Starting phenix.real_space_refine on Tue Aug 6 21:51:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tnh_41416/08_2024/8tnh_41416.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tnh_41416/08_2024/8tnh_41416.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tnh_41416/08_2024/8tnh_41416.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tnh_41416/08_2024/8tnh_41416.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tnh_41416/08_2024/8tnh_41416.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tnh_41416/08_2024/8tnh_41416.cif" } resolution = 3.32 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= 0.001 sd= 0.032 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 123 5.16 5 C 11001 2.51 5 N 2988 2.21 5 O 3555 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 153": "OE1" <-> "OE2" Residue "A PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 370": "OE1" <-> "OE2" Residue "B PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 648": "OE1" <-> "OE2" Residue "C TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 321": "OD1" <-> "OD2" Residue "C TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 634": "OE1" <-> "OE2" Residue "E GLU 153": "OE1" <-> "OE2" Residue "E ASP 321": "OD1" <-> "OD2" Residue "E ASP 325": "OD1" <-> "OD2" Residue "H GLU 6": "OE1" <-> "OE2" Residue "J TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 17667 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 3567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3567 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "B" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1009 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 1, 'TRANS': 125} Chain breaks: 1 Chain: "C" Number of atoms: 3567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3567 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "D" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1002 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "E" Number of atoms: 3567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3567 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "F" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1002 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "H" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 968 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "I" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 968 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "J" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 968 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} 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: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: "V" 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: "W" 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: "X" 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: "Y" 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: "Z" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "a" 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: "b" 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: "c" 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: "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: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 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: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "E" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 9.95, per 1000 atoms: 0.56 Number of scatterers: 17667 At special positions: 0 Unit cell: (136.53, 133.2, 126.54, 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 123 16.00 O 3555 8.00 N 2988 7.00 C 11001 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.04 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.04 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.04 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 433 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.04 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.05 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.05 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.04 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.04 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.05 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS H 50 " - pdb=" SG CYS H 100 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.04 Simple disulfide: pdb=" SG CYS I 50 " - pdb=" SG CYS I 100 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.04 Simple disulfide: pdb=" SG CYS J 50 " - pdb=" SG CYS J 100 " 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 ALPHA1-3 " BMA S 3 " - " MAN S 4 " " BMA Z 3 " - " MAN Z 4 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " 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 S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 133 " " NAG A 603 " - " ASN A 160 " " NAG A 604 " - " ASN A 234 " " NAG A 605 " - " ASN A 332 " " NAG A 606 " - " ASN A 392 " " NAG A 607 " - " ASN A 448 " " NAG A 608 " - " ASN A 339 " " NAG A 609 " - " ASN A 301 " " NAG A 610 " - " ASN A 197 " " NAG B 701 " - " ASN B 637 " " NAG C 601 " - " ASN C 133 " " NAG C 602 " - " ASN C 234 " " NAG C 603 " - " ASN C 392 " " NAG C 604 " - " ASN C 448 " " NAG C 605 " - " ASN C 339 " " NAG C 606 " - " ASN C 301 " " NAG C 607 " - " ASN C 197 " " NAG E 601 " - " ASN E 88 " " NAG E 602 " - " ASN E 133 " " NAG E 603 " - " ASN E 160 " " NAG E 604 " - " ASN E 234 " " NAG E 605 " - " ASN E 301 " " NAG E 606 " - " ASN E 392 " " NAG E 607 " - " ASN E 448 " " NAG E 608 " - " ASN E 339 " " NAG E 609 " - " ASN E 197 " " NAG G 1 " - " ASN A 156 " " NAG K 1 " - " ASN A 262 " " NAG L 1 " - " ASN A 276 " " NAG M 1 " - " ASN A 295 " " NAG N 1 " - " ASN A 363 " " NAG O 1 " - " ASN A 386 " " NAG P 1 " - " ASN C 88 " " NAG Q 1 " - " ASN C 156 " " NAG R 1 " - " ASN C 160 " " NAG S 1 " - " ASN C 262 " " NAG T 1 " - " ASN C 276 " " NAG U 1 " - " ASN C 295 " " NAG V 1 " - " ASN C 332 " " NAG W 1 " - " ASN C 363 " " NAG X 1 " - " ASN C 386 " " NAG Y 1 " - " ASN E 156 " " NAG Z 1 " - " ASN E 262 " " NAG a 1 " - " ASN E 276 " " NAG b 1 " - " ASN E 295 " " NAG c 1 " - " ASN E 332 " " NAG d 1 " - " ASN E 363 " " NAG e 1 " - " ASN E 386 " Time building additional restraints: 7.67 Conformation dependent library (CDL) restraints added in 3.2 seconds 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3926 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 44 sheets defined 19.8% alpha, 24.