Starting phenix.real_space_refine on Mon Dec 30 05:07:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dsa_27687/12_2024/8dsa_27687.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dsa_27687/12_2024/8dsa_27687.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dsa_27687/12_2024/8dsa_27687.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dsa_27687/12_2024/8dsa_27687.map" model { file = "/net/cci-nas-00/data/ceres_data/8dsa_27687/12_2024/8dsa_27687.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dsa_27687/12_2024/8dsa_27687.cif" } resolution = 3.48 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= 0.041 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): 0.05s 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: 8.66, per 1000 atoms: 0.72 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: 2.91 Conformation dependent library (CDL) restraints added in 1.5 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: 1.13 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: 3.63 Time building geometry restraints manager: 3.40 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: 4.680 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: 0.520 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 30.120 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6116 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 : 7.06 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 357 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 350 time to evaluate : 1.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ILE cc_start: 0.8039 (mt) cc_final: 0.7503 (mm) REVERT: A 131 LEU cc_start: 0.8425 (tt) cc_final: 0.8175 (tt) REVERT: A 143 TRP cc_start: 0.6701 (p90) cc_final: 0.6445 (p90) REVERT: B 35 MET cc_start: 0.6908 (mtp) cc_final: 0.6583 (mtt) REVERT: C 125 PHE cc_start: 0.7655 (t80) cc_final: 0.7378 (t80) REVERT: C 171 ARG cc_start: 0.8139 (tmt-80) cc_final: 0.7890 (tmt-80) REVERT: E 110 ASP cc_start: 0.5993 (m-30) cc_final: 0.5372 (m-30) REVERT: F 96 MET cc_start: 0.5211 (mpp) cc_final: 0.4965 (mmm) outliers start: 7 outliers final: 3 residues processed: 354 average time/residue: 0.2656 time to fit residues: 130.3903 Evaluate side-chains 242 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 239 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 58 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 71 optimal weight: 0.5980 chunk 56 optimal weight: 0.6980 chunk 108 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 126 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 370 ASN C 406 ASN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6309 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12385 Z= 0.238 Angle : 0.611 8.163 16773 Z= 0.324 Chirality : 0.042 0.246 1846 Planarity : 0.004 0.053 1985 Dihedral : 9.765 179.446 1676 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 5.02 % Allowed : 21.00 % Favored : 73.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.05 (0.22), residues: 1382 helix: 1.39 (0.16), residues: 959 sheet: 0.38 (0.51), residues: 107 loop : -1.25 (0.35), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 23 HIS 0.005 0.001 HIS A 312 PHE 0.027 0.002 PHE E 291 TYR 0.026 0.002 TYR F 262 ARG 0.005 0.000 ARG B 345 *********************** 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 321 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 255 time to evaluate : 1.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 TRP cc_start: 0.5714 (p90) cc_final: 0.4973 (p90) REVERT: A 131 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8051 (tt) REVERT: B 35 MET cc_start: 0.6965 (mtp) cc_final: 0.6589 (mtt) REVERT: B 275 PHE cc_start: 0.7104 (OUTLIER) cc_final: 0.6637 (t80) REVERT: B 331 PHE cc_start: 0.6151 (OUTLIER) cc_final: 0.5744 (m-10) REVERT: B 337 MET cc_start: 0.7180 (tmm) cc_final: 0.6434 (tmm) REVERT: C 25 ASP cc_start: 0.7508 (m-30) cc_final: 0.7300 (m-30) REVERT: C 104 HIS cc_start: 0.6759 (OUTLIER) cc_final: 0.6093 (t70) REVERT: C 110 ASP cc_start: 0.7075 (m-30) cc_final: 0.6764 (m-30) REVERT: C 161 LEU cc_start: 0.7210 (OUTLIER) cc_final: 0.6791 (pp) REVERT: C 388 LYS cc_start: 0.7279 (ttpt) cc_final: 0.7060 (tmmt) REVERT: D 157 VAL cc_start: 0.8170 (t) cc_final: 0.7828 (p) REVERT: D 243 LEU cc_start: 0.7447 (mt) cc_final: 0.7019 (mt) REVERT: D 364 ASP cc_start: 0.7004 (t0) cc_final: 0.6481 (t0) REVERT: E 291 PHE cc_start: 