Starting phenix.real_space_refine on Wed Mar 12 19:45:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dmi_27539/03_2025/8dmi_27539.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dmi_27539/03_2025/8dmi_27539.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dmi_27539/03_2025/8dmi_27539.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dmi_27539/03_2025/8dmi_27539.map" model { file = "/net/cci-nas-00/data/ceres_data/8dmi_27539/03_2025/8dmi_27539.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dmi_27539/03_2025/8dmi_27539.cif" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 81 5.16 5 C 5187 2.51 5 N 1347 2.21 5 O 1644 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8259 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1357 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain breaks: 3 Chain: "a" Number of atoms: 1200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1200 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 3, 'TRANS': 143} Chain breaks: 1 Chain: "B" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1357 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain breaks: 3 Chain: "b" Number of atoms: 1200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1200 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 3, 'TRANS': 143} Chain breaks: 1 Chain: "C" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1357 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain breaks: 3 Chain: "c" Number of atoms: 1200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1200 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 3, 'TRANS': 143} Chain breaks: 1 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "a" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "b" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "c" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.37, per 1000 atoms: 0.65 Number of scatterers: 8259 At special positions: 0 Unit cell: (88.11, 91.08, 92.07, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 81 16.00 O 1644 8.00 N 1347 7.00 C 5187 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 123 " - pdb=" SG CYS A 160 " distance=2.03 Simple disulfide: pdb=" SG CYS A 184 " - pdb=" SG CYS A 220 " distance=2.03 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS a 366 " distance=2.05 Simple disulfide: pdb=" SG CYS a 285 " - pdb=" SG CYS a 298 " distance=2.03 Simple disulfide: pdb=" SG CYS a 307 " - pdb=" SG CYS a 316 " distance=2.03 Simple disulfide: pdb=" SG CYS a 370 " - pdb=" SG CYS a 391 " distance=2.03 Simple disulfide: pdb=" SG CYS B 92 " - pdb=" SG CYS B 239 " distance=2.03 Simple disulfide: pdb=" SG CYS B 123 " - pdb=" SG CYS B 160 " distance=2.03 Simple disulfide: pdb=" SG CYS B 184 " - pdb=" SG CYS B 220 " distance=2.03 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS b 366 " distance=2.04 Simple disulfide: pdb=" SG CYS b 285 " - pdb=" SG CYS b 298 " distance=2.03 Simple disulfide: pdb=" SG CYS b 307 " - pdb=" SG CYS b 316 " distance=2.03 Simple disulfide: pdb=" SG CYS b 370 " - pdb=" SG CYS b 391 " distance=2.03 Simple disulfide: pdb=" SG CYS C 92 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 123 " - pdb=" SG CYS C 160 " distance=2.03 Simple disulfide: pdb=" SG CYS C 184 " - pdb=" SG CYS C 220 " distance=2.03 Simple disulfide: pdb=" SG CYS C 207 " - pdb=" SG CYS c 366 " distance=2.07 Simple disulfide: pdb=" SG CYS c 285 " - pdb=" SG CYS c 298 " distance=2.03 Simple disulfide: pdb=" SG CYS c 307 " - pdb=" SG CYS c 316 " distance=2.03 Simple disulfide: pdb=" SG CYS c 370 " - pdb=" SG CYS c 391 " 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 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A 301 " - " ASN A 124 " " NAG B 301 " - " ASN B 124 " " NAG C 301 " - " ASN C 124 " " NAG D 1 " - " ASN A 85 " " NAG E 1 " - " ASN A 95 " " NAG F 1 " - " ASN A 114 " " NAG G 1 " - " ASN A 171 " " NAG H 1 " - " ASN A 232 " " NAG I 1 " - " ASN a 371 " " NAG J 1 " - " ASN B 85 " " NAG K 1 " - " ASN B 95 " " NAG L 1 " - " ASN B 114 " " NAG M 1 " - " ASN B 171 " " NAG N 1 " - " ASN B 232 " " NAG O 1 " - " ASN b 371 " " NAG P 1 " - " ASN C 85 " " NAG Q 1 " - " ASN C 95 " " NAG R 1 " - " ASN C 114 " " NAG S 1 " - " ASN C 171 " " NAG T 1 " - " ASN C 232 " " NAG U 1 " - " ASN c 371 " " NAG a 701 " - " ASN a 401 " " NAG b 701 " - " ASN b 401 " " NAG c 701 " - " ASN c 401 " Time building additional restraints: 2.51 Conformation dependent library (CDL) restraints added in 893.0 milliseconds 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1818 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 9 sheets defined 35.3% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 136 through 148 Processing helix chain 'A' and resid 186 through 200 Processing helix chain 'A' and resid 244 through 253 Processing helix chain 'a' and resid 300 through 307 removed outlier: 4.153A pdb=" N VAL a 304 " --> pdb=" O GLY a 300 " (cutoff:3.500A) Processing helix chain 'a' and resid 313 through 330 removed outlier: 4.156A pdb=" N ASP a 317 " --> pdb=" O GLU a 313 " (cutoff:3.500A) Processing helix chain 'a' and resid 335 through 346 Processing helix chain 'a' and resid 352 through 365 Processing helix chain 'a' and resid 405 