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.44 Creating SS restraints... Processing helix chain 'A' and resid 58 through 62 removed outlier: 4.106A pdb=" N GLU A 62 " --> pdb=" O LYS A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 99 through 113 removed outlier: 3.685A pdb=" N GLN A 103 " --> pdb=" O ASN A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 335 through 349 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 377 through 381 removed outlier: 3.969A pdb=" N GLY A 380 " --> pdb=" O ASN A 377 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU A 381 " --> pdb=" O CYS A 378 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 377 through 381' Processing helix chain 'B' and resid 536 through 543 removed outlier: 4.465A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA B 541 " --> pdb=" O LEU B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 596 removed outlier: 3.863A pdb=" N LEU B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TRP B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 615 Processing helix chain 'B' and resid 618 through 625 removed outlier: 3.721A pdb=" N ASN B 625 " --> pdb=" O GLU B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 639 through 664 removed outlier: 3.990A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA B 662 " --> pdb=" O GLN B 658 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU B 663 " --> pdb=" O ASP B 659 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASP B 664 " --> pdb=" O LEU B 660 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 62 removed outlier: 4.024A pdb=" N GLU C 62 " --> pdb=" O LYS C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 98 No H-bonds generated for 'chain 'C' and resid 96 through 98' Processing helix chain 'C' and resid 99 through 113 removed outlier: 3.683A pdb=" N GLN C 103 " --> pdb=" O ASN C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 126 removed outlier: 4.004A pdb=" N CYS C 126 " --> pdb=" O THR C 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 123 through 126' Processing helix chain 'C' and resid 335 through 349 Processing helix chain 'C' and resid 475 through 479 Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 542 removed outlier: 4.096A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 597 removed outlier: 3.617A pdb=" N LEU D 576 " --> pdb=" O GLY D 572 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLY D 597 " --> pdb=" O LEU D 593 " (cutoff:3.500A) Processing helix chain 'D' and resid 619 through 624 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 664 removed outlier: 3.862A pdb=" N ILE D 642 " --> pdb=" O TYR D 638 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N TYR D 643 " --> pdb=" O THR D 639 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLY D 644 " --> pdb=" O GLN D 640 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 62 removed outlier: 4.032A pdb=" N GLU E 62 " --> pdb=" O LYS E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 74 removed outlier: 3.835A pdb=" N ALA E 73 " --> pdb=" O ALA E 70 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N CYS E 74 " --> pdb=" O THR E 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 70 through 74' Processing helix chain 'E' and resid 94 through 98 removed outlier: 3.820A pdb=" N ASN E 98 " --> pdb=" O MET E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 113 removed outlier: 3.714A pdb=" N GLN E 103 " --> pdb=" O ASN E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 151 removed outlier: 3.628A pdb=" N ARG E 151 " --> pdb=" O ASP E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 350 Processing helix chain 'E' and resid 368 through 373 removed outlier: 3.783A pdb=" N THR E 373 " --> pdb=" O LEU E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 480 removed outlier: 3.838A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 543 removed outlier: 3.728A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 596 removed outlier: 3.929A pdb=" N LEU F 576 " --> pdb=" O GLY F 572 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N TRP F 596 " --> pdb=" O LEU F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 619 through 625 removed outlier: 3.635A pdb=" N TRP F 623 " --> pdb=" O LEU F 619 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN F 625 " --> pdb=" O GLU F 621 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 641 through 664 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.676A pdb=" N THR H 87 " --> pdb=" O PRO H 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 87 removed outlier: 3.667A pdb=" N THR I 87 " --> pdb=" O PRO I 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 87 removed outlier: 3.729A pdb=" N THR J 87 " --> pdb=" O PRO J 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 4.666A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR B 606 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.290A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 121 through 122 removed outlier: 4.432A pdb=" N CYS A 201 " --> pdb=" O LEU A 122 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA7, first strand: chain 'A' and resid 271 through 272 removed outlier: 7.871A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 272 removed outlier: 10.142A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 302 through 312 removed outlier: 5.398A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 393 through 395 removed outlier: 3.632A pdb=" N SER A 393 " --> pdb=" O PHE A 361 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 423 through 424 Processing sheet with id=AB3, first strand: chain 'C' and resid 495 through 499 removed outlier: 