Starting phenix.real_space_refine on Tue Feb 20 03:44:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qus_14153/02_2024/7qus_14153_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qus_14153/02_2024/7qus_14153.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qus_14153/02_2024/7qus_14153.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qus_14153/02_2024/7qus_14153.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qus_14153/02_2024/7qus_14153_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qus_14153/02_2024/7qus_14153_updated.pdb" } resolution = 2.39 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= 0.005 sd= 0.161 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 120 5.16 5 C 16998 2.51 5 N 4377 2.21 5 O 5247 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 169": "OE1" <-> "OE2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 428": "OD1" <-> "OD2" Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 554": "OE1" <-> "OE2" Residue "A ASP 568": "OD1" <-> "OD2" Residue "A ASP 571": "OD1" <-> "OD2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 654": "OE1" <-> "OE2" Residue "A PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 950": "OD1" <-> "OD2" Residue "A GLU 1017": "OE1" <-> "OE2" Residue "A TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 169": "OE1" <-> "OE2" Residue "B PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 428": "OD1" <-> "OD2" Residue "B TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 554": "OE1" <-> "OE2" Residue "B ASP 568": "OD1" <-> "OD2" Residue "B ASP 571": "OD1" <-> "OD2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 654": "OE1" <-> "OE2" Residue "B PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 950": "OD1" <-> "OD2" Residue "B GLU 1017": "OE1" <-> "OE2" Residue "B TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 169": "OE1" <-> "OE2" Residue "C PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 428": "OD1" <-> "OD2" Residue "C TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 554": "OE1" <-> "OE2" Residue "C ASP 568": "OD1" <-> "OD2" Residue "C ASP 571": "OD1" <-> "OD2" Residue "C PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 654": "OE1" <-> "OE2" Residue "C PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 950": "OD1" <-> "OD2" Residue "C GLU 1017": "OE1" <-> "OE2" Residue "C TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 26742 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 8594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1101, 8594 Classifications: {'peptide': 1101} Link IDs: {'PTRANS': 49, 'TRANS': 1051} Chain breaks: 2 Chain: "B" Number of atoms: 8594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1101, 8594 Classifications: {'peptide': 1101} Link IDs: {'PTRANS': 49, 'TRANS': 1051} Chain breaks: 2 Chain: "C" Number of atoms: 8594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1101, 8594 Classifications: {'peptide': 1101} Link IDs: {'PTRANS': 49, 'TRANS': 1051} Chain breaks: 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: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 48 Unusual residues: {'FUC': 2, '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: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 48 Unusual residues: {'FUC': 2, '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: "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: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 48 Unusual residues: {'FUC': 2, '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: 188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 188 Unusual residues: {'EIC': 1, 'NAG': 12} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 188 Unusual residues: {'EIC': 1, 'NAG': 12} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "C" Number of atoms: 188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 188 Unusual residues: {'EIC': 1, 'NAG': 12} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 14.15, per 1000 atoms: 0.53 Number of scatterers: 26742 At special positions: 0 Unit cell: (151.7, 154.16, 165.64, 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 120 16.00 O 5247 8.00 N 4377 7.00 C 16998 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-3 " NAG G 1 " - " FUC G 2 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG K 1 " - " FUC K 2 " " NAG O 1 " - " FUC O 2 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG 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 3 " BETA1-6 " NAG G 1 " - " FUC G 4 " " NAG K 1 " - " FUC K 4 " " NAG O 1 " - " FUC O 4 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 149 " " NAG A1308 " - " ASN A 709 " " NAG A1309 " - " ASN A1074 " " NAG A1310 " - " ASN A1098 " " NAG A1311 " - " ASN A1134 " " NAG A1312 " - " ASN A 17 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 343 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 149 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B1074 " " NAG B1310 " - " ASN B1098 " " NAG B1311 " - " ASN B1134 " " NAG B1312 " - " ASN B 17 " " NAG C1302 " - " ASN C 61 " " NAG C1303 " - " ASN C 122 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 331 " " NAG C1306 " - " ASN C 343 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 149 " " NAG C1309 " - " ASN C 709 " " NAG C1310 " - " ASN C1074 " " NAG C1311 " - " ASN C1098 " " NAG C1312 " - " ASN C1134 " " NAG C1313 " - " ASN C 17 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A 165 " " NAG H 1 " - " ASN B 234 " " NAG I 1 " - " ASN B 717 " " NAG J 1 " - " ASN B 801 " " NAG K 1 " - " ASN B 165 " " NAG L 1 " - " ASN C 234 " " NAG M 1 " - " ASN C 717 " " NAG N 1 " - " ASN C 801 " " NAG O 1 " - " ASN C 165 " Time building additional restraints: 10.76 Conformation dependent library (CDL) restraints added in 5.1 seconds 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6162 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 63 helices and 39 sheets defined 21.3% alpha, 22.