through 426 Processing helix chain 'B' and resid 136 through 148 Processing helix chain 'B' and resid 186 through 200 Processing helix chain 'B' and resid 244 through 253 Processing helix chain 'b' and resid 300 through 307 removed outlier: 4.154A pdb=" N VAL b 304 " --> pdb=" O GLY b 300 " (cutoff:3.500A) Processing helix chain 'b' and resid 313 through 330 removed outlier: 4.155A pdb=" N ASP b 317 " --> pdb=" O GLU b 313 " (cutoff:3.500A) Processing helix chain 'b' and resid 335 through 346 Processing helix chain 'b' and resid 352 through 365 Processing helix chain 'b' and resid 405 through 426 Processing helix chain 'C' and resid 136 through 148 Processing helix chain 'C' and resid 186 through 200 Processing helix chain 'C' and resid 244 through 253 Processing helix chain 'c' and resid 300 through 307 removed outlier: 4.154A pdb=" N VAL c 304 " --> pdb=" O GLY c 300 " (cutoff:3.500A) Processing helix chain 'c' and resid 313 through 330 removed outlier: 4.156A pdb=" N ASP c 317 " --> pdb=" O GLU c 313 " (cutoff:3.500A) Processing helix chain 'c' and resid 335 through 346 Processing helix chain 'c' and resid 352 through 365 Processing helix chain 'c' and resid 405 through 426 Processing sheet with id=AA1, first strand: chain 'A' and resid 72 through 78 removed outlier: 3.527A pdb=" N GLU a 379 " --> pdb=" O GLN A 73 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 89 through 93 Processing sheet with id=AA3, first strand: chain 'a' and resid 394 through 395 Processing sheet with id=AA4, first strand: chain 'B' and resid 72 through 78 removed outlier: 3.510A pdb=" N GLU b 379 " --> pdb=" O GLN B 73 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 89 through 93 Processing sheet with id=AA6, first strand: chain 'b' and resid 394 through 395 Processing sheet with id=AA7, first strand: chain 'C' and resid 72 through 78 Processing sheet with id=AA8, first strand: chain 'C' and resid 89 through 93 Processing sheet with id=AA9, first strand: chain 'c' and resid 394 through 395 328 hydrogen bonds defined for protein. 939 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.12 Time building geometry restraints manager: 2.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2067 1.33 - 1.45: 1924 1.45 - 1.58: 4307 1.58 - 1.70: 6 1.70 - 1.82: 120 Bond restraints: 8424 Sorted by residual: bond pdb=" CB ASN B 114 " pdb=" CG ASN B 114 " ideal model delta sigma weight residual 1.516 1.609 -0.093 2.50e-02 1.60e+03 1.39e+01 bond pdb=" CB ASN C 114 " pdb=" CG ASN C 114 " ideal model delta sigma weight residual 1.516 1.609 -0.093 2.50e-02 1.60e+03 1.38e+01 bond pdb=" CB ASN A 114 " pdb=" CG ASN A 114 " ideal model delta sigma weight residual 1.516 1.608 -0.092 2.50e-02 1.60e+03 1.37e+01 bond pdb=" CA ASN A 114 " pdb=" CB ASN A 114 " ideal model delta sigma weight residual 1.530 1.565 -0.035 1.54e-02 4.22e+03 5.07e+00 bond pdb=" CA ASN C 114 " pdb=" CB ASN C 114 " ideal model delta sigma weight residual 1.530 1.564 -0.034 1.54e-02 4.22e+03 4.98e+00 ... (remaining 8419 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 11051 2.10 - 4.21: 250 4.21 - 6.31: 54 6.31 - 8.41: 6 8.41 - 10.52: 9 Bond angle restraints: 11370 Sorted by residual: angle pdb=" CA ASN A 114 " pdb=" CB ASN A 114 " pdb=" CG ASN A 114 " ideal model delta sigma weight residual 112.60 119.82 -7.22 1.00e+00 1.00e+00 5.21e+01 angle pdb=" CA ASN B 114 " pdb=" CB ASN B 114 " pdb=" CG ASN B 114 " ideal model delta sigma weight residual 112.60 119.77 -7.17 1.00e+00 1.00e+00 5.14e+01 angle pdb=" CA ASN C 114 " pdb=" CB ASN C 114 " pdb=" CG ASN C 114 " ideal model delta sigma weight residual 112.60 119.76 -7.16 1.00e+00 1.00e+00 5.13e+01 angle pdb=" N ILE C 117 " pdb=" CA ILE C 117 " pdb=" C ILE C 117 " ideal model delta sigma weight residual 113.71 109.94 3.77 9.50e-01 1.11e+00 1.57e+01 angle pdb=" N ILE A 117 " pdb=" CA ILE A 117 " pdb=" C ILE A 117 " ideal model delta sigma weight residual 113.71 109.95 3.76 9.50e-01 1.11e+00 1.57e+01 ... (remaining 11365 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.99: 4872 16.99 - 33.98: 509 33.98 - 50.97: 126 50.97 - 67.96: 55 67.96 - 84.96: 9 Dihedral angle restraints: 5571 sinusoidal: 2772 harmonic: 2799 Sorted by residual: dihedral pdb=" CB CYS B 207 " pdb=" SG CYS B 207 " pdb=" SG CYS b 366 " pdb=" CB CYS b 366 " ideal model delta sinusoidal sigma weight residual -86.00 -170.96 84.96 1 1.00e+01 1.00e-02 8.76e+01 dihedral pdb=" CB CYS B 123 " pdb=" SG CYS B 123 " pdb=" SG CYS B 160 " pdb=" CB CYS B 160 " ideal model delta sinusoidal sigma weight residual 93.00 8.85 84.15 1 1.00e+01 1.00e-02 8.62e+01 dihedral pdb=" CB CYS A 123 " pdb=" SG CYS A 123 " pdb=" SG CYS A 160 " pdb=" CB CYS A 160 " ideal model delta sinusoidal sigma weight residual 93.00 8.87 84.13 1 1.00e+01 1.00e-02 8.62e+01 ... (remaining 5568 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 1245 0.079 - 0.157: 100 0.157 - 0.236: 17 0.236 - 0.315: 6 0.315 - 0.393: 6 Chirality restraints: 1374 Sorted by residual: chirality pdb=" C5 NAG R 1 " pdb=" C4 NAG R 1 " pdb=" C6 NAG R 1 " pdb=" O5 NAG R 1 " both_signs ideal model delta sigma weight residual False -2.41 -2.02 -0.39 2.00e-01 2.50e+01 3.86e+00 chirality pdb=" C5 NAG F 1 " pdb=" C4 