Starting phenix.real_space_refine on Wed Feb 4 03:59:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ipm_60777/02_2026/9ipm_60777.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ipm_60777/02_2026/9ipm_60777.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ipm_60777/02_2026/9ipm_60777.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ipm_60777/02_2026/9ipm_60777.map" model { file = "/net/cci-nas-00/data/ceres_data/9ipm_60777/02_2026/9ipm_60777.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ipm_60777/02_2026/9ipm_60777.cif" } resolution = 3.56 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.009 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 12 5.49 5 S 78 5.16 5 C 5820 2.51 5 N 1350 2.21 5 O 1500 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8760 Number of models: 1 Model: "" Number of chains: 12 Chain: "E" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1381 Classifications: {'peptide': 171} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 164} Chain breaks: 1 Chain: "A" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1381 Classifications: {'peptide': 171} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 164} Chain breaks: 1 Chain: "B" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1381 Classifications: {'peptide': 171} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 164} Chain breaks: 1 Chain: "F" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1381 Classifications: {'peptide': 171} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 164} Chain breaks: 1 Chain: "C" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1381 Classifications: {'peptide': 171} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 164} Chain breaks: 1 Chain: "D" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1381 Classifications: {'peptide': 171} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 164} Chain breaks: 1 Chain: "E" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 79 Unusual residues: {'C14': 1, 'MC3': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 27 Chain: "A" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 79 Unusual residues: {'C14': 1, 'MC3': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 27 Chain: "B" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 79 Unusual residues: {'C14': 1, 'MC3': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 27 Chain: "F" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 79 Unusual residues: {'C14': 1, 'MC3': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 27 Chain: "C" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 79 Unusual residues: {'C14': 1, 'MC3': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 27 Chain: "D" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 79 Unusual residues: {'C14': 1, 'MC3': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 27 Time building chain proxies: 2.14, per 1000 atoms: 0.24 Number of scatterers: 8760 At special positions: 0 Unit cell: (97.92, 104.32, 80.64, 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 78 16.00 P 12 15.00 O 1500 8.00 N 1350 7.00 C 5820 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS E 55 " - pdb=" SG CYS E 242 " distance=2.03 Simple disulfide: pdb=" SG CYS E 62 " - pdb=" SG CYS E 236 " distance=2.03 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 231 " distance=2.03 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 242 " distance=2.03 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 236 " distance=2.03 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 231 " distance=2.03 Simple disulfide: pdb=" SG CYS B 55 " - pdb=" SG CYS B 242 " distance=2.03 Simple disulfide: pdb=" SG CYS B 62 " - pdb=" SG CYS B 236 " distance=2.03 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 231 " distance=2.03 Simple disulfide: pdb=" SG CYS F 55 " - pdb=" SG CYS F 242 " distance=2.03 Simple disulfide: pdb=" SG CYS F 62 " - pdb=" SG CYS F 236 " distance=2.03 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 231 " distance=2.03 Simple disulfide: pdb=" SG CYS C 55 " - pdb=" SG CYS C 242 " distance=2.03 Simple disulfide: pdb=" SG CYS C 62 " - pdb=" SG CYS C 236 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 231 " distance=2.03 Simple disulfide: pdb=" SG CYS D 55 " - pdb=" SG CYS D 242 " distance=2.03 Simple disulfide: pdb=" SG CYS D 62 " - pdb=" SG CYS D 236 " distance=2.03 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 231 " 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: 0.61 Conformation dependent library (CDL) restraints added in 235.7 milliseconds 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1932 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 6 sheets defined 77.3% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'E' and resid 19 through 48 removed outlier: 5.317A pdb=" N GLU E 43 " --> pdb=" O ALA E 39 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N THR E 44 " --> pdb=" O ILE E 40 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N VAL E 45 " --> pdb=" O VAL E 41 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TYR E 46 " --> pdb=" O GLY E 42 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP E 47 " --> pdb=" O GLU E 43 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ASP E 48 " --> pdb=" O THR E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 53 Processing helix chain 'E' and resid 61 through 71 removed outlier: 3.797A pdb=" N ALA E 65 " --> pdb=" O GLY E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 101 Proline residue: E 89 - end of helix Processing helix chain 'E' and resid 195 through 221 Processing helix chain 'E' and resid 246 through 276 Processing helix chain 'A' and resid 20 through 48 removed outlier: 5.316A pdb=" N GLU A 43 " --> pdb=" O ALA A 39 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N THR A 44 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N VAL A 45 " --> pdb=" O VAL A 41 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR A 46 " --> pdb=" O GLY A 42 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP A 47 " --> pdb=" O GLU A 43 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ASP A 48 " --> pdb=" O THR A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 53 Processing helix chain 'A' and resid 61 through 71 removed outlier: 3.796A pdb=" N ALA A 65 " --> pdb=" O GLY A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 101 Proline residue: A 89 - end of helix Processing helix chain 'A' and resid 195 through 221 Processing helix chain 'A' and resid 246 through 276 Processing helix chain 'B' and resid 20 through 48 removed outlier: 5.318A pdb=" N GLU B 43 " --> pdb=" O ALA B 39 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N THR B 44 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N VAL B 45 " --> pdb=" O VAL B 41 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TYR B 46 " --> pdb=" O GLY B 42 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP B 47 " --> pdb=" O GLU B 43 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ASP B 48 " --> pdb=" O THR B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 53 Processing helix chain 'B' and resid 61 through 71 removed outlier: 3.797A pdb=" N ALA B 65 " --> pdb=" O GLY B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 101 Proline residue: B 89 - end of helix Processing helix chain 'B' and resid 195 through 221 Processing helix chain 'B' and resid 246 through 276 Processing helix chain 'F' and resid 20 through 48 removed outlier: 5.317A pdb=" N GLU F 43 " --> pdb=" O ALA F 39 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N THR F 44 " --> pdb=" O ILE F 40 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N VAL F 45 " --> pdb=" O VAL F 41 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR F 46 " --> pdb=" O GLY F 42 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP F 47 " --> pdb=" O GLU F 43 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ASP F 48 " --> pdb=" O THR F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 53 Processing helix chain 'F' and resid 61 through 71 removed outlier: 3.797A pdb=" N ALA F 65 " --> pdb=" O GLY F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 101 Proline residue: F 89 - end of helix Processing helix chain 'F' and resid 195 through 221 Processing helix chain 'F' and resid 246 through 276 Processing helix chain 'C' and resid 20 through 48 removed outlier: 5.317A pdb=" N GLU C 43 " --> pdb=" O ALA C 39 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N THR C 44 " --> pdb=" O ILE C 40 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N VAL C 45 " --> pdb=" O VAL C 41 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TYR C 46 " --> pdb=" O GLY