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.28 Creating SS restraints... Processing helix chain 'A' and resid 295 through 303 Processing helix chain 'A' and resid 338 through 342 Processing helix chain 'A' and resid 365 through 369 Processing helix chain 'A' and resid 384 through 389 removed outlier: 4.451A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 409 No H-bonds generated for 'chain 'A' and resid 407 through 409' Processing helix chain 'A' and resid 417 through 421 Processing helix chain 'A' and resid 439 through 442 No H-bonds generated for 'chain 'A' and resid 439 through 442' Processing helix chain 'A' and resid 738 through 743 Processing helix chain 'A' and resid 747 through 755 removed outlier: 4.149A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 782 Processing helix chain 'A' and resid 817 through 825 Processing helix chain 'A' and resid 843 through 847 removed outlier: 3.730A pdb=" N ARG A 847 " --> pdb=" O ILE A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 856 Processing helix chain 'A' and resid 867 through 883 Processing helix chain 'A' and resid 887 through 890 Processing helix chain 'A' and resid 898 through 909 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 920 through 939 Processing helix chain 'A' and resid 946 through 967 removed outlier: 4.002A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N SER A 967 " --> pdb=" O VAL A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 983 Processing helix chain 'A' and resid 986 through 1032 removed outlier: 4.125A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 303 Processing helix chain 'B' and resid 338 through 342 Processing helix chain 'B' and resid 365 through 369 Processing helix chain 'B' and resid 384 through 389 removed outlier: 4.452A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 409 No H-bonds generated for 'chain 'B' and resid 407 through 409' Processing helix chain 'B' and resid 417 through 421 Processing helix chain 'B' and resid 439 through 442 No H-bonds generated for 'chain 'B' and resid 439 through 442' Processing helix chain 'B' and resid 738 through 743 Processing helix chain 'B' and resid 747 through 755 removed outlier: 4.148A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 782 Processing helix chain 'B' and resid 817 through 825 Processing helix chain 'B' and resid 843 through 847 removed outlier: 3.730A pdb=" N ARG B 847 " --> pdb=" O ILE B 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 856 Processing helix chain 'B' and resid 867 through 883 Processing helix chain 'B' and resid 887 through 890 Processing helix chain 'B' and resid 898 through 909 Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 920 through 939 Processing helix chain 'B' and resid 946 through 967 removed outlier: 4.002A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N SER B 967 " --> pdb=" O VAL B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 983 Processing helix chain 'B' and resid 986 through 1032 removed outlier: 4.125A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 303 Processing helix chain 'C' and resid 338 through 342 Processing helix chain 'C' and resid 365 through 369 Processing helix chain 'C' and resid 384 through 389 removed outlier: 4.452A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 409 No H-bonds generated for 'chain 'C' and resid 407 through 409' Processing helix chain 'C' and resid 417 through 421 Processing helix chain 'C' and resid 439 through 442 No H-bonds generated for 'chain 'C' and resid 439 through 442' Processing helix chain 'C' and resid 738 through 743 Processing helix chain 'C' and resid 747 through 755 removed outlier: 4.149A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 782 Processing helix chain 'C' and resid 817 through 825 Processing helix chain 'C' and resid 843 through 847 removed outlier: 3.730A pdb=" N ARG C 847 " --> pdb=" O ILE C 844 " (cutoff:3.500A) Processing helix chain 'C' and resid 849 through 856 Processing helix chain 'C' and resid 867 through 883 Processing helix chain 'C' and resid 887 through 890 Processing helix chain 'C' and resid 898 through 909 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 920 through 939 Processing helix chain 'C' and resid 946 through 967 removed outlier: 4.002A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N SER C 967 " --> pdb=" O VAL C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 977 through 983 Processing helix chain 'C' and resid 986 through 1032 removed outlier: 4.124A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 27 through 31 removed outlier: 4.029A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 47 through 56 removed outlier: 4.070A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 67 through 70 Processing sheet with id= D, first strand: chain 'A' and resid 83 through 85 Processing sheet with id= E, first strand: chain 'A' and resid 243 through 246 removed outlier: 6.760A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N HIS A 146 " --> pdb=" O TRP A 152 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N TRP A 152 " --> pdb=" O HIS A 146 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 311 through 315 removed outlier: 4.680A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.288A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.027A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 452 through 454 Processing sheet with id= J, first strand: chain 'A' and resid 691 through 696 removed outlier: 6.423A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.664A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.801A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.245A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 27 through 31 removed outlier: 4.028A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 47 through 56 removed outlier: 4.070A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 67 through 70 Processing sheet with id= Q, first strand: chain 'B' and resid 83 through 85 Processing sheet with id= R, first strand: chain 'B' and resid 243 through 246 removed outlier: 6.760A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N ARG B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N HIS B 146 " --> pdb=" O TRP B 152 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N TRP B 152 " --> pdb=" O HIS B 146 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 311 through 315 removed outlier: 4.680A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.287A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.027A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'B' and resid 452 through 454 Processing sheet with id= W, first strand: chain 'B' and resid 691 through 696 removed outlier: 6.423A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.664A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.801A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.246A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'C' and resid 27 through 31 removed outlier: 4.029A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'C' and resid 47 through 56 removed outlier: 4.070A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'C' and resid 67 through 70 Processing sheet with id= AD, first strand: chain 'C' and resid 83 through 85 Processing sheet with id= AE, first strand: chain 'C' and resid 243 through 246 removed outlier: 