NAG F 1 " pdb=" C6 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.41 -2.02 -0.39 2.00e-01 2.50e+01 3.83e+00 chirality pdb=" C5 NAG L 1 " pdb=" C4 NAG L 1 " pdb=" C6 NAG L 1 " pdb=" O5 NAG L 1 " both_signs ideal model delta sigma weight residual False -2.41 -2.02 -0.39 2.00e-01 2.50e+01 3.80e+00 ... (remaining 1371 not shown) Planarity restraints: 1389 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 114 " 0.053 2.00e-02 2.50e+03 6.31e-02 4.98e+01 pdb=" CG ASN C 114 " -0.123 2.00e-02 2.50e+03 pdb=" OD1 ASN C 114 " 0.033 2.00e-02 2.50e+03 pdb=" ND2 ASN C 114 " 0.009 2.00e-02 2.50e+03 pdb=" C1 NAG R 1 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 114 " 0.053 2.00e-02 2.50e+03 6.29e-02 4.95e+01 pdb=" CG ASN B 114 " -0.123 2.00e-02 2.50e+03 pdb=" OD1 ASN B 114 " 0.033 2.00e-02 2.50e+03 pdb=" ND2 ASN B 114 " 0.008 2.00e-02 2.50e+03 pdb=" C1 NAG L 1 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 114 " 0.053 2.00e-02 2.50e+03 6.28e-02 4.92e+01 pdb=" CG ASN A 114 " -0.122 2.00e-02 2.50e+03 pdb=" OD1 ASN A 114 " 0.033 2.00e-02 2.50e+03 pdb=" ND2 ASN A 114 " 0.008 2.00e-02 2.50e+03 pdb=" C1 NAG F 1 " 0.028 2.00e-02 2.50e+03 ... (remaining 1386 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 188 2.67 - 3.23: 7787 3.23 - 3.79: 12362 3.79 - 4.34: 16892 4.34 - 4.90: 28171 Nonbonded interactions: 65400 Sorted by model distance: nonbonded pdb=" ND1 HIS a 380 " pdb=" OG1 THR a 383 " model vdw 2.117 3.120 nonbonded pdb=" ND1 HIS c 380 " pdb=" OG1 THR c 383 " model vdw 2.118 3.120 nonbonded pdb=" ND1 HIS b 380 " pdb=" OG1 THR b 383 " model vdw 2.118 3.120 nonbonded pdb=" OG SER B 82 " pdb=" O7 NAG J 1 " model vdw 2.306 3.040 nonbonded pdb=" OG SER A 82 " pdb=" O7 NAG D 1 " model vdw 2.306 3.040 ... (remaining 65395 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 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.150 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: 0.000 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.340 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 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 : 0.004 0.093 8424 Z= 0.263 Angle : 0.815 10.517 11370 Z= 0.439 Chirality : 0.055 0.393 1374 Planarity : 0.009 0.119 1365 Dihedral : 14.468 68.731 3690 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.27), residues: 915 helix: 0.58 (0.28), residues: 351 sheet: -0.12 (0.54), residues: 93 loop : -2.10 (0.25), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 219 HIS 0.013 0.002 HIS B 136 PHE 0.016 0.002 PHE B 187 TYR 0.063 0.002 TYR A 227 ARG 0.031 0.003 ARG B 188 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 0.831 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.2575 time to fit residues: 68.2687 Evaluate side-chains 141 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 4.9990 chunk 70 optimal weight: 9.9990 chunk 39 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 72 optimal weight: 6.9990 chunk 28 optimal weight: 0.3980 chunk 44 optimal weight: 8.9990 chunk 54 optimal weight: 0.8980 chunk 84 optimal weight: 5.9990 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 359 ASN C 73 GLN C 237 ASN c 359 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.060251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.048313 restraints weight = 31518.713| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 4.28 r_work: 0.2747 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8424 Z= 0.262 Angle : 0.702 9.497 11370 Z= 0.358 Chirality : 0.046 0.246 1374 Planarity : 0.004 0.030 1365 Dihedral : 9.383 56.723 1899 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 0.69 % Allowed : 9.49 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.27), residues: 915 helix: 1.48 (0.28), residues: 357 sheet: 0.29 (0.56), residues: 90 loop : -1.71 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP c 392 HIS 0.007 0.001 HIS C 238 PHE 0.015 0.002 PHE C 122 TYR 0.020 0.001 TYR A 227 ARG 0.008 0.001 ARG C 190 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 160 time to evaluate : 0.930 Fit side-chains REVERT: A 72 TYR cc_start: 0.8909 (m-80) cc_final: 0.8583 (m-80) REVERT: A 103 MET cc_start: 0.9403 (tpt) cc_final: 0.9106 (tpt) REVERT: A 183 GLN cc_start: 0.7322 (mm110) cc_final: 0.7072 (mm110) REVERT: a 310 ASN cc_start: 0.8353 (t0) cc_final: 0.7183 (t0) REVERT: a 313 GLU cc_start: 0.8210 (mp0) cc_final: 0.7477 (mp0) REVERT: a 414 ASP cc_start: 0.9118 (m-30) cc_final: 0.8878 (p0) REVERT: B 72 TYR cc_start: 0.9095 (m-80) cc_final: 0.8883 (m-80) REVERT: B 168 ILE cc_start: 0.9497 (mt) cc_final: 0.9277 (mm) REVERT: b 310 ASN cc_start: 0.8077 (t0) cc_final: 0.7237 (t0) REVERT: b 412 GLU cc_start: 0.8962 (tp30) cc_final: 0.8685 (tp30) REVERT: b 416 MET cc_start: 0.9431 (ttp) cc_final: 0.9149 (ttp) REVERT: C 103 MET cc_start: 0.9369 (tpt) cc_final: 0.8405 (tpp) REVERT: C 222 GLN cc_start: 0.9155 (mm110) cc_final: 0.8947 (mm-40) REVERT: C 254 GLN cc_start: 0.8986 (tt0) cc_final: 0.8712 (pm20) REVERT: c 310 ASN cc_start: 0.8139 (t0) cc_final: 0.6974 (t0) outliers start: 6 outliers final: 4 residues processed: 163 average time/residue: 0.2159 time to fit residues: 47.4210 Evaluate side-chains 146 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 