Starting phenix.real_space_refine on Tue Feb 20 00:59:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mkl_23898/02_2024/7mkl_23898.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mkl_23898/02_2024/7mkl_23898.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mkl_23898/02_2024/7mkl_23898.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mkl_23898/02_2024/7mkl_23898.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mkl_23898/02_2024/7mkl_23898.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mkl_23898/02_2024/7mkl_23898.pdb" } resolution = 3.2 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= 0.002 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 751 atoms to isotropic. 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 16288 2.51 5 N 4164 2.21 5 O 5034 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 340": "OE1" <-> "OE2" Residue "A TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 775": "OD1" <-> "OD2" Residue "A GLU 988": "OE1" <-> "OE2" Residue "A GLU 1017": "OE1" <-> "OE2" Residue "A ASP 1118": "OD1" <-> "OD2" Residue "B TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 868": "OE1" <-> "OE2" Residue "B PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 398": "OD1" <-> "OD2" Residue "C TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 25597 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 7825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7825 Classifications: {'peptide': 1002} Link IDs: {'PCIS': 1, 'PTRANS': 52, 'TRANS': 948} Chain breaks: 7 Chain: "B" Number of atoms: 7606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 7606 Classifications: {'peptide': 972} Link IDs: {'PTRANS': 52, 'TRANS': 919} Chain breaks: 11 Chain: "C" Number of atoms: 7606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 7606 Classifications: {'peptide': 972} Link IDs: {'PTRANS': 52, 'TRANS': 919} Chain breaks: 11 Chain: "H" Number of atoms: 878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 878 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "L" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 800 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 97} 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: "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: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 13.03, per 1000 atoms: 0.51 Number of scatterers: 25597 At special positions: 0 Unit cell: (135.72, 131.08, 214.6, 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 5034 8.00 N 4164 7.00 C 16288 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 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=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.04 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " 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=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.04 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " 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=2.05 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.04 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 87 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " NAG-ASN " NAG A1201 " - " ASN A 61 " " NAG A1202 " - " ASN A 122 " " NAG A1203 " - " ASN A 165 " " NAG A1204 " - " ASN A 282 " " NAG A1205 " - " ASN A 331 " " NAG A1206 " - " ASN A 343 " " NAG A1207 " - " ASN A 603 " " NAG A1208 " - " ASN A 616 " " NAG A1209 " - " ASN A 657 " " NAG A1210 " - " ASN A 709 " " NAG A1211 " - " ASN A1074 " " NAG B1201 " - " ASN B 61 " " NAG B1202 " - " ASN B 122 " " NAG B1203 " - " ASN B 165 " " NAG B1204 " - " ASN B 282 " " NAG B1205 " - " ASN B 331 " " NAG B1206 " - " ASN B 343 " " NAG B1207 " - " ASN B 603 " " NAG B1208 " - " ASN B 616 " " NAG B1209 " - " ASN B 657 " " NAG B1210 " - " ASN B 709 " " NAG B1211 " - " ASN B1074 " " NAG C1201 " - " ASN C 61 " " NAG C1202 " - " ASN C 122 " " NAG C1203 " - " ASN C 165 " " NAG C1204 " - " ASN C 282 " " NAG C1205 " - " ASN C 331 " " NAG C1206 " - " ASN C 343 " " NAG C1207 " - " ASN C 603 " " NAG C1208 " - " ASN C 616 " " NAG C1209 " - " ASN C 657 " " NAG C1210 " - " ASN C 709 " " NAG C1211 " - " ASN C1074 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1098 " " NAG I 1 " - " ASN A1134 " " NAG J 1 " - " ASN B 234 " " NAG K 1 " - " ASN B 717 " " NAG M 1 " - " ASN B 801 " " NAG N 1 " - " ASN B1098 " " NAG O 1 " - " ASN B1134 " " NAG P 1 " - " ASN C 234 " " NAG Q 1 " - " ASN C 717 " " NAG R 1 " - " ASN C 801 " " NAG S 1 " - " ASN C1098 " " NAG T 1 " - " ASN C1134 " Time building additional restraints: 9.84 Conformation dependent library (CDL) restraints added in 4.2 seconds 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5930 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 44 sheets defined 24.5% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.85 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 365 through 372 Processing helix chain 'A' and resid 404 through 410 Processing helix chain 'A' and resid 416 through 422 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: 3.777A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.246A 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 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.180A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (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 removed outlier: 5.049A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.125A 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 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.544A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 501 through 501 No H-bonds generated for 'chain 'B' and resid 501 through 501' Processing helix chain 'B' and resid 503 through 505 No H-bonds generated for 'chain 'B' and resid 503 through 505' 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: 3.871A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.085A 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 