6.760A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N TYR C 144 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N GLU C 154 " --> pdb=" O TYR C 144 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N HIS C 146 " --> pdb=" O TRP C 152 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N TRP C 152 " --> pdb=" O HIS C 146 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'C' and resid 311 through 315 removed outlier: 4.680A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'C' and resid 324 through 328 removed outlier: 4.286A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.027A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'C' and resid 452 through 454 Processing sheet with id= AJ, first strand: chain 'C' and resid 691 through 696 removed outlier: 6.423A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.664A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.801A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.245A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) 972 hydrogen bonds defined for protein. 2673 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: 11.51 Time building geometry restraints manager: 11.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 8502 1.35 - 1.47: 7013 1.47 - 1.59: 11668 1.59 - 1.72: 0 1.72 - 1.84: 150 Bond restraints: 27333 Sorted by residual: bond pdb=" C13 EIC C1301 " pdb=" C14 EIC C1301 " ideal model delta sigma weight residual 1.496 1.553 -0.057 2.00e-02 2.50e+03 8.23e+00 bond pdb=" C13 EIC A1313 " pdb=" C14 EIC A1313 " ideal model delta sigma weight residual 1.496 1.553 -0.057 2.00e-02 2.50e+03 8.18e+00 bond pdb=" C13 EIC B1313 " pdb=" C14 EIC B1313 " ideal model delta sigma weight residual 1.496 1.553 -0.057 2.00e-02 2.50e+03 8.13e+00 bond pdb=" C1 FUC O 2 " pdb=" O5 FUC O 2 " ideal model delta sigma weight residual 1.400 1.455 -0.055 2.00e-02 2.50e+03 7.60e+00 bond pdb=" C1 FUC K 2 " pdb=" O5 FUC K 2 " ideal model delta sigma weight residual 1.400 1.455 -0.055 2.00e-02 2.50e+03 7.52e+00 ... (remaining 27328 not shown) Histogram of bond angle deviations from ideal: 99.68 - 110.21: 5307 110.21 - 120.74: 21880 120.74 - 131.27: 9952 131.27 - 141.80: 28 141.80 - 152.33: 3 Bond angle restraints: 37170 Sorted by residual: angle pdb=" C11 EIC C1301 " pdb=" C10 EIC C1301 " pdb=" C9 EIC C1301 " ideal model delta sigma weight residual 127.32 152.33 -25.01 3.00e+00 1.11e-01 6.95e+01 angle pdb=" C11 EIC B1313 " pdb=" C10 EIC B1313 " pdb=" C9 EIC B1313 " ideal model delta sigma weight residual 127.32 152.32 -25.00 3.00e+00 1.11e-01 6.94e+01 angle pdb=" C11 EIC A1313 " pdb=" C10 EIC A1313 " pdb=" C9 EIC A1313 " ideal model delta sigma weight residual 127.32 152.30 -24.98 3.00e+00 1.11e-01 6.93e+01 angle pdb=" C10 EIC A1313 " pdb=" C9 EIC A1313 " pdb=" C8 EIC A1313 " ideal model delta sigma weight residual 127.75 111.86 15.89 3.00e+00 1.11e-01 2.81e+01 angle pdb=" C10 EIC B1313 " pdb=" C9 EIC B1313 " pdb=" C8 EIC B1313 " ideal model delta sigma weight residual 127.75 111.87 15.88 3.00e+00 1.11e-01 2.80e+01 ... (remaining 37165 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 15023 17.95 - 35.89: 1540 35.89 - 53.84: 401 53.84 - 71.78: 106 71.78 - 89.73: 30 Dihedral angle restraints: 17100 sinusoidal: 7497 harmonic: 9603 Sorted by residual: dihedral pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " pdb=" SG CYS A 166 " pdb=" CB CYS A 166 " ideal model delta sinusoidal sigma weight residual -86.00 -49.16 -36.84 1 1.00e+01 1.00e-02 1.92e+01 dihedral pdb=" CB CYS C 131 " pdb=" SG CYS C 131 " pdb=" SG CYS C 166 " pdb=" CB CYS C 166 " ideal model delta sinusoidal sigma weight residual -86.00 -49.20 -36.80 1 1.00e+01 1.00e-02 1.91e+01 dihedral pdb=" CB CYS B 131 " pdb=" SG CYS B 131 " pdb=" SG CYS B 166 " pdb=" CB CYS B 166 " ideal model delta sinusoidal sigma weight residual -86.00 -49.22 -36.78 1 1.00e+01 1.00e-02 1.91e+01 ... (remaining 17097 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 3519 0.050 - 0.100: 661 0.100 - 0.149: 203 0.149 - 0.199: 3 0.199 - 0.249: 3 Chirality restraints: 4389 Sorted by residual: chirality pdb=" C4 NAG K 1 " pdb=" C3 NAG K 1 " pdb=" C5 NAG K 1 " pdb=" O4 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.53 -2.28 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" C4 NAG G 1 " pdb=" C3 NAG G 1 " pdb=" C5 NAG G 1 " pdb=" O4 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.53 -2.29 -0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" C4 NAG O 1 " pdb=" C3 NAG O 1 " pdb=" C5 NAG O 1 " pdb=" O4 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.53 -2.29 -0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 4386 not shown) Planarity restraints: 4776 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 478 " 0.030 5.00e-02 4.00e+02 4.65e-02 3.46e+00 pdb=" N PRO C 479 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO C 479 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 479 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 478 " 0.030 5.00e-02 4.00e+02 4.65e-02 3.46e+00 pdb=" N PRO A 479 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 479 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 479 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 478 " 0.030 5.00e-02 4.00e+02 4.63e-02 3.44e+00 pdb=" N PRO B 479 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO B 479 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 479 " 0.026 5.00e-02 4.00e+02 ... (remaining 4773 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2303 2.75 - 3.29: 25229 3.29 - 3.82: 46280 3.82 - 4.36: 56795 4.36 - 4.90: 95495 Nonbonded interactions: 226102 Sorted by model distance: nonbonded pdb=" OG1 THR A 547 " pdb=" OG SER B 982 " model vdw 2.212 2.440 nonbonded pdb=" OG1 THR C 645 " pdb=" O ARG C 646 " model vdw 2.260 2.440 nonbonded pdb=" OG1 THR A 645 " pdb=" O ARG A 646 " model vdw 2.260 2.440 nonbonded pdb=" OG1 THR B 645 " pdb=" O ARG B 646 " model vdw 2.261 2.440 nonbonded pdb=" OD1 ASN A 360 " pdb=" OG1 THR A 523 " model vdw 2.266 2.440 ... (remaining 226097 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 1139 or resid 1302 through 1312)) selection = (chain 'B' and (resid 14 through 1139 or resid 1302 through 1312)) selection = (chain 'C' and (resid 14 through 1139 or resid 1302 through 1312)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'L' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'G' selection = chain 'K' selection = chain 'O' } 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: 4.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 12.280 Check model and map are aligned: 0.450 Set scattering table: 0.270 Process input model: 72.270 Find NCS groups from input model: 2.140 Set up NCS constraints: 0.310 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:13.