142 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain a residue 304 VAL Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain c residue 299 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 29 optimal weight: 7.9990 chunk 67 optimal weight: 0.3980 chunk 39 optimal weight: 10.0000 chunk 5 optimal weight: 8.9990 chunk 64 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 2 optimal weight: 0.5980 chunk 76 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.060941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.049248 restraints weight = 31415.597| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 4.28 r_work: 0.2768 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8424 Z= 0.170 Angle : 0.625 9.535 11370 Z= 0.318 Chirality : 0.045 0.246 1374 Planarity : 0.003 0.027 1365 Dihedral : 8.577 56.590 1899 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.81 % Allowed : 10.07 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.28), residues: 915 helix: 1.71 (0.29), residues: 339 sheet: 0.44 (0.58), residues: 90 loop : -1.37 (0.26), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP b 392 HIS 0.005 0.001 HIS B 238 PHE 0.012 0.001 PHE C 122 TYR 0.015 0.001 TYR A 227 ARG 0.004 0.001 ARG a 358 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 163 time to evaluate : 0.853 Fit side-chains revert: symmetry clash REVERT: A 103 MET cc_start: 0.9320 (tpt) cc_final: 0.8899 (tpt) REVERT: A 139 MET cc_start: 0.8807 (tpp) cc_final: 0.8590 (tmm) REVERT: A 156 LYS cc_start: 0.8929 (mmmm) cc_final: 0.8546 (mmmm) REVERT: a 310 ASN cc_start: 0.8402 (t0) cc_final: 0.7094 (t0) REVERT: a 313 GLU cc_start: 0.8354 (mp0) cc_final: 0.7609 (mp0) REVERT: a 414 ASP cc_start: 0.9122 (m-30) cc_final: 0.8872 (p0) REVERT: B 72 TYR cc_start: 0.8973 (m-80) cc_final: 0.8661 (m-80) REVERT: b 310 ASN cc_start: 0.8114 (t0) cc_final: 0.7302 (t0) REVERT: b 412 GLU cc_start: 0.8895 (tp30) cc_final: 0.8623 (tp30) REVERT: b 416 MET cc_start: 0.9409 (ttp) cc_final: 0.9121 (ttp) REVERT: C 103 MET cc_start: 0.9361 (tpt) cc_final: 0.9116 (tpt) REVERT: C 156 LYS cc_start: 0.8880 (mmtm) cc_final: 0.8559 (mmmm) REVERT: C 222 GLN cc_start: 0.9192 (mm110) cc_final: 0.8973 (mm-40) REVERT: c 310 ASN cc_start: 0.8234 (t0) cc_final: 0.7090 (t0) REVERT: c 385 GLU cc_start: 0.8967 (tp30) cc_final: 0.8456 (tp30) outliers start: 7 outliers final: 4 residues processed: 166 average time/residue: 0.2005 time to fit residues: 45.1910 Evaluate side-chains 146 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 142 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain b residue 304 VAL Chi-restraints excluded: chain c residue 299 PHE Chi-restraints excluded: chain c residue 364 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 45 optimal weight: 9.9990 chunk 19 optimal weight: 0.0070 chunk 1 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 55 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 overall best weight: 2.1404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.058506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.046605 restraints weight = 32016.621| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 4.26 r_work: 0.2702 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8424 Z= 0.259 Angle : 0.667 9.461 11370 Z= 0.336 Chirality : 0.045 0.246 1374 Planarity : 0.004 0.056 1365 Dihedral : 8.157 57.200 1899 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.74 % Allowed : 12.04 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.28), residues: 915 helix: 1.85 (0.29), residues: 339 sheet: 0.79 (0.58), residues: 90 loop : -1.30 (0.26), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP c 392 HIS 0.004 0.001 HIS a 311 PHE 0.014 0.001 PHE B 245 TYR 0.025 0.001 TYR A 72 ARG 0.005 0.001 ARG C 205 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 147 time to evaluate : 0.972 Fit side-chains revert: symmetry clash REVERT: A 72 TYR cc_start: 0.8682 (m-80) cc_final: 0.8432 (m-80) REVERT: A 103 MET cc_start: 0.9343 (tpt) cc_final: 0.8845 (tpt) REVERT: A 156 LYS cc_start: 0.9006 (mmmm) cc_final: 0.8616 (mmmm) REVERT: A 256 LYS cc_start: 0.7274 (mmtt) cc_final: 0.6975 (mmtm) REVERT: a 310 ASN cc_start: 0.8596 (t0) cc_final: 0.7318 (t0) REVERT: a 313 GLU cc_start: 0.8446 (mp0) cc_final: 0.7681 (mp0) REVERT: a 416 MET cc_start: 0.9470 (ttp) cc_final: 0.9080 (tmm) REVERT: B 72 TYR cc_start: 0.9103 (m-80) cc_final: 0.8704 (m-80) REVERT: b 310 ASN cc_start: 0.8268 (t0) cc_final: 0.7479 (t0) REVERT: b 402 GLU cc_start: 0.9078 (mp0) cc_final: 0.8866 (mp0) REVERT: b 412 GLU cc_start: 0.9010 (tp30) cc_final: 0.8715 (tp30) REVERT: b 416 MET cc_start: 0.9452 (ttp) cc_final: 0.9139 (ttp) REVERT: C 78 GLU cc_start: 0.8213 (tp30) cc_final: 0.7998 (pm20) REVERT: C 103 MET cc_start: 0.9396 (tpt) cc_final: 0.9101 (tpt) REVERT: C 139 MET cc_start: 0.8973 (tpp) cc_final: 0.8643 (tmm) REVERT: C 156 LYS cc_start: 0.8919 (mmtm) cc_final: 0.8575 (mmmm) REVERT: c 310 ASN cc_start: 0.8267 (t0) cc_final: 0.7271 (t0) REVERT: c 362 ARG cc_start: 0.9014 (mmm-85) cc_final: 0.8764 (mtt-85) REVERT: c 385 GLU cc_start: 0.8995 (tp30) cc_final: 0.8689 (tp30) outliers start: 15 outliers final: 11 residues processed: 151 