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.018A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (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 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 5.030A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.892A 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 365 through 371 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.388A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.662A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) 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: 4.126A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.201A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.945A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (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 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.707A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 3.852A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'H' and resid 84 through 89 Processing helix chain 'L' and resid 48 through 52 removed outlier: 3.793A pdb=" N ASN L 52 " --> pdb=" O ASP L 49 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.535A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE A 194 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.899A 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: 4.372A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE B 326 " --> pdb=" O ASN B 540 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.523A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.119A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.547A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 328 removed outlier: 3.689A pdb=" N ARG A 328 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL A 539 " --> pdb=" O GLY A 550 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 355 through 358 removed outlier: 4.283A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TYR A 396 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER A 514 " --> pdb=" O TYR A 396 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A 510 " --> pdb=" O PHE A 400 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU A 513 " --> pdb=" O CYS A 432 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.245A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 712 through 728 removed outlier: 7.049A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB4, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.304A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE A1081 " --> pdb=" O HIS A1088 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB6, first strand: chain 'B' and resid 42 through 43 removed outlier: 3.770A pdb=" N ARG C 567 " --> pdb=" O PHE B 43 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG C 328 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.555A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N PHE B 55 " --> pdb=" O GLN B 271 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.870A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU B 118 " --> pdb=" O LYS B 129 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS B 129 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL B 120 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL B 127 " --> pdb=" O VAL B 120 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 224 through 229 removed outlier: 6.099A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER B 94 " --> pdb=" O ARG B 190 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 311 through 319 removed outlier: 3.693A pdb=" N GLY B 311 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR B 315 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY B 648 " --> pdb=" O THR B 645 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR B 645 " --> pdb=" O GLY B 648 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.747A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'B' and resid 378 through 379 removed outlier: 4.593A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL B 433 " --> pdb=" O LYS B 378 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AC5, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.738A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 711 through 728 removed outlier: 3.568A pdb=" N ILE B 714 " --> pdb=" O LYS B1073 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AC8, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.529A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE B1081 " --> pdb=" O HIS B1088 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD1, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.752A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 63 through 64 removed outlier: 3.785A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR C 91 " --> pdb=" O GLY C 268 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL C 90 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE C 194 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N SER C 94 " --> pdb=" O ARG C 190 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU C 189 " --> pdb=" O THR C 208 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR C 208 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.269A pdb=" N ARG C 237 " --> pdb=" O GLY C 107 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLN C 239 " --> pdb=" O ILE C 105 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ILE C 105 " --> pdb=" O GLN C 239 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 118 through 122 removed outlier: 3.718A pdb=" N VAL C 120 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL C 127 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ASN C 122 " --> pdb=" O ASN C 125 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR C 170 " --> pdb=" O ILE C 128 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.395A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.046A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL C 433 