Starting phenix.real_space_refine on Fri Aug 9 02:39:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v0n_42862/08_2024/8v0n_42862_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v0n_42862/08_2024/8v0n_42862.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v0n_42862/08_2024/8v0n_42862.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v0n_42862/08_2024/8v0n_42862.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v0n_42862/08_2024/8v0n_42862_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v0n_42862/08_2024/8v0n_42862_neut.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.038 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 111 5.16 5 C 15735 2.51 5 N 4056 2.21 5 O 4788 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 583": "OE1" <-> "OE2" Residue "A TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 398": "OD1" <-> "OD2" Residue "B TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 471": "OE1" <-> "OE2" Residue "B ASP 568": "OD1" <-> "OD2" Residue "B ASP 574": "OD1" <-> "OD2" Residue "B ASP 775": "OD1" <-> "OD2" Residue "B GLU 1092": "OE1" <-> "OE2" Residue "C TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 420": "OD1" <-> "OD2" Residue "C PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 571": "OD1" <-> "OD2" Residue "C ASP 574": "OD1" <-> "OD2" Residue "C PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 24690 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 8020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1028, 8020 Classifications: {'peptide': 1028} Link IDs: {'PTRANS': 51, 'TRANS': 976} Chain breaks: 6 Chain: "B" Number of atoms: 8020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1028, 8020 Classifications: {'peptide': 1028} Link IDs: {'PTRANS': 51, 'TRANS': 976} Chain breaks: 6 Chain: "C" Number of atoms: 8020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1028, 8020 Classifications: {'peptide': 1028} Link IDs: {'PTRANS': 51, 'TRANS': 976} Chain breaks: 6 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 13.05, per 1000 atoms: 0.53 Number of scatterers: 24690 At special positions: 0 Unit cell: (135, 127.44, 176.04, 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 111 16.00 O 4788 8.00 N 4056 7.00 C 15735 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 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=2.05 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 738 " - pdb=" SG CYS A 760 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 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=2.04 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=2.04 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 738 " - pdb=" SG CYS B 760 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 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=2.05 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 738 " - pdb=" SG CYS C 760 " 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=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A 343 " " NAG A1304 " - " ASN A 709 " " NAG A1305 " - " ASN A1074 " " NAG A1306 " - " ASN A1134 " " NAG A1307 " - " ASN A 282 " " NAG A1308 " - " ASN A 234 " " NAG A1309 " - " ASN A 616 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 331 " " NAG B1303 " - " ASN B 343 " " NAG B1304 " - " ASN B 616 " " NAG B1305 " - " ASN B 709 " " NAG B1306 " - " ASN B1074 " " NAG B1307 " - " ASN B1134 " " NAG B1308 " - " ASN B 282 " " NAG B1309 " - " ASN B 234 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 343 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C1074 " " NAG C1307 " - " ASN C1134 " " NAG C1308 " - " ASN C 282 " " NAG C1309 " - " ASN C 234 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN A1098 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN B 717 " " NAG H 1 " - " ASN B1098 " " NAG I 1 " - " ASN B 801 " " NAG J 1 " - " ASN C 717 " " NAG K 1 " - " ASN C1098 " " NAG L 1 " - " ASN C 801 " Time building additional restraints: 8.81 Conformation dependent library (CDL) restraints added in 4.5 seconds 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5778 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 43 sheets defined 26.2% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.51 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 4.015A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 371 Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.727A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.629A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 841 Processing helix chain 'A' and resid 848 through 856 removed outlier: 3.588A pdb=" N ALA A 852 " --> pdb=" O ASP A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.097A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.803A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.965A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.667A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.894A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 