average time/residue: 0.2062 time to fit residues: 42.3479 Evaluate side-chains 154 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 143 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain a residue 304 VAL Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain b residue 304 VAL Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain c residue 299 PHE Chi-restraints excluded: chain c residue 364 LEU Chi-restraints excluded: chain c residue 411 GLN Chi-restraints excluded: chain c residue 417 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 47 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 72 optimal weight: 10.0000 chunk 31 optimal weight: 8.9990 chunk 32 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 73 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.057568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.045681 restraints weight = 31928.031| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 4.27 r_work: 0.2681 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8424 Z= 0.231 Angle : 0.649 9.438 11370 Z= 0.326 Chirality : 0.045 0.243 1374 Planarity : 0.004 0.049 1365 Dihedral : 7.597 57.144 1899 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.31 % Allowed : 11.92 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.28), residues: 915 helix: 1.84 (0.30), residues: 339 sheet: 0.49 (0.59), residues: 96 loop : -1.27 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 235 HIS 0.005 0.001 HIS c 311 PHE 0.012 0.001 PHE B 245 TYR 0.020 0.001 TYR A 241 ARG 0.005 0.001 ARG c 358 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 146 time to evaluate : 1.044 Fit side-chains REVERT: A 103 MET cc_start: 0.9335 (tpt) cc_final: 0.8673 (tpt) REVERT: A 109 GLU cc_start: 0.9335 (OUTLIER) cc_final: 0.8629 (tm-30) REVERT: A 139 MET cc_start: 0.8900 (tpp) cc_final: 0.8611 (tmm) REVERT: a 310 ASN cc_start: 0.8590 (t0) cc_final: 0.7468 (t0) REVERT: a 313 GLU cc_start: 0.8458 (mp0) cc_final: 0.7593 (mp0) REVERT: a 353 ASP cc_start: 0.8918 (p0) cc_final: 0.8658 (p0) REVERT: a 414 ASP cc_start: 0.9138 (m-30) cc_final: 0.8851 (p0) REVERT: a 416 MET cc_start: 0.9469 (ttp) cc_final: 0.8970 (tmm) REVERT: B 156 LYS cc_start: 0.8955 (mmmm) cc_final: 0.8700 (mmmm) REVERT: b 310 ASN cc_start: 0.8418 (t0) cc_final: 0.7622 (t0) REVERT: b 412 GLU cc_start: 0.9001 (tp30) cc_final: 0.8734 (tp30) REVERT: b 416 MET cc_start: 0.9456 (ttp) cc_final: 0.9169 (ttp) REVERT: C 78 GLU cc_start: 0.8241 (tp30) cc_final: 0.8016 (pm20) REVERT: C 103 MET cc_start: 0.9428 (tpt) cc_final: 0.9068 (tpt) REVERT: C 156 LYS cc_start: 0.8950 (mmtm) cc_final: 0.8663 (mmmm) REVERT: c 310 ASN cc_start: 0.8510 (t0) cc_final: 0.7584 (t0) REVERT: c 362 ARG cc_start: 0.9076 (mmm-85) cc_final: 0.8843 (mtt-85) REVERT: c 379 GLU cc_start: 0.8871 (pt0) cc_final: 0.8524 (pt0) REVERT: c 385 GLU cc_start: 0.8981 (tp30) cc_final: 0.8473 (tp30) outliers start: 20 outliers final: 11 residues processed: 153 average time/residue: 0.2246 time to fit residues: 46.9451 Evaluate side-chains 148 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 136 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain a residue 357 MET Chi-restraints excluded: chain a residue 412 GLU Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain b residue 304 VAL Chi-restraints excluded: chain b residue 354 GLN Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain c residue 299 PHE Chi-restraints excluded: chain c residue 364 LEU Chi-restraints excluded: chain c residue 417 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 62 optimal weight: 8.9990 chunk 81 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 89 optimal weight: 9.9990 chunk 13 optimal weight: 6.9990 chunk 52 optimal weight: 0.6980 chunk 60 optimal weight: 8.9990 chunk 72 optimal weight: 9.9990 chunk 51 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 overall best weight: 2.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN A 183 GLN B 90 ASN B 183 GLN C 183 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.056418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.044787 restraints weight = 31994.928| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 4.23 r_work: 0.2647 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.3788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8424 Z= 0.278 Angle : 0.679 10.642 11370 Z= 0.340 Chirality : 0.045 0.241 1374 Planarity : 0.004 0.054 1365 Dihedral : 7.461 57.399 1899 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.31 % Allowed : 13.43 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.28), residues: 915 helix: 1.84 (0.29), residues: 336 sheet: 0.74 (0.61), residues: 96 loop : -1.36 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP b 392 HIS 0.006 0.001 HIS B 238 PHE 0.013 0.001 PHE B 245 TYR 0.014 0.001 TYR A 72 ARG 0.004 0.001 ARG C 196 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 144 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.9239 (mtp) cc_final: 0.9020 (mtp) REVERT: A 103 MET cc_start: 0.9366 (tpt) cc_final: 0.8674 (tpt) REVERT: A 109 GLU cc_start: 0.9372 (OUTLIER) cc_final: 0.8668 (tm-30) REVERT: A 256 LYS cc_start: 0.7326 (mmtt) cc_final: 0.7066 (mmtt) REVERT: a 290 MET