Starting phenix.real_space_refine on Mon Mar 11 12:31:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmi_27539/03_2024/8dmi_27539.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmi_27539/03_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmi_27539/03_2024/8dmi_27539.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmi_27539/03_2024/8dmi_27539.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmi_27539/03_2024/8dmi_27539.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmi_27539/03_2024/8dmi_27539.pdb" } 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 Residue "A TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 236": "OE1" <-> "OE2" Residue "a ASP 323": "OD1" <-> "OD2" Residue "a GLU 379": "OE1" <-> "OE2" Residue "B TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 236": "OE1" <-> "OE2" Residue "b ASP 323": "OD1" <-> "OD2" Residue "b GLU 379": "OE1" <-> "OE2" Residue "C TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 236": "OE1" <-> "OE2" Residue "c ASP 323": "OD1" <-> "OD2" Residue "c GLU 379": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 5.11, per 1000 atoms: 0.62 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 - 3.50 Amino acid : False - 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: 3.50 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 1.92 Time building geometry restraints manager: 3.77 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: 99.54 - 106.45: 165 106.45 - 113.35: 4748 113.35 - 120.25: 2945 120.25 - 127.16: 3410 127.16 - 134.06: 102 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 2.520 nonbonded pdb=" ND1 HIS c 380 " pdb=" OG1 THR c 383 " model vdw 2.118 2.520 nonbonded pdb=" ND1 HIS b 380 " pdb=" OG1 THR b 383 " model vdw 2.118 2.520 nonbonded pdb=" OG SER B 82 " pdb=" O7 NAG J 1 " model vdw 2.306 2.440 nonbonded pdb=" OG SER A 82 " pdb=" O7 NAG D 1 " model vdw 2.306 2.440 ... (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 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: 0.780 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: 3.310 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 24.800 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.340 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 0.909 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.2574 time to fit residues: 68.1251 Evaluate side-chains 141 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 0.937 ------------------------------------------------------------------------------- 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: 5.9990 chunk 70 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN a 359 ASN a 360 HIS B 164 ASN C 73 GLN C 164 ASN C 237 ASN c 359 ASN c 360 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 8424 Z= 0.437 Angle : 0.771 9.343 11370 Z= 0.386 Chirality : 0.047 0.246 1374 Planarity : 0.004 0.040 1365 Dihedral : 9.143 57.342 1899 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.39 % Allowed : 10.19 % 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: -0.31 (0.27), residues: 915 helix: 1.53 (0.28), residues: 357 sheet: 0.03 (0.56), residues: 96 loop : -1.76 (0.25), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP c 392 HIS 0.007 0.002 HIS C 238 PHE 0.020 0.002 PHE B 245 TYR 0.029 0.002 TYR A 227 ARG 0.007 0.001 ARG c 358 *********************** 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 157 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 145 time to evaluate : 0.970 Fit side-chains outliers start: 12 outliers final: 9 residues processed: 152 average time/residue: 0.2185 time to fit residues: 44.6548 Evaluate side-chains 137 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 128 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain a residue 304 VAL Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain C 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: 4.9990 chunk 26 optimal weight: 0.8980 chunk 70 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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: 0.8031 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8424 Z= 0.187 Angle : 0.622 9.451 11370 Z= 0.317 Chirality : 0.044 0.245 1374 Planarity : 0.003 0.025 1365 Dihedral : 8.411 56.537 1899 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.16 % Allowed : 12.04 % Favored : 86.81 % 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: 0.07 (0.28), residues: 915 helix: 1.71 (0.29), residues: 357 sheet: 0.21 (0.58), residues: 96 loop : -1.40 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP b 392 HIS 0.005 0.001 HIS C 238 PHE 0.010 0.001 PHE B 245 TYR 0.015 0.001 TYR A 227 ARG 0.004 0.001 ARG c 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 156 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 146 time to evaluate : 0.868 Fit side-chains REVERT: c 310 ASN cc_start: 0.7334 (t0) cc_final: 0.7006 (t0) outliers start: 10 outliers final: 3 residues processed: 149 average time/residue: 0.2213 time to fit residues: 44.2529 Evaluate side-chains 136 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 133 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain c residue 299 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 83 optimal weight: 7.9990 chunk 63 optimal weight: 5.9990 chunk 43 optimal weight: 8.9990 chunk 9 optimal weight: 6.9990 chunk 40 optimal weight: 7.9990 chunk 56 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 80 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 8424 Z= 0.405 Angle : 0.743 9.312 11370 Z= 0.367 Chirality : 0.046 0.240 1374 Planarity : 0.004 0.023 1365 Dihedral : 8.156 57.620 1899 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.66 % Allowed : 12.85 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.28), residues: 915 helix: 1.68 (0.28), residues: 354 sheet: 0.61 (0.60), residues: 96 loop : -1.52 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP b 392 HIS 0.005 0.001 HIS C 238 PHE 0.016 0.002 PHE B 245 TYR 0.025 0.002 TYR B 72 ARG 0.005 0.001 ARG A 