371 Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.742A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.660A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.816A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 835 through 841 Processing helix chain 'B' and resid 848 through 856 removed outlier: 3.596A pdb=" N ALA B 852 " --> pdb=" O ASP B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 4.013A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.188A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.716A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU B 959 " --> pdb=" O ASN B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.592A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 4.168A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 4.022A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 371 Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.542A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.633A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 835 through 841 Processing helix chain 'C' and resid 848 through 856 removed outlier: 3.704A pdb=" N ALA C 852 " --> pdb=" O ASP C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.764A pdb=" N ASN C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.625A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.093A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 28 removed outlier: 4.416A pdb=" N SER A 94 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG A 190 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.358A pdb=" N PHE A 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.098A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 316 removed outlier: 6.962A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.723A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.636A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 538 through 543 removed outlier: 3.572A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 660 removed outlier: 6.116A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 8.774A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.492A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.599A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.056A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.674A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 789 removed outlier: 5.729A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.868A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 8.991A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.727A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.117A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.553A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC5, first strand: chain 'B' and resid 538 through 543 removed outlier: 5.431A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.277A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.748A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.813A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AC9, first strand: chain 'B' and resid 718 through 722 removed outlier: 6.798A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 725 through 728 Processing sheet with id=AD2, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.559A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD4, first strand: chain 'C' and resid 25 through 30 removed outlier: 7.675A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 8.874A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 8.905A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.053A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 316 removed outlier: 7.035A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.954A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE1, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.602A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.076A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AE4, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.916A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE6, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE7, first strand: chain 'C' and resid 1094 through 1097 958 hydrogen bonds defined for protein. 