cc_start: 0.9069 (mtt) cc_final: 0.8856 (mtt) REVERT: a 310 ASN cc_start: 0.8752 (t0) cc_final: 0.7669 (t0) REVERT: a 313 GLU cc_start: 0.8548 (mp0) cc_final: 0.7734 (mp0) REVERT: a 379 GLU cc_start: 0.8834 (pt0) cc_final: 0.8536 (pt0) REVERT: a 416 MET cc_start: 0.9425 (ttp) cc_final: 0.9149 (tmm) REVERT: B 72 TYR cc_start: 0.9126 (m-80) cc_final: 0.8800 (m-80) REVERT: B 156 LYS cc_start: 0.9024 (mmmm) cc_final: 0.8730 (mmmm) REVERT: b 310 ASN cc_start: 0.8511 (t0) cc_final: 0.7649 (t0) REVERT: b 379 GLU cc_start: 0.8780 (pt0) cc_final: 0.8490 (pt0) REVERT: b 412 GLU cc_start: 0.9018 (tp30) cc_final: 0.8726 (tp30) REVERT: C 103 MET cc_start: 0.9431 (tpt) cc_final: 0.9037 (tpt) REVERT: C 156 LYS cc_start: 0.8983 (mmtm) cc_final: 0.8691 (mmmm) REVERT: c 310 ASN cc_start: 0.8594 (t0) cc_final: 0.7675 (t0) REVERT: c 379 GLU cc_start: 0.8841 (pt0) cc_final: 0.8527 (pt0) outliers start: 20 outliers final: 14 residues processed: 151 average time/residue: 0.2044 time to fit residues: 41.8645 Evaluate side-chains 157 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 142 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain a residue 304 VAL Chi-restraints excluded: chain a residue 357 MET Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain b residue 304 VAL Chi-restraints excluded: chain b residue 354 GLN Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain c residue 299 PHE Chi-restraints excluded: chain c residue 364 LEU Chi-restraints excluded: chain c residue 416 MET Chi-restraints excluded: chain c residue 417 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 57 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 88 optimal weight: 5.9990 chunk 67 optimal weight: 9.9990 chunk 89 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 29 optimal weight: 8.9990 chunk 7 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.056684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.045072 restraints weight = 31986.012| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 4.26 r_work: 0.2655 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8424 Z= 0.241 Angle : 0.682 9.828 11370 Z= 0.338 Chirality : 0.045 0.240 1374 Planarity : 0.004 0.047 1365 Dihedral : 7.384 57.272 1899 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.43 % Allowed : 14.81 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.28), residues: 915 helix: 1.81 (0.29), residues: 336 sheet: 0.78 (0.61), residues: 96 loop : -1.38 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP a 392 HIS 0.007 0.001 HIS C 238 PHE 0.011 0.001 PHE B 245 TYR 0.016 0.001 TYR A 72 ARG 0.005 0.000 ARG c 358 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 146 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.9243 (mtp) cc_final: 0.9038 (mtp) REVERT: A 103 MET cc_start: 0.9344 (tpt) cc_final: 0.8641 (tpt) REVERT: A 109 GLU cc_start: 0.9387 (OUTLIER) cc_final: 0.8692 (tm-30) REVERT: A 139 MET cc_start: 0.8960 (tpp) cc_final: 0.8306 (ttt) REVERT: A 256 LYS cc_start: 0.7241 (mmtt) cc_final: 0.6990 (mmtt) REVERT: a 290 MET cc_start: 0.9043 (mtt) cc_final: 0.8813 (mtt) REVERT: a 310 ASN cc_start: 0.8775 (t0) cc_final: 0.7700 (t0) REVERT: a 313 GLU cc_start: 0.8546 (mp0) cc_final: 0.7723 (mp0) REVERT: a 379 GLU cc_start: 0.8849 (pt0) cc_final: 0.8558 (pt0) REVERT: a 416 MET cc_start: 0.9408 (ttp) cc_final: 0.9017 (tmm) REVERT: B 156 LYS cc_start: 0.8963 (mmmm) cc_final: 0.8674 (mmmm) REVERT: b 310 ASN cc_start: 0.8573 (t0) cc_final: 0.7602 (t0) REVERT: b 379 GLU cc_start: 0.8787 (pt0) cc_final: 0.8481 (pt0) REVERT: b 412 GLU cc_start: 0.9021 (tp30) cc_final: 0.8733 (tp30) REVERT: C 103 MET cc_start: 0.9431 (tpt) cc_final: 0.9020 (tpt) REVERT: C 156 LYS cc_start: 0.8988 (mmtm) cc_final: 0.8695 (mmmm) REVERT: C 172 LEU cc_start: 0.9528 (tp) cc_final: 0.9147 (tt) REVERT: c 310 ASN cc_start: 0.8532 (t0) cc_final: 0.7589 (t0) REVERT: c 379 GLU cc_start: 0.8878 (pt0) cc_final: 0.8544 (pt0) outliers start: 21 outliers final: 13 residues processed: 156 average time/residue: 0.2492 time to fit residues: 53.8393 Evaluate side-chains 154 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 140 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain a residue 304 VAL Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain b residue 354 GLN Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain c residue 299 PHE Chi-restraints excluded: chain c residue 349 SER Chi-restraints excluded: chain c residue 351 ILE Chi-restraints excluded: chain c residue 364 LEU Chi-restraints excluded: chain c residue 416 MET Chi-restraints excluded: chain c residue 417 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 33 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 36 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 51 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 27 optimal weight: 9.