5.552A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.228A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AB6, first strand: chain 'C' and resid 91 through 94 removed outlier: 3.688A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 121 through 122 removed outlier: 4.513A pdb=" N CYS C 201 " --> pdb=" O LEU C 122 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 174 through 177 Processing sheet with id=AB9, first strand: chain 'C' and resid 271 through 272 Processing sheet with id=AC1, first strand: chain 'C' and resid 377 through 378 removed outlier: 3.542A pdb=" N GLU C 381 " --> pdb=" O CYS C 378 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG C 419 " --> pdb=" O TYR C 384 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 308 through 312 removed outlier: 6.807A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 393 through 395 removed outlier: 3.744A pdb=" N SER C 393 " --> pdb=" O PHE C 361 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 423 through 424 Processing sheet with id=AC5, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.410A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 45 through 47 removed outlier: 4.214A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AC8, first strand: chain 'E' and resid 91 through 93 Processing sheet with id=AC9, first strand: chain 'E' and resid 173 through 177 Processing sheet with id=AD1, first strand: chain 'E' and resid 161 through 162 removed outlier: 3.785A pdb=" N MET E 161 " --> pdb=" O GLN E 170 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 271 through 272 Processing sheet with id=AD3, first strand: chain 'E' and resid 416 through 417 removed outlier: 3.628A pdb=" N ILE E 443 " --> pdb=" O ARG E 298 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 304 through 305 Processing sheet with id=AD5, first strand: chain 'E' and resid 308 through 312 removed outlier: 4.387A pdb=" N GLY E 312 " --> pdb=" O GLN E 315 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN E 315 " --> pdb=" O GLY E 312 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'E' and resid 393 through 395 removed outlier: 3.745A pdb=" N SER E 393 " --> pdb=" O PHE E 361 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 377 through 378 removed outlier: 3.540A pdb=" N CYS E 378 " --> pdb=" O GLU E 381 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS E 421 " --> pdb=" O PHE E 382 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 423 through 424 removed outlier: 3.853A pdb=" N ILE E 424 " --> pdb=" O MET E 434 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AE1, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.268A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N ARG H 38 " --> pdb=" O GLU H 47 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N GLU H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.268A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR H 94 " --> pdb=" O TYR H 102 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TYR H 102 " --> pdb=" O THR H 94 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 3 through 8 Processing sheet with id=AE4, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.228A pdb=" N GLY I 10 " --> pdb=" O THR I 110 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.228A pdb=" N GLY I 10 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR I 94 " --> pdb=" O TYR I 102 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N TYR I 102 " --> pdb=" O THR I 94 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AE7, first strand: chain 'J' and resid 10 through 11 removed outlier: 6.300A pdb=" N GLY J 10 " --> pdb=" O THR J 110 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 10 through 11 removed outlier: 6.300A pdb=" N GLY J 10 " --> pdb=" O THR J 110 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N THR J 94 " --> pdb=" O TYR J 102 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N TYR J 102 " --> pdb=" O THR J 94 " (cutoff:3.500A) 548 hydrogen bonds defined for protein. 1413 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: 5.92 Time building geometry restraints manager: 8.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 3272 1.33 - 1.46: 6720 1.46 - 1.60: 7837 1.60 - 1.74: 2 1.74 - 1.88: 160 Bond restraints: 17991 Sorted by residual: bond pdb=" C THR C 123 " pdb=" N PRO C 124 " ideal model delta sigma weight residual 1.331 1.365 -0.034 7.90e-03 1.60e+04 1.82e+01 bond pdb=" CA ALA A 319 " pdb=" CB ALA A 319 " ideal model delta sigma weight residual 1.531 1.464 0.067 1.58e-02 4.01e+03 1.81e+01 bond pdb=" C TYR A 318 " pdb=" O TYR A 318 " ideal model delta sigma weight residual 1.234 1.189 0.045 1.19e-02 7.06e+03 1.41e+01 bond pdb=" CA ALA C 319 " pdb=" CB ALA C 319 " ideal model delta sigma weight residual 1.535 1.462 0.072 1.93e-02 2.68e+03 1.41e+01 bond pdb=" C TYR E 318 " pdb=" O TYR E 318 " ideal model delta sigma weight residual 1.235 1.196 0.039 1.26e-02 6.30e+03 9.81e+00 ... (remaining 17986 not shown) Histogram of bond angle deviations from ideal: 99.39 - 106.33: 411 106.33 - 113.26: 10280 113.26 - 120.20: 5845 120.20 - 127.14: 7673 127.14 - 134.08: 202 Bond angle restraints: 24411 Sorted by residual: angle pdb=" CA CYS C 296 " pdb=" CB CYS C 296 " pdb=" SG CYS C 296 " ideal model delta sigma weight residual 114.40 130.83 -16.43 2.30e+00 1.89e-01 5.10e+01 angle pdb=" C LYS C 155 " pdb=" N ASN C 156 " pdb=" CA ASN C 156 " ideal model delta sigma weight residual 122.93 114.23 8.70 1.45e+00 4.76e-01 3.60e+01 angle pdb=" CA CYS E 296 " pdb=" CB CYS E 296 " pdb=" SG CYS E 296 " ideal model delta sigma weight residual 114.40 127.28 -12.88 2.30e+00 1.89e-01 3.14e+01 angle pdb=" C ASN C 160 " pdb=" CA ASN C 160 " pdb=" CB ASN C 160 " ideal model delta sigma weight residual 111.70 118.28 -6.58 1.31e+00 5.83e-01 2.52e+01 angle pdb=" N CYS C 296 " pdb=" CA CYS C 296 " pdb=" C CYS C 296 " ideal model delta sigma weight residual 108.42 115.74 -7.32 1.54e+00 4.22e-01 2.26e+01 ... (remaining 24406 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.70: 10351 21.70 - 43.40: 1176 