005 0.000 ARG D 389 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2913.43 seconds wall clock time: 54 minutes 17.58 seconds (3257.58 seconds total)