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 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 = 0.3183 r_free = 0.3183 target = 0.057212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.045657 restraints weight = 32142.770| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 4.24 r_work: 0.2678 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.4018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8424 Z= 0.203 Angle : 0.675 9.450 11370 Z= 0.336 Chirality : 0.044 0.241 1374 Planarity : 0.004 0.042 1365 Dihedral : 7.291 57.185 1899 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.85 % Allowed : 15.74 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.28), residues: 915 helix: 1.82 (0.30), residues: 336 sheet: 0.10 (0.53), residues: 114 loop : -1.19 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 219 HIS 0.006 0.001 HIS C 238 PHE 0.009 0.001 PHE A 245 TYR 0.014 0.001 TYR A 72 ARG 0.005 0.000 ARG c 358 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 148 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 TYR cc_start: 0.9062 (m-80) cc_final: 0.8448 (m-80) REVERT: A 88 MET cc_start: 0.9234 (OUTLIER) cc_final: 0.9030 (mtp) REVERT: A 103 MET cc_start: 0.9310 (tpt) cc_final: 0.8695 (tpt) REVERT: A 109 GLU cc_start: 0.9380 (OUTLIER) cc_final: 0.8688 (tm-30) REVERT: A 139 MET cc_start: 0.8955 (tpp) cc_final: 0.8425 (tmm) REVERT: a 310 ASN cc_start: 0.8749 (t0) cc_final: 0.7638 (t0) REVERT: a 313 GLU cc_start: 0.8581 (mp0) cc_final: 0.7723 (mp0) REVERT: a 379 GLU cc_start: 0.8864 (pt0) cc_final: 0.8565 (pt0) REVERT: a 416 MET cc_start: 0.9426 (ttp) cc_final: 0.8705 (tmm) REVERT: B 72 TYR cc_start: 0.8808 (m-80) cc_final: 0.8360 (m-80) REVERT: B 156 LYS cc_start: 0.8990 (mmmm) cc_final: 0.8618 (mmmm) REVERT: b 310 ASN cc_start: 0.8602 (t0) cc_final: 0.7668 (t0) REVERT: b 379 GLU cc_start: 0.8818 (pt0) cc_final: 0.8521 (pt0) REVERT: b 412 GLU cc_start: 0.9000 (tp30) cc_final: 0.8721 (tp30) REVERT: b 416 MET cc_start: 0.9433 (ttp) cc_final: 0.9151 (tmm) REVERT: C 103 MET cc_start: 0.9415 (tpt) cc_final: 0.9045 (tpt) REVERT: C 156 LYS cc_start: 0.8982 (mmtm) cc_final: 0.8697 (mmmm) REVERT: C 172 LEU cc_start: 0.9505 (tp) cc_final: 0.9144 (tt) REVERT: c 310 ASN cc_start: 0.8551 (t0) cc_final: 0.7618 (t0) REVERT: c 354 GLN cc_start: 0.8881 (pt0) cc_final: 0.8679 (pt0) REVERT: c 379 GLU cc_start: 0.8879 (pt0) cc_final: 0.8573 (pt0) REVERT: c 385 GLU cc_start: 0.8966 (tp30) cc_final: 0.8520 (tp30) outliers start: 16 outliers final: 10 residues processed: 154 average time/residue: 0.2748 time to fit residues: 57.6605 Evaluate side-chains 154 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 142 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain a residue 304 VAL Chi-restraints excluded: chain a residue 349 SER Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain b residue 354 GLN Chi-restraints excluded: chain c residue 299 PHE Chi-restraints excluded: chain c residue 364 LEU Chi-restraints excluded: chain c residue 416 MET Chi-restraints excluded: chain c residue 417 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 50 optimal weight: 7.9990 chunk 15 optimal weight: 7.9990 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 3 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 13 optimal weight: 7.9990 chunk 41 optimal weight: 8.9990 chunk 26 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 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 = 0.3149 r_free = 0.3149 target = 0.055917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.044362 restraints weight = 32659.808| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 4.25 r_work: 0.2637 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.4194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8424 Z= 0.298 Angle : 0.734 9.340 11370 Z= 0.363 Chirality : 0.045 0.239 1374 Planarity : 0.004 0.051 1365 Dihedral : 7.404 57.305 1899 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.74 % Allowed : 16.20 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.29), residues: 915 helix: 1.52 (0.29), residues: 354 sheet: 0.22 (0.54), residues: 114 loop : -1.23 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP a 392 HIS 0.010 0.001 HIS B 238 PHE 0.012 0.001 PHE B 245 TYR 0.015 0.001 TYR A 72 ARG 0.004 0.001 ARG C 196 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 141 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.9248 (OUTLIER) cc_final: 0.9024 (mtp) REVERT: A 103 MET cc_start: 0.9328 (tpt) cc_final: 0.8779 (tpt) REVERT: A 109 GLU cc_start: 0.9402 (OUTLIER) cc_final: 0.8691 (tm-30) REVERT: a 310 ASN cc_start: 0.8799 (t0) cc_final: 0.7778 (t0) REVERT: a 313 GLU cc_start: 0.8595 (mp0) cc_final: 0.7747 (mp0) REVERT: a 379 GLU cc_start: 0.8857 (pt0) cc_final: 0.8538 (pt0) REVERT: B 72 TYR cc_start: 0.8895 (m-80) cc_final: 0.8451 (m-80) REVERT: B 156 LYS cc_start: 0.9068 (mmmm) cc_final: 0.8696 (mmmm) REVERT: b 310 ASN cc_start: 0.8643 (t0) cc_final: 0.7741 (t0) REVERT: b 379 GLU cc_start: 0.8803 (pt0) cc_final: 0.8496 (pt0) REVERT: b 412 GLU cc_start: 0.9041 (tp30) cc_final: 0.8769 (tp30) REVERT: b 416 MET cc_start: 0.9465 (ttp) cc_final: 0.9142 (tmm) REVERT: C 103 MET cc_start: 0.9441 (tpt) cc_final: 0.9059 (tpt) REVERT: C 156 LYS cc_start: 0.9062 (mmtm) cc_final: 0.8772 (mmmm) REVERT: C 172 LEU cc_start: 0.9542 (tp) cc_final: 0.9121 (tt) REVERT: c 310 ASN cc_start: 0.8554 (t0) cc_final: 0.7702 (t0) REVERT: c 379 GLU cc_start: 0.8869 (pt0) cc_final: 0.8502 (pt0) REVERT: c 385 GLU cc_start: 0.8991 (tp30) cc_final: 0.8547 (tp30) outliers