Starting phenix.real_space_refine on Sat Jul 26 01:39:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dmi_27539/07_2025/8dmi_27539.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dmi_27539/07_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_27539/07_2025/8dmi_27539.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dmi_27539/07_2025/8dmi_27539.map" model { file = "/net/cci-nas-00/data/ceres_data/8dmi_27539/07_2025/8dmi_27539.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dmi_27539/07_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-5711/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: 7.14, per 1000 atoms: 0.86 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: 2.82 Conformation dependent library (CDL) restraints added in 943.3 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: 0.90 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: 3.17 Time building geometry restraints manager: 3.22 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: 0.06 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: 0.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 25.290 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.070 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:5.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.270 ------------------------------------------------------------------------------- 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 8487 Z= 0.197 Angle : 0.885 14.733 11538 Z= 0.461 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 Details of bonding type rmsd link_NAG-ASN : bond 0.02360 ( 24) link_NAG-ASN : angle 2.58800 ( 72) link_BETA1-4 : bond 0.00760 ( 18) link_BETA1-4 : angle 1.83548 ( 54) hydrogen bonds : bond 0.14553 ( 328) hydrogen bonds : angle 5.00084 ( 939) SS BOND : bond 0.01059 ( 21) SS BOND : angle 4.44360 ( 42) covalent geometry : bond 0.00391 ( 8424) covalent geometry : angle 0.81468 (11370) *********************** 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 : 1.044 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.3203 time to fit residues: 85.1388 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 : 0.902 ------------------------------------------------------------------------------- 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: 0.4980 chunk 44 optimal weight: 8.9990 chunk 54 optimal weight: 0.8980 chunk 84 optimal weight: 5.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- 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 = 0.060308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.048290 restraints weight = 31567.076| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 4.28 r_work: 0.2742 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8487 Z= 0.193 Angle : 0.735 9.536 11538 Z= 0.367 Chirality : 0.046 0.238 1374 Planarity : 0.004 0.031 1365 Dihedral : 9.318 56.750 1899 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 0.81 % Allowed : 9.26 % Favored : 89.93 % 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: -0.28 (0.27), residues: 915 helix: 1.48 (0.28), residues: 357 sheet: 0.31 (0.56), residues: 90 loop : -1.71 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP c 392 HIS 0.007 0.001 HIS A 238 PHE 0.015 0.002 PHE C 122 TYR 0.020 0.001 TYR A 227 ARG 0.009 0.001 ARG C 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00312 ( 24) link_NAG-ASN : angle 1.82079 ( 72) link_BETA1-4 : bond 0.00408 ( 18) link_BETA1-4 : angle 1.62465 ( 54) hydrogen bonds : bond 0.04026 ( 328) hydrogen bonds : angle 4.05253 ( 939) SS BOND : bond 0.00521 ( 21) SS BOND : angle 1.89093 ( 42) covalent geometry : bond 0.00417 ( 8424) covalent geometry : angle 0.70766 (11370) *********************** 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 167 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 160 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 TYR cc_start: 0.8898 (m-80) cc_final: 0.8567 (m-80) REVERT: A 103 MET cc_start: 0.9403 (tpt) cc_final: 0.9108 (tpt) REVERT: A 183 GLN cc_start: 0.7327 (mm110) cc_final: 0.7071 (mm110) REVERT: a 310 ASN cc_start: 0.8389 (t0) cc_final: 0.7229 (t0) REVERT: a 313 GLU cc_start: 0.8210 (mp0) cc_final: 0.7488 (mp0) REVERT: a 414 ASP cc_start: 0.9123 (m-30) cc_final: 0.8879 (p0) REVERT: B 72 TYR cc_start: 0.9090 (m-80) cc_final: 0.8817 (m-80) REVERT: B 168 ILE cc_start: 0.9498 (mt) cc_final: 0.9281 (mm) REVERT: b 310 ASN cc_start: 0.8056 (t0) cc_final: 0.7214 (t0) REVERT: b 412 GLU cc_start: 0.8968 (tp30) cc_final: 0.8685 (tp30) REVERT: b 416 MET cc_start: 0.9431 (ttp) cc_final: 0.9152 (ttp) REVERT: C 103 MET cc_start: 0.9374 (tpt) cc_final: 0.9171 (tpt) REVERT: C 183 GLN cc_start: 0.7502 (mm110) cc_final: 0.7297 (mm110) REVERT: C 222 GLN cc_start: 0.9149 (mm110) cc_final: 0.8935 (mm-40) REVERT: C 254 GLN cc_start: 0.8982 (tt0) cc_final: 0.8701 (pm20) REVERT: c 310 ASN cc_start: 0.8169 (t0) cc_final: 0.6996 (t0) REVERT: c 313 GLU cc_start: 0.8209 (mp0) cc_final: 0.7577 (mp0) REVERT: c 402 GLU cc_start: 0.9033 (mp0) cc_final: 0.8825 (mp0) outliers start: 7 outliers final: 4 residues processed: 164 average time/residue: 0.2119 time to fit residues: 46.9374 Evaluate side-chains 148 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 144 time to evaluate : 0.926 ------------------------------------------------------------------------------- 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: 6.9990 chunk 67 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 chunk 5 optimal weight: 8.9990 chunk 64 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 92 optimal weight: 10.0000 chunk 2 optimal weight: 0.8980 chunk 76 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 = 0.3222 r_free = 0.3222 target = 0.059038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.047157 restraints weight = 31694.541| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 4.31 r_work: 0.2713 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8487 Z= 0.170 Angle : 0.667 9.459 11538 Z= 0.334 Chirality : 0.045 0.245 1374 Planarity : 0.004 0.039 1365 Dihedral : 8.427 56.984 1899 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.04 % Allowed : 10.53 % Favored : 88.43 % 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: 0.05 (0.28), residues: 915 helix: 1.73 (0.29), residues: 339 sheet: 0.56 (0.58), residues: 90 loop : -1.39 (0.26), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP b 392 HIS 0.005 0.001 HIS A 238 PHE 0.013 0.001 PHE C 245 TYR 0.016 0.001 TYR A 227 ARG 0.004 0.001 ARG b 362 Details of bonding type rmsd link_NAG-ASN : bond 0.00319 ( 24) link_NAG-ASN : angle 1.67463 ( 72) link_BETA1-4 : bond 0.00289 ( 18) link_BETA1-4 : angle 1.54603 ( 54) hydrogen bonds : bond 0.03735 ( 328) hydrogen bonds : angle 3.78841 ( 939) SS BOND : bond 0.00418 ( 21) SS BOND : angle 1.71908 ( 42) covalent geometry : bond 0.00371 ( 8424) covalent geometry : angle 0.64124 (11370) *********************** 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 161 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 152 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 TYR cc_start: 0.8862 (m-80) cc_final: 0.8656 (m-80) REVERT: A 103 MET cc_start: 0.9356 (tpt) cc_final: 0.8817 (tpt) REVERT: A 139 MET cc_start: 0.8925 (tpp) cc_final: 0.8654 (tmm) REVERT: A 156 LYS cc_start: 0.8969 (mmmm) cc_final: 0.8565 (mmmm) REVERT: a 310 ASN cc_start: 0.8572 (t0) cc_final: 0.7310 (t0) REVERT: a 313 GLU cc_start: 0.8356 (mp0) cc_final: 0.7592 (mp0) REVERT: a 364 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8889 (mm) REVERT: a 414 ASP cc_start: 0.9140 (m-30) cc_final: 0.8850 (p0) REVERT: B 72 TYR cc_start: 0.9106 (m-80) cc_final: 0.8736 (m-80) REVERT: B 168 ILE cc_start: 0.9537 (mt) cc_final: 0.9321 (mm) REVERT: b 310 ASN cc_start: 0.8279 (t0) cc_final: 0.7492 (t0) REVERT: b 323 ASP cc_start: 0.9330 (t0) cc_final: 0.9107 (t0) REVERT: b 412 GLU cc_start: 0.8963 (tp30) cc_final: 0.8703 (tp30) REVERT: b 416 MET cc_start: 0.9425 (ttp) cc_final: 0.9092 (ttp) REVERT: C 103 MET cc_start: 0.9408 (tpt) cc_final: 0.9109 (tpt) REVERT: C 156 LYS cc_start: 0.8961 (mmmm) cc_final: 0.8727 (mmmm) REVERT: C 222 GLN cc_start: 0.9186 (mm110) cc_final: 0.8310 (mm-40) REVERT: c 310 ASN cc_start: 0.8420 (t0) cc_final: 0.7214 (t0) REVERT: c 313 GLU cc_start: 0.8412 (mp0) cc_final: 0.7703 (mp0) REVERT: c 402 GLU cc_start: 0.9079 (mp0) cc_final: 0.8842 (mp0) outliers start: 9 outliers final: 7 residues processed: 156 average time/residue: 0.2223 time to fit residues: 46.8095 Evaluate side-chains 147 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 139 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain a residue 364 LEU 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 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: 6.9990 chunk 19 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 86 optimal weight: 9.9990 chunk 82 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 53 optimal weight: 8.