C 42 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP C 47 " --> pdb=" O GLU C 43 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ASP C 48 " --> pdb=" O THR C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 53 Processing helix chain 'C' and resid 61 through 71 removed outlier: 3.798A pdb=" N ALA C 65 " --> pdb=" O GLY C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 101 Proline residue: C 89 - end of helix Processing helix chain 'C' and resid 195 through 221 Processing helix chain 'C' and resid 246 through 276 Processing helix chain 'D' and resid 20 through 48 removed outlier: 5.317A pdb=" N GLU D 43 " --> pdb=" O ALA D 39 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N THR D 44 " --> pdb=" O ILE D 40 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N VAL D 45 " --> pdb=" O VAL D 41 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TYR D 46 " --> pdb=" O GLY D 42 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP D 47 " --> pdb=" O GLU D 43 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ASP D 48 " --> pdb=" O THR D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 53 Processing helix chain 'D' and resid 61 through 71 removed outlier: 3.797A pdb=" N ALA D 65 " --> pdb=" O GLY D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 101 Proline residue: D 89 - end of helix Processing helix chain 'D' and resid 195 through 221 Processing helix chain 'D' and resid 246 through 276 Processing sheet with id=AA1, first strand: chain 'E' and resid 54 through 55 removed outlier: 3.753A pdb=" N VAL E 240 " --> pdb=" O CYS E 231 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 54 through 55 removed outlier: 3.753A pdb=" N VAL A 240 " --> pdb=" O CYS A 231 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 54 through 55 removed outlier: 3.753A pdb=" N VAL B 240 " --> pdb=" O CYS B 231 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 54 through 55 removed outlier: 3.753A pdb=" N VAL F 240 " --> pdb=" O CYS F 231 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 54 through 55 removed outlier: 3.753A pdb=" N VAL C 240 " --> pdb=" O CYS C 231 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 54 through 55 removed outlier: 3.753A pdb=" N VAL D 240 " --> pdb=" O CYS D 231 " (cutoff:3.500A) 619 hydrogen bonds defined for protein. 1839 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.20 Time building geometry restraints manager: 0.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2401 1.34 - 1.45: 1457 1.45 - 1.57: 4962 1.57 - 1.69: 24 1.69 - 1.81: 102 Bond restraints: 8946 Sorted by residual: bond pdb=" C31 MC3 F 401 " pdb=" O2 MC3 F 401 " ideal model delta sigma weight residual 1.328 1.459 -0.131 2.00e-02 2.50e+03 4.28e+01 bond pdb=" C31 MC3 A 401 " pdb=" O2 MC3 A 401 " ideal model delta sigma weight residual 1.328 1.459 -0.131 2.00e-02 2.50e+03 4.28e+01 bond pdb=" C31 MC3 B 401 " pdb=" O2 MC3 B 401 " ideal model delta sigma weight residual 1.328 1.459 -0.131 2.00e-02 2.50e+03 4.28e+01 bond pdb=" C31 MC3 D 401 " pdb=" O2 MC3 D 401 " ideal model delta sigma weight residual 1.328 1.459 -0.131 2.00e-02 2.50e+03 4.28e+01 bond pdb=" C31 MC3 E 401 " pdb=" O2 MC3 E 401 " ideal model delta sigma weight residual 1.328 1.459 -0.131 2.00e-02 2.50e+03 4.27e+01 ... (remaining 8941 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 11474 2.26 - 4.53: 465 4.53 - 6.79: 85 6.79 - 9.05: 24 9.05 - 11.31: 30 Bond angle restraints: 12078 Sorted by residual: angle pdb=" O3P MC3 A 401 " pdb=" P MC3 A 401 " pdb=" O4P MC3 A 401 " ideal model delta sigma weight residual 93.26 104.57 -11.31 3.00e+00 1.11e-01 1.42e+01 angle pdb=" O3P MC3 E 401 " pdb=" P MC3 E 401 " pdb=" O4P MC3 E 401 " ideal model delta sigma weight residual 93.26 104.52 -11.26 3.00e+00 1.11e-01 1.41e+01 angle pdb=" O3P MC3 C 401 " pdb=" P MC3 C 401 " pdb=" O4P MC3 C 401 " ideal model delta sigma weight residual 93.26 104.52 -11.26 3.00e+00 1.11e-01 1.41e+01 angle pdb=" O3P MC3 D 401 " pdb=" P MC3 D 401 " pdb=" O4P MC3 D 401 " ideal model delta sigma weight residual 93.26 104.51 -11.25 3.00e+00 1.11e-01 1.41e+01 angle pdb=" O3P MC3 F 401 " pdb=" P MC3 F 401 " pdb=" O4P MC3 F 401 " ideal model delta sigma weight residual 93.26 104.50 -11.24 3.00e+00 1.11e-01 1.40e+01 ... (remaining 12073 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.60: 5166 34.60 - 69.20: 156 69.20 - 103.80: 24 103.80 - 138.40: 12 138.40 - 173.00: 6 Dihedral angle restraints: 5364 sinusoidal: 2358 harmonic: 3006 Sorted by residual: dihedral pdb=" N MC3 B 401 " pdb=" C4 MC3 B 401 " pdb=" C5 MC3 B 401 " pdb=" O4P MC3 B 401 " ideal model delta sinusoidal sigma weight residual -70.18 102.82 -173.00 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" N MC3 C 401 " pdb=" C4 MC3 C 401 " pdb=" C5 MC3 C 401 " pdb=" O4P MC3 C 401 " ideal model delta sinusoidal sigma weight residual -70.18 102.81 -172.99 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" N MC3 F 401 " pdb=" C4 MC3 F 401 " pdb=" C5 MC3 F 401 " pdb=" O4P MC3 F 401 " ideal model delta sinusoidal sigma weight residual -70.18 102.80 -172.98 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 5361 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 919 0.039 - 0.079: 297 0.079 - 0.118: 110 0.118 - 0.157: 18 0.157 - 0.197: 6 Chirality restraints: 1350 Sorted by residual: chirality pdb=" CA THR C 88 " pdb=" N THR C 88 " pdb=" C THR C 88 " pdb=" CB THR C 88 " both_signs ideal model delta sigma weight residual False 2.53 2.33 0.20 2.00e-01 2.50e+01 9.68e-01 chirality pdb=" CA THR B 88 " pdb=" N THR B 88 " pdb=" C THR B 88 " pdb=" CB THR B 88 " both_signs ideal model delta sigma weight residual False 2.53 2.33 0.20 2.00e-01 2.50e+01 9.58e-01 chirality pdb=" CA THR E 88 " pdb=" N THR E 88 " pdb=" C THR E 88 " pdb=" CB THR E 88 " both_signs ideal model delta sigma weight residual False 2.53 2.33 0.20 2.00e-01 2.50e+01 9.57e-01 ... (remaining 1347 not shown) Planarity restraints: 1440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 88 " 0.025 5.00e-02 4.00e+02 3.72e-02 2.21e+00 pdb=" N PRO C 89 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO C 89 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 89 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 88 " 0.025 5.00e-02 4.00e+02 3.72e-02 2.21e+00 pdb=" N PRO D 89 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO D 89 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 89 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR E 88 " -0.025 5.00e-02 4.00e+02 3.72e-02 2.21e+00 pdb=" N PRO E 89 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO E 89 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO E 89 " -0.021 5.00e-02 4.00e+02 ... (remaining 1437 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 784 2.74 - 3.28: 9503 3.28 - 3.82: 15233 3.82 - 4.36: 15579 4.36 - 4.90: 27489 Nonbonded interactions: 68588 Sorted by model distance: nonbonded pdb=" OE2 GLU B 49 " pdb=" OH TYR B 67 " model vdw 2.201 3.040 nonbonded pdb=" OE2 GLU F 49 " pdb=" OH TYR F 67 " model vdw 2.201 3.040 nonbonded pdb=" OE2 GLU D 49 " pdb=" OH TYR D 67 " model vdw 2.201 3.040 nonbonded pdb=" OE2 GLU C 49 " pdb=" OH TYR C 67 " model vdw 2.202 3.040 nonbonded pdb=" OE2 GLU A 49 " pdb=" OH TYR A 67 " model vdw 2.202 3.040 ... (remaining 68583 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: 0.03 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'A' selection = chain 'B' selection = chain 'F' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 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: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.230 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 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:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 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 : 0.008 0.131 8964 Z= 0.398 Angle : 1.112 11.314 12114 Z= 0.500 Chirality : 0.045 0.197 1350 Planarity : 0.004 0.037 1440 Dihedral : 19.346 173.001 3378 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.12 (0.24), residues: 1002 helix: 1.66 (0.18), residues: 726 sheet: None (None), residues: 0 loop : 0.95 (0.33), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 246 TYR 0.014 0.001 TYR F 199 PHE 0.012 0.002 PHE F 81 TRP 0.009 0.001 TRP B 277 HIS 0.004 0.002 HIS B 274 Details of bonding type rmsd covalent geometry : bond 0.00800 ( 8946) covalent geometry : angle 1.11314 (12078) SS BOND : bond 0.00237 ( 18) SS BOND : angle 0.54594 ( 36) hydrogen bonds : bond 0.10023 ( 619) hydrogen bonds : angle 4.30338 ( 1839) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 451 time to evaluate : 0.274 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 21 MET cc_start: 0.9001 (pmm) cc_final: 0.8774 (pmm) REVERT: E 93 PHE cc_start: 0.8455 (t80) cc_final: 0.8245 (t80) REVERT: E 99 HIS cc_start: 0.8547 (t-90) cc_final: 0.8191 (t-90) REVERT: E 229 TYR cc_start: 0.8992 (t80) cc_final: 0.8664 (t80) REVERT: E 230 GLU cc_start: 0.8574 (mp0) cc_final: 0.8238 (mp0) REVERT: E 233 ARG cc_start: 0.8413 (mtt180) cc_final: 0.8150 (mtt-85) REVERT: E 239 GLU cc_start: 0.8399 (tm-30) cc_final: 0.7998 (tm-30) REVERT: E 256 PHE cc_start: 0.8672 (t80) cc_final: 0.8461 (t80) REVERT: A 21 MET cc_start: 0.8998 (pmm) cc_final: 0.8751 (pmm) REVERT: A 93 PHE cc_start: 0.8510 (t80) cc_final: 0.8301 (t80) REVERT: A 99 HIS cc_start: 0.8646 (t-90) cc_final: 0.8352 (t-90) REVERT: A 239 GLU cc_start: 0.8434 (tm-30) cc_final: 0.8007 (tm-30) REVERT: B 21 MET cc_start: 0.8991 (pmm) cc_final: 0.8761 (pmm) REVERT: B 99 HIS cc_start: 0.8539 (t-90) cc_final: 0.8226 (t-90) REVERT: B 229 TYR cc_start: 0.9028 (t80) cc_final: 0.8764 (t80) REVERT: B 230 GLU cc_start: 0.8630 (mp0) cc_final: 0.8355 (mp0) REVERT: B 239 GLU cc_start: 0.8529 (tm-30) cc_final: 0.8130 (tm-30) REVERT: B 256 PHE cc_start: 0.8682 (t80) cc_final: 0.8457 (t80) REVERT: F 21 MET cc_start: 0.9013 (pmm) cc_final: 0.8809 (pmm) REVERT: F 40 ILE cc_start: 0.9670 (mm) cc_final: 0.9448 (mm) REVERT: F 99 HIS cc_start: 0.8677 (t-90) cc_final: 0.8360 (t-90) REVERT: F 229 TYR cc_start: 0.9010 (t80) cc_final: 0.8726 (t80) REVERT: F 239 GLU cc_start: 0.8373 (tm-30) cc_final: 0.7982 (tm-30) REVERT: F 256 PHE cc_start: 0.8627 (t80) cc_final: 0.8403 (t80) REVERT: C 21 MET cc_start: 0.9021 (pmm) cc_final: 0.8765 (pmm) REVERT: C 40 ILE cc_start: 0.9669 (mm) cc_final: 0.9456 (mm) REVERT: C 99 HIS cc_start: 0.8656 (t-90) cc_final: 0.8314 (t-90) REVERT: C 229 TYR cc_start: 0.8979 (t80) cc_final: 0.8710 (t80) REVERT: C 239 GLU cc_start: 0.8344 (tm-30) cc_final: 0.7951 (tm-30) REVERT: C 256 PHE cc_start: 0.8605 (t80) cc_final: 0.8383 (t80) REVERT: D 21 MET cc_start: 0.9029 (pmm) cc_final: 0.8819 (pmm) REVERT: D 93 PHE cc_start: 0.8493 (t80) cc_final: 0.8267 (t80) REVERT: D 99 HIS cc_start: 0.8604 (t-90) cc_final: 0.8263 (t-90) REVERT: D 239 GLU cc_start: 0.8412 (tm-30) cc_final: 0.8000 (tm-30) outliers start: 0 outliers final: 0 residues processed: 451 average time/residue: 0.0782 time to fit residues: 48.6742 Evaluate side-chains 299 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 299 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 8.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.0980 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 10.0000 chunk 100 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 268 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 = 0.3441 r_free = 0.3441 target = 0.100992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.079420 restraints weight = 18011.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.082979 restraints weight = 8090.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.085645 restraints weight = 4955.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.087230 restraints weight = 3534.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.088515 restraints weight = 2879.490| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8964 Z= 0.160 Angle : 0.685 5.612 12114 Z= 0.364 Chirality : 0.045 0.199 1350 Planarity : 0.006 0.070 1440 Dihedral : 20.914 168.773 1500 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 4.09 % Allowed : 15.59 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.29 (0.24), residues: 1002 helix: 1.62 (0.17), residues: 732 sheet: 2.31 (0.58), residues: 60 loop : 1.19 (0.42), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 246 TYR 0.023 0.002 TYR B 234 PHE 0.017 0.002 PHE F 33 TRP 0.025 0.002 TRP D 277 HIS 0.008 0.003 HIS E 274 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 8946) covalent geometry : angle 0.68502 (12078) SS BOND : bond 0.00279 ( 18) SS BOND : angle 0.50368 ( 36) hydrogen bonds : bond 0.04404 ( 619) hydrogen bonds : angle 3.71822 ( 1839) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 338 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 99 HIS cc_start: 0.8589 (t-90) cc_final: 0.8166 (t-90) REVERT: E 205 PHE cc_start: 0.8644 (OUTLIER) cc_final: 0.8354 (t80) REVERT: E 229 TYR cc_start: 0.8941 (t80) cc_final: 0.8589 (t80) REVERT: E 230 GLU cc_start: 0.8633 (mp0) cc_final: 0.8357 (mp0) REVERT: E 233 ARG cc_start: 0.8244 (mtt180) cc_final: 0.8017 (mtt-85) REVERT: E 239 GLU cc_start: 0.8524 (tm-30) cc_final: 0.8094 (tm-30) REVERT: A 21 MET cc_start: 0.8933 (pmm) cc_final: 0.8686 (pmm) REVERT: A 99 HIS cc_start: 0.8712 (t-90) cc_final: 0.8343 (t-90) REVERT: A 205 PHE cc_start: 0.8738 (OUTLIER) cc_final: 0.8429 (t80) REVERT: A 239 GLU cc_start: 0.8544 (tm-30) cc_final: 0.8084 (tm-30) REVERT: B 21 MET cc_start: 0.8977 (pmm) cc_final: 0.8724 (pmm) REVERT: B 99 HIS cc_start: 0.8575 (t-90) cc_final: 0.8202 (t-90) REVERT: B 205 PHE cc_start: 0.8681 (OUTLIER) cc_final: 0.8364 (t80) REVERT: B 230 GLU cc_start: 0.8703 (mp0) cc_final: 0.8429 (mp0) REVERT: B 239 GLU cc_start: 0.8595 (tm-30) cc_final: 0.8207 (tm-30) REVERT: F 99 HIS cc_start: 0.8732 (t-90) cc_final: 0.8311 (t-90) REVERT: F 205 PHE cc_start: 0.8673 (OUTLIER) cc_final: 0.8338 (t80) REVERT: F 229 TYR cc_start: 0.8993 (t80) cc_final: 0.8590 (t80) REVERT: F 230 GLU cc_start: 0.8557 (mp0) cc_final: 0.8305 (mp0) REVERT: F 233 ARG cc_start: 0.8197 (mtt180) cc_final: 0.7919 (mtt-85) REVERT: F 239 GLU cc_start: 0.8519 (tm-30) cc_final: 0.8061 (tm-30) REVERT: C 21 MET cc_start: 0.9009 (pmm) cc_final: 0.8796 (pmm) REVERT: C 40 ILE cc_start: 0.9659 (mm) cc_final: 0.9456 (mm) REVERT: C 93 PHE cc_start: 0.8548 (t80) cc_final: 0.8339 (t80) REVERT: C 94 ILE cc_start: 0.8578 (mm) cc_final: 0.8372 (tt) REVERT: C 99 HIS cc_start: 0.8716 (t-90) cc_final: 0.8307 (t-90) REVERT: C 205 PHE cc_start: 0.8676 (OUTLIER) cc_final: 0.8357 (t80) REVERT: C 229 TYR cc_start: 0.8955 (t80) cc_final: 0.8516 (t80) REVERT: C 230 GLU cc_start: 0.8593 (mp0) cc_final: 0.8307 (mp0) REVERT: C 233 ARG cc_start: 0.8362 (mtt180) cc_final: 0.8100 (mtt-85) REVERT: C 239 GLU cc_start: 0.8528 (tm-30) cc_final: 0.8091 (tm-30) REVERT: D 21 MET cc_start: 0.8965 (pmm) cc_final: 0.8756 (pmm) REVERT: D 99 HIS cc_start: 0.8670 (t-90) cc_final: 0.8253 (t-90) REVERT: D 205 PHE cc_start: 0.8665 (OUTLIER) cc_final: 0.8374 (t80) REVERT: D 239 GLU cc_start: 0.8543 (tm-30) cc_final: 0.8119 (tm-30) outliers start: 38 outliers final: 32 residues processed: 365 average time/residue: 0.0904 time to fit residues: 44.5299 Evaluate side-chains 317 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 279 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 22 ILE Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 205 PHE Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 274 HIS Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 205 PHE Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 205 PHE Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 274 HIS Chi-restraints excluded: chain B residue 281 LYS Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 205 PHE Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 274 HIS Chi-restraints excluded: chain F residue 281 LYS Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 205 PHE Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 281 LYS Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 205 PHE Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 274 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 52 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 25 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 42 optimal weight: 9.9990 chunk 55 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 92 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 268 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 = 0.3595 r_free = 0.3595 target = 0.107658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.083720 restraints weight = 19094.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.087225 restraints weight = 8791.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.089563 restraints weight = 5538.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.090976 restraints weight = 4162.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.092422 restraints weight = 3480.118| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8964 Z= 0.206 Angle : 0.667 6.156 12114 Z= 0.361 Chirality : 0.046 0.198 1350 Planarity : 0.005 0.045 1440 Dihedral : 18.541 158.451 1500 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 7.42 % Allowed : 20.54 % Favored : 72.