0.4819 (m-10) cc_final: 0.3864 (p90) REVERT: E 343 MET cc_start: 0.2604 (mtp) cc_final: 0.2403 (mtp) REVERT: F 300 MET cc_start: 0.6383 (mmt) cc_final: 0.6042 (mmp) outliers start: 66 outliers final: 30 residues processed: 303 average time/residue: 0.2397 time to fit residues: 103.8505 Evaluate side-chains 261 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 226 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 134 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 19 ILE Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 155 HIS Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 343 MET Chi-restraints excluded: chain D residue 363 SER Chi-restraints excluded: chain E residue 41 PHE Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 292 ASP 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: 1.9990 chunk 105 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 126 optimal weight: 0.5980 chunk 136 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 125 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 chunk 101 optimal weight: 20.0000 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 GLN D 104 HIS ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6416 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 12385 Z= 0.272 Angle : 0.611 8.753 16773 Z= 0.323 Chirality : 0.042 0.205 1846 Planarity : 0.004 0.051 1985 Dihedral : 9.513 176.853 1673 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 5.71 % Allowed : 21.77 % Favored : 72.53 % 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: 1.17 (0.22), residues: 1382 helix: 1.48 (0.16), residues: 965 sheet: 0.69 (0.51), residues: 105 loop : -1.36 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP E 24 HIS 0.007 0.001 HIS A 104 PHE 0.031 0.002 PHE E 291 TYR 0.034 0.002 TYR F 262 ARG 0.004 0.000 ARG B 345 *********************** 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 321 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 246 time to evaluate : 1.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8199 (tt) REVERT: B 35 MET cc_start: 0.6888 (mtp) cc_final: 0.6595 (mtt) REVERT: B 115 GLU cc_start: 0.6698 (OUTLIER) cc_final: 0.6349 (pt0) REVERT: B 275 PHE cc_start: 0.7084 (OUTLIER) cc_final: 0.6621 (t80) REVERT: B 308 TYR cc_start: 0.7558 (OUTLIER) cc_final: 0.7145 (m-80) REVERT: B 331 PHE cc_start: 0.6199 (OUTLIER) cc_final: 0.5877 (t80) REVERT: B 337 MET cc_start: 0.6834 (tmm) cc_final: 0.6286 (tmm) REVERT: C 104 HIS cc_start: 0.6984 (OUTLIER) cc_final: 0.6294 (t70) REVERT: C 388 LYS cc_start: 0.7216 (ttpt) cc_final: 0.6957 (tmmt) REVERT: D 396 GLU cc_start: 0.7327 (pm20) cc_final: 0.7068 (pt0) REVERT: E 52 MET cc_start: 0.4560 (ppp) cc_final: 0.3604 (ttp) REVERT: E 299 ILE cc_start: 0.3773 (OUTLIER) cc_final: 0.2966 (pt) REVERT: E 343 MET cc_start: 0.2600 (mtp) cc_final: 0.2096 (mtp) REVERT: F 96 MET cc_start: 0.6492 (mmm) cc_final: 0.5310 (ptp) REVERT: F 300 MET cc_start: 0.6376 (mmt) cc_final: 0.5938 (mmp) REVERT: F 303 TYR cc_start: 0.5394 (m-80) cc_final: 0.5050 (m-80) REVERT: F 318 LYS cc_start: 0.7995 (mmmt) cc_final: 0.7679 (mmmt) outliers start: 75 outliers final: 44 residues processed: 294 average time/residue: 0.2591 time to fit residues: 109.2574 Evaluate side-chains 278 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 227 time to evaluate : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 136 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 341 TRP Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 308 TYR Chi-restraints excluded: chain B residue 331 PHE Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 327 SER 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 102 ASP Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 363 SER Chi-restraints excluded: chain E residue 41 PHE Chi-restraints excluded: chain E residue 273 ILE Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain F residue 17 PHE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 292 ASP Chi-restraints excluded: chain F residue 343 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 124 optimal weight: 0.0030 chunk 95 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 13 optimal weight: 7.9990 chunk 60 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 126 optimal weight: 0.8980 chunk 134 optimal weight: 4.9990 chunk 66 optimal weight: 0.5980 chunk 120 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 