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- 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 = 0.3161 r_free = 0.3161 target = 0.056363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.044430 restraints weight = 32216.404| |-----------------------------------------------------------------------------| r_work (start): 0.2805 rms_B_bonded: 4.24 r_work: 0.2638 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 8487 Z= 0.260 Angle : 0.749 9.374 11538 Z= 0.368 Chirality : 0.046 0.241 1374 Planarity : 0.005 0.069 1365 Dihedral : 8.078 57.630 1899 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.20 % Allowed : 12.50 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.28), residues: 915 helix: 1.81 (0.29), residues: 336 sheet: -0.08 (0.52), residues: 114 loop : -1.34 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP b 392 HIS 0.005 0.001 HIS c 311 PHE 0.019 0.002 PHE B 245 TYR 0.015 0.001 TYR A 227 ARG 0.009 0.001 ARG B 205 Details of bonding type rmsd link_NAG-ASN : bond 0.00261 ( 24) link_NAG-ASN : angle 1.77387 ( 72) link_BETA1-4 : bond 0.00299 ( 18) link_BETA1-4 : angle 1.62067 ( 54) hydrogen bonds : bond 0.03968 ( 328) hydrogen bonds : angle 3.84775 ( 939) SS BOND : bond 0.00570 ( 21) SS BOND : angle 2.20430 ( 42) covalent geometry : bond 0.00565 ( 8424) covalent geometry : angle 0.72031 (11370) *********************** 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 166 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 147 time to evaluate : 0.939 Fit side-chains revert: symmetry clash REVERT: A 103 MET cc_start: 0.9393 (tpt) cc_final: 0.8663 (tpt) REVERT: A 156 LYS cc_start: 0.9083 (mmmm) cc_final: 0.8703 (mmmm) REVERT: A 256 LYS cc_start: 0.7353 (mmtt) cc_final: 0.7057 (mmtt) REVERT: a 310 ASN cc_start: 0.8621 (t0) cc_final: 0.7440 (t0) REVERT: a 313 GLU cc_start: 0.8370 (mp0) cc_final: 0.7589 (mp0) REVERT: B 168 ILE cc_start: 0.9643 (mt) cc_final: 0.9440 (mm) REVERT: b 310 ASN cc_start: 0.8412 (t0) cc_final: 0.7640 (t0) REVERT: b 323 ASP cc_start: 0.9396 (t0) cc_final: 0.9174 (t0) REVERT: b 412 GLU cc_start: 0.9057 (tp30) cc_final: 0.8776 (tp30) REVERT: b 416 MET cc_start: 0.9470 (ttp) cc_final: 0.9123 (ttp) REVERT: C 78 GLU cc_start: 0.8235 (tp30) cc_final: 0.7997 (pm20) REVERT: C 103 MET cc_start: 0.9459 (tpt) cc_final: 0.9054 (tpt) REVERT: C 156 LYS cc_start: 0.9010 (mmmm) cc_final: 0.8710 (mmmm) REVERT: c 310 ASN cc_start: 0.8502 (t0) cc_final: 0.7316 (t0) REVERT: c 313 GLU cc_start: 0.8539 (mp0) cc_final: 0.7765 (mp0) REVERT: c 362 ARG cc_start: 0.9104 (mmm-85) cc_final: 0.8873 (mtt-85) REVERT: c 402 GLU cc_start: 0.9126 (mp0) cc_final: 0.8867 (mp0) outliers start: 19 outliers final: 10 residues processed: 153 average time/residue: 0.2204 time to fit residues: 45.3999 Evaluate side-chains 151 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 141 time to evaluate : 0.885 ------------------------------------------------------------------------------- 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 351 ILE 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: 0.8980 chunk 86 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 72 optimal weight: 7.9990 chunk 31 optimal weight: 7.9990 chunk 32 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 30 optimal weight: 8.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 GLN B 183 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.057732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.046054 restraints weight = 31269.802| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 4.25 r_work: 0.2681 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.3565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8487 Z= 0.139 Angle : 0.687 9.501 11538 Z= 0.339 Chirality : 0.045 0.245 1374 Planarity : 0.004 0.051 1365 Dihedral : 7.722 57.263 1899 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.50 % Allowed : 14.24 % 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: 0.14 (0.28), residues: 915 helix: 1.89 (0.29), residues: 336 sheet: 0.51 (0.60), residues: 96 loop : -1.38 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP a 392 HIS 0.006 0.001 HIS A 238 PHE 0.010 0.001 PHE B 245 TYR 0.011 0.001 TYR B 227 ARG 0.004 0.001 ARG B 205 Details of bonding type rmsd link_NAG-ASN : bond 0.00387 ( 24) link_NAG-ASN : angle 1.72215 ( 72) link_BETA1-4 : bond 0.00335 ( 18) link_BETA1-4 : angle 1.56248 ( 54) hydrogen bonds : bond 0.03464 ( 328) hydrogen bonds : angle 3.65659 ( 939) SS BOND : bond 0.00386 ( 21) SS BOND : angle 2.00836 ( 42) covalent geometry : bond 0.00301 ( 