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.47 (0.24), residues: 1002 helix: 1.80 (0.17), residues: 726 sheet: 1.73 (0.58), residues: 60 loop : 1.31 (0.43), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 69 TYR 0.030 0.002 TYR B 229 PHE 0.017 0.001 PHE C 33 TRP 0.030 0.002 TRP C 277 HIS 0.007 0.002 HIS B 274 Details of bonding type rmsd covalent geometry : bond 0.00498 ( 8946) covalent geometry : angle 0.66755 (12078) SS BOND : bond 0.00372 ( 18) SS BOND : angle 0.41274 ( 36) hydrogen bonds : bond 0.04317 ( 619) hydrogen bonds : angle 3.59708 ( 1839) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 316 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 21 MET cc_start: 0.8765 (pmm) cc_final: 0.8553 (pmm) REVERT: E 99 HIS cc_start: 0.8637 (t-90) cc_final: 0.8230 (t-90) REVERT: E 197 ARG cc_start: 0.8278 (ttt180) cc_final: 0.8034 (ttt180) REVERT: E 205 PHE cc_start: 0.8733 (OUTLIER) cc_final: 0.8412 (t80) REVERT: E 229 TYR cc_start: 0.9065 (t80) cc_final: 0.8724 (t80) REVERT: E 230 GLU cc_start: 0.8633 (mp0) cc_final: 0.8404 (mp0) REVERT: E 239 GLU cc_start: 0.8519 (tm-30) cc_final: 0.8103 (tm-30) REVERT: A 99 HIS cc_start: 0.8706 (t-90) cc_final: 0.8348 (t-90) REVERT: A 205 PHE cc_start: 0.8781 (OUTLIER) cc_final: 0.8464 (t80) REVERT: A 239 GLU cc_start: 0.8540 (tm-30) cc_final: 0.8120 (tm-30) REVERT: B 99 HIS cc_start: 0.8611 (t-90) cc_final: 0.8251 (t-90) REVERT: B 205 PHE cc_start: 0.8749 (OUTLIER) cc_final: 0.8433 (t80) REVERT: B 230 GLU cc_start: 0.8724 (mp0) cc_final: 0.8507 (mp0) REVERT: B 239 GLU cc_start: 0.8557 (tm-30) cc_final: 0.8207 (tm-30) REVERT: F 99 HIS cc_start: 0.8748 (t-90) cc_final: 0.8349 (t-90) REVERT: F 205 PHE cc_start: 0.8706 (OUTLIER) cc_final: 0.8387 (t80) REVERT: F 229 TYR cc_start: 0.9125 (t80) cc_final: 0.8644 (t80) REVERT: F 230 GLU cc_start: 0.8546 (mp0) cc_final: 0.8271 (mp0) REVERT: F 239 GLU cc_start: 0.8509 (tm-30) cc_final: 0.8113 (tm-30) REVERT: C 40 ILE cc_start: 0.9686 (mm) cc_final: 0.9473 (mm) REVERT: C 99 HIS cc_start: 0.8731 (t-90) cc_final: 0.8325 (t-90) REVERT: C 205 PHE cc_start: 0.8715 (OUTLIER) cc_final: 0.8396 (t80) REVERT: C 229 TYR cc_start: 0.9057 (t80) cc_final: 0.8576 (t80) REVERT: C 230 GLU cc_start: 0.8562 (mp0) cc_final: 0.8260 (mp0) REVERT: C 239 GLU cc_start: 0.8508 (tm-30) cc_final: 0.8110 (tm-30) REVERT: C 264 CYS cc_start: 0.9155 (t) cc_final: 0.8832 (t) REVERT: D 69 ARG cc_start: 0.8860 (mmm-85) cc_final: 0.8646 (mmm-85) REVERT: D 99 HIS cc_start: 0.8691 (t-90) cc_final: 0.8279 (t-90) REVERT: D 205 PHE cc_start: 0.8701 (OUTLIER) cc_final: 0.8435 (t80) REVERT: D 229 TYR cc_start: 0.8954 (t80) cc_final: 0.8106 (t80) REVERT: D 230 GLU cc_start: 0.8613 (mp0) cc_final: 0.8318 (mp0) REVERT: D 239 GLU cc_start: 0.8538 (tm-30) cc_final: 0.8031 (tm-30) outliers start: 69 outliers final: 62 residues processed: 364 average time/residue: 0.0930 time to fit residues: 45.2467 Evaluate side-chains 348 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 280 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 86 VAL Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 205 PHE Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 263 ILE Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 274 HIS Chi-restraints excluded: chain E residue 281 LYS Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 205 PHE Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 205 PHE Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 274 HIS Chi-restraints excluded: chain B residue 281 LYS Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 205 PHE Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 244 VAL Chi-restraints excluded: chain F residue 263 ILE Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 274 HIS Chi-restraints excluded: chain F residue 281 LYS Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 205 PHE Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 281 LYS Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 205 PHE Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 274 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 28 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 268 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 = 0.3542 r_free = 0.3542 target = 0.102660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.082376 restraints weight = 17984.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.085862 restraints weight = 7874.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.088507 restraints weight = 4774.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.090137 restraints weight = 3355.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.091349 restraints weight = 2688.344| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8964 Z= 0.153 Angle : 0.647 6.005 12114 Z= 0.349 Chirality : 0.045 0.195 1350 Planarity : 0.005 0.039 1440 Dihedral : 17.987 154.464 1500 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 5.38 % Allowed : 26.67 % Favored : 67.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.44 (0.25), residues: 1002 helix: 1.78 (0.17), residues: 726 sheet: 1.17 (0.52), residues: 60 loop : 1.48 (0.44), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 69 TYR 0.030 0.002 TYR B 229 PHE 0.013 0.001 PHE C 33 TRP 0.042 0.004 TRP A 277 HIS 0.007 0.002 HIS C 274 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 8946) covalent geometry : angle 0.64721 (12078) SS BOND : bond 0.00248 ( 18) SS BOND : angle 0.40670 ( 36) hydrogen bonds : bond 0.04011 ( 619) hydrogen bonds : angle 3.57194 ( 1839) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 335 time to evaluate : 0.327 Fit side-chains revert: symmetry clash REVERT: E 69 ARG cc_start: 0.8417 (mmt90) cc_final: 0.8191 (mmm-85) REVERT: E 99 HIS cc_start: 0.8628 (t-90) cc_final: 0.8220 (t-90) REVERT: E 205 PHE cc_start: 0.8693 (OUTLIER) cc_final: 0.8435 (t80) REVERT: E 229 TYR cc_start: 0.9004 (t80) cc_final: 0.8682 (t80) REVERT: E 230 GLU cc_start: 0.8652 (mp0) cc_final: 0.8354 (mp0) REVERT: E 239 GLU cc_start: 0.8575 (tm-30) cc_final: 0.8279 (tm-30) REVERT: A 21 MET cc_start: 0.8679 (pmm) cc_final: 0.8260 (pmm) REVERT: A 69 ARG cc_start: 0.8827 (mmm-85) cc_final: 0.8427 (mmm-85) REVERT: A 99 HIS cc_start: 0.8677 (t-90) cc_final: 0.8311 (t-90) REVERT: A 205 PHE cc_start: 0.8730 (OUTLIER) cc_final: 0.8479 (t80) REVERT: A 229 TYR cc_start: 0.8892 (t80) cc_final: 0.7998 (t80) REVERT: A 230 GLU cc_start: 0.8702 (mp0) cc_final: 0.8371 (mp0) REVERT: A 233 ARG cc_start: 0.8794 (mmm-85) cc_final: 0.8377 (mmm-85) REVERT: A 239 GLU cc_start: 0.8536 (tm-30) cc_final: 0.8013 (tm-30) REVERT: B 69 ARG cc_start: 0.8846 (mmm-85) cc_final: 0.8589 (mmm-85) REVERT: B 94 ILE cc_start: 0.8566 (mt) cc_final: 0.8364 (tt) REVERT: B 99 HIS cc_start: 0.8618 (t-90) cc_final: 0.8240 (t-90) REVERT: B 205 PHE cc_start: 0.8696 (OUTLIER) cc_final: 0.8457 (t80) REVERT: B 229 TYR cc_start: 0.8355 (t80) cc_final: 0.8109 (t80) REVERT: B 239 GLU cc_start: 0.8573 (tm-30) cc_final: 0.8110 (tm-30) REVERT: F 69 ARG cc_start: 0.8405 (mmt90) cc_final: 0.8146 (mmm-85) REVERT: F 99 HIS cc_start: 0.8709 (t-90) cc_final: 0.8322 (t-90) REVERT: F 205 PHE cc_start: 0.8671 (OUTLIER) cc_final: 0.8399 (t80) REVERT: F 229 TYR cc_start: 0.9042 (t80) cc_final: 0.8505 (t80) REVERT: F 230 GLU cc_start: 0.8600 (mp0) cc_final: 0.8305 (mp0) REVERT: F 239 GLU cc_start: 0.8548 (tm-30) cc_final: 0.8157 (tm-30) REVERT: F 264 CYS cc_start: 0.9156 (t) cc_final: 0.8846 (t) REVERT: C 36 LEU cc_start: 0.9635 (OUTLIER) cc_final: 0.9380 (tt) REVERT: C 40 ILE cc_start: 0.9683 (mm) cc_final: 0.9403 (mm) REVERT: C 69 ARG cc_start: 0.8323 (mmt90) cc_final: 0.8016 (mmm-85) REVERT: C 99 HIS cc_start: 0.8702 (t-90) cc_final: 0.8322 (t-90) REVERT: C 205 PHE cc_start: 0.8686 (OUTLIER) cc_final: 0.8422 (t80) REVERT: C 229 TYR cc_start: 0.8951 (t80) cc_final: 0.8403 (t80) REVERT: C 230 GLU cc_start: 0.8610 (mp0) cc_final: 0.8379 (mp0) REVERT: C 239 GLU cc_start: 0.8584 (tm-30) cc_final: 0.8309 (tm-30) REVERT: C 264 CYS cc_start: 0.9181 (t) cc_final: 0.8871 (t) REVERT: D 21 MET cc_start: 0.8528 (pmm) cc_final: 0.8294 (pmm) REVERT: D 99 HIS cc_start: 0.8656 (t-90) cc_final: 0.8259 (t-90) REVERT: D 205 PHE cc_start: 0.8646 (OUTLIER) cc_final: 0.8400 (t80) REVERT: D 230 GLU cc_start: 0.8710 (mp0) cc_final: 0.8499 (mp0) REVERT: D 239 GLU cc_start: 0.8540 (tm-30) cc_final: 0.8083 (tm-30) outliers start: 50 outliers final: 41 residues processed: 364 average time/residue: 0.0896 time to fit residues: 44.4548 Evaluate side-chains 349 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 301 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 205 PHE Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 263 ILE Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 274 HIS Chi-restraints excluded: chain E residue 281 LYS Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 205 PHE Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain B residue 205 PHE Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 274 HIS Chi-restraints excluded: chain B residue 281 LYS Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 205 PHE Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 266 VAL Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 274 HIS Chi-restraints excluded: chain F residue 281 LYS Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 205 PHE Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 281 LYS Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 205 PHE Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 263 ILE Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 274 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 29 optimal weight: 10.0000 chunk 8 optimal weight: 20.0000 chunk 65 optimal weight: 2.9990 chunk 78 optimal weight: 8.9990 chunk 80 optimal weight: 0.4980 chunk 10 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 85 optimal weight: 10.0000 chunk 48 optimal weight: 0.