43.40 - 65.09: 237 65.09 - 86.79: 59 86.79 - 108.49: 18 Dihedral angle restraints: 11841 sinusoidal: 5754 harmonic: 6087 Sorted by residual: dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual -86.00 -173.47 87.47 1 1.00e+01 1.00e-02 9.18e+01 dihedral pdb=" CB CYS C 54 " pdb=" SG CYS C 54 " pdb=" SG CYS C 74 " pdb=" CB CYS C 74 " ideal model delta sinusoidal sigma weight residual -86.00 -4.82 -81.18 1 1.00e+01 1.00e-02 8.13e+01 dihedral pdb=" CA ASN C 160 " pdb=" C ASN C 160 " pdb=" N MET C 161 " pdb=" CA MET C 161 " ideal model delta harmonic sigma weight residual -180.00 -142.88 -37.12 0 5.00e+00 4.00e-02 5.51e+01 ... (remaining 11838 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.238: 2947 0.238 - 0.476: 14 0.476 - 0.715: 0 0.715 - 0.953: 0 0.953 - 1.191: 1 Chirality restraints: 2962 Sorted by residual: chirality pdb=" C1 NAG Q 1 " pdb=" ND2 ASN C 156 " pdb=" C2 NAG Q 1 " pdb=" O5 NAG Q 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.21 -1.19 2.00e-01 2.50e+01 3.55e+01 chirality pdb=" C1 NAG C 607 " pdb=" ND2 ASN C 197 " pdb=" C2 NAG C 607 " pdb=" O5 NAG C 607 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" CA ASP E 321A" pdb=" N ASP E 321A" pdb=" C ASP E 321A" pdb=" CB ASP E 321A" both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.26e+00 ... (remaining 2959 not shown) Planarity restraints: 3091 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 160 " 0.067 2.00e-02 2.50e+03 6.03e-02 4.55e+01 pdb=" CG ASN C 160 " -0.079 2.00e-02 2.50e+03 pdb=" OD1 ASN C 160 " 0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN C 160 " -0.057 2.00e-02 2.50e+03 pdb=" C1 NAG R 1 " 0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 156 " -0.042 2.00e-02 2.50e+03 3.98e-02 1.98e+01 pdb=" CG ASN C 156 " 0.047 2.00e-02 2.50e+03 pdb=" OD1 ASN C 156 " -0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN C 156 " 0.045 2.00e-02 2.50e+03 pdb=" C1 NAG Q 1 " -0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 339 " 0.038 2.00e-02 2.50e+03 3.59e-02 1.61e+01 pdb=" CG ASN A 339 " -0.037 2.00e-02 2.50e+03 pdb=" OD1 ASN A 339 " 0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN A 339 " -0.045 2.00e-02 2.50e+03 pdb=" C1 NAG A 608 " 0.040 2.00e-02 2.50e+03 ... (remaining 3088 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1246 2.73 - 3.27: 16167 3.27 - 3.82: 25524 3.82 - 4.36: 29141 4.36 - 4.90: 53977 Nonbonded interactions: 126055 Sorted by model distance: nonbonded pdb=" O SER C 375 " pdb=" OG SER C 375 " model vdw 2.191 3.040 nonbonded pdb=" NH2 ARG B 617 " pdb=" OE1 GLU B 634 " model vdw 2.199 3.120 nonbonded pdb=" OE1 GLN C 258 " pdb=" OG1 THR C 387 " model vdw 2.222 3.040 nonbonded pdb=" N GLU C 49 " pdb=" OE1 GLU C 49 " model vdw 2.244 3.120 nonbonded pdb=" O SER E 375 " pdb=" OG SER E 375 " model vdw 2.251 3.040 ... (remaining 126050 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' and (resid 31 through 505 or resid 601 through 607)) selection = chain 'C' selection = (chain 'E' and (resid 31 through 505 or resid 601 through 607)) } ncs_group { reference = (chain 'B' and resid 519 through 664) selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'S' selection = chain 'Z' } 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: 1.170 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: 0.020 Extract box with map and model: 0.650 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 49.100 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.110 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: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 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 : 0.005 0.073 17991 Z= 0.309 Angle : 0.773 16.426 24411 Z= 0.404 Chirality : 0.057 1.191 2962 Planarity : 0.004 0.055 3042 Dihedral : 18.142 108.487 7798 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.05 % Favored : 90.71 % Rotamer: Outliers : 0.48 % Allowed : 32.14 % Favored : 67.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -1.36 (0.19), residues: 2077 helix: 1.96 (0.31), residues: 333 sheet: -0.75 (0.21), residues: 654 loop : -1.99 (0.18), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 596 HIS 0.003 0.001 HIS J 100C PHE 0.023 0.001 PHE J 98 TYR 0.017 0.001 TYR C 484 ARG 0.007 0.000 ARG A 151 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 335 time to evaluate : 2.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.7559 (t0) cc_final: 0.7012 (t0) REVERT: B 588 ARG cc_start: 0.6581 (ttm110) cc_final: 0.6330 (ttm-80) REVERT: C 478 ASN cc_start: 0.8427 (m-40) cc_final: 0.8095 (t0) REVERT: H 79 TYR cc_start: 0.8715 (m-80) cc_final: 0.8140 (m-80) REVERT: H 95 ASP cc_start: 0.8524 (t0) cc_final: 0.8314 (m-30) REVERT: I 18 LEU cc_start: 0.8503 (mt) cc_final: 0.8202 (mp) REVERT: I 79 TYR cc_start: 0.8513 (m-80) cc_final: 0.8123 (m-80) REVERT: J 28 ASP cc_start: 0.8240 (p0) cc_final: 0.7389 (p0) REVERT: J 79 TYR cc_start: 0.8656 (m-80) cc_final: 0.8018 (m-80) outliers start: 9 outliers final: 2 residues processed: 342 average time/residue: 0.3543 time to fit residues: 172.6524 Evaluate side-chains 205 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 203 time to evaluate : 2.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 156 ASN Chi-restraints excluded: chain I residue 50 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 6.9990 chunk 156 optimal weight: 5.9990 chunk 87 optimal weight: 7.9990 chunk 53 optimal weight: 7.9990 chunk 105 optimal weight: 0.0070 chunk 83 optimal weight: 7.9990 chunk 162 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 98 optimal weight: 0.9980 chunk 120 optimal weight: 0.3980 chunk 187 optimal weight: 0.4980 overall best weight: 1.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS A 258 GLN A 293 GLN A 330 HIS A 348 GLN B 651 ASN C 67 ASN ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 ASN C 293 GLN C 302 ASN C 348 GLN C 411 ASN D 625 ASN ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 ASN F 590 GLN F 591 GLN F 637 ASN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 82BASN J 57 GLN J 82BASN J 108 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 17991 Z= 0.226 Angle : 0.697 13.636 24411 Z= 0.356 Chirality : 0.047 0.329 2962 Planarity : 0.004 0.041 3042 Dihedral : 10.257 75.757 3852 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.18 % Favored : 91.67 % Rotamer: Outliers : 4.45 % Allowed : 30.04 % Favored : 65.