8424) covalent geometry : angle 0.65844 (11370) *********************** 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 160 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 147 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 MET cc_start: 0.9373 (tpt) cc_final: 0.8678 (tpt) REVERT: A 109 GLU cc_start: 0.9357 (tt0) cc_final: 0.8705 (tm-30) REVERT: A 139 MET cc_start: 0.8841 (tpp) cc_final: 0.8576 (tmm) REVERT: a 290 MET cc_start: 0.8998 (mtt) cc_final: 0.8753 (mtt) REVERT: a 310 ASN cc_start: 0.8645 (t0) cc_final: 0.7509 (t0) REVERT: a 313 GLU cc_start: 0.8469 (mp0) cc_final: 0.7650 (mp0) REVERT: a 379 GLU cc_start: 0.8818 (pt0) cc_final: 0.8544 (pt0) REVERT: a 414 ASP cc_start: 0.9120 (m-30) cc_final: 0.8841 (p0) REVERT: b 310 ASN cc_start: 0.8437 (t0) cc_final: 0.7673 (t0) REVERT: b 323 ASP cc_start: 0.9399 (t0) cc_final: 0.9137 (t0) REVERT: b 412 GLU cc_start: 0.8989 (tp30) cc_final: 0.8728 (tp30) REVERT: C 103 MET cc_start: 0.9423 (tpt) cc_final: 0.8939 (tpt) REVERT: C 156 LYS cc_start: 0.9038 (mmmm) cc_final: 0.8701 (mmmm) REVERT: C 172 LEU cc_start: 0.9499 (tp) cc_final: 0.9079 (tt) REVERT: c 310 ASN cc_start: 0.8554 (t0) cc_final: 0.7354 (t0) REVERT: c 313 GLU cc_start: 0.8635 (mp0) cc_final: 0.7872 (mp0) REVERT: c 362 ARG cc_start: 0.9066 (mmm-85) cc_final: 0.8820 (mtt-85) REVERT: c 379 GLU cc_start: 0.8825 (pt0) cc_final: 0.8434 (pt0) REVERT: c 385 GLU cc_start: 0.8990 (tp30) cc_final: 0.8616 (tp30) REVERT: c 402 GLU cc_start: 0.9132 (mp0) cc_final: 0.8869 (mp0) outliers start: 13 outliers final: 8 residues processed: 152 average time/residue: 0.2184 time to fit residues: 45.6363 Evaluate side-chains 146 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 138 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain a residue 304 VAL 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 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: 10.0000 chunk 81 optimal weight: 7.9990 chunk 23 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 13 optimal weight: 8.9990 chunk 52 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 72 optimal weight: 7.9990 chunk 51 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN C 183 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.056920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.045110 restraints weight = 31748.011| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 4.31 r_work: 0.2651 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.3795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8487 Z= 0.171 Angle : 0.691 10.371 11538 Z= 0.341 Chirality : 0.044 0.242 1374 Planarity : 0.004 0.052 1365 Dihedral : 7.527 57.299 1899 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.20 % Allowed : 14.93 % Favored : 82.87 % 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: 1.85 (0.29), residues: 336 sheet: 0.03 (0.53), residues: 114 loop : -1.28 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP a 392 HIS 0.005 0.001 HIS C 238 PHE 0.010 0.001 PHE B 245 TYR 0.010 0.001 TYR A 227 ARG 0.004 0.000 ARG c 358 Details of bonding type rmsd link_NAG-ASN : bond 0.00275 ( 24) link_NAG-ASN : angle 1.70374 ( 72) link_BETA1-4 : bond 0.00291 ( 18) link_BETA1-4 : angle 1.62044 ( 54) hydrogen bonds : bond 0.03535 ( 328) hydrogen bonds : angle 3.66281 ( 939) SS BOND : bond 0.00454 ( 21) SS BOND : angle 1.97244 ( 42) covalent geometry : bond 0.00374 ( 8424) covalent geometry : angle 0.66302 (11370) *********************** 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: 19 poor density : 145 time to evaluate : 0.913 Fit side-chains revert: symmetry clash REVERT: A 103 MET cc_start: 0.9377 (tpt) cc_final: 0.8668 (tpt) REVERT: A 109 GLU cc_start: 0.9383 (OUTLIER) cc_final: 0.8727 (tm-30) REVERT: A 139 MET cc_start: 0.8898 (tpp) cc_final: 0.8526 (tmm) REVERT: A 256 LYS cc_start: 0.7150 (mmtt) cc_final: 0.6789 (mmtt) REVERT: a 310 ASN cc_start: 0.8705 (t0) cc_final: 0.7632 (t0) REVERT: a 313 GLU cc_start: 0.8534 (mp0) cc_final: 0.7725 (mp0) REVERT: a 364 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.9021 (mm) REVERT: a 379 GLU cc_start: 0.8844 (pt0) cc_final: 0.8513 (pt0) REVERT: a 414 ASP cc_start: 0.9140 (m-30) cc_final: 0.8913 (p0) REVERT: a 416 MET cc_start: 0.9470 (ttp) cc_final: 0.9226 (tmm) REVERT: b 310 ASN cc_start: 0.8559 (t0) cc_final: 0.7690 (t0) REVERT: b 323 ASP cc_start: 0.9423 (t0) cc_final: 0.9156 (t0) REVERT: b 379 GLU cc_start: 0.8779 (pt0) cc_final: 0.8461 (pt0) REVERT: b 412 GLU cc_start: 0.9006 (tp30) cc_final: 