196 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 139 time to evaluate : 0.987 Fit side-chains outliers start: 23 outliers final: 15 residues processed: 148 average time/residue: 0.2180 time to fit residues: 43.6044 Evaluate side-chains 142 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 127 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain a residue 304 VAL Chi-restraints excluded: chain a residue 354 GLN Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain b residue 304 VAL Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain c residue 291 ILE 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 74 optimal weight: 0.1980 chunk 51 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 45 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 GLN C 183 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8424 Z= 0.179 Angle : 0.638 9.459 11370 Z= 0.320 Chirality : 0.044 0.243 1374 Planarity : 0.003 0.026 1365 Dihedral : 7.701 56.721 1899 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.62 % Allowed : 14.24 % Favored : 84.14 % 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: 0.23 (0.29), residues: 915 helix: 1.86 (0.29), residues: 354 sheet: 0.63 (0.61), residues: 96 loop : -1.40 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 219 HIS 0.005 0.001 HIS B 238 PHE 0.011 0.001 PHE B 245 TYR 0.015 0.001 TYR A 72 ARG 0.003 0.000 ARG c 358 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 140 time to evaluate : 0.956 Fit side-chains REVERT: a 364 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8389 (mm) REVERT: c 420 MET cc_start: 0.8913 (tmm) cc_final: 0.8695 (tmm) outliers start: 14 outliers final: 6 residues processed: 149 average time/residue: 0.2080 time to fit residues: 42.6403 Evaluate side-chains 134 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 127 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain a residue 364 LEU Chi-restraints excluded: chain b residue 354 GLN Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain c residue 299 PHE Chi-restraints excluded: chain c residue 347 VAL 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: 1.9990 chunk 80 optimal weight: 3.9990 chunk 17 optimal weight: 8.9990 chunk 52 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 89 optimal weight: 0.0020 chunk 74 optimal weight: 8.9990 chunk 41 optimal weight: 8.9990 chunk 7 optimal weight: 1.9990 chunk 29 optimal weight: 8.9990 chunk 47 optimal weight: 7.9990 overall best weight: 2.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 183 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.3984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 8424 Z= 0.294 Angle : 0.684 12.037 11370 Z= 0.338 Chirality : 0.044 0.240 1374 Planarity : 0.003 0.035 1365 Dihedral : 7.697 57.181 1899 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.31 % Allowed : 14.93 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.28), residues: 915 helix: 1.85 (0.29), residues: 354 sheet: 0.69 (0.61), residues: 96 loop : -1.43 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP a 392 HIS 0.007 0.001 HIS C 238 PHE 0.013 0.001 PHE B 245 TYR 0.019 0.001 TYR B 72 ARG 0.007 0.001 ARG B 205 *********************** 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 152 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 132 time to evaluate : 1.047 Fit side-chains REVERT: c 420 MET cc_start: 0.8937 (tmm) cc_final: 0.8718 (tmm) outliers start: 20 outliers final: 13 residues processed: 143 average time/residue: 0.2077 time to fit residues: 40.9109 Evaluate side-chains 144 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 131 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 237 ASN Chi-restraints excluded: chain a residue 304 VAL Chi-restraints excluded: chain a residue 354 GLN Chi-restraints excluded: chain B residue 103 MET Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain b residue 354 GLN Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain c residue 299 PHE Chi-restraints excluded: chain c residue 347 VAL Chi-restraints excluded: chain c residue 412 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 86 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 50 optimal weight: 7.9990 chunk 75 optimal weight: 8.9990 chunk 89 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 55 optimal weight: 0.0870 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 360 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8424 Z= 0.172 Angle : 0.646 9.490 11370 Z= 0.321 Chirality : 0.044 0.243 1374 Planarity : 0.003 0.034 1365 Dihedral : 7.445 56.727 1899 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.74 % Allowed : 16.55 % 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: 0.46 (0.29), residues: 915 helix: 2.16 (0.29), residues: 336 sheet: 0.80 (0.61), residues: 96 loop : -1.22 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 219 HIS 0.005 0.001 HIS C 238 PHE 0.009 0.001 PHE B 245 TYR 0.020 0.001 TYR A 72 ARG 0.004 0.001 ARG a 358 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 133 time to evaluate : 0.956 Fit side-chains REVERT: c 420 MET cc_start: 0.8934 (tmm) cc_final: 0.8729 (tmm) outliers start: 15 outliers final: 11 residues processed: 138 average time/residue: 0.2042 time to fit residues: 38.7332 Evaluate side-chains 135 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 124 time to evaluate : 0.917 ------------------------------------------------------------------------------- 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 B residue 103 MET Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain C residue 103 MET 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 412 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 35 optimal weight: 6.9990 chunk 53 optimal weight: 0.8980 chunk 27 optimal weight: 0.1980 chunk 17 optimal weight: 9.9990 chunk 56 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 70 optimal weight: 10.0000 chunk 81 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 354 