start: 15 outliers final: 12 residues processed: 146 average time/residue: 0.2650 time to fit residues: 52.5352 Evaluate side-chains 152 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 138 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain a residue 304 VAL Chi-restraints excluded: chain a residue 349 SER Chi-restraints excluded: chain a residue 412 GLU Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain b residue 354 GLN Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain c residue 299 PHE Chi-restraints excluded: chain c residue 349 SER Chi-restraints excluded: chain c residue 364 LEU Chi-restraints excluded: chain c residue 416 MET Chi-restraints excluded: chain c residue 417 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 46 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 67 optimal weight: 20.0000 chunk 23 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 62 optimal weight: 8.9990 chunk 88 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.054854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.043258 restraints weight = 32038.130| |-----------------------------------------------------------------------------| r_work (start): 0.2771 rms_B_bonded: 4.28 r_work: 0.2599 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.4442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 8424 Z= 0.364 Angle : 0.774 10.728 11370 Z= 0.383 Chirality : 0.046 0.237 1374 Planarity : 0.004 0.050 1365 Dihedral : 7.628 57.466 1899 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 1.97 % Allowed : 15.51 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.28), residues: 915 helix: 1.36 (0.29), residues: 354 sheet: 0.32 (0.55), residues: 114 loop : -1.36 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP c 392 HIS 0.009 0.001 HIS C 238 PHE 0.013 0.001 PHE C 245 TYR 0.011 0.001 TYR A 241 ARG 0.005 0.001 ARG A 196 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 144 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 GLU cc_start: 0.7784 (pm20) cc_final: 0.7342 (pm20) REVERT: A 88 MET cc_start: 0.9255 (OUTLIER) cc_final: 0.9047 (mtp) REVERT: A 103 MET cc_start: 0.9334 (tpt) cc_final: 0.8695 (tpt) REVERT: a 310 ASN cc_start: 0.8845 (t0) cc_final: 0.7837 (t0) REVERT: a 313 GLU cc_start: 0.8628 (mp0) cc_final: 0.7813 (mp0) REVERT: a 379 GLU cc_start: 0.8866 (pt0) cc_final: 0.8562 (pt0) REVERT: a 416 MET cc_start: 0.9473 (ttp) cc_final: 0.9159 (tmm) REVERT: B 72 TYR cc_start: 0.9008 (m-80) cc_final: 0.8592 (m-80) REVERT: B 156 LYS cc_start: 0.9119 (mmmm) cc_final: 0.8799 (mmmt) REVERT: b 310 ASN cc_start: 0.8728 (t0) cc_final: 0.7887 (t0) REVERT: b 379 GLU cc_start: 0.8827 (pt0) cc_final: 0.8533 (pt0) REVERT: b 412 GLU cc_start: 0.9076 (tp30) cc_final: 0.8807 (tp30) REVERT: b 416 MET cc_start: 0.9472 (ttp) cc_final: 0.9151 (tmm) REVERT: C 78 GLU cc_start: 0.7921 (pm20) cc_final: 0.7112 (pm20) REVERT: C 103 MET cc_start: 0.9448 (tpt) cc_final: 0.8981 (tpt) REVERT: C 156 LYS cc_start: 0.9150 (mmtm) cc_final: 0.8856 (mmmm) REVERT: c 310 ASN cc_start: 0.8665 (t0) cc_final: 0.7879 (t0) REVERT: c 379 GLU cc_start: 0.8882 (pt0) cc_final: 0.8500 (pt0) outliers start: 17 outliers final: 13 residues processed: 149 average time/residue: 0.2232 time to fit residues: 44.6737 Evaluate side-chains 154 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 140 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain a residue 304 VAL Chi-restraints excluded: chain a residue 349 SER Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain b residue 354 GLN Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain c residue 299 PHE Chi-restraints excluded: chain c residue 349 SER Chi-restraints excluded: chain c residue 364 LEU Chi-restraints excluded: chain c residue 416 MET Chi-restraints excluded: chain c residue 417 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 51 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 67 optimal weight: 7.9990 chunk 27 optimal weight: 7.9990 chunk 30 optimal weight: 0.9980 chunk 53 optimal weight: 8.9990 chunk 64 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 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 = 0.3145 r_free = 0.3145 target = 0.055767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.044205 restraints weight = 32186.060| |-----------------------------------------------------------------------------| r_work (start): 0.2804 rms_B_bonded: 4.26 r_work: 0.2632 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.4463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8424 Z= 0.239 Angle : 0.728 9.563 11370 Z= 0.364 Chirality : 0.045 0.240 1374 Planarity : 0.004 0.079 1365 Dihedral : 7.580 57.343 1899 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.74 % Allowed : 16.20 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.28), residues: 915 helix: 1.41 (0.29), residues: 354 sheet: 0.31 (0.54), residues: 114 loop : -1.34 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 219 HIS 0.008 0.001 HIS B 238 PHE 0.010 0.001 PHE A 245 TYR 0.017 0.001 TYR A 241 ARG 0.005 0.000 ARG c 358 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3174.59 seconds wall clock time: 56 minutes 32.23 seconds (3392.23 seconds total)