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 27333 Z= 0.236 Angle : 0.604 25.007 37170 Z= 0.279 Chirality : 0.043 0.249 4389 Planarity : 0.004 0.046 4728 Dihedral : 15.760 89.727 10812 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.56 % Favored : 96.26 % Rotamer: Outliers : 1.46 % Allowed : 17.50 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.14), residues: 3285 helix: 1.80 (0.20), residues: 702 sheet: 0.54 (0.19), residues: 723 loop : -0.92 (0.14), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.004 0.001 HIS A1101 PHE 0.014 0.001 PHE A 823 TYR 0.014 0.001 TYR B1067 ARG 0.006 0.000 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 305 time to evaluate : 2.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ASN cc_start: 0.8089 (t0) cc_final: 0.7604 (t0) REVERT: A 613 GLN cc_start: 0.8391 (mt0) cc_final: 0.7901 (mt0) REVERT: A 827 THR cc_start: 0.8576 (p) cc_final: 0.8321 (t) REVERT: B 529 LYS cc_start: 0.7948 (tttm) cc_final: 0.7666 (tppt) REVERT: C 29 THR cc_start: 0.8454 (t) cc_final: 0.8252 (m) REVERT: C 370 ASN cc_start: 0.8259 (t0) cc_final: 0.7823 (m-40) REVERT: C 571 ASP cc_start: 0.8027 (m-30) cc_final: 0.7809 (t70) REVERT: C 613 GLN cc_start: 0.8168 (mt0) cc_final: 0.7684 (mt0) REVERT: C 675 GLN cc_start: 0.7301 (mm110) cc_final: 0.7063 (mm110) REVERT: C 869 MET cc_start: 0.9189 (mtt) cc_final: 0.8912 (mtt) REVERT: C 986 LYS cc_start: 0.7974 (ttmt) cc_final: 0.7686 (ttpt) REVERT: C 990 GLU cc_start: 0.7360 (tt0) cc_final: 0.6969 (tt0) outliers start: 42 outliers final: 19 residues processed: 339 average time/residue: 1.1645 time to fit residues: 471.6879 Evaluate side-chains 250 residues out of total 2868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 231 time to evaluate : 2.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1127 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 278 optimal weight: 1.9990 chunk 250 optimal weight: 0.7980 chunk 138 optimal weight: 0.7980 chunk 85 optimal weight: 0.4980 chunk 168 optimal weight: 7.9990 chunk 133 optimal weight: 20.0000 chunk 258 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 157 optimal weight: 4.9990 chunk 192 optimal weight: 1.9990 chunk 299 optimal weight: 8.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 164 ASN A 314 GLN A 440 ASN A 556 ASN A 613 GLN A 658 ASN A 872 GLN A 926 GLN A1101 HIS A1106 GLN B 99 ASN B 314 GLN B 334 ASN B 613 GLN B 658 ASN ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1058 HIS B1101 HIS C 99 ASN C 164 ASN C 314 GLN C 474 GLN C 556 ASN C 613 GLN C 658 ASN C 914 ASN C 926 GLN C1058 HIS C1101 HIS C1106 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 27333 Z= 0.232 Angle : 0.563 7.356 37170 Z= 0.292 Chirality : 0.046 0.348 4389 Planarity : 0.004 0.049 4728 Dihedral : 7.182 59.588 4990 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.87 % Favored : 95.92 % Rotamer: Outliers : 3.87 % Allowed : 15.24 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.14), residues: 3285 helix: 1.39 (0.20), residues: 705 sheet: 0.34 (0.19), residues: 735 loop : -1.01 (0.13), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 436 HIS 0.005 0.001 HIS A1058 PHE 0.023 0.002 PHE C 817 TYR 0.024 0.002 TYR A1067 ARG 0.007 0.000 ARG C 190 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 253 time to evaluate : 3.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ASN cc_start: 0.8154 (t0) cc_final: 0.7621 (t0) REVERT: A 177 MET cc_start: 0.7192 (OUTLIER) cc_final: 0.6218 (tmt) REVERT: A 613 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.7982 (mt0) REVERT: A 795 LYS cc_start: 0.6107 (OUTLIER) cc_final: 0.5839 (mmmt) REVERT: A 827 THR cc_start: 0.8664 (OUTLIER) cc_final: 0.8428 (t) REVERT: A 833 PHE cc_start: 0.7163 (m-80) cc_final: 0.6864 (m-80) REVERT: A 1091 ARG cc_start: 0.7501 (OUTLIER) cc_final: 0.6994 (ptp-170) REVERT: A 1113 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.8079 (mt0) REVERT: B 52 GLN cc_start: 0.8870 (OUTLIER) cc_final: 0.8594 (tp40) REVERT: B 177 MET cc_start: 0.7193 (OUTLIER) cc_final: 0.5009 (tmt) REVERT: B 346 ARG cc_start: 0.7241 (OUTLIER) cc_final: 0.6811 (ttp80) REVERT: B 357 ARG cc_start: 0.8851 (OUTLIER) cc_final: 0.7149 (ttm170) REVERT: B 493 GLN cc_start: 0.8564 (mt0) cc_final: 0.8354 (tt0) REVERT: B 571 ASP cc_start: 0.8322 (OUTLIER) cc_final: 0.8062 (t0) REVERT: B 964 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.8302 (mtpt) REVERT: C 177 MET cc_start: 0.7367 (OUTLIER) cc_final: 0.6732 (tmt) REVERT: C 370 ASN cc_start: 0.8531 (t0) cc_final: 0.8081 (m110) REVERT: C 571 ASP cc_start: 0.8146 (OUTLIER) cc_final: 0.7908 (t70) REVERT: C 613 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.7963 (mt0) REVERT: C 1029 MET cc_start: 0.9239 (tpp) cc_final: 0.9025 (tpp) outliers start: 111 outliers final: 36 residues processed: 334 average time/residue: 1.1959 time to fit residues: 473.5171 Evaluate side-chains 276 residues out of total 2868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 225 time to evaluate : 3.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 795 LYS Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1091 ARG Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 346 ARG Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1045 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 166 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 249 optimal weight: 0.9980 chunk 204 optimal weight: 5.9990 chunk 82 optimal weight: 0.5980 chunk 300 optimal weight: 0.4980 chunk 324 optimal weight: 4.9990 chunk 267 optimal weight: 4.9990 chunk 297 optimal weight: 0.0770 chunk 102 optimal weight: 0.8980 chunk 240 optimal weight: 0.4980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 314 GLN A 613 GLN A 658 ASN B 99 ASN B 164 ASN B 334 ASN B 613 GLN ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 HIS C 99 ASN C 314 GLN C 556 ASN C 613 GLN C 804 GLN C1010 GLN C1106 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 27333 Z= 0.137 Angle : 0.488 7.467 37170 Z= 0.255 Chirality : 0.043 0.285 4389 Planarity : 0.003 0.046 4728 Dihedral : 6.518 59.772 4976 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.01 % Favored : 96.77 % Rotamer: Outliers : 3.14 % Allowed : 15.79 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.14), residues: 3285 helix: 1.78 (0.20), residues: 687 sheet: 0.36 (0.19), residues: 732 loop : -0.95 (0.13), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.002 0.001 HIS C 66 PHE 0.014 0.001 PHE C 817 TYR 0.016 0.001 TYR B1067 ARG 0.009 0.000 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 239 time to evaluate : 3.