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.777A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AD9, first strand: chain 'C' and resid 654 through 655 removed outlier: 3.660A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 711 through 728 removed outlier: 3.622A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE3, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.303A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE C1081 " --> pdb=" O HIS C1088 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AE5, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.702A pdb=" N LEU H 18 " --> pdb=" O MET H 82 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N MET H 82 " --> pdb=" O LEU H 18 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE H 20 " --> pdb=" O LEU H 80 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLN H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 46 through 48 removed outlier: 3.591A pdb=" N GLY H 33 " --> pdb=" O ASP H 98 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL H 37 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN H 39 " --> pdb=" O LYS H 92 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYS H 92 " --> pdb=" O GLN H 39 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 3 through 5 removed outlier: 3.979A pdb=" N VAL L 19 " --> pdb=" O ILE L 74 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ILE L 74 " --> pdb=" O VAL L 19 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N MET L 21 " --> pdb=" O LEU L 72 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LEU L 72 " --> pdb=" O MET L 21 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N CYS L 23 " --> pdb=" O TYR L 70 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR L 70 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR L 71 " --> pdb=" O SER L 64 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N SER L 62 " --> pdb=" O THR L 73 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'L' and resid 45 through 47 removed outlier: 4.519A pdb=" N LEU L 45 " --> pdb=" O GLN L 36 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLN L 36 " --> pdb=" O LEU L 45 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLN L 88 " --> pdb=" O TYR L 33 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N TYR L 35 " --> pdb=" O TYR L 86 " (cutoff:3.500A) 891 hydrogen bonds defined for protein. 2511 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: 10.07 Time building geometry restraints manager: 10.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 8082 1.35 - 1.47: 6865 1.47 - 1.60: 11073 1.60 - 1.73: 0 1.73 - 1.86: 140 Bond restraints: 26160 Sorted by residual: bond pdb=" C1 NAG R 2 " pdb=" O5 NAG R 2 " ideal model delta sigma weight residual 1.406 1.513 -0.107 2.00e-02 2.50e+03 2.86e+01 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.482 -0.076 2.00e-02 2.50e+03 1.43e+01 bond pdb=" C1 NAG B1202 " pdb=" O5 NAG B1202 " ideal model delta sigma weight residual 1.406 1.470 -0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.55e+00 bond pdb=" C1 NAG T 1 " pdb=" O5 NAG T 1 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.74e+00 ... (remaining 26155 not shown) Histogram of bond angle deviations from ideal: 96.73 - 104.18: 423 104.18 - 111.64: 12128 111.64 - 119.09: 8992 119.09 - 126.55: 13758 126.55 - 134.00: 299 Bond angle restraints: 35600 Sorted by residual: angle pdb=" CA CYS A 432 " pdb=" CB CYS A 432 " pdb=" SG CYS A 432 " ideal model delta sigma weight residual 114.40 133.86 -19.46 2.30e+00 1.89e-01 7.16e+01 angle pdb=" CA CYS B 738 " pdb=" CB CYS B 738 " pdb=" SG CYS B 738 " ideal model delta sigma weight residual 114.40 126.86 -12.46 2.30e+00 1.89e-01 2.93e+01 angle pdb=" CA CYS C 432 " pdb=" CB CYS C 432 " pdb=" SG CYS C 432 " ideal model delta sigma weight residual 114.40 125.98 -11.58 2.30e+00 1.89e-01 2.54e+01 angle pdb=" CA CYS B 432 " pdb=" CB CYS B 432 " pdb=" SG CYS B 432 " ideal model delta sigma weight residual 114.40 124.90 -10.50 2.30e+00 1.89e-01 2.09e+01 angle pdb=" C LYS A 386 " pdb=" N LEU A 387 " pdb=" CA LEU A 387 " ideal model delta sigma weight residual 122.58 113.22 9.36 2.07e+00 2.33e-01 2.05e+01 ... (remaining 35595 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.74: 15558 22.74 - 45.47: 649 45.47 - 68.21: 145 68.21 - 90.94: 40 90.94 - 113.68: 14 Dihedral angle restraints: 16406 sinusoidal: 7204 harmonic: 9202 Sorted by residual: dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 -2.50 -83.50 1 1.00e+01 1.00e-02 8.51e+01 dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual 93.00 173.33 -80.33 1 1.00e+01 1.00e-02 7.99e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -156.64 70.64 1 1.00e+01 1.00e-02 6.42e+01 ... (remaining 16403 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.211: 4217 0.211 - 0.422: 17 0.422 - 0.633: 1 0.633 - 0.844: 0 0.844 - 1.055: 1 Chirality restraints: 4236 Sorted by residual: chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN C 234 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.34 -1.06 2.00e-01 2.50e+01 2.79e+01 chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN B1134 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.85 -0.55 2.00e-01 2.50e+01 7.69e+00 chirality pdb=" C1 NAG A1203 " pdb=" ND2 ASN A 165 " pdb=" C2 NAG A1203 " pdb=" O5 NAG A1203 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.51e+00 ... (remaining 4233 not shown) Planarity restraints: 4562 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 898 " 0.085 5.00e-02 4.00e+02 1.28e-01 2.62e+01 pdb=" N PRO A 899 " -0.221 5.00e-02 4.00e+02 pdb=" CA PRO A 899 " 0.067 5.00e-02 4.00e+02 pdb=" CD PRO A 899 " 0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN B1134 " -0.007 2.00e-02 2.50e+03 3.67e-02 1.69e+01 pdb=" CG ASN B1134 " -0.032 2.00e-02 2.50e+03 pdb=" OD1 ASN B1134 " 0.043 2.00e-02 2.50e+03 pdb=" ND2 ASN B1134 " -0.046 2.00e-02 2.50e+03 pdb=" C1 NAG O 1 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 816 " 0.065 5.00e-02 4.00e+02 9.78e-02 