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.22 (0.19), residues: 2077 helix: 1.96 (0.29), residues: 337 sheet: -0.85 (0.21), residues: 624 loop : -1.70 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 69 HIS 0.006 0.001 HIS J 100C PHE 0.015 0.001 PHE A 382 TYR 0.014 0.001 TYR H 60 ARG 0.006 0.001 ARG E 327 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 223 time to evaluate : 2.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.9218 (OUTLIER) cc_final: 0.8643 (m100) REVERT: A 114 GLN cc_start: 0.8003 (tm-30) cc_final: 0.7782 (tm-30) REVERT: C 185 ASN cc_start: 0.6766 (t0) cc_final: 0.6446 (t0) REVERT: E 185 ASN cc_start: 0.6809 (t0) cc_final: 0.6587 (t0) REVERT: E 426 MET cc_start: 0.7734 (ttp) cc_final: 0.7448 (ptt) REVERT: I 82 MET cc_start: 0.8202 (mpp) cc_final: 0.7953 (mpp) REVERT: I 82 ASN cc_start: 0.8743 (OUTLIER) cc_final: 0.8523 (t0) REVERT: I 95 ASP cc_start: 0.8218 (m-30) cc_final: 0.7727 (m-30) REVERT: J 28 ASP cc_start: 0.8197 (p0) cc_final: 0.7992 (p0) REVERT: J 30 GLU cc_start: 0.7569 (mp0) cc_final: 0.7223 (mp0) outliers start: 83 outliers final: 29 residues processed: 299 average time/residue: 0.3071 time to fit residues: 137.1045 Evaluate side-chains 223 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 192 time to evaluate : 2.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 156 ASN Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 418 CYS Chi-restraints excluded: chain D residue 570 VAL Chi-restraints excluded: chain D residue 603 ILE Chi-restraints excluded: chain D residue 604 CYS Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 433 CYS Chi-restraints excluded: chain E residue 465 THR Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 82 ASN Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 82 ASN Chi-restraints excluded: chain J residue 100 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 104 optimal weight: 8.9990 chunk 58 optimal weight: 7.9990 chunk 156 optimal weight: 0.7980 chunk 128 optimal weight: 6.9990 chunk 51 optimal weight: 0.8980 chunk 188 optimal weight: 0.9990 chunk 203 optimal weight: 0.3980 chunk 167 optimal weight: 6.9990 chunk 186 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 151 optimal weight: 4.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 ASN C 72 HIS C 105 HIS ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 478 ASN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 82BASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 17991 Z= 0.215 Angle : 0.672 16.931 24411 Z= 0.342 Chirality : 0.046 0.268 2962 Planarity : 0.004 0.039 3042 Dihedral : 9.021 59.941 3851 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.04 % Favored : 91.82 % Rotamer: Outliers : 3.81 % Allowed : 29.45 % Favored : 66.74 % 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: -1.11 (0.19), residues: 2077 helix: 2.21 (0.30), residues: 325 sheet: -0.72 (0.21), residues: 651 loop : -1.70 (0.18), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 479 HIS 0.005 0.001 HIS J 100C PHE 0.014 0.001 PHE A 382 TYR 0.014 0.001 TYR J 79 ARG 0.005 0.000 ARG D 542 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 212 time to evaluate : 2.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8096 (tm-30) cc_final: 0.7827 (tm-30) REVERT: C 185 ASN cc_start: 0.6331 (t0) cc_final: 0.6089 (t0) REVERT: E 104 MET cc_start: 0.8644 (OUTLIER) cc_final: 0.8359 (tmm) REVERT: E 185 ASN cc_start: 0.6783 (t0) cc_final: 0.6517 (t0) REVERT: E 426 MET cc_start: 0.7609 (ttp) cc_final: 0.7402 (ptt) REVERT: H 18 LEU cc_start: 0.9184 (tp) cc_final: 0.8944 (tp) REVERT: I 5 GLN cc_start: 0.8436 (tm-30) cc_final: 0.8227 (tm-30) REVERT: J 28 ASP cc_start: 0.8198 (p0) cc_final: 0.7966 (p0) outliers start: 71 outliers final: 38 residues processed: 271 average time/residue: 0.3299 time to fit residues: 134.7132 Evaluate side-chains 231 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 192 time to evaluate : 2.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 156 ASN Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 418 CYS Chi-restraints excluded: chain D residue 603 ILE Chi-restraints excluded: chain D residue 604 CYS Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 104 MET Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 433 CYS Chi-restraints excluded: chain E residue 465 THR Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 50 CYS Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain J residue 27 LEU Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 82 ASN Chi-restraints excluded: chain J residue 100 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 186 optimal weight: 5.9990 chunk 141 optimal weight: 5.9990 chunk 97 optimal weight: 8.9990 chunk 20 optimal weight: 6.9990 chunk 89 optimal weight: 10.0000 chunk 126 optimal weight: 5.9990 chunk 188 optimal weight: 0.9980 chunk 200 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 179 optimal weight: 0.4980 chunk 53 optimal weight: 8.9990 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 ASN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 82BASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 17991 Z= 0.327 Angle : 0.701 16.621 24411 Z= 0.355 Chirality : 0.045 0.259 2962 Planarity : 0.004 0.038 3042 Dihedral : 8.242 59.828 3851 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.71 % Favored : 91.24 % Rotamer: Outliers : 3.65 % Allowed : 30.90 % Favored : 65.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.08 (0.19), residues: 2077 helix: 2.18 (0.30), residues: 330 sheet: -0.73 (0.21), residues: 663 loop : -1.66 (0.19), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP C 479 HIS 0.004 0.001 HIS J 100C PHE 0.019 0.001 PHE C 159 TYR 0.015 0.001 TYR J 102 ARG 0.005 0.000 ARG C 327 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 195 time to evaluate : 3.