2637 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: 10.22 Time building geometry restraints manager: 9.68 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: 7854 1.35 - 1.48: 6562 1.48 - 1.61: 10679 1.61 - 1.74: 0 1.74 - 1.86: 138 Bond restraints: 25233 Sorted by residual: bond pdb=" C VAL B 620 " pdb=" N PRO B 621 " ideal model delta sigma weight residual 1.326 1.382 -0.056 1.44e-02 4.82e+03 1.49e+01 bond pdb=" C1 NAG A1309 " pdb=" O5 NAG A1309 " ideal model delta sigma weight residual 1.406 1.463 -0.057 2.00e-02 2.50e+03 8.12e+00 bond pdb=" C1 NAG C1309 " pdb=" O5 NAG C1309 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.65e+00 bond pdb=" CA VAL C 620 " pdb=" C VAL C 620 " ideal model delta sigma weight residual 1.520 1.543 -0.023 8.80e-03 1.29e+04 7.04e+00 bond pdb=" C1 NAG C1301 " pdb=" O5 NAG C1301 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.54e+00 ... (remaining 25228 not shown) Histogram of bond angle deviations from ideal: 96.76 - 104.40: 379 104.40 - 112.04: 12294 112.04 - 119.68: 8929 119.68 - 127.31: 12513 127.31 - 134.95: 205 Bond angle restraints: 34320 Sorted by residual: angle pdb=" N ASP B 198 " pdb=" CA ASP B 198 " pdb=" CB ASP B 198 " ideal model delta sigma weight residual 114.17 108.10 6.07 1.14e+00 7.69e-01 2.83e+01 angle pdb=" N ILE C 235 " pdb=" CA ILE C 235 " pdb=" C ILE C 235 " ideal model delta sigma weight residual 113.47 108.18 5.29 1.01e+00 9.80e-01 2.75e+01 angle pdb=" C ASP B 198 " pdb=" CA ASP B 198 " pdb=" CB ASP B 198 " ideal model delta sigma weight residual 110.06 117.00 -6.94 1.44e+00 4.82e-01 2.32e+01 angle pdb=" C GLY C 744 " pdb=" N ASP C 745 " pdb=" CA ASP C 745 " ideal model delta sigma weight residual 121.54 130.45 -8.91 1.91e+00 2.74e-01 2.18e+01 angle pdb=" CG1 ILE B 119 " pdb=" CB ILE B 119 " pdb=" CG2 ILE B 119 " ideal model delta sigma weight residual 110.70 97.56 13.14 3.00e+00 1.11e-01 1.92e+01 ... (remaining 34315 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.20: 14073 18.20 - 36.40: 1278 36.40 - 54.61: 233 54.61 - 72.81: 49 72.81 - 91.01: 24 Dihedral angle restraints: 15657 sinusoidal: 6678 harmonic: 8979 Sorted by residual: dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual -86.00 -15.02 -70.98 1 1.00e+01 1.00e-02 6.47e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -19.75 -66.25 1 1.00e+01 1.00e-02 5.73e+01 dihedral pdb=" CA CYS C 617 " pdb=" C CYS C 617 " pdb=" N THR C 618 " pdb=" CA THR C 618 " ideal model delta harmonic sigma weight residual 180.00 143.16 36.84 0 5.00e+00 4.00e-02 5.43e+01 ... (remaining 15654 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 3781 0.107 - 0.214: 242 0.214 - 0.321: 9 0.321 - 0.428: 5 0.428 - 0.536: 1 Chirality restraints: 4038 Sorted by residual: chirality pdb=" C1 NAG A1308 " pdb=" ND2 ASN A 234 " pdb=" C2 NAG A1308 " pdb=" O5 NAG A1308 " both_signs ideal model delta sigma weight residual False -2.40 -1.86 -0.54 2.00e-01 2.50e+01 7.17e+00 chirality pdb=" CB ILE B 119 " pdb=" CA ILE B 119 " pdb=" CG1 ILE B 119 " pdb=" CG2 ILE B 119 " both_signs ideal model delta sigma weight residual False 2.64 3.05 -0.41 2.00e-01 2.50e+01 4.13e+00 chirality pdb=" C1 NAG A1309 " pdb=" ND2 ASN A 616 " pdb=" C2 NAG A1309 " pdb=" O5 NAG A1309 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 4.04e+00 ... (remaining 4035 not shown) Planarity restraints: 4413 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 234 " -0.008 2.00e-02 2.50e+03 3.52e-02 1.55e+01 pdb=" CG ASN A 234 " 0.039 2.00e-02 2.50e+03 pdb=" OD1 ASN A 234 " -0.039 2.00e-02 2.50e+03 pdb=" ND2 ASN A 234 " 0.043 2.00e-02 2.50e+03 pdb=" C1 NAG A1308 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 808 " 0.061 5.00e-02 4.00e+02 9.29e-02 1.38e+01 pdb=" N PRO B 809 " -0.161 5.00e-02 4.00e+02 pdb=" CA PRO B 809 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO B 809 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 198 " 0.015 2.00e-02 2.50e+03 2.93e-02 8.57e+00 pdb=" C ASP B 198 " -0.051 2.00e-02 2.50e+03 pdb=" O ASP B 198 " 0.019 2.00e-02 2.50e+03 pdb=" N GLY B 199 " 0.017 2.00e-02 2.50e+03 ... (remaining 4410 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 6432 2.81 - 3.33: 19910 3.33 - 3.85: 39427 3.85 - 4.38: 43552 4.38 - 4.90: 79280 Nonbonded interactions: 188601 Sorted by model distance: nonbonded pdb=" O THR C 393 " pdb=" OG1 THR C 523 " model vdw 2.286 3.040 nonbonded pdb=" O THR A 393 " pdb=" OG1 THR A 523 " model vdw 2.304 3.040 nonbonded pdb=" O ALA C 879 " pdb=" OG1 THR C 883 " model vdw 2.312 3.040 nonbonded pdb=" OG SER C 31 " pdb=" OG SER C 60 " model vdw 2.319 3.040 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.322 3.040 ... (remaining 188596 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.810 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 64.660 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 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 0.059 25233 Z= 0.279 Angle : 0.773 13.137 34320 Z= 0.406 Chirality : 0.056 0.536 4038 Planarity : 0.006 0.093 4377 Dihedral : 14.359 91.012 9762 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % 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: -1.17 (0.14), residues: 3042 helix: 0.08 (0.18), residues: 696 sheet: 0.41 (0.20), residues: 621 loop : -1.66 (0.14), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 64 HIS 0.005 0.001 HIS C 339 PHE 0.038 0.002 PHE B 238 TYR 0.029 0.001 TYR A 495 ARG 0.017 0.001 ARG C 567 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 253 time to evaluate : 2.