Starting phenix.real_space_refine on Sat Dec 28 09:40:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dmi_27539/12_2024/8dmi_27539.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dmi_27539/12_2024/8dmi_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_27539/12_2024/8dmi_27539.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dmi_27539/12_2024/8dmi_27539.map" model { file = "/net/cci-nas-00/data/ceres_data/8dmi_27539/12_2024/8dmi_27539.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dmi_27539/12_2024/8dmi_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-5532/modules/chem_data/mon_lib" Total number of atoms: 8259 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1357 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain breaks: 3 Chain: "a" Number of atoms: 1200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1200 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 3, 'TRANS': 143} Chain breaks: 1 Chain: "B" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1357 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain breaks: 3 Chain: "b" Number of atoms: 1200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1200 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 3, 'TRANS': 143} Chain breaks: 1 Chain: "C" Number of atoms: 1357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1357 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 2, 'TRANS': 167} Chain breaks: 3 Chain: "c" Number of atoms: 1200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1200 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 3, 'TRANS': 143} Chain breaks: 1 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "a" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "b" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "c" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.74, per 1000 atoms: 0.69 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: 2.80 Conformation dependent library (CDL) restraints added in 942.5 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: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 136 through 148 Processing helix chain 'A' and resid 186 through 200 Processing helix chain 'A' and resid 244 through 253 Processing helix chain 'a' and resid 300 through 307 removed outlier: 4.153A pdb=" N VAL a 304 " --> pdb=" O GLY a 300 " (cutoff:3.500A) Processing helix chain 'a' and resid 313 through 330 removed outlier: 4.156A pdb=" N ASP a 317 " --> pdb=" O GLU a 313 " (cutoff:3.500A) Processing helix chain 'a' and resid 335 through 346 Processing helix chain 'a' and resid 352 through 365 Processing helix chain 'a' and resid 405 through 426 Processing helix chain 'B' and resid 136 through 148 Processing helix chain 'B' and resid 186 through 200 Processing helix chain 'B' and resid 244 through 253 Processing helix chain 'b' and resid 300 through 307 removed outlier: 4.154A pdb=" N VAL b 304 " --> pdb=" O GLY b 300 " (cutoff:3.500A) Processing helix chain 'b' and resid 313 through 330 removed outlier: 4.155A pdb=" N ASP b 317 " --> pdb=" O GLU b 313 " (cutoff:3.500A) Processing helix chain 'b' and resid 335 through 346 Processing helix chain 'b' and resid 352 through 365 Processing helix chain 'b' and resid 405 through 426 Processing helix chain 'C' and resid 136 through 148 Processing helix chain 'C' and resid 186 through 200 Processing helix chain 'C' and resid 244 through 253 Processing helix chain 'c' and resid 300 through 307 removed outlier: 4.154A pdb=" N VAL c 304 " --> pdb=" O GLY c 300 " (cutoff:3.500A) Processing helix chain 'c' and resid 313 through 330 removed outlier: 4.156A pdb=" N ASP c 317 " --> pdb=" O GLU c 313 " (cutoff:3.500A) Processing helix chain 'c' and resid 335 through 346 Processing helix chain 'c' and resid 352 through 365 Processing helix chain 'c' and resid 405 through 426 Processing sheet with id=AA1, first strand: chain 'A' and resid 72 through 78 removed outlier: 3.527A pdb=" N GLU a 379 " --> pdb=" O GLN A 73 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 89 through 93 Processing sheet with id=AA3, first strand: chain 'a' and resid 394 through 395 Processing sheet with id=AA4, first strand: chain 'B' and resid 72 through 78 removed outlier: 3.510A pdb=" N GLU b 379 " --> pdb=" O GLN B 73 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 89 through 93 Processing sheet with id=AA6, first strand: chain 'b' and resid 394 through 395 Processing sheet with id=AA7, first strand: chain 'C' and resid 72 through 78 Processing sheet with id=AA8, first strand: chain 'C' and resid 89 through 93 Processing sheet with id=AA9, first strand: chain 'c' and resid 394 through 395 328 hydrogen bonds defined for protein. 