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ASN cc_start: 0.8148 (t0) cc_final: 0.7610 (t0) REVERT: A 177 MET cc_start: 0.7118 (OUTLIER) cc_final: 0.5598 (tmt) REVERT: A 755 GLN cc_start: 0.7198 (OUTLIER) cc_final: 0.5602 (mp10) REVERT: A 827 THR cc_start: 0.8591 (OUTLIER) cc_final: 0.8361 (t) REVERT: A 833 PHE cc_start: 0.7207 (m-80) cc_final: 0.6912 (m-80) REVERT: A 983 ARG cc_start: 0.8206 (mtp85) cc_final: 0.7962 (mtp-110) REVERT: A 1091 ARG cc_start: 0.7488 (OUTLIER) cc_final: 0.6687 (ptp-170) REVERT: B 177 MET cc_start: 0.7144 (OUTLIER) cc_final: 0.4494 (tmt) REVERT: B 244 LEU cc_start: 0.6247 (OUTLIER) cc_final: 0.5835 (pp) REVERT: B 357 ARG cc_start: 0.8829 (OUTLIER) cc_final: 0.7124 (ttm170) REVERT: B 613 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.8125 (mt0) REVERT: C 177 MET cc_start: 0.7339 (OUTLIER) cc_final: 0.6632 (tmt) REVERT: C 370 ASN cc_start: 0.8508 (t0) cc_final: 0.8031 (m110) REVERT: C 571 ASP cc_start: 0.8126 (OUTLIER) cc_final: 0.7873 (t70) REVERT: C 755 GLN cc_start: 0.7136 (mp10) cc_final: 0.6900 (mp10) REVERT: C 1010 GLN cc_start: 0.8767 (OUTLIER) cc_final: 0.7905 (mp10) outliers start: 90 outliers final: 31 residues processed: 307 average time/residue: 1.1949 time to fit residues: 439.1120 Evaluate side-chains 262 residues out of total 2868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 220 time to evaluate : 2.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1091 ARG Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1091 ARG Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1010 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 296 optimal weight: 7.9990 chunk 225 optimal weight: 10.0000 chunk 155 optimal weight: 0.0030 chunk 33 optimal weight: 7.9990 chunk 143 optimal weight: 0.2980 chunk 201 optimal weight: 4.9990 chunk 301 optimal weight: 0.6980 chunk 318 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 285 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 overall best weight: 0.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 658 ASN A1106 GLN B 613 GLN B 804 GLN ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 HIS C 99 ASN C 675 GLN C 804 GLN C1106 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27333 Z= 0.191 Angle : 0.528 10.947 37170 Z= 0.275 Chirality : 0.044 0.298 4389 Planarity : 0.004 0.049 4728 Dihedral : 6.329 58.298 4975 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.56 % Favored : 96.23 % Rotamer: Outliers : 3.10 % Allowed : 15.83 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.14), residues: 3285 helix: 1.60 (0.20), residues: 705 sheet: 0.42 (0.19), residues: 726 loop : -0.97 (0.13), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 886 HIS 0.002 0.001 HIS B 245 PHE 0.013 0.001 PHE C 817 TYR 0.021 0.001 TYR A1067 ARG 0.009 0.000 ARG C 190 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 230 time to evaluate : 2.939 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: A 177 MET cc_start: 0.7072 (OUTLIER) cc_final: 0.5618 (tmt) REVERT: A 755 GLN cc_start: 0.7164 (OUTLIER) cc_final: 0.5552 (mp10) REVERT: A 827 THR cc_start: 0.8609 (OUTLIER) cc_final: 0.8373 (t) REVERT: A 933 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.8116 (mtpt) REVERT: A 983 ARG cc_start: 0.8479 (mtp85) cc_final: 0.8248 (mtp-110) REVERT: A 1091 ARG cc_start: 0.7537 (OUTLIER) cc_final: 0.6888 (ptp-170) REVERT: B 52 GLN cc_start: 0.8869 (OUTLIER) cc_final: 0.8601 (tp40) REVERT: B 244 LEU cc_start: 0.6404 (OUTLIER) cc_final: 0.5967 (pp) REVERT: B 357 ARG cc_start: 0.8837 (OUTLIER) cc_final: 0.7128 (ttm170) REVERT: B 571 ASP cc_start: 0.8300 (OUTLIER) cc_final: 0.7944 (t70) REVERT: B 613 GLN cc_start: 0.8098 (OUTLIER) cc_final: 0.7889 (mt0) REVERT: B 755 GLN cc_start: 0.7247 (OUTLIER) cc_final: 0.6189 (mp10) REVERT: B 964 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.8290 (mtpt) REVERT: B 1045 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8512 (tmtt) REVERT: C 177 MET cc_start: 0.7318 (OUTLIER) cc_final: 0.6623 (tmt) REVERT: C 370 ASN cc_start: 0.8497 (t0) cc_final: 0.8012 (m110) REVERT: C 571 ASP cc_start: 0.8153 (OUTLIER) cc_final: 0.7890 (t70) REVERT: C 795 LYS cc_start: 0.5863 (OUTLIER) cc_final: 0.5514 (tttm) REVERT: C 1010 GLN cc_start: 0.8758 (OUTLIER) cc_final: 0.7982 (mp10) outliers start: 89 outliers final: 40 residues processed: 290 average time/residue: 1.1919 time to fit residues: 410.0156 Evaluate side-chains 283 residues out of total 2868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 226 time to evaluate : 2.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 933 LYS Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1091 ARG Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1091 ARG Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 795 LYS Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1091 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 265 optimal weight: 6.9990 chunk 181 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 237 optimal weight: 5.9990 chunk 131 optimal weight: 0.5980 chunk 272 optimal weight: 3.9990 chunk 220 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 162 optimal weight: 3.9990 chunk 286 optimal weight: 0.1980 chunk 80 optimal weight: 9.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 913 GLN A1058 HIS B 613 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 HIS C 52 GLN C 99 ASN C 314 GLN C 613 GLN C 804 GLN C1106 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 27333 Z= 0.353 Angle : 0.627 9.826 37170 Z= 0.327 Chirality : 0.049 0.421 4389 Planarity : 0.004 0.053 4728 Dihedral : 6.698 59.845 4975 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.99 % Favored : 95.74 % Rotamer: Outliers : 3.59 % Allowed : 14.92 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.14), residues: 3285 helix: 1.21 (0.19), residues: 705 sheet: 0.26 (0.18), residues: 795 loop : -1.07 (0.14), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 886 HIS 0.005 0.001 HIS C 245 PHE 0.016 0.002 PHE B 759 TYR 0.026 0.002 TYR C1067 ARG 0.011 0.001 ARG A1039 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 238 time to evaluate : 2.735 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 118 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8474 (tp) REVERT: A 177 MET cc_start: 0.7084 (OUTLIER) cc_final: 0.5600 (tmt) REVERT: A 554 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7482 (mp0) REVERT: A 827 THR cc_start: 0.8670 (OUTLIER) cc_final: 0.8397 (t) REVERT: A 933 LYS cc_start: 0.8412 (OUTLIER) cc_final: 0.8129 (mtpt) REVERT: A 1091 ARG cc_start: 0.7722 (OUTLIER) cc_final: 0.6787 (ptp-170) REVERT: A 1113 GLN cc_start: 0.8709 (OUTLIER) cc_final: 