0.8724 (tp30) REVERT: C 103 MET cc_start: 0.9435 (tpt) cc_final: 0.9002 (tpt) REVERT: C 156 LYS cc_start: 0.9078 (mmmm) cc_final: 0.8761 (mmmm) REVERT: C 172 LEU cc_start: 0.9526 (tp) cc_final: 0.9140 (tt) REVERT: c 310 ASN cc_start: 0.8568 (t0) cc_final: 0.7395 (t0) REVERT: c 313 GLU cc_start: 0.8660 (mp0) cc_final: 0.7865 (mp0) REVERT: c 362 ARG cc_start: 0.9102 (mmm-85) cc_final: 0.8856 (mtt-85) REVERT: c 379 GLU cc_start: 0.8857 (pt0) cc_final: 0.8538 (pt0) REVERT: c 385 GLU cc_start: 0.9002 (tp30) cc_final: 0.8627 (tp30) REVERT: c 402 GLU cc_start: 0.9154 (mp0) cc_final: 0.8880 (mp0) outliers start: 19 outliers final: 11 residues processed: 154 average time/residue: 0.2099 time to fit residues: 44.2029 Evaluate side-chains 157 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 144 time to evaluate : 0.849 ------------------------------------------------------------------------------- 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 364 LEU 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 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 417 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 57 optimal weight: 1.9990 chunk 72 optimal weight: 8.9990 chunk 32 optimal weight: 0.8980 chunk 88 optimal weight: 6.9990 chunk 67 optimal weight: 10.0000 chunk 89 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 30 optimal weight: 8.9990 chunk 29 optimal weight: 9.9990 chunk 7 optimal weight: 4.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN B 164 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.054558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.042873 restraints weight = 32276.841| |-----------------------------------------------------------------------------| r_work (start): 0.2754 rms_B_bonded: 4.25 r_work: 0.2583 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.4265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.039 8487 Z= 0.310 Angle : 0.806 9.271 11538 Z= 0.394 Chirality : 0.047 0.240 1374 Planarity : 0.004 0.059 1365 Dihedral : 7.807 57.604 1899 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 3.01 % Allowed : 14.58 % 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: -0.10 (0.28), residues: 915 helix: 1.61 (0.29), residues: 336 sheet: 0.23 (0.55), residues: 114 loop : -1.49 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP a 392 HIS 0.008 0.002 HIS c 311 PHE 0.017 0.002 PHE B 245 TYR 0.014 0.001 TYR c 372 ARG 0.005 0.001 ARG C 196 Details of bonding type rmsd link_NAG-ASN : bond 0.00344 ( 24) link_NAG-ASN : angle 1.97103 ( 72) link_BETA1-4 : bond 0.00361 ( 18) link_BETA1-4 : angle 1.80608 ( 54) hydrogen bonds : bond 0.04419 ( 328) hydrogen bonds : angle 3.99247 ( 939) SS BOND : bond 0.00602 ( 21) SS BOND : angle 2.47169 ( 42) covalent geometry : bond 0.00680 ( 8424) covalent geometry : angle 0.77282 (11370) *********************** 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 175 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 149 time to evaluate : 0.841 Fit side-chains revert: symmetry clash REVERT: A 72 TYR cc_start: 0.9136 (m-80) cc_final: 0.8854 (m-80) REVERT: A 103 MET cc_start: 0.9402 (tpt) cc_final: 0.8579 (tpt) REVERT: A 256 LYS cc_start: 0.7361 (mmtt) cc_final: 0.7098 (mmtt) REVERT: a 290 MET cc_start: 0.9101 (mtt) cc_final: 0.8893 (mtt) REVERT: a 310 ASN cc_start: 0.8799 (t0) cc_final: 0.7800 (t0) REVERT: a 313 GLU cc_start: 0.8527 (mp0) cc_final: 0.7709 (mp0) REVERT: a 364 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.9086 (mm) REVERT: a 414 ASP cc_start: 0.9199 (m-30) cc_final: 0.8985 (p0) REVERT: a 416 MET cc_start: 0.9472 (ttp) cc_final: 0.9082 (tmm) REVERT: B 72 TYR cc_start: 0.9152 (m-80) cc_final: 0.8862 (m-80) REVERT: b 310 ASN cc_start: 0.8707 (t0) cc_final: 0.7811 (t0) REVERT: b 379 GLU cc_start: 0.8768 (pt0) cc_final: 0.8443 (pt0) REVERT: b 412 GLU cc_start: 0.9084 (tp30) cc_final: 0.8816 (tp30) REVERT: b 416 MET cc_start: 0.9463 (ttp) cc_final: 0.9154 (tmm) REVERT: C 103 MET cc_start: 0.9459 (tpt) cc_final: 0.8968 (tpt) REVERT: C 156 LYS cc_start: 0.9154 (mmmm) cc_final: 0.8862 (mmmm) REVERT: c 310 ASN cc_start: 0.8720 (t0) cc_final: 0.7717 (t0) REVERT: c 313 GLU cc_start: 0.8685 (mp0) cc_final: 0.7738 (mp0) REVERT: c 362 ARG cc_start: 0.9240 (mmm-85) cc_final: 0.8982 (mtt-85) REVERT: c 379 GLU cc_start: 0.8871 (pt0) cc_final: 0.8551 (pt0) REVERT: c 402 GLU cc_start: 0.9142 (mp0) cc_final: 0.8862 (mp0) outliers start: 26 outliers final: 14 residues processed: 160 average time/residue: 