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.6944 (t80) cc_final: 0.6239 (t80) REVERT: A 586 ASP cc_start: 0.8263 (m-30) cc_final: 0.7989 (m-30) REVERT: A 780 GLU cc_start: 0.7808 (tt0) cc_final: 0.7496 (tt0) REVERT: B 460 LYS cc_start: 0.7403 (mttt) cc_final: 0.6736 (mttm) REVERT: B 574 ASP cc_start: 0.7936 (t0) cc_final: 0.7730 (t0) REVERT: B 955 ASN cc_start: 0.7266 (m110) cc_final: 0.6905 (m-40) REVERT: C 32 PHE cc_start: 0.6975 (m-80) cc_final: 0.6704 (m-80) REVERT: C 564 GLN cc_start: 0.7600 (mm110) cc_final: 0.7392 (mm110) REVERT: C 574 ASP cc_start: 0.7203 (t70) cc_final: 0.6917 (m-30) outliers start: 0 outliers final: 0 residues processed: 253 average time/residue: 0.3603 time to fit residues: 144.2071 Evaluate side-chains 195 residues out of total 2679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 3.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 3.9990 chunk 231 optimal weight: 0.9990 chunk 128 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 156 optimal weight: 4.9990 chunk 123 optimal weight: 3.9990 chunk 239 optimal weight: 8.9990 chunk 92 optimal weight: 0.5980 chunk 145 optimal weight: 0.0370 chunk 178 optimal weight: 0.9990 chunk 277 optimal weight: 4.9990 overall best weight: 0.9264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 935 GLN B 30 ASN B 115 GLN B 613 GLN C 115 GLN C 394 ASN C 405 ASN C 613 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.0778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25233 Z= 0.179 Angle : 0.517 9.665 34320 Z= 0.265 Chirality : 0.044 0.294 4038 Planarity : 0.004 0.063 4377 Dihedral : 6.887 57.613 4248 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 0.60 % Allowed : 5.64 % Favored : 93.77 % 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: -0.55 (0.15), residues: 3042 helix: 1.25 (0.19), residues: 726 sheet: 0.45 (0.19), residues: 663 loop : -1.53 (0.14), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 64 HIS 0.005 0.001 HIS C1048 PHE 0.013 0.001 PHE A 192 TYR 0.016 0.001 TYR B1067 ARG 0.004 0.000 ARG B 237 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 221 time to evaluate : 2.845 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.7033 (t80) cc_final: 0.6302 (t80) REVERT: A 498 ARG cc_start: 0.6922 (mmt90) cc_final: 0.6510 (mmt90) REVERT: A 586 ASP cc_start: 0.8281 (m-30) cc_final: 0.8016 (m-30) REVERT: A 780 GLU cc_start: 0.7838 (tt0) cc_final: 0.7596 (tt0) REVERT: B 360 ASN cc_start: 0.7895 (t0) cc_final: 0.7622 (t0) REVERT: B 574 ASP cc_start: 0.8026 (t0) cc_final: 0.7747 (t0) REVERT: B 591 SER cc_start: 0.8881 (OUTLIER) cc_final: 0.8287 (p) REVERT: B 955 ASN cc_start: 0.7253 (m110) cc_final: 0.6872 (m-40) REVERT: B 964 LYS cc_start: 0.8439 (tptm) cc_final: 0.8032 (ttmt) REVERT: C 32 PHE cc_start: 0.6900 (m-80) cc_final: 0.6620 (m-80) REVERT: C 269 TYR cc_start: 0.6977 (m-10) cc_final: 0.6721 (m-80) REVERT: C 458 LYS cc_start: 0.8351 (mmmm) cc_final: 0.8115 (tppt) REVERT: C 564 GLN cc_start: 0.7664 (mm110) cc_final: 0.7445 (mm110) outliers start: 16 outliers final: 11 residues processed: 231 average time/residue: 0.3419 time to fit residues: 128.3453 Evaluate side-chains 214 residues out of total 2679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 202 time to evaluate : 2.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 588 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 154 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 231 optimal weight: 4.9990 chunk 189 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 278 optimal weight: 3.9990 chunk 300 optimal weight: 3.9990 chunk 247 optimal weight: 3.9990 chunk 276 optimal weight: 10.0000 chunk 94 optimal weight: 3.9990 chunk 223 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 544 ASN A 901 GLN B 218 GLN B 239 GLN B 901 GLN B 960 ASN B1135 ASN C 26 GLN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 25233 Z= 0.378 Angle : 0.615 9.339 34320 Z= 0.318 Chirality : 0.048 0.278 4038 Planarity : 0.004 0.055 4377 Dihedral : 6.630 58.421 4248 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 1.23 % Allowed : 9.03 % Favored : 89.73 % 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: -0.63 (0.15), residues: 3042 helix: 1.36 (0.20), residues: 723 sheet: 0.12 (0.19), residues: 693 loop : -1.54 (0.14), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 64 HIS 0.006 0.001 HIS C1048 PHE 0.023 0.002 PHE A 497 TYR 0.021 0.002 TYR B1067 ARG 0.005 0.000 ARG C 567 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 210 time to evaluate : 2.638 Fit side-chains revert: symmetry clash REVERT: A 170 TYR cc_start: 0.7319 (t80) cc_final: 0.6466 (t80) REVERT: A 281 GLU cc_start: 