0.7891 (mm-40) REVERT: B 52 GLN cc_start: 0.8900 (OUTLIER) cc_final: 0.8333 (tt0) REVERT: B 357 ARG cc_start: 0.8865 (OUTLIER) cc_final: 0.7428 (tpm170) REVERT: B 370 ASN cc_start: 0.8388 (t0) cc_final: 0.8045 (m-40) REVERT: B 571 ASP cc_start: 0.8387 (OUTLIER) cc_final: 0.8061 (t70) REVERT: B 795 LYS cc_start: 0.5930 (OUTLIER) cc_final: 0.5715 (mtpt) REVERT: B 804 GLN cc_start: 0.8378 (mt0) cc_final: 0.8169 (mt0) REVERT: B 933 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.8207 (mtmm) REVERT: B 964 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8352 (mtpt) REVERT: C 177 MET cc_start: 0.7320 (OUTLIER) cc_final: 0.6682 (tmt) REVERT: C 571 ASP cc_start: 0.8225 (OUTLIER) cc_final: 0.7928 (t70) REVERT: C 606 ASN cc_start: 0.8693 (OUTLIER) cc_final: 0.8481 (m-40) REVERT: C 1010 GLN cc_start: 0.8776 (OUTLIER) cc_final: 0.7958 (mp10) REVERT: C 1091 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.6443 (ptp-170) REVERT: C 1113 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.8115 (mm110) outliers start: 103 outliers final: 42 residues processed: 310 average time/residue: 1.2108 time to fit residues: 445.5134 Evaluate side-chains 285 residues out of total 2868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 224 time to evaluate : 2.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 933 LYS Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1091 ARG Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 795 LYS Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 933 LYS Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1091 ARG Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 606 ASN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1091 ARG Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1113 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 107 optimal weight: 0.8980 chunk 287 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 187 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 319 optimal weight: 2.9990 chunk 265 optimal weight: 4.9990 chunk 147 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 105 optimal weight: 0.5980 chunk 167 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN B 99 ASN B 804 GLN ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 HIS C 99 ASN C 556 ASN C 804 GLN C 914 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27333 Z= 0.181 Angle : 0.556 16.086 37170 Z= 0.289 Chirality : 0.044 0.353 4389 Planarity : 0.004 0.050 4728 Dihedral : 6.233 58.250 4975 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.04 % Favored : 96.68 % Rotamer: Outliers : 2.96 % Allowed : 15.79 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.14), residues: 3285 helix: 1.48 (0.20), residues: 705 sheet: 0.25 (0.18), residues: 795 loop : -1.07 (0.14), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 886 HIS 0.002 0.001 HIS A 66 PHE 0.015 0.001 PHE B 823 TYR 0.020 0.001 TYR A1067 ARG 0.009 0.000 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 236 time to evaluate : 2.832 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: A 118 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8469 (tp) REVERT: A 827 THR cc_start: 0.8564 (OUTLIER) cc_final: 0.8324 (t) REVERT: A 1045 LYS cc_start: 0.8762 (OUTLIER) cc_final: 0.8484 (tmmt) REVERT: A 1091 ARG cc_start: 0.7708 (OUTLIER) cc_final: 0.6845 (ptp-170) REVERT: A 1113 GLN cc_start: 0.8713 (OUTLIER) cc_final: 0.7905 (mm-40) REVERT: B 52 GLN cc_start: 0.8861 (OUTLIER) cc_final: 0.8588 (tp40) REVERT: B 177 MET cc_start: 0.7227 (OUTLIER) cc_final: 0.4213 (tmt) REVERT: B 357 ARG cc_start: 0.8857 (OUTLIER) cc_final: 0.7102 (ttm170) REVERT: B 370 ASN cc_start: 0.8351 (t0) cc_final: 0.8006 (m-40) REVERT: B 571 ASP cc_start: 0.8305 (m-30) cc_final: 0.7982 (t70) REVERT: B 933 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.8180 (mtmm) REVERT: B 964 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8277 (mtpt) REVERT: B 1045 LYS cc_start: 0.8773 (OUTLIER) cc_final: 0.8494 (tmtt) REVERT: C 177 MET cc_start: 0.7352 (OUTLIER) cc_final: 0.6666 (tmt) REVERT: C 571 ASP cc_start: 0.8165 (OUTLIER) cc_final: 0.7866 (t70) REVERT: C 606 ASN cc_start: 0.8668 (OUTLIER) cc_final: 0.8464 (m-40) REVERT: C 1010 GLN cc_start: 0.8736 (OUTLIER) cc_final: 0.7966 (mp10) outliers start: 85 outliers final: 41 residues processed: 299 average time/residue: 1.2268 time to fit residues: 434.1618 Evaluate side-chains 283 residues out of total 2868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 227 time to evaluate : 2.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 795 LYS Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1091 ARG Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 933 LYS Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1091 ARG Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 606 ASN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1091 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 307 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 181 optimal weight: 5.9990 chunk 233 optimal weight: 7.9990 chunk 180 optimal weight: 3.9990 chunk 268 optimal weight: 3.9990 chunk 178 optimal weight: 1.9990 chunk 318 optimal weight: 3.9990 chunk 199 optimal weight: 0.9990 chunk 193 optimal weight: 4.9990 chunk 146 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 207 HIS B 99 ASN B 207 HIS B 314 GLN B 613 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 GLN B1101 HIS C 99 ASN C 314 GLN C 613 GLN C 675 GLN C 804 GLN C1101 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.082 27333 Z= 0.438 Angle : 0.667 16.336 37170 Z= 0.347 Chirality : 0.051 0.414 4389 Planarity : 0.004 0.054 4728 Dihedral : 6.682 59.910 4975 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.17 % Favored : 95.56 % Rotamer: Outliers : 3.10 % Allowed : 15.55 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.14), residues: 3285 helix: 1.15 (0.19), residues: 705 sheet: 0.26 (0.18), residues: 798 loop : -1.13 (0.13), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 886 HIS 0.005 0.001 HIS C 245 PHE 0.017 0.002 PHE B 823 TYR 0.028 0.002 TYR A1067 ARG 0.009 0.001 ARG C 190 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 228 time to evaluate : 3.020 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: A 118 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8474 (tp) REVERT: A 370 ASN cc_start: 0.8459 (t0) cc_final: 0.8046 (m-40) REVERT: A 554 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7501 (mp0) REVERT: A 827 THR cc_start: 0.8658 (OUTLIER) cc_final: 0.8357 (t) REVERT: A 933 LYS cc_start: 0.8424 (OUTLIER) cc_final: 0.8126 (mtpt) REVERT: A 1045 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8414 (tmmt) REVERT: A 1091 ARG cc_start: 0.7776 (OUTLIER) cc_final: 0.6812 (ptp-170) REVERT: A 1113 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.7946 (mm-40) REVERT: B 52 GLN cc_start: 0.8928 (OUTLIER) cc_final: 0.8363 (tt0) REVERT: B 177 MET cc_start: 0.7223 (OUTLIER) cc_final: 0.4637 (tmt) REVERT: B 357 ARG cc_start: 0.8884 (OUTLIER) cc_final: 0.7442 (tpm170) REVERT: B 571 ASP cc_start: 0.8377 (OUTLIER) cc_final: 0.8063 (t70) REVERT: B 613 GLN cc_start: 0.8863 (OUTLIER) cc_final: 0.8160 (mt0) REVERT: B 804 GLN cc_start: 0.8424 (mt0) cc_final: 0.8198 (mt0) REVERT: B 964 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8346 (mtpt) REVERT: C 177 MET cc_start: 0.7351 (OUTLIER) cc_final: 0.6761 (tmt) REVERT: C 571 ASP cc_start: 0.8257 (OUTLIER) cc_final: 0.7955 (t70) REVERT: C 1010 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.7968 (mp10) REVERT: C 1091 ARG cc_start: 0.7821 (OUTLIER) cc_final: 0.6412 (ptp-170) REVERT: C 1113 GLN cc_start: 0.8753 (OUTLIER) cc_final: 0.8127 (mm110) outliers start: 89 outliers final: 45 residues processed: 289 average time/residue: 1.2261 time to fit residues: 422.2760 Evaluate side-chains 280 residues out of total 2868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 217 time to evaluate : 2.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 795 LYS Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 933 LYS Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1091 ARG Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1091 ARG Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1091 ARG Chi-restraints excluded: chain C residue 1113 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 196 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 189 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 202 optimal weight: 1.9990 chunk 216 optimal weight: 0.9990 chunk 157 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 250 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 314 GLN A 613 GLN B 99 ASN B 804 GLN B1010 GLN B1101 HIS C 99 ASN C 314 GLN C 556 ASN C 613 GLN C 675 GLN C 804 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 27333 Z= 0.182 Angle : 0.539 11.532 37170 Z= 0.282 Chirality : 0.044 0.349 4389 Planarity : 0.004 0.050 4728 Dihedral : 6.139 57.988 4975 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.32 % Favored : 96.50 % Rotamer: Outliers : 2.48 % Allowed : 16.35 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.14), residues: 3285 helix: 1.43 (0.20), residues: 705 sheet: 0.22 (0.18), residues: 822 loop : -1.12 (0.14), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 886 HIS 0.002 0.001 HIS A 66 PHE 0.016 0.001 PHE B 823 TYR 0.019 0.001 TYR A1067 ARG 0.009 0.000 ARG C 190 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 230 time to evaluate : 3.148 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 143 VAL cc_start: 0.8348 (OUTLIER) cc_final: 0.8097 (p) REVERT: A 370 ASN cc_start: 0.8394 (t0) cc_final: 0.8025 (m-40) REVERT: A 827 THR cc_start: 0.8550 (OUTLIER) cc_final: 0.8271 (t) REVERT: A 933 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.8102 (mtpt) REVERT: A 1045 LYS cc_start: 0.8758 (OUTLIER) cc_final: 0.8486 (tmmt) REVERT: A 1091 ARG cc_start: 0.7710 (OUTLIER) cc_final: 0.6862 (ptp-170) REVERT: A 1113 GLN cc_start: 0.8736 (OUTLIER) cc_final: 0.7946 (mm-40) REVERT: B 52 GLN cc_start: 0.8858 (OUTLIER) cc_final: 0.8580 (tp40) REVERT: B 357 ARG cc_start: 0.8847 (OUTLIER) cc_final: 0.7129 (ttm170) REVERT: B 370 ASN cc_start: 0.8342 (t0) cc_final: 0.7976 (m-40) REVERT: B 571 ASP cc_start: 0.8305 (OUTLIER) cc_final: 0.7996 (t70) REVERT: B 613 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.8337 (mp10) REVERT: B 964 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.8263 (mtpt) REVERT: B 1010 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.8044 (mp10) REVERT: B 1045 LYS cc_start: 0.8753 (OUTLIER) cc_final: 0.8469 (tmtt) REVERT: B 1113 GLN cc_start: 0.8745 (OUTLIER) cc_final: 0.7920 (mm-40) REVERT: C 177 MET cc_start: 0.7293 (OUTLIER) cc_final: 0.6036 (tmt) REVERT: C 571 ASP cc_start: 0.8177 (OUTLIER) cc_final: 0.7875 (t70) REVERT: C 1010 GLN cc_start: 0.8745 (OUTLIER) cc_final: 0.7970 (mp10) REVERT: C 1113 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.8082 (mm110) outliers start: 71 outliers final: 39 residues processed: 282 average time/residue: 1.2498 time to fit residues: 417.8243 Evaluate side-chains 281 residues out of total 2868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 224 time to evaluate : 2.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 795 LYS Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 933 LYS Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1091 ARG Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1091 ARG Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1091 ARG Chi-restraints excluded: chain C residue 1113 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 289 optimal weight: 0.9980 chunk 304 optimal weight: 5.9990 chunk 278 optimal weight: 4.9990 chunk 296 optimal weight: 2.9990 chunk 178 optimal weight: 2.9990 chunk 129 optimal weight: 0.6980 chunk 232 optimal weight: 4.9990 chunk 90 optimal weight: 6.9990 chunk 267 optimal weight: 0.7980 chunk 280 optimal weight: 5.9990 chunk 295 optimal weight: 1.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 314 GLN A 321 GLN A 613 GLN B 99 ASN B 613 GLN B 804 GLN B1101 HIS C 99 ASN C 556 ASN C 675 GLN C 804 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 27333 Z= 0.250 Angle : 0.580 19.434 37170 Z= 0.301 Chirality : 0.046 0.365 4389 Planarity : 0.004 0.051 4728 Dihedral : 6.173 58.882 4975 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.77 % Favored : 96.04 % Rotamer: Outliers : 2.51 % Allowed : 16.39 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.14), residues: 3285 helix: 1.41 (0.20), residues: 705 sheet: 0.20 (0.18), residues: 828 loop : -1.11 (0.14), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 886 HIS 0.003 0.001 HIS B 245 PHE 0.017 0.002 PHE B 823 TYR 0.023 0.002 TYR A1067 ARG 0.010 0.000 ARG C 190 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 221 time to evaluate : 3.233 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: A 143 VAL cc_start: 0.8366 (OUTLIER) cc_final: 0.8120 (p) REVERT: A 370 ASN cc_start: 0.8449 (t0) cc_final: 0.8062 (m-40) REVERT: A 554 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7428 (mp0) REVERT: A 827 THR cc_start: 0.8567 (OUTLIER) cc_final: 0.8277 (t) REVERT: A 933 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.8121 (mtpt) REVERT: A 1045 LYS cc_start: 0.8774 (OUTLIER) cc_final: 0.8549 (tmmt) REVERT: A 1091 ARG cc_start: 