288 ASN C 49 GLN D 104 HIS D 105 GLN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 406 ASN E 132 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6379 moved from start: 0.4006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12385 Z= 0.202 Angle : 0.566 8.718 16773 Z= 0.299 Chirality : 0.040 0.201 1846 Planarity : 0.003 0.046 1985 Dihedral : 9.014 170.413 1673 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 4.95 % Allowed : 23.44 % Favored : 71.61 % 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: 1.71 (0.16), residues: 955 sheet: 0.88 (0.50), residues: 105 loop : -1.29 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 24 HIS 0.010 0.001 HIS D 104 PHE 0.023 0.001 PHE C 125 TYR 0.032 0.001 TYR F 262 ARG 0.005 0.000 ARG A 306 *********************** 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 307 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 242 time to evaluate : 1.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 TRP cc_start: 0.5556 (p-90) cc_final: 0.5313 (p90) REVERT: A 104 HIS cc_start: 0.6779 (OUTLIER) cc_final: 0.6343 (t70) REVERT: A 131 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8291 (tt) REVERT: B 35 MET cc_start: 0.6937 (mtp) cc_final: 0.6603 (mtt) REVERT: B 275 PHE cc_start: 0.7232 (OUTLIER) cc_final: 0.6716 (t80) REVERT: B 337 MET cc_start: 0.6592 (tmm) cc_final: 0.6240 (tmm) REVERT: C 104 HIS cc_start: 0.6769 (OUTLIER) cc_final: 0.6147 (t70) REVERT: C 110 ASP cc_start: 0.7242 (m-30) cc_final: 0.6844 (m-30) REVERT: C 161 LEU cc_start: 0.7168 (OUTLIER) cc_final: 0.6853 (pp) REVERT: C 388 LYS cc_start: 0.7215 (ttpt) cc_final: 0.6938 (tmmt) REVERT: D 157 VAL cc_start: 0.8398 (t) cc_final: 0.8093 (p) REVERT: D 396 GLU cc_start: 0.7260 (pm20) cc_final: 0.7052 (pt0) REVERT: E 52 MET cc_start: 0.4614 (ppp) cc_final: 0.3663 (ttp) REVERT: E 299 ILE cc_start: 0.3711 (OUTLIER) cc_final: 0.2959 (pt) REVERT: E 343 MET cc_start: 0.2171 (mtp) cc_final: 0.1513 (mtp) REVERT: F 51 LYS cc_start: 0.6173 (OUTLIER) cc_final: 0.5533 (pttp) REVERT: F 96 MET cc_start: 0.6311 (mmm) cc_final: 0.5468 (ptp) REVERT: F 145 TRP cc_start: 0.4830 (t-100) cc_final: 0.4627 (t-100) REVERT: F 303 TYR cc_start: 0.5796 (m-80) cc_final: 0.5398 (m-80) REVERT: F 318 LYS cc_start: 0.8067 (mmmt) cc_final: 0.7755 (mmmt) REVERT: F 328 SER cc_start: 0.7134 (t) cc_final: 0.6461 (p) outliers start: 65 outliers final: 41 residues processed: 283 average time/residue: 0.2543 time to fit residues: 103.8933 Evaluate side-chains 268 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 220 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 136 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 341 TRP Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 363 SER Chi-restraints excluded: chain E residue 24 TRP Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain F residue 17 PHE Chi-restraints excluded: chain F residue 51 LYS Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 106 GLN Chi-restraints excluded: chain F residue 261 MET Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 292 ASP Chi-restraints excluded: chain F residue 343 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 111 optimal weight: 7.9990 chunk 76 optimal weight: 0.5980 chunk 1 optimal weight: 7.9990 chunk 100 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 92 optimal weight: 0.5980 chunk 0 optimal weight: 8.9990 chunk 68 optimal weight: 0.8980 chunk 120 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 GLN B 49 GLN C 49 GLN D 104 HIS ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6457 moved from start: 0.4404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 12385 Z= 0.272 Angle : 0.603 7.627 16773 Z= 0.320 Chirality : 0.043 0.214 1846 Planarity : 0.004 0.050 1985 Dihedral : 8.767 159.829 1673 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 6.16 % Allowed : 22.75 % Favored : 71.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.22), residues: 1382 helix: 1.61 (0.16), residues: 961 sheet: 0.78 (0.50), residues: 105 loop : -1.44 (0.35), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP E 24 HIS 0.006 0.001 HIS A 104 PHE 0.040 0.002 PHE F 27 TYR 0.036 0.002 TYR F 330 ARG 0.005 0.000 ARG A 306 *********************** 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 314 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 233 time to evaluate : 1.