0.7820 (tt0) cc_final: 0.7616 (tm-30) REVERT: A 498 ARG cc_start: 0.6981 (mmt90) cc_final: 0.6630 (mmt90) REVERT: A 780 GLU cc_start: 0.8117 (tt0) cc_final: 0.7878 (tt0) REVERT: B 360 ASN cc_start: 0.8114 (t0) cc_final: 0.7816 (t0) REVERT: B 574 ASP cc_start: 0.8228 (t0) cc_final: 0.7906 (t0) REVERT: B 591 SER cc_start: 0.8903 (OUTLIER) cc_final: 0.8333 (p) REVERT: B 752 LEU cc_start: 0.9134 (mp) cc_final: 0.8870 (mp) REVERT: B 955 ASN cc_start: 0.7068 (m110) cc_final: 0.6816 (m110) REVERT: C 319 ARG cc_start: 0.7680 (ttm110) cc_final: 0.7433 (ptp-110) REVERT: C 414 GLN cc_start: 0.7354 (mt0) cc_final: 0.6323 (mp10) REVERT: C 859 THR cc_start: 0.8587 (OUTLIER) cc_final: 0.8196 (p) REVERT: C 900 MET cc_start: 0.8220 (mtp) cc_final: 0.7909 (mtp) outliers start: 33 outliers final: 21 residues processed: 234 average time/residue: 0.3762 time to fit residues: 146.8082 Evaluate side-chains 218 residues out of total 2679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 195 time to evaluate : 2.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 881 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 275 optimal weight: 1.9990 chunk 209 optimal weight: 7.9990 chunk 144 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 186 optimal weight: 1.9990 chunk 279 optimal weight: 1.9990 chunk 295 optimal weight: 0.4980 chunk 145 optimal weight: 0.0170 chunk 264 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 overall best weight: 1.0422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 30 ASN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25233 Z= 0.196 Angle : 0.515 9.329 34320 Z= 0.264 Chirality : 0.044 0.267 4038 Planarity : 0.004 0.048 4377 Dihedral : 6.139 57.438 4248 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.90 % Allowed : 11.35 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.15), residues: 3042 helix: 1.59 (0.20), residues: 738 sheet: 0.26 (0.19), residues: 687 loop : -1.41 (0.14), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.003 0.001 HIS B1048 PHE 0.025 0.001 PHE C 92 TYR 0.017 0.001 TYR A1067 ARG 0.003 0.000 ARG C 567 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 208 time to evaluate : 2.531 Fit side-chains revert: symmetry clash REVERT: A 170 TYR cc_start: 0.7283 (t80) cc_final: 0.6355 (t80) REVERT: A 498 ARG cc_start: 0.6890 (mmt90) cc_final: 0.6547 (mmt90) REVERT: A 780 GLU cc_start: 0.8069 (tt0) cc_final: 0.7829 (tt0) REVERT: B 360 ASN cc_start: 0.8074 (t0) cc_final: 0.7762 (t0) REVERT: B 493 GLN cc_start: 0.7786 (tp-100) cc_final: 0.7552 (tp-100) REVERT: B 574 ASP cc_start: 0.8054 (t0) cc_final: 0.7787 (t0) REVERT: B 591 SER cc_start: 0.8870 (m) cc_final: 0.8269 (p) REVERT: B 752 LEU cc_start: 0.9099 (mp) cc_final: 0.8850 (mp) REVERT: B 902 MET cc_start: 0.8847 (mmm) cc_final: 0.8549 (mmt) REVERT: B 955 ASN cc_start: 0.7127 (m110) cc_final: 0.6763 (m110) REVERT: C 319 ARG cc_start: 0.7593 (ttm110) cc_final: 0.7379 (ptp-110) REVERT: C 414 GLN cc_start: 0.7251 (mt0) cc_final: 0.6339 (mp10) outliers start: 24 outliers final: 18 residues processed: 225 average time/residue: 0.3510 time to fit residues: 129.5996 Evaluate side-chains 215 residues out of total 2679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 197 time to evaluate : 2.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 588 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 246 optimal weight: 5.9990 chunk 167 optimal weight: 0.7980 chunk 4 optimal weight: 6.9990 chunk 220 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 252 optimal weight: 3.9990 chunk 204 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 151 optimal weight: 4.9990 chunk 265 optimal weight: 4.9990 chunk 74 optimal weight: 0.6980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 926 GLN B 563 GLN C 30 ASN C 394 ASN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 25233 Z= 0.309 Angle : 0.565 9.258 34320 Z= 0.289 Chirality : 0.046 0.271 4038 Planarity : 0.004 0.046 4377 Dihedral : 6.114 57.530 4248 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 1.68 % Allowed : 12.09 % Favored : 86.23 % 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: -0.47 (0.15), residues: 3042 helix: 1.48 (0.20), residues: 741 sheet: 0.17 (0.19), residues: 684 loop : -1.45 (0.15), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.004 0.001 HIS C1048 PHE 0.018 0.002 PHE A1042 TYR 0.020 0.001 TYR B1067 ARG 0.004 0.000 ARG C 567 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 209 time to evaluate : 2.783 Fit side-chains revert: symmetry clash REVERT: A 170 TYR cc_start: 0.7223 (t80) cc_final: 0.6355 (t80) REVERT: A 177 MET cc_start: 0.3608 (mtt) cc_final: 0.2762 (mtm) REVERT: A 498 ARG cc_start: 0.6899 (mmt90) cc_final: 0.6526 (mmt90) REVERT: A 780 GLU cc_start: 0.8036 (tt0) cc_final: 0.7791 (tt0) REVERT: B 360 ASN cc_start: 0.8176 (t0) cc_final: 