939 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.20 Time building geometry restraints manager: 3.09 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.000 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.180 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 8424 Z= 0.263 Angle : 0.815 10.517 11370 Z= 0.439 Chirality : 0.055 0.393 1374 Planarity : 0.009 0.119 1365 Dihedral : 14.468 68.731 3690 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.27), residues: 915 helix: 0.58 (0.28), residues: 351 sheet: -0.12 (0.54), residues: 93 loop : -2.10 (0.25), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 219 HIS 0.013 0.002 HIS B 136 PHE 0.016 0.002 PHE B 187 TYR 0.063 0.002 TYR A 227 ARG 0.031 0.003 ARG B 188 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 0.882 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.2565 time to fit residues: 68.0328 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 : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 4.9990 chunk 70 optimal weight: 9.9990 chunk 39 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 72 optimal weight: 6.9990 chunk 28 optimal weight: 0.3980 chunk 44 optimal weight: 8.9990 chunk 54 optimal weight: 0.8980 chunk 84 optimal weight: 5.9990 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 359 ASN C 73 GLN C 237 ASN c 359 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8424 Z= 0.262 Angle : 0.702 9.497 11370 Z= 0.358 Chirality : 0.046 0.246 1374 Planarity : 0.004 0.030 1365 Dihedral : 9.383 56.723 1899 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 0.69 % Allowed : 9.49 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.27), residues: 915 helix: 1.48 (0.28), residues: 357 sheet: 0.29 (0.56), residues: 90 loop : -1.71 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP c 392 HIS 0.007 0.001 HIS C 238 PHE 0.015 0.002 PHE C 122 TYR 0.020 0.001 TYR A 227 ARG 0.008 0.001 ARG C 190 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 160 time to evaluate : 0.920 Fit side-chains REVERT: a 310 ASN cc_start: 0.7569 (t0) cc_final: 0.6936 (t0) REVERT: a 313 GLU cc_start: 0.6971 (mp0) cc_final: 0.6700 (mp0) REVERT: b 310 ASN cc_start: 0.7391 (t0) cc_final: 0.6870 (t0) REVERT: c 310 ASN cc_start: 0.7334 (t0) cc_final: 0.6802 (t0) outliers start: 6 outliers final: 4 residues processed: 163 average time/residue: 0.2257 time to fit residues: 49.5260 Evaluate side-chains 143 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 139 time to evaluate : 1.190 ------------------------------------------------------------------------------- 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 46 optimal weight: 7.9990 chunk 26 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 chunk 28 optimal weight: 6.9990 chunk 67 optimal weight: 10.0000 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8424 Z= 0.176 Angle : 0.641 10.226 11370 Z= 0.325 Chirality : 0.045 0.247 1374 Planarity : 0.004 0.027 1365 Dihedral : 8.550 56.627 1899 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.04 % Allowed : 10.42 % Favored : 88.54 % 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: 0.02 (0.28), residues: 915 helix: 1.66 (0.29), residues: 339 sheet: 0.47 (0.58), residues: 90 loop : -1.35 (0.26), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP b 392 HIS 0.005 0.001 HIS B 238 PHE 0.013 0.001 PHE C 245 TYR 0.015 0.001 TYR A 227 ARG 0.004 0.001 ARG a 358 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 153 time to evaluate : 0.921 Fit side-chains revert: symmetry clash REVERT: a 310 ASN cc_start: 0.7688 (t0) cc_final: 0.7053 (t0) REVERT: a 313 GLU cc_start: 0.6942 (mp0) cc_final: 0.6716 (mp0) REVERT: b 310 ASN cc_start: 0.7462 (t0) cc_final: 0.7251 (t0) REVERT: c 310 ASN cc_start: 0.7412 (t0) cc_final: 0.7011 (t0) outliers start: 9 outliers final: 7 residues processed: 156 average time/residue: 0.2283 time to fit residues: 47.9257 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 : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain b residue 304 VAL Chi-restraints excluded: chain 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 83 optimal weight: 6.9990 chunk 63 optimal weight: 0.8980 chunk 43 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 chunk 89 optimal weight: 0.6980 chunk 44 optimal weight: 4.9990 chunk 80 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8424 Z= 0.181 Angle : 0.659 9.544 11370 Z= 0.332 Chirality : 0.045 0.250 1374 Planarity : 0.004 0.053 1365 Dihedral : 8.091 56.971 1899 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.74 % Allowed : 12.50 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.28), residues: 915 helix: 1.76 (0.29), residues: 339 sheet: 0.72 (0.58), residues: 90 loop : -1.26 (0.26), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP c 392 HIS 0.004 0.001 HIS B 238 PHE 0.010 0.001 PHE C 245 TYR 0.020 0.001 TYR A 72 ARG 0.005 0.001 ARG C 205 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 148 time to evaluate : 0.924 Fit side-chains revert: symmetry clash REVERT: A 256 LYS cc_start: 0.5840 (mmtt) cc_final: 0.5597 (mmtm) REVERT: a 310 ASN cc_start: 0.7569 (t0) cc_final: 0.7003 (t0) REVERT: a 313 GLU cc_start: 0.6985 (mp0) cc_final: 0.6744 (mp0) REVERT: b 313 GLU cc_start: 0.7069 (mp0) cc_final: 0.6779 (mp0) outliers start: 15 outliers final: 7 residues processed: 152 average time/residue: 0.2155 time to fit residues: 44.5373 Evaluate side-chains 142 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 135 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 299 PHE Chi-restraints excluded: chain c residue 364 LEU 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 74 optimal weight: 3.9990 chunk 51 optimal weight: 9.9990 chunk 1 optimal weight: 4.9990 chunk 66 optimal weight: 8.9990 chunk 37 optimal weight: 7.9990 chunk 76 optimal weight: 2.9990 chunk 62 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 45 optimal weight: 1.9990 chunk 80 optimal weight: 10.0000 chunk 22 optimal weight: 8.