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 ASN ** D 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.099842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.079158 restraints weight = 17744.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.082660 restraints weight = 7875.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.085269 restraints weight = 4765.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.086999 restraints weight = 3384.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.088165 restraints weight = 2685.666| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8964 Z= 0.146 Angle : 0.639 5.933 12114 Z= 0.345 Chirality : 0.045 0.194 1350 Planarity : 0.005 0.071 1440 Dihedral : 17.631 152.567 1500 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 6.99 % Allowed : 30.00 % Favored : 63.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.32 (0.24), residues: 1002 helix: 1.75 (0.17), residues: 726 sheet: 0.72 (0.55), residues: 60 loop : 1.36 (0.42), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 69 TYR 0.024 0.001 TYR F 234 PHE 0.011 0.001 PHE C 33 TRP 0.008 0.001 TRP A 277 HIS 0.007 0.002 HIS E 274 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 8946) covalent geometry : angle 0.63963 (12078) SS BOND : bond 0.00236 ( 18) SS BOND : angle 0.38815 ( 36) hydrogen bonds : bond 0.03881 ( 619) hydrogen bonds : angle 3.55353 ( 1839) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 332 time to evaluate : 0.234 Fit side-chains revert: symmetry clash REVERT: E 93 PHE cc_start: 0.8498 (t80) cc_final: 0.8273 (t80) REVERT: E 99 HIS cc_start: 0.8642 (t-90) cc_final: 0.8240 (t-90) REVERT: E 205 PHE cc_start: 0.8626 (OUTLIER) cc_final: 0.8411 (t80) REVERT: E 229 TYR cc_start: 0.8938 (t80) cc_final: 0.8643 (t80) REVERT: E 230 GLU cc_start: 0.8737 (mp0) cc_final: 0.8489 (mp0) REVERT: E 239 GLU cc_start: 0.8644 (tm-30) cc_final: 0.8132 (tm-30) REVERT: A 21 MET cc_start: 0.8769 (pmm) cc_final: 0.8350 (pmm) REVERT: A 46 TYR cc_start: 0.9094 (m-80) cc_final: 0.8825 (m-80) REVERT: A 69 ARG cc_start: 0.8782 (mmm-85) cc_final: 0.8492 (mmm-85) REVERT: A 99 HIS cc_start: 0.8708 (t-90) cc_final: 0.8353 (t-90) REVERT: A 205 PHE cc_start: 0.8679 (OUTLIER) cc_final: 0.8462 (t80) REVERT: A 230 GLU cc_start: 0.8853 (mp0) cc_final: 0.8623 (mp0) REVERT: A 239 GLU cc_start: 0.8551 (tm-30) cc_final: 0.8126 (tm-30) REVERT: B 69 ARG cc_start: 0.8825 (mmm-85) cc_final: 0.7747 (tpp80) REVERT: B 99 HIS cc_start: 0.8620 (t-90) cc_final: 0.8246 (t-90) REVERT: B 205 PHE cc_start: 0.8633 (OUTLIER) cc_final: 0.8406 (t80) REVERT: B 229 TYR cc_start: 0.8463 (t80) cc_final: 0.8159 (t80) REVERT: B 230 GLU cc_start: 0.8867 (mp0) cc_final: 0.8581 (mp0) REVERT: B 239 GLU cc_start: 0.8619 (tm-30) cc_final: 0.8328 (tm-30) REVERT: F 46 TYR cc_start: 0.9096 (m-80) cc_final: 0.8876 (m-80) REVERT: F 99 HIS cc_start: 0.8733 (t-90) cc_final: 0.8361 (t-90) REVERT: F 205 PHE cc_start: 0.8652 (OUTLIER) cc_final: 0.8393 (t80) REVERT: F 229 TYR cc_start: 0.8959 (t80) cc_final: 0.8330 (t80) REVERT: F 230 GLU cc_start: 0.8698 (mp0) cc_final: 0.8365 (mp0) REVERT: F 239 GLU cc_start: 0.8592 (tm-30) cc_final: 0.8119 (tm-30) REVERT: F 264 CYS cc_start: 0.9152 (t) cc_final: 0.8841 (t) REVERT: C 36 LEU cc_start: 0.9624 (OUTLIER) cc_final: 0.9375 (tt) REVERT: C 40 ILE cc_start: 0.9668 (mm) cc_final: 0.9382 (mm) REVERT: C 69 ARG cc_start: 0.8415 (mmt90) cc_final: 0.8111 (mmm-85) REVERT: C 99 HIS cc_start: 0.8710 (t-90) cc_final: 0.8315 (t-90) REVERT: C 205 PHE cc_start: 0.8651 (OUTLIER) cc_final: 0.8425 (t80) REVERT: C 229 TYR cc_start: 0.8888 (t80) cc_final: 0.8291 (t80) REVERT: C 230 GLU cc_start: 0.8716 (mp0) cc_final: 0.8308 (mp0) REVERT: C 239 GLU cc_start: 0.8637 (tm-30) cc_final: 0.8118 (tm-30) REVERT: D 21 MET cc_start: 0.8710 (pmm) cc_final: 0.8410 (pmm) REVERT: D 40 ILE cc_start: 0.9660 (OUTLIER) cc_final: 0.9458 (mm) REVERT: D 99 HIS cc_start: 0.8657 (t-90) cc_final: 0.8296 (t-90) REVERT: D 197 ARG cc_start: 0.8593 (ptm160) cc_final: 0.8002 (ttt90) REVERT: D 205 PHE cc_start: 0.8585 (OUTLIER) cc_final: 0.8355 (t80) REVERT: D 230 GLU cc_start: 0.8812 (mp0) cc_final: 0.8580 (mp0) REVERT: D 239 GLU cc_start: 0.8590 (tm-30) cc_final: 0.8184 (tm-30) outliers start: 65 outliers final: 49 residues processed: 372 average time/residue: 0.0924 time to fit residues: 46.5631 Evaluate side-chains 371 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 314 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 205 PHE Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 274 HIS Chi-restraints excluded: chain E residue 281 LYS Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 205 PHE Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 205 PHE Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 274 HIS Chi-restraints excluded: chain B residue 281 LYS Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 205 PHE Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 244 VAL Chi-restraints excluded: chain F residue 266 VAL Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 274 HIS Chi-restraints excluded: chain F residue 281 LYS Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 205 PHE Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 281 LYS Chi-restraints excluded: chain D residue 40 ILE Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 205 PHE Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 274 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 92 optimal weight: 8.9990 chunk 15 optimal weight: 0.7980 chunk 13 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.104906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.085089 restraints weight = 17862.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.088557 restraints weight = 7681.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.091104 restraints weight = 4597.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.092905 restraints weight = 3254.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.093962 restraints weight = 2525.560| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8964 Z= 0.151 Angle : 0.659 6.264 12114 Z= 0.350 Chirality : 0.045 0.194 1350 Planarity : 0.004 0.042 1440 Dihedral : 17.372 151.203 1500 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 7.20 % Allowed : 29.78 % Favored : 63.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.35 (0.24), residues: 1002 helix: 1.79 (0.17), residues: 726 sheet: 0.49 (0.56), residues: 60 loop : 1.36 (0.42), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 69 TYR 0.043 0.002 TYR C 46 PHE 0.011 0.001 PHE C 33 TRP 0.026 0.002 TRP F 277 HIS 0.007 0.002 HIS D 75 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 8946) covalent geometry : angle 0.65984 (12078) SS BOND : bond 0.00224 ( 18) SS BOND : angle 0.39461 ( 36) hydrogen bonds : bond 0.03835 ( 619) hydrogen bonds : angle 3.52695 ( 1839) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 325 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 21 MET cc_start: 0.8791 (pmm) cc_final: 0.8417 (pmm) REVERT: E 69 ARG cc_start: 0.8743 (mmm-85) cc_final: 0.8428 (mmm-85) REVERT: E 99 HIS cc_start: 0.8632 (t-90) cc_final: 0.8240 (t-90) REVERT: E 205 PHE cc_start: 0.8607 (OUTLIER) cc_final: 0.8388 (t80) REVERT: E 229 TYR cc_start: 0.8920 (t80) cc_final: 0.8646 (t80) REVERT: E 230 GLU cc_start: 0.8803 (mp0) cc_final: 0.8534 (mp0) REVERT: E 233 ARG cc_start: 0.8840 (mmm-85) cc_final: 0.8622 (mmm-85) REVERT: E 239 GLU cc_start: 0.8622 (tm-30) cc_final: 0.8178 (tm-30) REVERT: A 21 MET cc_start: 0.8763 (pmm) cc_final: 0.8339 (pmm) REVERT: A 99 HIS cc_start: 0.8712 (t-90) cc_final: 0.8371 (t-90) REVERT: A 205 PHE cc_start: 0.8649 (OUTLIER) cc_final: 0.8439 (t80) REVERT: A 229 TYR cc_start: 0.8681 (t80) cc_final: 0.7765 (t80) REVERT: A 230 GLU cc_start: 0.8894 (mp0) cc_final: 0.8501 (mp0) REVERT: A 239 GLU cc_start: 0.8570 (tm-30) cc_final: 0.8121 (tm-30) REVERT: B 99 HIS cc_start: 0.8631 (t-90) cc_final: 0.8258 (t-90) REVERT: B 205 PHE cc_start: 0.8606 (OUTLIER) cc_final: 0.8401 (t80) REVERT: B 229 TYR cc_start: 0.8463 (t80) cc_final: 0.8174 (t80) REVERT: B 230 GLU cc_start: 0.8916 (mp0) cc_final: 0.8604 (mp0) REVERT: B 239 GLU cc_start: 0.8661 (tm-30) cc_final: 0.8262 (tm-30) REVERT: F 36 LEU cc_start: 0.9619 (OUTLIER) cc_final: 0.9389 (tt) REVERT: F 40 ILE cc_start: 0.9642 (OUTLIER) cc_final: 0.9421 (mm) REVERT: F 46 TYR cc_start: 0.9117 (m-80) cc_final: 0.8906 (m-80) REVERT: F 69 ARG cc_start: 0.8738 (mmm-85) cc_final: 0.8326 (mmm-85) REVERT: F 99 HIS cc_start: 0.8722 (t-90) cc_final: 0.8362 (t-90) REVERT: F 205 PHE cc_start: 0.8627 (OUTLIER) cc_final: 0.8393 (t80) REVERT: F 229 TYR cc_start: 0.8929 (t80) cc_final: 0.8201 (t80) REVERT: F 230 GLU cc_start: 0.8755 (mp0) cc_final: 0.8386 (mp0) REVERT: F 239 GLU cc_start: 0.8583 (tm-30) cc_final: 0.8207 (tm-30) REVERT: F 264 CYS cc_start: 0.9153 (t) cc_final: 0.8844 (t) REVERT: C 21 MET cc_start: 0.8780 (pmm) cc_final: 0.8449 (pmm) REVERT: C 40 ILE cc_start: 0.9660 (mm) cc_final: 0.9425 (mm) REVERT: C 99 HIS cc_start: 0.8712 (t-90) cc_final: 0.8323 (t-90) REVERT: C 205 PHE cc_start: 0.8617 (OUTLIER) cc_final: 0.8395 (t80) REVERT: C 229 TYR cc_start: 0.8844 (t80) cc_final: 0.8194 (t80) REVERT: C 230 GLU cc_start: 0.8764 (mp0) cc_final: 0.8345 (mp0) REVERT: C 233 ARG cc_start: 0.8790 (mmm-85) cc_final: 0.8436 (mmm-85) REVERT: C 239 GLU cc_start: 0.8612 (tm-30) cc_final: 0.8227 (tm-30) REVERT: D 21 MET cc_start: 0.8697 (pmm) cc_final: 0.8366 (pmm) REVERT: D 99 HIS cc_start: 0.8668 (t-90) cc_final: 0.8293 (t-90) REVERT: D 197 ARG cc_start: 0.8543 (ptm160) cc_final: 0.7904 (ttt180) REVERT: D 205 PHE cc_start: 0.8576 (OUTLIER) cc_final: 0.8368 (t80) REVERT: D 230 GLU cc_start: 0.8877 (mp0) cc_final: 0.8631 (mp0) REVERT: D 239 GLU cc_start: 0.8584 (tm-30) cc_final: 0.8226 (tm-30) outliers start: 67 outliers final: 52 residues processed: 364 average time/residue: 0.0881 time to fit residues: 43.4848 Evaluate side-chains 373 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 313 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 205 PHE Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 274 HIS Chi-restraints excluded: chain E residue 281 LYS Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 205 PHE Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 205 PHE Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 274 HIS Chi-restraints excluded: chain B residue 281 LYS Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 40 ILE Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 205 PHE Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 244 VAL Chi-restraints excluded: chain F residue 266 VAL Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 274 HIS Chi-restraints excluded: chain F residue 281 LYS Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 205 PHE Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 281 LYS Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 205 PHE Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 274 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 92 optimal weight: 9.9990 chunk 84 optimal weight: 0.9980 chunk 27 optimal weight: 7.9990 chunk 63 optimal weight: 20.0000 chunk 75 optimal weight: 10.0000 chunk 80 optimal weight: 0.9980 chunk 30 optimal weight: 8.9990 chunk 11 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 17 optimal weight: 20.0000 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 232 ASN ** F 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 232 ASN ** C 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.101528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.081097 restraints weight = 17914.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.084515 restraints weight = 7842.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.087046 restraints weight = 4806.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.088797 restraints weight = 3460.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.089909 restraints weight = 2732.870| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8964 Z= 0.162 Angle : 0.683 7.114 12114 Z= 0.360 Chirality : 0.045 0.195 1350 Planarity : 0.004 0.038 1440 Dihedral : 17.211 150.294 1500 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 6.45 % Allowed : 30.97 % Favored : 62.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.38 (0.24), residues: 1002 helix: 1.80 (0.17), residues: 726 sheet: 0.64 (0.56), residues: 60 loop : 1.40 (0.43), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 69 TYR 0.030 0.002 TYR C 234 PHE 0.009 0.001 PHE C 33 TRP 0.034 0.002 TRP D 277 HIS 0.007 0.002 HIS E 274 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 8946) covalent geometry : angle 0.68321 (12078) SS BOND : bond 0.00263 ( 18) SS BOND : angle 0.40139 ( 36) hydrogen bonds : bond 0.03884 ( 619) hydrogen bonds : angle 3.52351 ( 1839) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 319 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 21 MET cc_start: 0.8800 (pmm) cc_final: 0.8409 (pmm) REVERT: E 69 ARG cc_start: 0.8730 (mmm-85) cc_final: 0.8437 (mmm-85) REVERT: E 99 HIS cc_start: 0.8642 (t-90) cc_final: 0.8274 (t-90) REVERT: E 205 PHE cc_start: 0.8626 (OUTLIER) cc_final: 0.8414 (t80) REVERT: E 229 TYR cc_start: 0.8946 (t80) cc_final: 0.8705 (t80) REVERT: E 230 GLU cc_start: 0.8790 (mp0) cc_final: 0.8520 (mp0) REVERT: E 239 GLU cc_start: 0.8598 (tm-30) cc_final: 0.8164 (tm-30) REVERT: A 21 MET cc_start: 0.8727 (pmm) cc_final: 0.8301 (pmm) REVERT: A 69 ARG cc_start: 0.8778 (mmm-85) cc_final: 0.8577 (mmm-85) REVERT: A 99 HIS cc_start: 0.8710 (t-90) cc_final: 0.8374 (t-90) REVERT: A 205 PHE cc_start: 0.8673 (OUTLIER) cc_final: 0.8471 (t80) REVERT: A 230 GLU cc_start: 0.8905 (mp0) cc_final: 0.8689 (mp0) REVERT: A 239 GLU cc_start: 0.8570 (tm-30) cc_final: 0.8112 (tm-30) REVERT: B 99 HIS cc_start: 0.8633 (t-90) cc_final: 0.8279 (t-90) REVERT: B 205 PHE cc_start: 0.8629 (OUTLIER) cc_final: 0.8428 (t80) REVERT: B 229 TYR cc_start: 0.8580 (t80) cc_final: 0.8273 (t80) REVERT: B 230 GLU cc_start: 0.8919 (mp0) cc_final: 0.8591 (mp0) REVERT: B 239 GLU cc_start: 0.8642 (tm-30) cc_final: 0.8307 (tm-30) REVERT: F 36 LEU cc_start: 0.9626 (OUTLIER) cc_final: 0.9408 (tt) REVERT: F 40 ILE cc_start: 0.9661 (OUTLIER) cc_final: 0.9442 (mm) REVERT: F 46 TYR cc_start: 0.9151 (m-80) cc_final: 0.8688 (m-80) REVERT: F 69 ARG cc_start: 0.8747 (mmm-85) cc_final: 0.8402 (mmm-85) REVERT: F 99 HIS cc_start: 0.8731 (t-90) cc_final: 0.8372 (t-90) REVERT: F 205 PHE cc_start: 0.8659 (OUTLIER) cc_final: 0.8432 (t80) REVERT: F 229 TYR cc_start: 0.9004 (t80) cc_final: 0.8322 (t80) REVERT: F 230 GLU cc_start: 0.8777 (mp0) cc_final: 0.8360 (mp0) REVERT: F 239 GLU cc_start: 0.8588 (tm-30) cc_final: 0.8201 (tm-30) REVERT: F 264 CYS cc_start: 0.9162 (t) cc_final: 0.8872 (t) REVERT: C 21 MET cc_start: 0.8725 (pmm) cc_final: 0.8387 (pmm) REVERT: C 36 LEU cc_start: 0.9618 (OUTLIER) cc_final: 0.9374 (tt) REVERT: C 40 ILE cc_start: 0.9682 (mm) cc_final: 0.9395 (mm) REVERT: C 99 HIS cc_start: 0.8710 (t-90) cc_final: 0.8322 (t-90) REVERT: C 205 PHE cc_start: 0.8639 (OUTLIER) cc_final: 0.8422 (t80) REVERT: C 229 TYR cc_start: 0.8891 (t80) cc_final: 0.8217 (t80) REVERT: C 230 GLU cc_start: 0.8751 (mp0) cc_final: 0.8346 (mp0) REVERT: C 233 ARG cc_start: 0.8830 (mmm-85) cc_final: 0.8608 (mmm-85) REVERT: C 239 GLU cc_start: 0.8602 (tm-30) cc_final: 0.8218 (tm-30) REVERT: D 99 HIS cc_start: 0.8664 (t-90) cc_final: 0.8300 (t-90) REVERT: D 205 PHE cc_start: 0.8602 (OUTLIER) cc_final: 0.8392 (t80) REVERT: D 230 GLU cc_start: 0.8878 (mp0) cc_final: 0.8626 (mp0) REVERT: D 239 GLU cc_start: 0.8591 (tm-30) cc_final: 0.8243 (tm-30) outliers start: 60 outliers final: 50 residues processed: 353 average time/residue: 0.0856 time to fit residues: 40.9474 Evaluate side-chains 361 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 302 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 205 PHE Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 274 HIS Chi-restraints excluded: chain E residue 281 LYS Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 205 PHE Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 205 PHE Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 274 HIS Chi-restraints excluded: chain B residue 281 LYS Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 40 ILE Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 205 PHE Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 244 VAL Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 274 HIS Chi-restraints excluded: chain F residue 281 LYS Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 205 PHE Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 281 LYS Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 205 PHE Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 274 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 52 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 85 optimal weight: 8.9990 chunk 96 optimal weight: 4.9990 chunk 47 optimal weight: 0.0870 chunk 46 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 overall best weight: 1.