0.7858 (t0) REVERT: B 420 ASP cc_start: 0.8144 (m-30) cc_final: 0.7729 (t70) REVERT: B 574 ASP cc_start: 0.8004 (t0) cc_final: 0.7735 (t0) REVERT: B 591 SER cc_start: 0.8897 (m) cc_final: 0.8300 (p) REVERT: B 902 MET cc_start: 0.8872 (mmm) cc_final: 0.8643 (tpt) REVERT: B 955 ASN cc_start: 0.7021 (m110) cc_final: 0.6752 (m110) REVERT: C 394 ASN cc_start: 0.8159 (OUTLIER) cc_final: 0.7787 (m110) REVERT: C 859 THR cc_start: 0.8661 (OUTLIER) cc_final: 0.8323 (p) REVERT: C 900 MET cc_start: 0.8284 (mtp) cc_final: 0.7965 (mtp) outliers start: 45 outliers final: 35 residues processed: 243 average time/residue: 0.3399 time to fit residues: 136.1271 Evaluate side-chains 234 residues out of total 2679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 197 time to evaluate : 2.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 907 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 99 optimal weight: 3.9990 chunk 266 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 173 optimal weight: 6.9990 chunk 73 optimal weight: 0.8980 chunk 296 optimal weight: 0.7980 chunk 245 optimal weight: 5.9990 chunk 137 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 97 optimal weight: 0.5980 chunk 155 optimal weight: 4.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 474 GLN B 563 GLN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25233 Z= 0.215 Angle : 0.527 9.254 34320 Z= 0.270 Chirality : 0.044 0.297 4038 Planarity : 0.004 0.045 4377 Dihedral : 5.967 57.098 4248 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.64 % Allowed : 12.92 % Favored : 85.44 % 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: -0.34 (0.15), residues: 3042 helix: 1.64 (0.20), residues: 738 sheet: 0.24 (0.19), residues: 684 loop : -1.37 (0.15), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.003 0.001 HIS B1048 PHE 0.015 0.001 PHE A1042 TYR 0.018 0.001 TYR B1067 ARG 0.003 0.000 ARG C 567 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 206 time to evaluate : 2.795 Fit side-chains revert: symmetry clash REVERT: A 170 TYR cc_start: 0.7238 (t80) cc_final: 0.6326 (t80) REVERT: A 177 MET cc_start: 0.3699 (mtt) cc_final: 0.2814 (mtm) REVERT: A 517 LEU cc_start: 0.6975 (OUTLIER) cc_final: 0.6702 (mm) REVERT: A 780 GLU cc_start: 0.8030 (tt0) cc_final: 0.7802 (tt0) REVERT: B 360 ASN cc_start: 0.8177 (t0) cc_final: 0.7859 (t0) REVERT: B 420 ASP cc_start: 0.8117 (m-30) cc_final: 0.7724 (t70) REVERT: B 568 ASP cc_start: 0.7154 (t0) cc_final: 0.6779 (t0) REVERT: B 574 ASP cc_start: 0.7967 (t0) cc_final: 0.7700 (t0) REVERT: B 591 SER cc_start: 0.8879 (m) cc_final: 0.8265 (p) REVERT: B 955 ASN cc_start: 0.7032 (m110) cc_final: 0.6727 (m110) REVERT: C 859 THR cc_start: 0.8653 (OUTLIER) cc_final: 0.8324 (p) outliers start: 44 outliers final: 35 residues processed: 238 average time/residue: 0.3299 time to fit residues: 129.5491 Evaluate side-chains 236 residues out of total 2679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 199 time to evaluate : 2.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 907 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 285 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 chunk 168 optimal weight: 2.9990 chunk 216 optimal weight: 9.9990 chunk 167 optimal weight: 0.9980 chunk 249 optimal weight: 5.9990 chunk 165 optimal weight: 3.9990 chunk 294 optimal weight: 1.9990 chunk 184 optimal weight: 1.9990 chunk 179 optimal weight: 3.9990 chunk 136 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 926 GLN B 563 GLN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 25233 Z= 0.291 Angle : 0.556 9.227 34320 Z= 0.285 Chirality : 0.045 0.296 4038 Planarity : 0.004 0.045 4377 Dihedral : 6.008 57.095 4248 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 1.79 % Allowed : 13.55 % Favored : 84.66 % 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: -0.40 (0.15), residues: 3042 helix: 1.56 (0.20), residues: 738 sheet: 0.21 (0.19), residues: 684 loop : -1.40 (0.15), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.004 0.001 HIS A1064 PHE 0.016 0.001 PHE A1042 TYR 0.019 0.001 TYR B1067 ARG 0.003 0.000 ARG C 567 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 206 time to evaluate : 2.516 Fit side-chains revert: symmetry clash REVERT: A 170 TYR cc_start: 0.7394 (t80) cc_final: 0.6478 (t80) REVERT: A 177 MET cc_start: 0.3678 (mtt) cc_final: 0.2757 (mtm) REVERT: A 517 LEU cc_start: 0.7033 (OUTLIER) cc_final: 0.6736 (mm) REVERT: A 780 GLU cc_start: 0.8031 (tt0) cc_final: 0.7805 (tt0) REVERT: B 360 ASN cc_start: 0.8236 (t0) cc_final: 0.7924 (t0) REVERT: B 420 ASP cc_start: 0.8135 (m-30) cc_final: 0.7719 (t0) REVERT: B 568 ASP cc_start: 0.7189 (t0) cc_final: 0.6810 (t0) REVERT: B 574 ASP cc_start: 0.7975 (t0) cc_final: 0.7709 (t0) REVERT: B 591 SER cc_start: 0.8897 (m) cc_final: 0.8284 (p) REVERT: B 902 MET cc_start: 0.8735 (tpt) cc_final: 0.8422 (mmm) REVERT: B 955 ASN cc_start: 0.7001 (m110) cc_final: 0.6738 (m110) REVERT: C 414 GLN cc_start: 0.7270 (mt0) cc_final: 0.6269 (mp10) REVERT: C 859 THR cc_start: 0.8660 (OUTLIER) cc_final: 0.8323 (p) outliers start: 48 outliers final: 41 residues processed: 244 average time/residue: 0.3186 time to fit residues: 128.4451 Evaluate side-chains 243 residues out of total 2679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 200 time to evaluate : 2.