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8811 (tmm) cc_final: 0.8555 (tmm) REVERT: A 114 GLN cc_start: 0.8200 (tm-30) cc_final: 0.7910 (tm-30) REVERT: A 278 THR cc_start: 0.9425 (OUTLIER) cc_final: 0.9209 (p) REVERT: C 185 ASN cc_start: 0.6458 (t0) cc_final: 0.6168 (t0) REVERT: E 185 ASN cc_start: 0.6993 (t0) cc_final: 0.6742 (t0) REVERT: I 74 GLU cc_start: 0.8624 (pp20) cc_final: 0.8355 (pp20) REVERT: I 95 ASP cc_start: 0.8381 (m-30) cc_final: 0.8144 (m-30) outliers start: 68 outliers final: 46 residues processed: 251 average time/residue: 0.3283 time to fit residues: 125.1365 Evaluate side-chains 227 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 180 time to evaluate : 1.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain B residue 542 ARG Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 418 CYS Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 455 THR Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain D residue 603 ILE Chi-restraints excluded: chain D residue 604 CYS Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 433 CYS Chi-restraints excluded: chain E residue 465 THR Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain H residue 50 CYS Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain J residue 27 LEU Chi-restraints excluded: chain J residue 37 ILE Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 82 ASN Chi-restraints excluded: chain J residue 100 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 166 optimal weight: 9.9990 chunk 113 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 148 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 170 optimal weight: 6.9990 chunk 138 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 102 optimal weight: 9.9990 chunk 179 optimal weight: 0.0060 chunk 50 optimal weight: 5.9990 overall best weight: 0.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 82BASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 17991 Z= 0.194 Angle : 0.661 15.423 24411 Z= 0.335 Chirality : 0.045 0.250 2962 Planarity : 0.004 0.036 3042 Dihedral : 7.560 59.939 3849 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.23 % Favored : 91.67 % Rotamer: Outliers : 2.74 % Allowed : 31.17 % Favored : 66.09 % 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: -1.08 (0.19), residues: 2077 helix: 1.98 (0.30), residues: 330 sheet: -0.63 (0.21), residues: 666 loop : -1.66 (0.19), residues: 1081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 479 HIS 0.003 0.001 HIS J 100C PHE 0.016 0.001 PHE C 159 TYR 0.013 0.001 TYR A 39 ARG 0.006 0.001 ARG J 96 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 203 time to evaluate : 2.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8738 (tmm) cc_final: 0.8457 (tmm) REVERT: A 114 GLN cc_start: 0.8213 (tm-30) cc_final: 0.7938 (tm-30) REVERT: C 185 ASN cc_start: 0.6262 (t0) cc_final: 0.6010 (t0) REVERT: E 185 ASN cc_start: 0.6862 (t0) cc_final: 0.6612 (t0) REVERT: H 102 TYR cc_start: 0.8721 (m-80) cc_final: 0.8469 (m-80) REVERT: I 74 GLU cc_start: 0.8566 (pp20) cc_final: 0.8327 (pp20) REVERT: J 28 ASP cc_start: 0.8469 (p0) cc_final: 0.8189 (p0) REVERT: J 30 GLU cc_start: 0.7757 (mp0) cc_final: 0.7537 (mp0) outliers start: 51 outliers final: 34 residues processed: 249 average time/residue: 0.2926 time to fit residues: 110.5312 Evaluate side-chains 220 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 186 time to evaluate : 1.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 157 CYS Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 418 CYS Chi-restraints excluded: chain D residue 603 ILE Chi-restraints excluded: chain D residue 604 CYS Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 433 CYS Chi-restraints excluded: chain E residue 465 THR Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain H residue 50 CYS Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 82 ASN Chi-restraints excluded: chain J residue 100 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 67 optimal weight: 0.2980 chunk 180 optimal weight: 9.9990 chunk 39 optimal weight: 6.9990 chunk 117 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 200 optimal weight: 3.9990 chunk 166 optimal weight: 10.0000 chunk 92 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 105 optimal weight: 9.9990 overall best weight: 3.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 440 GLN J 82BASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 17991 Z= 0.325 Angle : 0.700 14.742 24411 Z= 0.357 Chirality : 0.045 0.242 2962 Planarity : 0.004 0.047 3042 Dihedral : 7.403 58.497 3849 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.15 % Favored : 90.76 % Rotamer: Outliers : 3.65 % Allowed : 30.90 % Favored : 65.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.03 (0.19), residues: 2077 helix: 1.92 (0.29), residues: 332 sheet: -0.61 (0.21), residues: 672 loop : -1.59 (0.19), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 479 HIS 0.003 0.001 HIS H 100C PHE 0.015 0.001 PHE A 382 TYR 0.025 0.002 TYR I 102 ARG 0.007 0.001 ARG D 542 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 191 time to evaluate : 2.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.8786 (tmm) cc_final: 0.8559 (tmm) REVERT: A 114 GLN cc_start: 0.8249 (tm-30) cc_final: 0.7954 (tm-30) REVERT: A 150 MET cc_start: 0.9034 (mpp) cc_final: 0.8380 (mmt) REVERT: C 185 ASN cc_start: 0.6450 (t0) cc_final: 0.6211 (t0) REVERT: I 74 GLU cc_start: 0.8614 (pp20) cc_final: 0.8353 (pp20) REVERT: I 82 MET cc_start: 0.8382 (mpp) cc_final: 0.8119 (mpp) outliers start: 68 outliers final: 50 residues processed: 250 average time/residue: 0.2915 time to fit residues: 110.4763 Evaluate side-chains 223 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 173 time to evaluate : 1.