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 HIS cc_start: 0.7089 (OUTLIER) cc_final: 0.6640 (t70) REVERT: A 131 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8257 (tt) REVERT: A 144 PHE cc_start: 0.6997 (OUTLIER) cc_final: 0.6563 (m-80) REVERT: B 35 MET cc_start: 0.6882 (mtp) cc_final: 0.6610 (mtt) REVERT: B 275 PHE cc_start: 0.7207 (OUTLIER) cc_final: 0.6722 (t80) REVERT: B 308 TYR cc_start: 0.7565 (OUTLIER) cc_final: 0.7161 (m-80) REVERT: C 104 HIS cc_start: 0.6985 (OUTLIER) cc_final: 0.6302 (t70) REVERT: C 161 LEU cc_start: 0.7114 (OUTLIER) cc_final: 0.6825 (pp) REVERT: C 388 LYS cc_start: 0.7319 (ttpt) cc_final: 0.6757 (mttt) REVERT: D 239 GLN cc_start: 0.7465 (pm20) cc_final: 0.7113 (pm20) REVERT: D 356 ILE cc_start: 0.4731 (OUTLIER) cc_final: 0.4002 (mt) REVERT: D 374 PHE cc_start: 0.6823 (OUTLIER) cc_final: 0.6207 (m-10) REVERT: E 52 MET cc_start: 0.4788 (ppp) cc_final: 0.3823 (ttp) REVERT: E 136 PHE cc_start: 0.4497 (OUTLIER) cc_final: 0.4118 (m-80) REVERT: E 299 ILE cc_start: 0.3780 (OUTLIER) cc_final: 0.3050 (pt) REVERT: F 51 LYS cc_start: 0.6428 (OUTLIER) cc_final: 0.5842 (pttp) REVERT: F 96 MET cc_start: 0.6153 (mmm) cc_final: 0.5584 (ptp) REVERT: F 300 MET cc_start: 0.6557 (mmt) cc_final: 0.6230 (mmp) REVERT: F 303 TYR cc_start: 0.5792 (m-80) cc_final: 0.5522 (m-80) REVERT: F 318 LYS cc_start: 0.8025 (mmmt) cc_final: 0.7772 (mmmt) REVERT: F 328 SER cc_start: 0.6690 (t) cc_final: 0.6230 (p) outliers start: 81 outliers final: 53 residues processed: 289 average time/residue: 0.2524 time to fit residues: 105.2949 Evaluate side-chains 281 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 216 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 136 PHE Chi-restraints excluded: chain A residue 144 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 341 TRP Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 134 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 308 TYR Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 274 LYS Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 363 SER Chi-restraints excluded: chain D residue 374 PHE Chi-restraints excluded: chain E residue 17 TYR Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 41 PHE Chi-restraints excluded: chain E residue 136 PHE Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain F residue 17 PHE Chi-restraints excluded: chain F residue 51 LYS Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 106 GLN Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 261 MET Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 330 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 45 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 78 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 134 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 44 optimal weight: 0.5980 chunk 70 optimal weight: 5.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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** E 49 GLN F 298 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6472 moved from start: 0.4802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 12385 Z= 0.270 Angle : 0.610 9.893 16773 Z= 0.322 Chirality : 0.043 0.196 1846 Planarity : 0.004 0.047 1985 Dihedral : 8.210 135.696 1673 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 5.63 % Allowed : 24.12 % 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: 1.27 (0.22), residues: 1382 helix: 1.61 (0.16), residues: 959 sheet: 0.77 (0.49), residues: 105 loop : -1.50 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 24 HIS 0.006 0.001 HIS A 104 PHE 0.020 0.002 PHE F 27 TYR 0.026 0.002 TYR A 124 ARG 0.003 0.000 ARG A 306 *********************** 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 294 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 220 time to evaluate : 1.