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 574 ASP Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 907 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 182 optimal weight: 1.9990 chunk 117 optimal weight: 4.9990 chunk 176 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 187 optimal weight: 1.9990 chunk 200 optimal weight: 0.8980 chunk 145 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 231 optimal weight: 2.9990 chunk 268 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1088 HIS B 563 GLN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25233 Z= 0.168 Angle : 0.509 9.256 34320 Z= 0.260 Chirality : 0.044 0.287 4038 Planarity : 0.003 0.046 4377 Dihedral : 5.767 57.205 4248 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.75 % Allowed : 14.04 % Favored : 84.21 % 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: -0.20 (0.15), residues: 3042 helix: 1.83 (0.20), residues: 738 sheet: 0.29 (0.19), residues: 684 loop : -1.31 (0.15), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.003 0.001 HIS C1048 PHE 0.015 0.001 PHE B 168 TYR 0.025 0.001 TYR B 170 ARG 0.003 0.000 ARG C 567 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 209 time to evaluate : 2.853 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.7401 (t80) cc_final: 0.6491 (t80) REVERT: A 177 MET cc_start: 0.3571 (mtt) cc_final: 0.2662 (mtm) REVERT: A 517 LEU cc_start: 0.6952 (OUTLIER) cc_final: 0.6697 (mm) REVERT: A 780 GLU cc_start: 0.8039 (tt0) cc_final: 0.7828 (tt0) REVERT: A 913 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.7828 (pt0) REVERT: B 360 ASN cc_start: 0.8232 (t0) cc_final: 0.7915 (t0) REVERT: B 420 ASP cc_start: 0.8118 (m-30) cc_final: 0.7732 (t0) REVERT: B 568 ASP cc_start: 0.7126 (t0) cc_final: 0.6852 (t0) REVERT: B 591 SER cc_start: 0.8842 (m) cc_final: 0.8235 (p) REVERT: B 955 ASN cc_start: 0.7007 (m110) cc_final: 0.6719 (m-40) REVERT: C 319 ARG cc_start: 0.7806 (ptp90) cc_final: 0.7089 (ptm160) REVERT: C 414 GLN cc_start: 0.7308 (mt0) cc_final: 0.6289 (mp10) REVERT: C 859 THR cc_start: 0.8566 (OUTLIER) cc_final: 0.8248 (p) outliers start: 47 outliers final: 37 residues processed: 249 average time/residue: 0.3400 time to fit residues: 140.3722 Evaluate side-chains 241 residues out of total 2679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 201 time to evaluate : 2.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 1043 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 282 optimal weight: 0.9990 chunk 257 optimal weight: 0.5980 chunk 274 optimal weight: 0.9990 chunk 165 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 215 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 248 optimal weight: 2.9990 chunk 259 optimal weight: 2.9990 chunk 273 optimal weight: 4.9990 chunk 180 optimal weight: 0.6980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 563 GLN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 25233 Z= 0.168 Angle : 0.507 9.293 34320 Z= 0.260 Chirality : 0.044 0.291 4038 Planarity : 0.003 0.046 4377 Dihedral : 5.650 56.873 4248 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 1.64 % Allowed : 14.18 % Favored : 84.17 % 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: -0.11 (0.15), residues: 3042 helix: 1.93 (0.20), residues: 741 sheet: 0.36 (0.19), residues: 699 loop : -1.30 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.002 0.001 HIS B1048 PHE 0.016 0.001 PHE A 192 TYR 0.024 0.001 TYR B 170 ARG 0.003 0.000 ARG C 567 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 211 time to evaluate : 2.630 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 PHE cc_start: 0.5696 (m-80) cc_final: 0.5380 (m-80) REVERT: A 170 TYR cc_start: 0.7306 (t80) cc_final: 0.6404 (t80) REVERT: A 177 MET cc_start: 0.4056 (mtt) cc_final: 0.3009 (mtm) REVERT: A 192 PHE cc_start: 0.7223 (m-10) cc_final: 0.6900 (m-80) REVERT: A 517 LEU cc_start: 0.7125 (OUTLIER) cc_final: 0.6907 (mm) REVERT: A 586 ASP cc_start: 0.8273 (m-30) cc_final: 0.8061 (m-30) REVERT: A 780 GLU cc_start: 0.8038 (tt0) cc_final: 0.7831 (tt0) REVERT: A 1116 THR cc_start: 0.7818 (OUTLIER) cc_final: 0.7609 (p) REVERT: B 360 ASN cc_start: 0.8234 (t0) cc_final: 0.7906 (t0) REVERT: B 420 ASP cc_start: 0.8103 (m-30) cc_final: 0.7721 (t0) REVERT: B 568 ASP cc_start: 0.7173 (t0) cc_final: 0.6908 (t0) REVERT: B 591 SER cc_start: 0.8823 (m) cc_final: 0.8211 (p) REVERT: B 955 ASN cc_start: 0.7043 (m110) cc_final: 0.6838 (m-40) REVERT: C 319 ARG cc_start: 0.7812 (ptp90) cc_final: 0.7074 (ptm160) REVERT: C 414 GLN cc_start: 0.7247 (mt0) cc_final: 0.6273 (mp10) REVERT: C 859 THR cc_start: 0.8572 (OUTLIER) cc_final: 0.8265 (p) REVERT: C 900 MET cc_start: 0.8184 (mtp) cc_final: 0.7926 (mtp) outliers start: 44 outliers final: 39 residues processed: 248 average time/residue: 0.3412 time to fit residues: 139.9663 Evaluate side-chains 247 residues out of total 2679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 205 time to evaluate : 3.