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 ASN ** D 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.104717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.084331 restraints weight = 18456.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.087702 restraints weight = 8551.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.090055 restraints weight = 5342.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.091822 restraints weight = 3918.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.092834 restraints weight = 3096.590| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8964 Z= 0.148 Angle : 0.677 6.845 12114 Z= 0.356 Chirality : 0.045 0.194 1350 Planarity : 0.004 0.038 1440 Dihedral : 17.140 149.945 1500 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 6.02 % Allowed : 32.80 % Favored : 61.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.39 (0.24), residues: 1002 helix: 1.82 (0.17), residues: 726 sheet: 0.69 (0.58), residues: 60 loop : 1.30 (0.42), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 69 TYR 0.029 0.002 TYR C 234 PHE 0.013 0.001 PHE E 93 TRP 0.027 0.002 TRP C 277 HIS 0.007 0.002 HIS E 274 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 8946) covalent geometry : angle 0.67784 (12078) SS BOND : bond 0.00204 ( 18) SS BOND : angle 0.37952 ( 36) hydrogen bonds : bond 0.03808 ( 619) hydrogen bonds : angle 3.55440 ( 1839) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 315 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 21 MET cc_start: 0.8767 (pmm) cc_final: 0.8370 (pmm) REVERT: E 44 THR cc_start: 0.9164 (m) cc_final: 0.8957 (p) REVERT: E 69 ARG cc_start: 0.8698 (mmm-85) cc_final: 0.8327 (mmm-85) REVERT: E 99 HIS cc_start: 0.8645 (t-90) cc_final: 0.8256 (t-90) REVERT: E 205 PHE cc_start: 0.8615 (OUTLIER) cc_final: 0.8411 (t80) REVERT: E 230 GLU cc_start: 0.8752 (mp0) cc_final: 0.8489 (mp0) REVERT: E 239 GLU cc_start: 0.8581 (tm-30) cc_final: 0.8158 (tm-30) REVERT: A 21 MET cc_start: 0.8706 (pmm) cc_final: 0.8265 (pmm) REVERT: A 99 HIS cc_start: 0.8692 (t-90) cc_final: 0.8359 (t-90) REVERT: A 205 PHE cc_start: 0.8661 (OUTLIER) cc_final: 0.8459 (t80) REVERT: A 239 GLU cc_start: 0.8508 (tm-30) cc_final: 0.8093 (tm-30) REVERT: B 99 HIS cc_start: 0.8620 (t-90) cc_final: 0.8264 (t-90) REVERT: B 229 TYR cc_start: 0.8612 (t80) cc_final: 0.8325 (t80) REVERT: B 230 GLU cc_start: 0.8901 (mp0) cc_final: 0.8571 (mp0) REVERT: B 239 GLU cc_start: 0.8596 (tm-30) cc_final: 0.8275 (tm-30) REVERT: F 36 LEU cc_start: 0.9616 (OUTLIER) cc_final: 0.9412 (tt) REVERT: F 40 ILE cc_start: 0.9679 (OUTLIER) cc_final: 0.9470 (mm) REVERT: F 99 HIS cc_start: 0.8733 (t-90) cc_final: 0.8388 (t-90) REVERT: F 205 PHE cc_start: 0.8642 (OUTLIER) cc_final: 0.8427 (t80) REVERT: F 229 TYR cc_start: 0.8978 (t80) cc_final: 0.8238 (t80) REVERT: F 230 GLU cc_start: 0.8731 (mp0) cc_final: 0.8311 (mp0) REVERT: F 239 GLU cc_start: 0.8570 (tm-30) cc_final: 0.8228 (tm-30) REVERT: C 21 MET cc_start: 0.8716 (pmm) cc_final: 0.8383 (pmm) REVERT: C 36 LEU cc_start: 0.9607 (OUTLIER) cc_final: 0.9378 (tt) REVERT: C 40 ILE cc_start: 0.9692 (mm) cc_final: 0.9414 (mm) REVERT: C 99 HIS cc_start: 0.8705 (t-90) cc_final: 0.8328 (t-90) REVERT: C 205 PHE cc_start: 0.8623 (OUTLIER) cc_final: 0.8419 (t80) REVERT: C 229 TYR cc_start: 0.8915 (t80) cc_final: 0.8233 (t80) REVERT: C 230 GLU cc_start: 0.8695 (mp0) cc_final: 0.8281 (mp0) REVERT: C 239 GLU cc_start: 0.8566 (tm-30) cc_final: 0.8218 (tm-30) REVERT: D 21 MET cc_start: 0.8627 (pmm) cc_final: 0.8129 (pmm) REVERT: D 99 HIS cc_start: 0.8668 (t-90) cc_final: 0.8309 (t-90) REVERT: D 230 GLU cc_start: 0.8820 (mp0) cc_final: 0.8609 (mp0) REVERT: D 239 GLU cc_start: 0.8551 (tm-30) cc_final: 0.8151 (tm-30) outliers start: 56 outliers final: 45 residues processed: 347 average time/residue: 0.0959 time to fit residues: 44.9170 Evaluate side-chains 355 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 303 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 205 PHE Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 244 VAL Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 274 HIS Chi-restraints excluded: chain E residue 281 LYS Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain A residue 205 PHE Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 274 HIS Chi-restraints excluded: chain B residue 281 LYS Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 40 ILE Chi-restraints excluded: chain F residue 205 PHE Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 244 VAL Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 274 HIS Chi-restraints excluded: chain F residue 281 LYS Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 205 PHE Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 281 LYS Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 274 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 71 optimal weight: 0.0040 chunk 49 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 chunk 93 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 17 optimal weight: 20.0000 chunk 27 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 47 optimal weight: 0.0370 overall best weight: 1.2076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 232 ASN ** C 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.103384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.083129 restraints weight = 17779.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.086612 restraints weight = 7777.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.088869 restraints weight = 4736.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.090727 restraints weight = 3507.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.091692 restraints weight = 2735.722| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 8964 Z= 0.150 Angle : 0.685 7.183 12114 Z= 0.362 Chirality : 0.045 0.194 1350 Planarity : 0.004 0.037 1440 Dihedral : 16.959 149.670 1500 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 5.70 % Allowed : 33.87 % Favored : 60.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.37 (0.24), residues: 1002 helix: 1.81 (0.17), residues: 726 sheet: 0.69 (0.60), residues: 60 loop : 1.29 (0.42), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 69 TYR 0.031 0.002 TYR C 234 PHE 0.014 0.001 PHE D 93 TRP 0.033 0.002 TRP D 277 HIS 0.006 0.002 HIS E 274 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 8946) covalent geometry : angle 0.68610 (12078) SS BOND : bond 0.00178 ( 18) SS BOND : angle 0.37516 ( 36) hydrogen bonds : bond 0.03781 ( 619) hydrogen bonds : angle 3.56046 ( 1839) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 314 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 21 MET cc_start: 0.8858 (pmm) cc_final: 0.8459 (pmm) REVERT: E 44 THR cc_start: 0.9147 (m) cc_final: 0.8941 (p) REVERT: E 69 ARG cc_start: 0.8674 (mmm-85) cc_final: 0.8323 (mmm-85) REVERT: E 99 HIS cc_start: 0.8635 (t-90) cc_final: 0.8379 (t-90) REVERT: E 229 TYR cc_start: 0.8338 (t80) cc_final: 0.7913 (t80) REVERT: E 230 GLU cc_start: 0.8911 (mp0) cc_final: 0.8609 (mp0) REVERT: E 239 GLU cc_start: 0.8646 (tm-30) cc_final: 0.8227 (tm-30) REVERT: A 21 MET cc_start: 0.8802 (pmm) cc_final: 0.8346 (pmm) REVERT: A 99 HIS cc_start: 0.8699 (t-90) cc_final: 0.8368 (t-90) REVERT: A 239 GLU cc_start: 0.8603 (tm-30) cc_final: 0.8184 (tm-30) REVERT: B 41 VAL cc_start: 0.9466 (m) cc_final: 0.9229 (p) REVERT: B 69 ARG cc_start: 0.8801 (mmm-85) cc_final: 0.8461 (mmm-85) REVERT: B 99 HIS cc_start: 0.8633 (t-90) cc_final: 0.8316 (t-90) REVERT: B 229 TYR cc_start: 0.8494 (t80) cc_final: 0.8133 (t80) REVERT: B 230 GLU cc_start: 0.9024 (mp0) cc_final: 0.8630 (mp0) REVERT: B 239 GLU cc_start: 0.8662 (tm-30) cc_final: 0.8347 (tm-30) REVERT: F 36 LEU cc_start: 0.9596 (OUTLIER) cc_final: 0.9394 (tt) REVERT: F 40 ILE cc_start: 0.9645 (OUTLIER) cc_final: 0.9434 (mm) REVERT: F 69 ARG cc_start: 0.8657 (mmm-85) cc_final: 0.8203 (mmm-85) REVERT: F 99 HIS cc_start: 0.8734 (t-90) cc_final: 0.8390 (t-90) REVERT: F 229 TYR