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 164 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.3858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.037 8424 Z= 0.452 Angle : 0.793 10.360 11370 Z= 0.393 Chirality : 0.048 0.240 1374 Planarity : 0.005 0.072 1365 Dihedral : 7.934 57.875 1899 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 3.01 % Allowed : 12.04 % Favored : 84.95 % 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: 1.40 (0.29), residues: 354 sheet: 0.03 (0.53), residues: 114 loop : -1.40 (0.27), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP b 392 HIS 0.009 0.002 HIS c 311 PHE 0.018 0.002 PHE B 245 TYR 0.017 0.002 TYR A 241 ARG 0.006 0.001 ARG B 188 *********************** 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 162 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 136 time to evaluate : 0.988 Fit side-chains REVERT: A 103 MET cc_start: 0.7950 (OUTLIER) cc_final: 0.7618 (tpt) REVERT: a 310 ASN cc_start: 0.7695 (t0) cc_final: 0.7123 (t0) REVERT: C 103 MET cc_start: 0.8019 (tpt) cc_final: 0.7783 (tpt) outliers start: 26 outliers final: 15 residues processed: 145 average time/residue: 0.2130 time to fit residues: 42.1194 Evaluate side-chains 144 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 MET 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 172 LEU Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 204 MET 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 309 VAL Chi-restraints excluded: chain c residue 351 ILE Chi-restraints excluded: chain c residue 364 LEU Chi-restraints excluded: chain c residue 416 MET Chi-restraints excluded: chain c residue 417 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 30 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 29 optimal weight: 0.0770 chunk 47 optimal weight: 0.6980 overall best weight: 1.5544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN A 183 GLN C 183 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.3903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8424 Z= 0.221 Angle : 0.682 9.443 11370 Z= 0.342 Chirality : 0.045 0.243 1374 Planarity : 0.004 0.046 1365 Dihedral : 7.600 57.399 1899 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.43 % Allowed : 14.47 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.28), residues: 915 helix: 1.75 (0.29), residues: 336 sheet: 0.69 (0.61), residues: 96 loop : -1.43 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP a 392 HIS 0.005 0.001 HIS C 238 PHE 0.013 0.001 PHE B 245 TYR 0.015 0.001 TYR A 72 ARG 0.004 0.001 ARG a 358 *********************** 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 161 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 140 time to evaluate : 1.009 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 13 residues processed: 148 average time/residue: 0.2093 time to fit residues: 42.3092 Evaluate side-chains 140 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 127 time to evaluate : 0.990 ------------------------------------------------------------------------------- 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 411 GLN Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain b residue 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 416 MET Chi-restraints excluded: chain c residue 417 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 86 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 51 optimal weight: 8.9990 chunk 65 optimal weight: 7.9990 chunk 50 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.4149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 8424 Z= 0.362 Angle : 0.774 19.018 11370 Z= 0.378 Chirality : 0.046 0.237 1374 Planarity : 0.004 0.053 1365 Dihedral : 7.679 57.555 1899 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.78 % Allowed : 14.81 % 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: -0.00 (0.28), residues: 915 helix: 1.68 (0.29), residues: 336 sheet: 0.23 (0.54), residues: 114 loop : -1.40 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP b 392 HIS 0.007 0.002 HIS a 311 PHE 0.015 0.001 PHE B 245 TYR 0.023 0.001 TYR A 72 ARG 0.004 0.001 ARG C 196 *********************** 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 153 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 129 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 17 residues processed: 139 average time/residue: 0.2117 time to fit residues: 40.1110 Evaluate side-chains 144 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 127 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain a residue 304 VAL Chi-restraints excluded: chain a residue 349 SER Chi-restraints excluded: chain a residue 357 MET Chi-restraints excluded: chain a residue 411 GLN Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain b residue 304 VAL Chi-restraints excluded: chain b residue 354 GLN Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain c residue 299 PHE Chi-restraints excluded: chain c residue 349 SER Chi-restraints excluded: chain c residue 364 LEU Chi-restraints excluded: chain c residue 416 MET Chi-restraints excluded: chain c residue 417 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 35 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 chunk 17 optimal weight: 8.9990 chunk 56 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 44 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 70 optimal weight: 0.9990 chunk 81 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.4158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8424 Z= 0.211 Angle : 0.726 18.022 11370 Z= 0.356 Chirality : 0.045 0.241 1374 Planarity : 0.004 0.040 1365 Dihedral : 7.485 57.343 1899 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.08 % Allowed : 16.20 % Favored : 81.71 % 