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 HIS cc_start: 0.7132 (OUTLIER) cc_final: 0.6642 (t70) REVERT: A 131 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8195 (tt) REVERT: A 144 PHE cc_start: 0.7090 (OUTLIER) cc_final: 0.6643 (m-80) REVERT: A 262 ARG cc_start: 0.3796 (mmm160) cc_final: 0.3457 (mmm160) REVERT: A 337 MET cc_start: 0.5440 (tpt) cc_final: 0.5128 (tpt) REVERT: B 35 MET cc_start: 0.7026 (mtp) cc_final: 0.6765 (mtt) REVERT: B 275 PHE cc_start: 0.7190 (OUTLIER) cc_final: 0.6716 (t80) REVERT: B 308 TYR cc_start: 0.7653 (OUTLIER) cc_final: 0.7162 (m-80) REVERT: B 337 MET cc_start: 0.6933 (tmm) cc_final: 0.6294 (tmm) REVERT: C 104 HIS cc_start: 0.7004 (OUTLIER) cc_final: 0.6309 (t70) REVERT: C 108 TYR cc_start: 0.7681 (t80) cc_final: 0.7375 (t80) REVERT: C 161 LEU cc_start: 0.7216 (OUTLIER) cc_final: 0.6908 (pp) REVERT: C 388 LYS cc_start: 0.7236 (ttpt) cc_final: 0.6685 (mttt) REVERT: D 157 VAL cc_start: 0.8519 (t) cc_final: 0.8172 (p) REVERT: D 301 SER cc_start: 0.8048 (p) cc_final: 0.7737 (m) REVERT: D 356 ILE cc_start: 0.4667 (OUTLIER) cc_final: 0.3966 (mt) REVERT: D 374 PHE cc_start: 0.6821 (OUTLIER) cc_final: 0.6126 (m-10) REVERT: E 52 MET cc_start: 0.4914 (ppp) cc_final: 0.3736 (ttp) REVERT: E 299 ILE cc_start: 0.4056 (OUTLIER) cc_final: 0.3209 (pt) REVERT: F 299 ASP cc_start: 0.7217 (t0) cc_final: 0.6924 (t0) REVERT: F 300 MET cc_start: 0.6808 (mmt) cc_final: 0.6490 (mmp) REVERT: F 303 TYR cc_start: 0.5969 (m-80) cc_final: 0.5685 (m-80) outliers start: 74 outliers final: 54 residues processed: 272 average time/residue: 0.2391 time to fit residues: 93.9429 Evaluate side-chains 270 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 206 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 136 PHE Chi-restraints excluded: chain A residue 144 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 341 TRP Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 134 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 308 TYR Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 274 LYS Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 363 SER Chi-restraints excluded: chain D residue 374 PHE Chi-restraints excluded: chain E residue 17 TYR Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 41 PHE Chi-restraints excluded: chain E residue 97 ILE 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 F residue 17 PHE Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 106 GLN Chi-restraints excluded: chain F residue 273 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 129 optimal weight: 0.4980 chunk 15 optimal weight: 0.4980 chunk 76 optimal weight: 0.4980 chunk 98 optimal weight: 0.6980 chunk 113 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 133 optimal weight: 0.7980 chunk 83 optimal weight: 0.1980 chunk 81 optimal weight: 0.6980 chunk 61 optimal weight: 0.5980 chunk 82 optimal weight: 0.9980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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** D 377 HIS ** F 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6390 moved from start: 0.4915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12385 Z= 0.182 Angle : 0.569 8.908 16773 Z= 0.302 Chirality : 0.041 0.182 1846 Planarity : 0.003 0.047 1985 Dihedral : 7.379 89.931 1673 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 4.79 % Allowed : 25.88 % Favored : 69.33 % 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: 1.55 (0.22), residues: 1382 helix: 1.79 (0.16), residues: 957 sheet: 0.97 (0.49), residues: 105 loop : -1.33 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 24 HIS 0.005 0.001 HIS E 132 PHE 0.014 0.001 PHE A 331 TYR 0.030 0.001 TYR B 325 ARG 0.004 0.000 ARG A 306 *********************** 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 286 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 223 time to evaluate : 1.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 HIS cc_start: 0.6778 (OUTLIER) cc_final: 0.6306 (t70) REVERT: A 131 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8204 (tt) REVERT: A 144 PHE cc_start: 0.7025 (OUTLIER) cc_final: 0.6696 (m-80) REVERT: A 337 MET cc_start: 0.5456 (tpt) cc_final: 0.5173 (tpt) REVERT: B 35 MET cc_start: 0.6943 (mtp) cc_final: 0.6646 (mtt) REVERT: B 275 PHE cc_start: 0.7305 (OUTLIER) cc_final: 0.6865 (t80) REVERT: B 337 MET cc_start: 0.6851 (tmm) cc_final: 0.6275 (tmm) REVERT: C 104 HIS cc_start: 0.6871 (OUTLIER) cc_final: 0.6014 (t70) REVERT: C 108 TYR cc_start: 0.7557 (t80) cc_final: 0.7316 (t80) REVERT: C 388 LYS cc_start: 0.7210 (ttpt) cc_final: 0.6925 (tmmt) REVERT: D 37 MET cc_start: 0.5317 (tmm) cc_final: 0.5115 (tpt) REVERT: D 156 PHE cc_start: 0.7616 (t80) cc_final: 0.7301 (t80) REVERT: D 157 VAL cc_start: 0.8435 (t) cc_final: 0.8112 (p) REVERT: D 301 SER cc_start: 0.7964 (p) cc_final: 0.7681 (m) REVERT: D 374 PHE cc_start: 0.6750 (OUTLIER) cc_final: 0.6113 (m-10) REVERT: E 52 MET cc_start: 0.4726 (ppp) cc_final: 0.3741 (ttp) REVERT: E 136 PHE cc_start: 0.4554 (OUTLIER) cc_final: 0.4174 (m-80) REVERT: E 299 ILE cc_start: 0.3565 (OUTLIER) cc_final: 0.2330 (mm) REVERT: E 343 MET cc_start: 0.2685 (mtp) cc_final: 0.2092 (mtp) REVERT: F 96 MET cc_start: 0.5821 (mtm) cc_final: 0.5556 (ptt) REVERT: F 300 MET cc_start: 0.7002 (mmt) cc_final: 0.6615 (mmp) REVERT: F 303 TYR cc_start: 0.5924 (m-80) cc_final: 0.5652 (m-80) outliers start: 63 outliers final: 43 residues processed: 269 average time/residue: 0.2528 time to fit residues: 97.4790 Evaluate side-chains 258 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 207 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 136 PHE Chi-restraints excluded: chain A residue 144 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 341 TRP Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 134 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 C residue 19 ILE Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 102 ASP 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 314 LEU Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain D residue 363 SER Chi-restraints excluded: chain D residue 374 PHE Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 41 PHE Chi-restraints excluded: chain E residue 136 PHE Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain F residue 17 PHE Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 106 GLN Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 330 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 53 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 85 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 105 optimal weight: 0.8980 chunk 121 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 377 HIS ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 GLN F 288 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6445 moved from start: 0.5134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12385 Z= 0.236 Angle : 0.602 8.969 16773 Z= 0.318 Chirality : 0.042 0.183 1846 Planarity : 0.004 0.044 1985 Dihedral : 7.194 78.910 1673 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 5.86 % Allowed : 24.66 % Favored : 69.48 % 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: 1.69 (0.16), residues: 964 sheet: 0.96 (0.50), residues: 105 loop : -1.51 (0.35), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 24 HIS 0.007 0.001 HIS F 314 PHE 0.026 0.002 PHE A 331 TYR 0.026 0.002 TYR B 325 ARG 0.005 0.000 ARG C 306 *********************** 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 289 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 212 time to evaluate : 1.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 HIS cc_start: 0.7039 (OUTLIER) cc_final: 0.6541 (t70) REVERT: A 144 PHE cc_start: 0.6908 (OUTLIER) cc_final: 0.6635 (m-80) REVERT: A 337 MET cc_start: 0.5483 (tpt) cc_final: 0.5230 (tpt) REVERT: B 35 MET cc_start: 0.7013 (mtp) cc_final: 0.6696 (mtt) REVERT: B 274 LYS cc_start: 0.5804 (tttt) cc_final: 0.4407 (mmtt) REVERT: B 275 PHE cc_start: 0.7407 (OUTLIER) cc_final: 0.6939 (t80) REVERT: B 308 TYR cc_start: 0.7698 (OUTLIER) cc_final: 0.7074 (m-80) REVERT: B 337 MET cc_start: 0.6857 (tmm) cc_final: 0.6302 (tmm) REVERT: C 104 HIS cc_start: 0.6877 (OUTLIER) cc_final: 0.6202 (t70) REVERT: C 108 TYR cc_start: 0.7668 (t80) cc_final: 0.7320 (t80) REVERT: C 161 LEU cc_start: 0.7156 (OUTLIER) cc_final: 0.6898 (pp) REVERT: C 388 LYS cc_start: 0.7323 (ttpt) cc_final: 0.6753 (mttt) REVERT: D 156 PHE cc_start: 0.7660 (t80) cc_final: 0.7355 (t80) REVERT: D 157 VAL cc_start: 0.8466 (t) cc_final: 0.8162 (p) REVERT: D 301 SER cc_start: 0.8037 (p) cc_final: 0.7725 (m) REVERT: D 374 PHE cc_start: 0.6665 (OUTLIER) cc_final: 0.6031 (m-10) REVERT: E 52 MET cc_start: 0.4944 (ppp) cc_final: 0.3763 (ttp) REVERT: E 136 PHE cc_start: 0.4621 (OUTLIER) cc_final: 0.4201 (m-80) REVERT: E 299 ILE cc_start: 0.3563 (OUTLIER) cc_final: 0.2744 (pt) REVERT: E 343 MET cc_start: 0.2919 (mtp) cc_final: 0.2176 (mtp) REVERT: F 279 TYR cc_start: 0.4564 (t80) cc_final: 0.4166 (t80) outliers start: 77 outliers final: 48 residues processed: 269 average time/residue: 0.2369 time to fit residues: 91.6387 Evaluate side-chains 264 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 207 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 144 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 341 TRP Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 134 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 