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 418 CYS Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 455 THR Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain D residue 603 ILE Chi-restraints excluded: chain D residue 604 CYS Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 104 MET Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 433 CYS Chi-restraints excluded: chain E residue 465 THR Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain H residue 50 CYS Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 82 ASN Chi-restraints excluded: chain J residue 100 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 193 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 114 optimal weight: 7.9990 chunk 146 optimal weight: 8.9990 chunk 113 optimal weight: 8.9990 chunk 168 optimal weight: 5.9990 chunk 111 optimal weight: 0.7980 chunk 199 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 82BASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 17991 Z= 0.245 Angle : 0.681 14.671 24411 Z= 0.348 Chirality : 0.045 0.247 2962 Planarity : 0.004 0.049 3042 Dihedral : 7.110 58.408 3849 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.23 % Favored : 91.67 % Rotamer: Outliers : 3.70 % Allowed : 30.90 % Favored : 65.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.01 (0.19), residues: 2077 helix: 1.98 (0.29), residues: 329 sheet: -0.53 (0.21), residues: 654 loop : -1.64 (0.19), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 479 HIS 0.003 0.001 HIS J 100C PHE 0.014 0.001 PHE A 382 TYR 0.025 0.001 TYR I 102 ARG 0.007 0.000 ARG D 542 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 192 time to evaluate : 2.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLN cc_start: 0.8226 (tm-30) cc_final: 0.7921 (tm-30) REVERT: C 185 ASN cc_start: 0.6395 (t0) cc_final: 0.6157 (t0) REVERT: E 150 MET cc_start: 0.8528 (mpp) cc_final: 0.8179 (mpp) REVERT: I 28 ASP cc_start: 0.8319 (p0) cc_final: 0.8019 (p0) REVERT: I 74 GLU cc_start: 0.8587 (pp20) cc_final: 0.8348 (pp20) REVERT: I 82 MET cc_start: 0.8384 (mpp) cc_final: 0.7975 (mpp) outliers start: 69 outliers final: 52 residues processed: 251 average time/residue: 0.2937 time to fit residues: 112.1487 Evaluate side-chains 228 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 176 time to evaluate : 2.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 418 CYS Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain D residue 603 ILE Chi-restraints excluded: chain D residue 604 CYS Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 161 MET Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 433 CYS Chi-restraints excluded: chain E residue 465 THR Chi-restraints excluded: chain F residue 584 GLU Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain H residue 50 CYS Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain J residue 50 CYS Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 82 ASN Chi-restraints excluded: chain J residue 100 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 123 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 119 optimal weight: 7.9990 chunk 60 optimal weight: 0.2980 chunk 39 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 126 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 98 optimal weight: 9.9990 chunk 18 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 82BASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 17991 Z= 0.281 Angle : 0.718 14.923 24411 Z= 0.368 Chirality : 0.046 0.285 2962 Planarity : 0.004 0.049 3042 Dihedral : 7.029 59.858 3849 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.24 % Favored : 90.66 % Rotamer: Outliers : 3.22 % Allowed : 31.71 % Favored : 65.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.05 (0.19), residues: 2077 helix: 1.72 (0.29), residues: 331 sheet: -0.51 (0.21), residues: 639 loop : -1.61 (0.19), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 479 HIS 0.004 0.001 HIS H 100C PHE 0.014 0.001 PHE A 382 TYR 0.013 0.001 TYR J 60 ARG 0.008 0.000 ARG D 542 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 188 time to evaluate : 2.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 185 ASN cc_start: 0.6671 (t0) cc_final: 0.6452 (t0) REVERT: E 150 MET cc_start: 0.8591 (mpp) cc_final: 0.8251 (mpp) REVERT: I 82 MET cc_start: 0.8385 (mpp) cc_final: 0.7911 (mpp) REVERT: I 102 TYR cc_start: 0.8560 (m-80) cc_final: 0.8337 (m-10) REVERT: J 28 ASP cc_start: 0.8649 (p0) cc_final: 0.8118 (p0) REVERT: J 73 ASN cc_start: 0.8557 (p0) cc_final: 0.8202 (p0) outliers start: 60 outliers final: 54 residues processed: 239 average time/residue: 0.2942 time to fit residues: 106.3936 Evaluate side-chains 232 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 178 time to evaluate : 2.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 418 CYS Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain D residue 603 ILE Chi-restraints excluded: chain D residue 604 CYS Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 161 MET Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 433 CYS Chi-restraints excluded: chain E residue 465 THR Chi-restraints excluded: chain F residue 584 GLU Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain H residue 50 CYS Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain J residue 50 CYS Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 82 ASN Chi-restraints excluded: chain J residue 100 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 181 optimal weight: 3.9990 chunk 191 optimal weight: 6.9990 chunk 174 optimal weight: 6.9990 chunk 185 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 145 optimal weight: 5.9990 chunk 57 optimal weight: 7.9990 chunk 168 optimal weight: 6.9990 chunk 175 optimal weight: 0.4980 chunk 122 optimal weight: 0.0000 overall best weight: 2.2990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 5 GLN J 82BASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 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 : 0.004 0.088 17991 Z= 0.271 Angle : 0.737 14.408 24411 Z= 0.375 Chirality : 0.046 0.269 2962 Planarity : 0.004 0.056 3042 Dihedral : 6.929 58.133 3849 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.71 % Favored : 91.19 % Rotamer: Outliers : 3.33 % Allowed : 31.38 % Favored : 65.