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 1043 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 290 optimal weight: 5.9990 chunk 177 optimal weight: 2.9990 chunk 137 optimal weight: 0.8980 chunk 202 optimal weight: 1.9990 chunk 304 optimal weight: 4.9990 chunk 280 optimal weight: 3.9990 chunk 242 optimal weight: 0.6980 chunk 25 optimal weight: 5.9990 chunk 187 optimal weight: 3.9990 chunk 148 optimal weight: 0.1980 chunk 192 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1135 ASN C 405 ASN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 25233 Z= 0.179 Angle : 0.513 9.342 34320 Z= 0.262 Chirality : 0.044 0.295 4038 Planarity : 0.003 0.045 4377 Dihedral : 5.594 56.830 4248 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.98 % Allowed : 14.04 % Favored : 83.99 % 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: -0.09 (0.15), residues: 3042 helix: 1.93 (0.20), residues: 741 sheet: 0.38 (0.19), residues: 699 loop : -1.29 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.003 0.001 HIS B1048 PHE 0.016 0.001 PHE C 371 TYR 0.023 0.001 TYR B 170 ARG 0.004 0.000 ARG A 498 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6084 Ramachandran restraints generated. 3042 Oldfield, 0 Emsley, 3042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 209 time to evaluate : 2.856 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 PHE cc_start: 0.5732 (m-80) cc_final: 0.5291 (m-80) REVERT: A 170 TYR cc_start: 0.7310 (t80) cc_final: 0.6414 (t80) REVERT: A 177 MET cc_start: 0.4060 (mtt) cc_final: 0.2971 (mtm) REVERT: A 192 PHE cc_start: 0.7237 (m-10) cc_final: 0.6843 (m-80) REVERT: A 205 SER cc_start: 0.8547 (m) cc_final: 0.8269 (m) REVERT: A 517 LEU cc_start: 0.7127 (OUTLIER) cc_final: 0.6919 (mm) REVERT: A 780 GLU cc_start: 0.8037 (tt0) cc_final: 0.7831 (tt0) REVERT: A 1116 THR cc_start: 0.7821 (OUTLIER) cc_final: 0.7617 (p) REVERT: B 360 ASN cc_start: 0.8238 (t0) cc_final: 0.7914 (t0) REVERT: B 420 ASP cc_start: 0.8113 (m-30) cc_final: 0.7740 (t0) REVERT: B 568 ASP cc_start: 0.7098 (t0) cc_final: 0.6827 (t0) REVERT: B 955 ASN cc_start: 0.7044 (m110) cc_final: 0.6835 (m-40) REVERT: C 319 ARG cc_start: 0.7907 (ptp90) cc_final: 0.7101 (ptm160) REVERT: C 414 GLN cc_start: 0.7253 (mt0) cc_final: 0.6276 (mp10) REVERT: C 859 THR cc_start: 0.8584 (OUTLIER) cc_final: 0.8274 (p) REVERT: C 900 MET cc_start: 0.8196 (mtp) cc_final: 0.7945 (mtp) outliers start: 53 outliers final: 46 residues processed: 252 average time/residue: 0.3107 time to fit residues: 130.2710 Evaluate side-chains 254 residues out of total 2679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 205 time to evaluate : 2.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 501 TYR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 1043 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 306 random chunks: chunk 258 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 223 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 67 optimal weight: 0.0270 chunk 243 optimal weight: 0.0980 chunk 101 optimal weight: 1.9990 chunk 249 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 213 optimal weight: 9.9990 overall best weight: 1.0242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 GLN B 563 GLN C 405 ASN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.159799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.114835 restraints weight = 31739.244| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.75 r_work: 0.3056 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25233 Z= 0.189 Angle : 0.515 10.645 34320 Z= 0.263 Chirality : 0.044 0.295 4038 Planarity : 0.003 0.045 4377 Dihedral : 5.568 56.791 4248 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.90 % Allowed : 14.22 % Favored : 83.87 % 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: -0.16 (0.15), residues: 3042 helix: 1.79 (0.20), residues: 759 sheet: 0.36 (0.19), residues: 699 loop : -1.33 (0.15), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.004 0.001 HIS C1048 PHE 0.017 0.001 PHE C 371 TYR 0.022 0.001 TYR B 170 ARG 0.004 0.000 ARG A 498 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4567.08 seconds wall clock time: 83 minutes 13.08 seconds (4993.08 seconds total)