308 TYR Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 274 LYS Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain D residue 363 SER Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 374 PHE Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 41 PHE Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 136 PHE 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 F residue 17 PHE Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 106 GLN Chi-restraints excluded: chain F residue 145 TRP Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 330 TYR 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: 0.6980 chunk 124 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 98 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 chunk 118 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 chunk 132 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6441 moved from start: 0.5311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12385 Z= 0.240 Angle : 0.625 10.510 16773 Z= 0.330 Chirality : 0.042 0.189 1846 Planarity : 0.004 0.045 1985 Dihedral : 6.962 76.589 1673 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 4.72 % Allowed : 26.26 % Favored : 69.03 % 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: 1.39 (0.22), residues: 1382 helix: 1.68 (0.16), residues: 963 sheet: 0.98 (0.50), residues: 105 loop : -1.52 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A 24 HIS 0.005 0.001 HIS E 132 PHE 0.025 0.002 PHE A 331 TYR 0.025 0.002 TYR D 284 ARG 0.005 0.000 ARG A 306 *********************** 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 272 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 210 time to evaluate : 1.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 HIS cc_start: 0.6980 (OUTLIER) cc_final: 0.6429 (t70) REVERT: A 337 MET cc_start: 0.5455 (tpt) cc_final: 0.5198 (tpt) REVERT: B 35 MET cc_start: 0.6974 (mtp) cc_final: 0.6741 (mtt) REVERT: B 274 LYS cc_start: 0.5740 (tttt) cc_final: 0.4374 (mmtt) REVERT: B 275 PHE cc_start: 0.7517 (OUTLIER) cc_final: 0.7048 (t80) REVERT: B 308 TYR cc_start: 0.7784 (OUTLIER) cc_final: 0.7073 (m-80) REVERT: B 337 MET cc_start: 0.6869 (tmm) cc_final: 0.6336 (tmm) REVERT: C 104 HIS cc_start: 0.6906 (OUTLIER) cc_final: 0.6137 (t70) REVERT: C 108 TYR cc_start: 0.7511 (t80) cc_final: 0.7275 (t80) REVERT: C 306 ARG cc_start: 0.7161 (ttm-80) cc_final: 0.6938 (ttm-80) REVERT: C 388 LYS cc_start: 0.7325 (ttpt) cc_final: 0.6740 (mttt) REVERT: D 156 PHE cc_start: 0.7786 (t80) cc_final: 0.7469 (t80) REVERT: D 157 VAL cc_start: 0.8477 (t) cc_final: 0.8144 (p) REVERT: D 301 SER cc_start: 0.8031 (p) cc_final: 0.7725 (m) REVERT: D 374 PHE cc_start: 0.6727 (OUTLIER) cc_final: 0.5954 (m-10) REVERT: E 52 MET cc_start: 0.4883 (ppp) cc_final: 0.3548 (ttp) REVERT: E 299 ILE cc_start: 0.3685 (OUTLIER) cc_final: 0.2451 (mm) REVERT: E 343 MET cc_start: 0.2950 (mtp) cc_final: 0.2298 (mtp) outliers start: 62 outliers final: 52 residues processed: 256 average time/residue: 0.2460 time to fit residues: 90.3637 Evaluate side-chains 263 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 205 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 136 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 341 TRP Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 308 TYR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 239 GLN Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 274 LYS Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 374 PHE Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 41 PHE Chi-restraints excluded: chain E residue 109 VAL 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 F residue 17 PHE Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 106 GLN Chi-restraints excluded: chain F residue 145 TRP Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 330 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 80 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 138 optimal weight: 0.9990 chunk 127 optimal weight: 4.9990 chunk 110 optimal weight: 0.7980 chunk 11 optimal weight: 7.9990 chunk 85 optimal weight: 0.8980 chunk 67 optimal weight: 0.8980 chunk 87 optimal weight: 0.7980 chunk 117 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6452 moved from start: 0.5465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12385 Z= 0.246 Angle : 0.650 15.353 16773 Z= 0.340 Chirality : 0.042 0.195 