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: 1.80 (0.29), residues: 336 sheet: 0.21 (0.54), residues: 114 loop : -1.32 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 219 HIS 0.007 0.001 HIS B 238 PHE 0.010 0.001 PHE B 245 TYR 0.018 0.001 TYR A 72 ARG 0.004 0.001 ARG c 358 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 1.259 Fit side-chains revert: symmetry clash REVERT: A 103 MET cc_start: 0.7855 (tpt) cc_final: 0.7617 (tpt) outliers start: 18 outliers final: 11 residues processed: 141 average time/residue: 0.2322 time to fit residues: 45.7698 Evaluate side-chains 137 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 126 time to evaluate : 0.995 ------------------------------------------------------------------------------- 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 172 LEU Chi-restraints excluded: chain b residue 354 GLN 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 Chi-restraints excluded: chain c residue 416 MET Chi-restraints excluded: chain c residue 417 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 50 optimal weight: 7.9990 chunk 36 optimal weight: 8.9990 chunk 65 optimal weight: 7.9990 chunk 25 optimal weight: 0.9990 chunk 75 optimal weight: 0.0060 chunk 79 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 chunk 88 optimal weight: 0.9990 overall best weight: 1.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.4174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8424 Z= 0.205 Angle : 0.725 17.258 11370 Z= 0.353 Chirality : 0.044 0.243 1374 Planarity : 0.004 0.045 1365 Dihedral : 7.414 57.234 1899 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.50 % Allowed : 16.55 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.28), residues: 915 helix: 1.80 (0.29), residues: 336 sheet: 0.20 (0.53), residues: 114 loop : -1.25 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 219 HIS 0.007 0.001 HIS B 238 PHE 0.009 0.001 PHE C 245 TYR 0.023 0.001 TYR B 72 ARG 0.003 0.001 ARG c 362 *********************** 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 143 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 130 time to evaluate : 1.070 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 9 residues processed: 136 average time/residue: 0.2349 time to fit residues: 43.7970 Evaluate side-chains 132 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 123 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain C residue 193 ASP 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 Chi-restraints excluded: chain c residue 416 MET Chi-restraints excluded: chain c residue 417 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 53 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 92 optimal weight: 10.0000 chunk 85 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 58 optimal weight: 9.9990 chunk 78 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 311 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.4270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8424 Z= 0.195 Angle : 0.725 16.095 11370 Z= 0.355 Chirality : 0.044 0.242 1374 Planarity : 0.004 0.060 1365 Dihedral : 7.316 57.202 1899 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.39 % Allowed : 16.78 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.29), residues: 915 helix: 1.83 (0.30), residues: 336 sheet: 0.21 (0.53), residues: 114 loop : -1.21 (0.28), residues: 465 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 0.010 0.001 PHE A 245 TYR 0.022 0.001 TYR B 72 ARG 0.004 0.001 ARG c 358 ********************** 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 142 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 0.965 Fit side-chains revert: symmetry clash REVERT: A 103 MET cc_start: 0.7206 (tpt) cc_final: 0.6925 (tpt) outliers start: 12 outliers final: 10 residues processed: 135 average time/residue: 0.2169 time to fit residues: 39.9675 Evaluate side-chains 133 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 123 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain b residue 354 GLN Chi-restraints excluded: chain c residue 299 PHE Chi-restraints excluded: chain c residue 347 VAL Chi-restraints excluded: chain c residue 351 ILE Chi-restraints excluded: chain c residue 364 LEU Chi-restraints excluded: chain c residue 416 MET Chi-restraints excluded: chain c residue 417 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 22 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 64 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.056032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.044628 restraints weight = 31886.613| |-----------------------------------------------------------------------------| r_work (start): 0.2815 rms_B_bonded: 4.18 r_work: 0.2649 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.4408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8424 Z= 0.283 Angle : 0.755 14.554 11370 Z= 0.369 Chirality : 0.045 0.241 1374 Planarity : 0.004 0.060 1365 Dihedral : 7.388 57.243 1899 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.62 % Allowed : 16.44 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.28), residues: 915 helix: 1.84 (0.29), residues: 336 sheet: 0.30 (0.54), residues: 114 loop : -1.32 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 219 HIS 0.008 0.001 HIS B 238 PHE 0.011 0.001 PHE B 245 TYR 0.020 0.001 TYR B 72 ARG 0.005 0.001 ARG B 196 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1778.77 seconds wall clock time: 33 minutes 43.16 seconds (2023.16 seconds total)