cc_start: 0.8852 (t80) cc_final: 0.8087 (t80) REVERT: F 230 GLU cc_start: 0.8879 (mp0) cc_final: 0.8389 (mp0) REVERT: F 239 GLU cc_start: 0.8630 (tm-30) cc_final: 0.8273 (tm-30) REVERT: C 21 MET cc_start: 0.8800 (pmm) cc_final: 0.8394 (pmm) REVERT: C 36 LEU cc_start: 0.9586 (OUTLIER) cc_final: 0.9357 (tt) REVERT: C 40 ILE cc_start: 0.9663 (mm) cc_final: 0.9377 (mm) REVERT: C 99 HIS cc_start: 0.8693 (t-90) cc_final: 0.8325 (t-90) REVERT: C 229 TYR cc_start: 0.8773 (t80) cc_final: 0.8047 (t80) REVERT: C 230 GLU cc_start: 0.8828 (mp0) cc_final: 0.8374 (mp0) REVERT: C 239 GLU cc_start: 0.8653 (tm-30) cc_final: 0.8280 (tm-30) REVERT: D 21 MET cc_start: 0.8738 (pmm) cc_final: 0.8254 (pmm) REVERT: D 99 HIS cc_start: 0.8653 (t-90) cc_final: 0.8319 (t-90) REVERT: D 230 GLU cc_start: 0.8960 (mp0) cc_final: 0.8656 (mp0) REVERT: D 233 ARG cc_start: 0.8689 (mmm-85) cc_final: 0.8346 (mmm-85) REVERT: D 239 GLU cc_start: 0.8632 (tm-30) cc_final: 0.8265 (tm-30) outliers start: 53 outliers final: 44 residues processed: 343 average time/residue: 0.0820 time to fit residues: 38.0025 Evaluate side-chains 350 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 303 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 274 HIS Chi-restraints excluded: chain E residue 281 LYS Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 274 HIS Chi-restraints excluded: chain B residue 281 LYS Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 40 ILE Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 244 VAL Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 274 HIS Chi-restraints excluded: chain F residue 281 LYS Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 281 LYS Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 274 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 44 optimal weight: 6.9990 chunk 66 optimal weight: 7.9990 chunk 52 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 42 optimal weight: 8.9990 chunk 85 optimal weight: 0.5980 chunk 64 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 ASN ** D 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.105981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.086403 restraints weight = 17533.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.089940 restraints weight = 7500.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.092580 restraints weight = 4448.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.094289 restraints weight = 3092.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.095547 restraints weight = 2424.302| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8964 Z= 0.147 Angle : 0.714 7.643 12114 Z= 0.372 Chirality : 0.045 0.192 1350 Planarity : 0.004 0.036 1440 Dihedral : 16.778 149.472 1500 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 15.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 5.27 % Allowed : 34.73 % Favored : 60.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.33 (0.24), residues: 1002 helix: 1.63 (0.17), residues: 738 sheet: 0.74 (0.62), residues: 60 loop : 1.87 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 69 TYR 0.031 0.001 TYR C 234 PHE 0.014 0.001 PHE D 93 TRP 0.078 0.003 TRP B 277 HIS 0.006 0.002 HIS E 274 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 8946) covalent geometry : angle 0.71490 (12078) SS BOND : bond 0.00141 ( 18) SS BOND : angle 0.40701 ( 36) hydrogen bonds : bond 0.03764 ( 619) hydrogen bonds : angle 3.56479 ( 1839) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 321 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 21 MET cc_start: 0.8754 (pmm) cc_final: 0.8373 (pmm) REVERT: E 44 THR cc_start: 0.9140 (m) cc_final: 0.8932 (p) REVERT: E 69 ARG cc_start: 0.8719 (mmm-85) cc_final: 0.8454 (mmm-85) REVERT: E 99 HIS cc_start: 0.8622 (t-90) cc_final: 0.8280 (t-90) REVERT: E 230 GLU cc_start: 0.8910 (mp0) cc_final: 0.8702 (mp0) REVERT: E 239 GLU cc_start: 0.8571 (tm-30) cc_final: 0.8267 (tm-30) REVERT: A 21 MET cc_start: 0.8732 (pmm) cc_final: 0.8269 (pmm) REVERT: A 22 ILE cc_start: 0.9437 (pt) cc_final: 0.9189 (pt) REVERT: A 99 HIS cc_start: 0.8690 (t-90) cc_final: 0.8361 (t-90) REVERT: A 239 GLU cc_start: 0.8543 (tm-30) cc_final: 0.8132 (tm-30) REVERT: B 69 ARG cc_start: 0.8830 (mmm-85) cc_final: 0.8558 (mmm-85) REVERT: B 99 HIS cc_start: 0.8695 (t-90) cc_final: 0.8343 (t-90) REVERT: B 229 TYR cc_start: 0.8520 (t80) cc_final: 0.8209 (t80) REVERT: B 230 GLU cc_start: 0.8988 (mp0) cc_final: 0.8573 (mp0) REVERT: B 239 GLU cc_start: 0.8608 (tm-30) cc_final: 0.8241 (tm-30) REVERT: F 40 ILE cc_start: 0.9656 (OUTLIER) cc_final: 0.9446 (mm) REVERT: F 69 ARG cc_start: 0.8621 (mmm-85) cc_final: 0.8167 (mmm-85) REVERT: F 229 TYR cc_start: 0.8847 (t80) cc_final: 0.8084 (t80) REVERT: F 230 GLU cc_start: 0.8844 (mp0) cc_final: 0.8353 (mp0) REVERT: F 239 GLU cc_start: 0.8588 (tm-30) cc_final: 0.8235 (tm-30) REVERT: C 21 MET cc_start: 0.8696 (pmm) cc_final: 0.8340 (pmm) REVERT: C 36 LEU cc_start: 0.9578 (OUTLIER) cc_final: 0.9365 (tt) REVERT: C 40 ILE cc_start: 0.9675 (mm) cc_final: 0.9372 (mm) REVERT: C 99 HIS cc_start: 0.8693 (t-90) cc_final: 0.8332 (t-90) REVERT: C 229 TYR cc_start: 0.8804 (t80) cc_final: 0.8056 (t80) REVERT: C 230 GLU cc_start: 0.8774 (mp0) cc_final: 0.8299 (mp0) REVERT: C 233 ARG cc_start: 0.8794 (mmm-85) cc_final: 0.8204 (mmt90) REVERT: C 239 GLU cc_start: 0.8596 (tm-30) cc_final: 0.8240 (tm-30) REVERT: D 21 MET cc_start: 0.8642 (pmm) cc_final: 0.8156 (pmm) REVERT: D 99 HIS cc_start: 0.8692 (t-90) cc_final: 0.8342 (t-90) REVERT: D 230 GLU cc_start: 0.8931 (mp0) cc_final: 0.8681 (mp0) REVERT: D 233 ARG cc_start: 0.8622 (mmm-85) cc_final: 0.8345 (mmm-85) REVERT: D 239 GLU cc_start: 0.8579 (tm-30) cc_final: 0.8155 (tm-30) outliers start: 49 outliers final: 43 residues processed: 344 average time/residue: 0.0854 time to fit residues: 39.6625 Evaluate side-chains 354 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 309 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 274 HIS Chi-restraints excluded: chain E residue 281 LYS Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain A residue 281 LYS Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 68 ASP Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 244 VAL Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 274 HIS Chi-restraints excluded: chain F residue 40 ILE Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 244 VAL Chi-restraints excluded: chain F residue 269 LEU Chi-restraints excluded: chain F residue 274 HIS Chi-restraints excluded: chain F residue 281 LYS Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 281 LYS Chi-restraints excluded: chain D residue 74 SER Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 274 HIS Chi-restraints excluded: chain D residue 281 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 101 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 chunk 80 optimal weight: 0.0040 chunk 89 optimal weight: 9.9990 chunk 0 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 49 optimal weight: 9.9990 chunk 78 optimal weight: 2.9990 chunk 50 optimal weight: 8.9990 overall best weight: 1.1798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 232 ASN ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 232 ASN ** C 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.100872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.080050 restraints weight = 17793.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.083533 restraints weight = 8072.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.086127 restraints weight = 4967.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.087795 restraints weight = 3565.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.089043 restraints weight = 2856.081| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8964 Z= 0.152 Angle : 0.725 8.758 12114 Z= 0.376 Chirality : 0.046 0.203 1350 Planarity : 0.004 0.036 1440 Dihedral : 16.514 149.393 1500 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 5.27 % Allowed : 36.24 % Favored : 58.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.31 (0.24), residues: 1002 helix: 1.63 (0.17), residues: 738 sheet: 0.78 (0.64), residues: 60 loop : 1.79 (0.41), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 69 TYR 0.040 0.002 TYR E 229 PHE 0.016 0.001 PHE D 93 TRP 0.026 0.002 TRP B 277 HIS 0.007 0.002 HIS C 274 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 8946) covalent geometry : angle 0.72572 (12078) SS BOND : bond 0.00166 ( 18) SS BOND : angle 0.41862 ( 36) hydrogen bonds : bond 0.03806 ( 619) hydrogen bonds : angle 3.56136 ( 1839) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1459.01 seconds wall clock time: 25 minutes 47.81 seconds (1547.81 seconds total)