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.4083 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= 0.182 Angle : 0.669 18.283 11370 Z= 0.323 Chirality : 0.043 0.244 1374 Planarity : 0.003 0.030 1365 Dihedral : 7.362 56.826 1899 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.85 % Allowed : 17.13 % Favored : 81.02 % 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: 0.56 (0.29), residues: 915 helix: 2.25 (0.29), residues: 336 sheet: 0.89 (0.61), residues: 96 loop : -1.18 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 219 HIS 0.006 0.001 HIS A 238 PHE 0.007 0.001 PHE A 245 TYR 0.018 0.001 TYR A 72 ARG 0.003 0.000 ARG B 196 *********************** 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 147 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 131 time to evaluate : 0.903 Fit side-chains outliers start: 16 outliers final: 13 residues processed: 137 average time/residue: 0.2026 time to fit residues: 37.8603 Evaluate side-chains 141 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 128 time to evaluate : 0.883 ------------------------------------------------------------------------------- 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 B residue 103 MET Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain b residue 354 GLN Chi-restraints excluded: chain C residue 103 MET 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 412 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 85 optimal weight: 4.9990 chunk 50 optimal weight: 7.9990 chunk 36 optimal weight: 9.9990 chunk 65 optimal weight: 8.9990 chunk 25 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.4240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8424 Z= 0.242 Angle : 0.699 16.930 11370 Z= 0.338 Chirality : 0.044 0.240 1374 Planarity : 0.003 0.032 1365 Dihedral : 7.403 56.866 1899 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.62 % Allowed : 17.25 % 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: 0.55 (0.29), residues: 915 helix: 2.25 (0.29), residues: 336 sheet: 1.06 (0.63), residues: 96 loop : -1.24 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP a 392 HIS 0.007 0.001 HIS A 238 PHE 0.010 0.001 PHE B 245 TYR 0.019 0.001 TYR A 72 ARG 0.005 0.001 ARG B 196 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 130 time to evaluate : 0.972 Fit side-chains REVERT: c 420 MET cc_start: 0.8925 (tmm) cc_final: 0.8681 (tmm) outliers start: 14 outliers final: 12 residues processed: 135 average time/residue: 0.2207 time to fit residues: 40.4362 Evaluate side-chains 137 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 125 time to evaluate : 0.991 ------------------------------------------------------------------------------- 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 B residue 103 MET Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain b residue 354 GLN Chi-restraints excluded: chain C residue 103 MET 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 412 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 53 optimal weight: 7.9990 chunk 41 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 92 optimal weight: 9.9990 chunk 85 optimal weight: 4.9990 chunk 73 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 58 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.4318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8424 Z= 0.243 Angle : 0.706 16.180 11370 Z= 0.342 Chirality : 0.044 0.240 1374 Planarity : 0.003 0.031 1365 Dihedral : 7.450 56.855 1899 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.39 % Allowed : 17.94 % Favored : 80.67 % 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: 0.46 (0.29), residues: 915 helix: 2.00 (0.29), residues: 354 sheet: 1.07 (0.63), residues: 96 loop : -1.29 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 219 HIS 0.008 0.001 HIS C 238 PHE 0.010 0.001 PHE B 245 TYR 0.021 0.001 TYR A 72 ARG 0.004 0.000 ARG B 196 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 129 time to evaluate : 0.963 Fit side-chains REVERT: c 420 MET cc_start: 0.8971 (tmm) cc_final: 0.8724 (tmm) outliers start: 12 outliers final: 12 residues processed: 132 average time/residue: 0.2131 time to fit residues: 38.4513 Evaluate side-chains 140 residues out of total 864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 128 time to evaluate : 0.966 ------------------------------------------------------------------------------- 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 B residue 103 MET Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain b residue 354 GLN Chi-restraints excluded: chain C residue 103 MET 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 412 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 22 optimal weight: 0.4980 chunk 68 optimal weight: 9.9990 chunk 10 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 73 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 75 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 311 HIS ** 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 = 0.3164 r_free = 0.3164 target = 0.056761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.045302 restraints weight = 31674.279| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 4.25 r_work: 0.2658 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.4404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8424 Z= 0.240 Angle : 0.700 14.412 11370 Z= 0.342 Chirality : 0.044 0.239 1374 Planarity : 0.003 0.031 1365 Dihedral : 7.464 56.862 1899 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.74 % Allowed : 17.48 % Favored : 80.79 % 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: 0.44 (0.29), residues: 915 helix: 2.01 (0.29), residues: 354 sheet: 1.09 (0.63), residues: 96 loop : -1.34 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP a 289 HIS 0.006 0.001 HIS C 238 PHE 0.013 0.001 PHE B 245 TYR 0.020 0.001 TYR A 72 ARG 0.004 0.001 ARG B 196 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1831.12 seconds wall clock time: 34 minutes 21.35 seconds (2061.35 seconds total)