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.11 (0.19), residues: 2077 helix: 1.65 (0.29), residues: 331 sheet: -0.58 (0.22), residues: 600 loop : -1.60 (0.19), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 479 HIS 0.004 0.001 HIS J 100C PHE 0.013 0.001 PHE A 382 TYR 0.016 0.001 TYR I 102 ARG 0.008 0.000 ARG D 542 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 187 time to evaluate : 2.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ASN cc_start: 0.9059 (t0) cc_final: 0.8840 (p0) REVERT: A 150 MET cc_start: 0.9067 (mpp) cc_final: 0.8373 (mmp) REVERT: E 150 MET cc_start: 0.8664 (mpp) cc_final: 0.8326 (mpp) REVERT: I 28 ASP cc_start: 0.8230 (p0) cc_final: 0.7999 (p0) REVERT: I 82 MET cc_start: 0.8372 (mpp) cc_final: 0.7894 (mpp) REVERT: I 102 TYR cc_start: 0.8526 (m-80) cc_final: 0.8276 (m-10) REVERT: J 73 ASN cc_start: 0.8533 (p0) cc_final: 0.7879 (p0) outliers start: 62 outliers final: 53 residues processed: 237 average time/residue: 0.2896 time to fit residues: 104.0815 Evaluate side-chains 229 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 176 time to evaluate : 1.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 418 CYS Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain D residue 603 ILE Chi-restraints excluded: chain D residue 604 CYS Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 161 MET Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 433 CYS Chi-restraints excluded: chain E residue 465 THR Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 27 LEU Chi-restraints excluded: chain H residue 50 CYS Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain J residue 50 CYS Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 82 ASN Chi-restraints excluded: chain J residue 100 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 196 optimal weight: 9.9990 chunk 119 optimal weight: 9.9990 chunk 93 optimal weight: 2.9990 chunk 136 optimal weight: 6.9990 chunk 206 optimal weight: 0.1980 chunk 189 optimal weight: 6.9990 chunk 164 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 126 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 130 optimal weight: 6.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 330 HIS D 651 ASN ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 82BASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 17991 Z= 0.309 Angle : 0.759 13.908 24411 Z= 0.388 Chirality : 0.046 0.259 2962 Planarity : 0.004 0.056 3042 Dihedral : 6.896 58.125 3849 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.44 % Favored : 90.47 % Rotamer: Outliers : 3.00 % Allowed : 31.97 % Favored : 65.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.15 (0.19), residues: 2077 helix: 1.62 (0.29), residues: 328 sheet: -0.57 (0.22), residues: 606 loop : -1.63 (0.19), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 479 HIS 0.003 0.001 HIS J 100C PHE 0.021 0.001 PHE D 522 TYR 0.017 0.001 TYR I 102 ARG 0.009 0.000 ARG D 542 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4154 Ramachandran restraints generated. 2077 Oldfield, 0 Emsley, 2077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 181 time to evaluate : 1.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ASN cc_start: 0.9001 (t0) cc_final: 0.8702 (p0) REVERT: E 150 MET cc_start: 0.8744 (mpp) cc_final: 0.8405 (mpp) REVERT: H 28 ASP cc_start: 0.8803 (p0) cc_final: 0.8365 (p0) REVERT: H 30 GLU cc_start: 0.8229 (pm20) cc_final: 0.8008 (mp0) REVERT: I 28 ASP cc_start: 0.8258 (p0) cc_final: 0.7989 (p0) REVERT: I 82 MET cc_start: 0.8368 (mpp) cc_final: 0.7895 (mpp) REVERT: J 73 ASN cc_start: 0.8616 (p0) cc_final: 0.8193 (p0) outliers start: 56 outliers final: 49 residues processed: 226 average time/residue: 0.2832 time to fit residues: 97.2934 Evaluate side-chains 226 residues out of total 1864 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 177 time to evaluate : 1.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 418 CYS Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain D residue 604 CYS Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 433 CYS Chi-restraints excluded: chain E residue 465 THR Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 50 CYS Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 52 SER Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain J residue 50 CYS Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 52 SER Chi-restraints excluded: chain J residue 82 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 7.9990 chunk 50 optimal weight: 0.8980 chunk 151 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 164 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 168 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 30 optimal weight: 0.0050 chunk 144 optimal weight: 1.9990 overall best weight: 1.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 82BASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.048250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2609 r_free = 0.2609 target = 0.035858 restraints weight = 85406.325| |-----------------------------------------------------------------------------| r_work (start): 0.2589 rms_B_bonded: 6.22 r_work: 0.2405 rms_B_bonded: 6.16 restraints_weight: 2.0000 r_work (final): 0.2405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 17991 Z= 0.220 Angle : 0.741 14.215 24411 Z= 0.378 Chirality : 0.046 0.252 2962 Planarity : 0.004 0.055 3042 Dihedral : 6.697 58.573 3849 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.23 % Favored : 91.67 % Rotamer: Outliers : 2.20 % Allowed : 32.67 % Favored : 65.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.08 (0.19), residues: 2077 helix: 1.59 (0.29), residues: 328 sheet: -0.51 (0.22), residues: 606 loop : -1.57 (0.19), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 427 HIS 0.004 0.001 HIS J 100C PHE 0.014 0.001 PHE D 522 TYR 0.018 0.001 TYR I 102 ARG 0.007 0.000 ARG D 542 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3580.02 seconds wall clock time: 65 minutes 10.25 seconds (3910.25 seconds total)