0.2226 time to fit residues: 48.0233 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 : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain a residue 304 VAL Chi-restraints excluded: chain a residue 349 SER Chi-restraints excluded: chain a residue 364 LEU 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 347 VAL Chi-restraints excluded: chain b residue 354 GLN Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain c residue 299 PHE Chi-restraints excluded: chain c residue 347 VAL Chi-restraints excluded: chain c residue 349 SER Chi-restraints excluded: chain c residue 351 ILE Chi-restraints excluded: chain c residue 364 LEU 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: 0.9980 chunk 2 optimal weight: 0.8980 chunk 36 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.056705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.045045 restraints weight = 31805.678| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 4.25 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: 0.8528 moved from start: 0.4184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8487 Z= 0.137 Angle : 0.730 10.042 11538 Z= 0.355 Chirality : 0.045 0.243 1374 Planarity : 0.003 0.034 1365 Dihedral : 7.550 57.258 1899 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.74 % Allowed : 15.97 % Favored : 82.29 % 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: 1.76 (0.29), residues: 336 sheet: 0.88 (0.61), residues: 96 loop : -1.45 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 219 HIS 0.004 0.001 HIS B 238 PHE 0.007 0.001 PHE C 245 TYR 0.016 0.001 TYR c 284 ARG 0.006 0.001 ARG a 358 Details of bonding type rmsd link_NAG-ASN : bond 0.00473 ( 24) link_NAG-ASN : angle 1.78281 ( 72) link_BETA1-4 : bond 0.00373 ( 18) link_BETA1-4 : angle 1.65829 ( 54) hydrogen bonds : bond 0.03369 ( 328) hydrogen bonds : angle 3.64500 ( 939) SS BOND : bond 0.00331 ( 21) SS BOND : angle 2.05830 ( 42) covalent geometry : bond 0.00299 ( 8424) covalent geometry : angle 0.70133 (11370) *********************** 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: 15 poor density : 149 time to evaluate : 1.132 Fit side-chains revert: symmetry clash REVERT: A 72 TYR cc_start: 0.9015 (m-80) cc_final: 0.8814 (m-10) REVERT: A 88 MET cc_start: 0.9173 (OUTLIER) cc_final: 0.8921 (mtp) REVERT: A 103 MET cc_start: 0.9324 (tpt) cc_final: 0.8549 (tpt) REVERT: A 139 MET cc_start: 0.8949 (tpp) cc_final: 0.8265 (ttt) REVERT: A 256 LYS cc_start: 0.7400 (mmtt) cc_final: 0.7019 (mmtt) REVERT: a 310 ASN cc_start: 0.8772 (t0) cc_final: 0.7669 (t0) REVERT: a 313 GLU cc_start: 0.8637 (mp0) cc_final: 0.7845 (mp0) REVERT: a 354 GLN cc_start: 0.9055 (mt0) cc_final: 0.8828 (mt0) REVERT: a 364 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8930 (mm) REVERT: a 414 ASP cc_start: 0.9164 (m-30) cc_final: 0.8958 (p0) REVERT: a 416 MET cc_start: 0.9448 (ttp) cc_final: 0.9102 (tmm) REVERT: B 72 TYR cc_start: 0.8944 (m-80) cc_final: 0.8668 (m-80) REVERT: b 310 ASN cc_start: 0.8668 (t0) cc_final: 0.7824 (t0) REVERT: b 323 ASP cc_start: 0.9423 (t0) cc_final: 0.9133 (t0) REVERT: b 379 GLU cc_start: 0.8839 (pt0) cc_final: 0.8527 (pt0) REVERT: b 412 GLU cc_start: 0.9006 (tp30) cc_final: 0.8734 (tp30) REVERT: b 416 MET cc_start: 0.9378 (ttp) cc_final: 0.9158 (tmm) REVERT: C 78 GLU cc_start: 0.7657 (pm20) cc_final: 0.6858 (pm20) REVERT: C 103 MET cc_start: 0.9426 (tpt) cc_final: 0.8950 (tpt) REVERT: C 156 LYS cc_start: 0.9075 (mmmm) cc_final: 0.8812 (mmmm) REVERT: C 172 LEU cc_start: 0.9525 (tp) cc_final: 0.9163 (tt) REVERT: c 310 ASN cc_start: 0.8523 (t0) cc_final: 0.7179 (t0) REVERT: c 313 GLU cc_start: 0.8630 (mp0) cc_final: 0.7746 (mp0) REVERT: c 379 GLU cc_start: 0.8892 (pt0) cc_final: 0.8495 (pt0) REVERT: c 385 GLU cc_start: 0.8953 (tp30) cc_final: 0.8337 (tp30) outliers start: 15 outliers final: 5 residues processed: 156 average time/residue: 0.2392 time to fit residues: 50.7004 Evaluate side-chains 145 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 138 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain a residue 304 VAL Chi-restraints excluded: chain a residue 364 LEU Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain c residue 299 PHE Chi-restraints excluded: chain c residue 364 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 50 optimal weight: 8.9990 chunk 15 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 3 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 26 optimal weight: 0.7980 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 