1846 Planarity : 0.004 0.045 1985 Dihedral : 6.914 74.557 1673 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.95 % Allowed : 26.33 % Favored : 68.72 % 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: 1.36 (0.22), residues: 1382 helix: 1.67 (0.16), residues: 963 sheet: 0.98 (0.50), residues: 105 loop : -1.57 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 24 HIS 0.004 0.001 HIS E 132 PHE 0.021 0.002 PHE A 331 TYR 0.039 0.002 TYR B 325 ARG 0.004 0.000 ARG A 306 ********************** 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 280 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 215 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 HIS cc_start: 0.6987 (OUTLIER) cc_final: 0.6447 (t70) REVERT: A 337 MET cc_start: 0.5463 (tpt) cc_final: 0.5150 (tpt) REVERT: B 35 MET cc_start: 0.6969 (mtp) cc_final: 0.6734 (mtt) REVERT: B 274 LYS cc_start: 0.5841 (tttt) cc_final: 0.4466 (mmtt) REVERT: B 275 PHE cc_start: 0.7484 (OUTLIER) cc_final: 0.6955 (t80) REVERT: B 308 TYR cc_start: 0.7789 (OUTLIER) cc_final: 0.7090 (m-80) REVERT: B 337 MET cc_start: 0.6736 (tmm) cc_final: 0.6186 (tmm) REVERT: C 104 HIS cc_start: 0.6920 (OUTLIER) cc_final: 0.6279 (t70) REVERT: C 388 LYS cc_start: 0.7344 (ttpt) cc_final: 0.6754 (mttt) REVERT: D 156 PHE cc_start: 0.7733 (t80) cc_final: 0.7409 (t80) REVERT: D 157 VAL cc_start: 0.8454 (t) cc_final: 0.8131 (p) REVERT: D 279 ILE cc_start: 0.5329 (OUTLIER) cc_final: 0.4994 (mm) REVERT: D 292 ASP cc_start: 0.7236 (m-30) cc_final: 0.6863 (p0) REVERT: D 301 SER cc_start: 0.8055 (p) cc_final: 0.7763 (m) REVERT: D 374 PHE cc_start: 0.6797 (OUTLIER) cc_final: 0.6022 (m-10) REVERT: E 52 MET cc_start: 0.4768 (ppp) cc_final: 0.3526 (ttp) REVERT: E 299 ILE cc_start: 0.3764 (OUTLIER) cc_final: 0.2890 (pt) REVERT: E 343 MET cc_start: 0.3092 (mtp) cc_final: 0.1992 (mtp) outliers start: 65 outliers final: 55 residues processed: 260 average time/residue: 0.2465 time to fit residues: 91.5626 Evaluate side-chains 268 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 206 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 136 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 341 TRP Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 308 TYR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 239 GLN Chi-restraints excluded: chain D residue 268 THR 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 283 VAL Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 348 LEU Chi-restraints excluded: chain D residue 363 SER Chi-restraints excluded: chain D residue 368 VAL Chi-restraints excluded: chain D residue 374 PHE Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 41 PHE Chi-restraints excluded: chain E residue 109 VAL 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 F residue 17 PHE Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 106 GLN Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 145 TRP Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 330 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 33 optimal weight: 0.8980 chunk 101 optimal weight: 20.0000 chunk 16 optimal weight: 0.3980 chunk 30 optimal weight: 6.9990 chunk 110 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 96 optimal weight: 0.1980 chunk 6 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4633 r_free = 0.4633 target = 0.208756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.167601 restraints weight = 18551.428| |-----------------------------------------------------------------------------| r_work (start): 0.4189 rms_B_bonded: 2.91 r_work: 0.3985 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6743 moved from start: 0.5547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12385 Z= 0.209 Angle : 0.639 14.812 16773 Z= 0.332 Chirality : 0.041 0.182 1846 Planarity : 0.004 0.044 1985 Dihedral : 6.638 74.518 1671 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 4.49 % Allowed : 27.09 % Favored : 68.42 % 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: 1.47 (0.22), residues: 1382 helix: 1.75 (0.16), residues: 962 sheet: 1.12 (0.51), residues: 105 loop : -1.52 (0.34), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 24 HIS 0.005 0.001 HIS D 104 PHE 0.021 0.002 PHE A 331 TYR 0.025 0.001 TYR D 284 ARG 0.004 0.000 ARG A 306 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3005.44 seconds wall clock time: 55 minutes 47.35 seconds (3347.35 seconds total)