0.7718 (OUTLIER) cc_final: 0.6768 (ptp-170) REVERT: A 1113 GLN cc_start: 0.8740 (OUTLIER) cc_final: 0.7952 (mm-40) REVERT: B 52 GLN cc_start: 0.8873 (OUTLIER) cc_final: 0.8598 (tp40) REVERT: B 357 ARG cc_start: 0.8853 (OUTLIER) cc_final: 0.7066 (ttm170) REVERT: B 370 ASN cc_start: 0.8343 (t0) cc_final: 0.7973 (m-40) REVERT: B 571 ASP cc_start: 0.8330 (OUTLIER) cc_final: 0.8024 (t70) REVERT: B 613 GLN cc_start: 0.8768 (OUTLIER) cc_final: 0.8165 (mt0) REVERT: B 964 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8290 (mtpt) REVERT: B 1010 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.8079 (mp10) REVERT: C 177 MET cc_start: 0.7337 (OUTLIER) cc_final: 0.6623 (tmt) REVERT: C 571 ASP cc_start: 0.8195 (OUTLIER) cc_final: 0.7888 (t70) REVERT: C 1010 GLN cc_start: 0.8782 (OUTLIER) cc_final: 0.8001 (mp10) REVERT: C 1091 ARG cc_start: 0.7765 (OUTLIER) cc_final: 0.6237 (ptp-170) REVERT: C 1113 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.8088 (mm110) outliers start: 72 outliers final: 47 residues processed: 273 average time/residue: 1.2396 time to fit residues: 402.4470 Evaluate side-chains 284 residues out of total 2868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 219 time to evaluate : 3.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 795 LYS Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 933 LYS Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1091 ARG Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1091 ARG Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1091 ARG Chi-restraints excluded: chain C residue 1113 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 194 optimal weight: 2.9990 chunk 313 optimal weight: 2.9990 chunk 191 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 217 optimal weight: 1.9990 chunk 328 optimal weight: 7.9990 chunk 302 optimal weight: 2.9990 chunk 261 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 202 optimal weight: 0.6980 chunk 160 optimal weight: 3.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 954 GLN B 99 ASN B 207 HIS B 613 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN C 556 ASN C 675 GLN C 804 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 27333 Z= 0.304 Angle : 0.611 18.931 37170 Z= 0.317 Chirality : 0.047 0.383 4389 Planarity : 0.004 0.052 4728 Dihedral : 6.286 59.883 4975 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.62 % Favored : 96.19 % Rotamer: Outliers : 2.44 % Allowed : 16.49 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.14), residues: 3285 helix: 1.32 (0.19), residues: 705 sheet: 0.24 (0.18), residues: 822 loop : -1.14 (0.14), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 886 HIS 0.003 0.001 HIS C 245 PHE 0.017 0.002 PHE B 823 TYR 0.025 0.002 TYR A1067 ARG 0.010 0.001 ARG C 190 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6570 Ramachandran restraints generated. 3285 Oldfield, 0 Emsley, 3285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 217 time to evaluate : 2.845 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: A 143 VAL cc_start: 0.8389 (OUTLIER) cc_final: 0.8184 (p) REVERT: A 370 ASN cc_start: 0.8441 (t0) cc_final: 0.8056 (m-40) REVERT: A 554 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7453 (mp0) REVERT: A 827 THR cc_start: 0.8655 (OUTLIER) cc_final: 0.8336 (t) REVERT: A 933 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.8132 (mtpt) REVERT: A 1045 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8553 (tmmt) REVERT: A 1091 ARG cc_start: 0.7751 (OUTLIER) cc_final: 0.6803 (ptp-170) REVERT: A 1113 GLN cc_start: 0.8759 (OUTLIER) cc_final: 0.7962 (mm-40) REVERT: B 52 GLN cc_start: 0.8887 (OUTLIER) cc_final: 0.8347 (tm-30) REVERT: B 357 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.7084 (ttm170) REVERT: B 370 ASN cc_start: 0.8351 (t0) cc_final: 0.7978 (m-40) REVERT: B 571 ASP cc_start: 0.8336 (OUTLIER) cc_final: 0.8030 (t70) REVERT: B 613 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.8209 (mt0) REVERT: B 964 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8313 (mtpt) REVERT: B 1010 GLN cc_start: 0.8783 (OUTLIER) cc_final: 0.8052 (mp10) REVERT: C 177 MET cc_start: 0.7321 (OUTLIER) cc_final: 0.6679 (tmt) REVERT: C 571 ASP cc_start: 0.8219 (OUTLIER) cc_final: 0.7910 (t70) REVERT: C 1010 GLN cc_start: 0.8799 (OUTLIER) cc_final: 0.8023 (mp10) REVERT: C 1091 ARG cc_start: 0.7784 (OUTLIER) cc_final: 0.6265 (ptp-170) REVERT: C 1113 GLN cc_start: 0.8749 (OUTLIER) cc_final: 0.8134 (mm110) outliers start: 70 outliers final: 47 residues processed: 268 average time/residue: 1.2842 time to fit residues: 414.4020 Evaluate side-chains 280 residues out of total 2868 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 215 time to evaluate : 2.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 795 LYS Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 933 LYS Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1045 LYS Chi-restraints excluded: chain A residue 1091 ARG Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1091 ARG Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 828 LEU Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1091 ARG Chi-restraints excluded: chain C residue 1113 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 207 optimal weight: 2.9990 chunk 278 optimal weight: 5.9990 chunk 80 optimal weight: 9.9990 chunk 241 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 262 optimal weight: 2.9990 chunk 109 optimal weight: 8.9990 chunk 269 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 954 GLN A1135 ASN B 99 ASN B 207 HIS B 613 GLN B 675 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 HIS C 99 ASN C 556 ASN C 675 GLN C 804 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.139251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.101547 restraints weight = 26913.813| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.86 r_work: 0.3002 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 27333 Z= 0.256 Angle : 0.594 17.982 37170 Z= 0.309 Chirality : 0.046 0.356 4389 Planarity : 0.004 0.051 4728 Dihedral : 6.233 59.644 4975 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.71 % Favored : 96.10 % Rotamer: Outliers : 2.48 % Allowed : 16.42 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.14), residues: 3285 helix: 1.35 (0.20), residues: 705 sheet: 0.23 (0.18), residues: 822 loop : -1.14 (0.14), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 886 HIS 0.003 0.001 HIS B 245 PHE 0.018 0.002 PHE B 823 TYR 0.023 0.002 TYR A1067 ARG 0.009 0.000 ARG C 190 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8655.99 seconds wall clock time: 155 minutes 43.71 seconds (9343.71 seconds total)