183 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.055954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.044292 restraints weight = 32296.673| |-----------------------------------------------------------------------------| r_work (start): 0.2804 rms_B_bonded: 4.27 r_work: 0.2635 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.4281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8487 Z= 0.182 Angle : 0.751 9.681 11538 Z= 0.362 Chirality : 0.045 0.240 1374 Planarity : 0.004 0.085 1365 Dihedral : 7.580 57.332 1899 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.50 % Allowed : 17.13 % Favored : 81.37 % 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: 0.12 (0.28), residues: 915 helix: 1.80 (0.29), residues: 336 sheet: 0.90 (0.61), residues: 96 loop : -1.43 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP a 392 HIS 0.008 0.001 HIS B 238 PHE 0.010 0.001 PHE B 245 TYR 0.014 0.001 TYR c 372 ARG 0.009 0.001 ARG C 205 Details of bonding type rmsd link_NAG-ASN : bond 0.00275 ( 24) link_NAG-ASN : angle 1.69871 ( 72) link_BETA1-4 : bond 0.00264 ( 18) link_BETA1-4 : angle 1.71208 ( 54) hydrogen bonds : bond 0.03497 ( 328) hydrogen bonds : angle 3.63281 ( 939) SS BOND : bond 0.00466 ( 21) SS BOND : angle 2.18983 ( 42) covalent geometry : bond 0.00402 ( 8424) covalent geometry : angle 0.72265 (11370) *********************** 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: 13 poor density : 143 time to evaluate : 1.085 Fit side-chains revert: symmetry clash REVERT: A 72 TYR cc_start: 0.9122 (m-80) cc_final: 0.8800 (m-80) REVERT: A 103 MET cc_start: 0.9347 (tpt) cc_final: 0.8574 (tpt) REVERT: A 139 MET cc_start: 0.8975 (tpp) cc_final: 0.8250 (ttt) REVERT: a 310 ASN cc_start: 0.8801 (t0) cc_final: 0.7747 (t0) REVERT: a 313 GLU cc_start: 0.8608 (mp0) cc_final: 0.7800 (mp0) REVERT: a 364 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.8920 (mm) REVERT: a 416 MET cc_start: 0.9455 (ttp) cc_final: 0.9047 (tmm) REVERT: B 72 TYR cc_start: 0.9015 (m-80) cc_final: 0.8764 (m-80) REVERT: b 310 ASN cc_start: 0.8682 (t0) cc_final: 0.7842 (t0) REVERT: b 323 ASP cc_start: 0.9421 (t0) cc_final: 0.9131 (t0) REVERT: b 379 GLU cc_start: 0.8833 (pt0) cc_final: 0.8510 (pt0) REVERT: b 412 GLU cc_start: 0.9036 (tp30) cc_final: 0.8773 (tp30) REVERT: b 416 MET cc_start: 0.9427 (ttp) cc_final: 0.9129 (tmm) REVERT: C 103 MET cc_start: 0.9423 (tpt) cc_final: 0.8997 (tpt) REVERT: C 156 LYS cc_start: 0.9110 (mmmm) cc_final: 0.8846 (mmmm) REVERT: C 172 LEU cc_start: 0.9529 (tp) cc_final: 0.9190 (tt) REVERT: C 256 LYS cc_start: 0.7560 (mmtt) cc_final: 0.7331 (mmtm) REVERT: c 310 ASN cc_start: 0.8610 (t0) cc_final: 0.7344 (t0) REVERT: c 313 GLU cc_start: 0.8649 (mp0) cc_final: 0.7692 (mp0) REVERT: c 362 ARG cc_start: 0.9183 (mmm-85) cc_final: 0.8926 (mtt-85) REVERT: c 379 GLU cc_start: 0.8893 (pt0) cc_final: 0.8528 (pt0) REVERT: c 385 GLU cc_start: 0.8982 (tp30) cc_final: 0.8361 (tp30) outliers start: 13 outliers final: 9 residues processed: 148 average time/residue: 0.2394 time to fit residues: 47.8155 Evaluate side-chains 150 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 140 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 304 VAL Chi-restraints excluded: chain a residue 364 LEU 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 109 GLU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 46 optimal weight: 0.6980 chunk 20 optimal weight: 5.9990 chunk 67 optimal weight: 8.9990 chunk 23 optimal weight: 6.9990 chunk 3 optimal weight: 8.9990 chunk 47 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 62 optimal weight: 9.9990 chunk 88 optimal weight: 0.7980 chunk 70 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3167 r_free = 0.3167 target = 0.056725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.045108 restraints weight = 31524.076| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 4.25 r_work: 0.2659 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.4314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8487 Z= 0.146 Angle : 0.749 10.537 11538 Z= 0.364 Chirality : 0.045 0.242 1374 Planarity : 0.004 0.069 1365 Dihedral : 7.469 57.154 1899 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.16 % Allowed : 17.71 % Favored : 81.13 % 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: 0.11 (0.28), residues: 915 helix: 1.73 (0.29), residues: 336 sheet: 0.86 (0.61), residues: 96 loop : -1.37 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 219 HIS 0.009 0.001 HIS B 238 PHE 0.008 0.001 PHE A 245 TYR 0.014 0.001 TYR c 372 ARG 0.006 0.001 ARG C 205 Details of bonding type rmsd link_NAG-ASN : bond 0.00369 ( 24) link_NAG-ASN : angle 1.65302 ( 72) link_BETA1-4 : bond 0.00317 ( 18) link_BETA1-4 : angle 1.67509 ( 54) hydrogen bonds : bond 0.03297 ( 328) hydrogen bonds : angle 3.58116 ( 939) SS BOND : bond 0.00377 ( 21) SS BOND : angle 2.04926 ( 42) covalent geometry : bond 0.00325 ( 8424) covalent geometry : angle 0.72292 (11370) ********************** 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 155 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 145 time to evaluate : 0.972 Fit side-chains revert: symmetry clash REVERT: A 72 TYR cc_start: 0.9113 (m-80) cc_final: 0.8794 (m-80) REVERT: A 88 MET cc_start: 0.9173 (OUTLIER) cc_final: 0.8902 (mtp) REVERT: A 103 MET cc_start: 0.9310 (tpt) cc_final: 0.8642 (tpt) REVERT: A 139 MET cc_start: 0.8902 (tpp) cc_final: 0.8190 (ttt) REVERT: a 310 ASN cc_start: 0.8804 (t0) cc_final: 0.7760 (t0) REVERT: a 313 GLU cc_start: 0.8636 (mp0) cc_final: 0.7797 (mp0) REVERT: a 364 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8865 (mm) REVERT: a 416 MET cc_start: 0.9467 (ttp) cc_final: 0.9036 (tmm) REVERT: B 72 TYR cc_start: 0.8970 (m-80) cc_final: 0.8654 (m-80) REVERT: b 310 ASN cc_start: 0.8636 (t0) cc_final: 0.7920 (t0) REVERT: b 323 ASP cc_start: 0.9406 (t0) cc_final: 0.9107 (t0) REVERT: b 379 GLU cc_start: 0.8832 (pt0) cc_final: 0.8504 (pt0) REVERT: b 412 GLU cc_start: 0.9008 (tp30) cc_final: 0.8746 (tp30) REVERT: b 416 MET cc_start: 0.9383 (ttp) cc_final: 0.9159 (tmm) REVERT: C 78 GLU cc_start: 0.7483 (pm20) cc_final: 0.6702 (pm20) REVERT: C 103 MET cc_start: 0.9419 (tpt) cc_final: 0.9028 (tpt) REVERT: C 139 MET cc_start: 0.8866 (tpp) cc_final: 0.8587 (tmm) REVERT: C 156 LYS cc_start: 0.9092 (mmmm) cc_final: 0.8823 (mmmm) REVERT: C 172 LEU cc_start: 0.9508 (tp) cc_final: 0.9173 (tt) REVERT: C 256 LYS cc_start: 0.7546 (mmtt) cc_final: 0.7310 (mmtm) REVERT: c 310 ASN cc_start: 0.8556 (t0) cc_final: 0.7293 (t0) REVERT: c 313 GLU cc_start: 0.8605 (mp0) cc_final: 0.7630 (mp0) REVERT: c 362 ARG cc_start: 0.9160 (mmm-85) cc_final: 0.8902 (mtt-85) REVERT: c 379 GLU cc_start: 0.8900 (pt0) cc_final: 0.8535 (pt0) REVERT: c 385 GLU cc_start: 0.8933 (tp30) cc_final: 0.8323 (tp30) outliers start: 10 outliers final: 7 residues processed: 150 average time/residue: 0.2081 time to fit residues: 42.3126 Evaluate side-chains 150 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 141 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain a residue 304 VAL Chi-restraints excluded: chain a residue 364 LEU Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain c residue 299 PHE Chi-restraints excluded: chain c residue 347 VAL Chi-restraints excluded: chain c residue 351 ILE Chi-restraints excluded: chain c residue 364 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 51 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 67 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 71 optimal weight: 4.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 = 0.3157 r_free = 0.3157 target = 0.056144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.044629 restraints weight = 31943.184| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 4.22 r_work: 0.2649 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.4415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8487 Z= 0.171 Angle : 0.760 11.216 11538 Z= 0.368 Chirality : 0.045 0.245 1374 Planarity : 0.004 0.056 1365 Dihedral : 7.473 57.132 1899 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.39 % Allowed : 17.01 % Favored : 81.60 % 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: 0.11 (0.28), residues: 915 helix: 1.75 (0.29), residues: 336 sheet: 0.29 (0.54), residues: 114 loop : -1.30 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 219 HIS 0.008 0.001 HIS B 238 PHE 0.010 0.001 PHE A 245 TYR 0.015 0.001 TYR c 372 ARG 0.005 0.001 ARG C 205 Details of bonding type rmsd link_NAG-ASN : bond 0.00279 ( 24) link_NAG-ASN : angle 1.63569 ( 72) link_BETA1-4 : bond 0.00255 ( 18) link_BETA1-4 : angle 1.70837 ( 54) hydrogen bonds : bond 0.03455 ( 328) hydrogen bonds : angle 3.60353 ( 939) SS BOND : bond 0.00437 ( 21) SS BOND : angle 2.07025 ( 42) covalent geometry : bond 0.00381 ( 8424) covalent geometry : angle 0.73407 (11370) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3715.56 seconds wall clock time: 66 minutes 3.43 seconds (3963.43 seconds total)