1.53e+01 pdb=" N PRO A 817 " -0.169 5.00e-02 4.00e+02 pdb=" CA PRO A 817 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO A 817 " 0.054 5.00e-02 4.00e+02 ... (remaining 4559 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 86 2.47 - 3.08: 17186 3.08 - 3.68: 35944 3.68 - 4.29: 51071 4.29 - 4.90: 85344 Nonbonded interactions: 189631 Sorted by model distance: nonbonded pdb=" O PRO B 85 " pdb=" OH TYR B 269 " model vdw 1.862 2.440 nonbonded pdb=" O PHE B 329 " pdb=" NE2 GLN B 580 " model vdw 2.150 2.520 nonbonded pdb=" OD1 ASN A 360 " pdb=" OG1 THR A 523 " model vdw 2.170 2.440 nonbonded pdb=" OE2 GLU B 96 " pdb=" N ILE B 100 " model vdw 2.176 2.520 nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.177 2.440 ... (remaining 189626 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 444 or resid 447 through 454 or resid 462 throu \ gh 468 or resid 489 through 501 or resid 503 through 1147 or resid 1201 through \ 1211)) selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } 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: 1.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.130 Construct map_model_manager: 0.010 Extract box with map and model: 6.690 Check model and map are aligned: 0.380 Set scattering table: 0.220 Process input model: 64.710 Find NCS groups from input model: 1.780 Set up NCS constraints: 0.220 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5698 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 0.107 26160 Z= 0.293 Angle : 0.820 19.465 35600 Z= 0.431 Chirality : 0.056 1.055 4236 Planarity : 0.006 0.128 4514 Dihedral : 13.439 113.679 10359 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.60 % Cis-general : 0.00 % Twisted Proline : 0.60 % 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 (0.14), residues: 3096 helix: 0.76 (0.19), residues: 696 sheet: 1.21 (0.19), residues: 629 loop : -0.29 (0.14), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 353 HIS 0.011 0.001 HIS B1048 PHE 0.026 0.002 PHE C 92 TYR 0.034 0.002 TYR B 423 ARG 0.014 0.001 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 342 time to evaluate : 2.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 394 ASN cc_start: 0.6632 (p0) cc_final: 0.5888 (p0) REVERT: A 568 ASP cc_start: 0.7320 (t0) cc_final: 0.7083 (t0) REVERT: B 265 TYR cc_start: 0.5243 (p90) cc_final: 0.4592 (p90) REVERT: B 558 LYS cc_start: 0.5761 (tmtt) cc_final: 0.5508 (tptp) REVERT: B 781 VAL cc_start: 0.4733 (t) cc_final: 0.4449 (t) outliers start: 0 outliers final: 0 residues processed: 342 average time/residue: 0.3504 time to fit residues: 190.8700 Evaluate side-chains 297 residues out of total 2774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 297 time to evaluate : 2.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 265 optimal weight: 0.9980 chunk 238 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 81 optimal weight: 0.6980 chunk 161 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 246 optimal weight: 0.5980 chunk 95 optimal weight: 0.6980 chunk 150 optimal weight: 0.0870 chunk 183 optimal weight: 1.9990 chunk 286 optimal weight: 0.7980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN ** A 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN B 450 ASN ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 824 ASN C 317 ASN C 787 GLN H 35 HIS ** L 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5763 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 26160 Z= 0.207 Angle : 0.666 15.011 35600 Z= 0.343 Chirality : 0.055 1.672 4236 Planarity : 0.005 0.074 4514 Dihedral : 9.874 93.385 4697 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.15 % Allowed : 4.54 % Favored : 94.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.14), residues: 3096 helix: 1.70 (0.20), residues: 690 sheet: 0.82 (0.19), residues: 656 loop : -0.32 (0.14), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 436 HIS 0.008 0.001 HIS B1083 PHE 0.025 0.002 PHE A 855 TYR 0.019 0.002 TYR A 279 ARG 0.007 0.000 ARG C 646 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 308 time to evaluate : 2.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 568 ASP cc_start: 0.7360 (t0) cc_final: 0.7087 (t0) REVERT: B 265 TYR cc_start: 0.5021 (p90) cc_final: 0.4474 (p90) REVERT: B 465 GLU cc_start: 0.7615 (mm-30) cc_final: 0.7293 (mm-30) REVERT: B 781 VAL cc_start: 0.5088 (t) cc_final: 0.4764 (t) REVERT: C 552 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7574 (mp) REVERT: C 902 MET cc_start: 0.3982 (tpp) cc_final: 0.3670 (tpt) outliers start: 32 outliers final: 20 residues processed: 324 average time/residue: 0.3550 time to fit residues: 185.9969 Evaluate side-chains 302 residues out of total 2774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 281 time to evaluate : 2.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1134 ASN Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 877 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 158 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 238 optimal weight: 2.9990 chunk 194 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 chunk 286 optimal weight: 2.9990 chunk 309 optimal weight: 5.9990 chunk 255 optimal weight: 0.9990 chunk 284 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 229 optimal weight: 0.8980 overall best weight: 0.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 655 HIS ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 GLN A 935 GLN A1101 HIS B 239 GLN B 824 ASN ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5899 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 26160 Z= 0.250 Angle : 0.661 12.424 35600 Z= 0.343 Chirality : 0.051 0.671 4236 Planarity : 0.005 0.062 4514 Dihedral : 9.313 89.889 4697 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.62 % Allowed : 7.43 % Favored : 90.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 0.17 (0.14), residues: 3096 helix: 1.52 (0.20), residues: 685 sheet: 0.57 (0.19), residues: 639 loop : -0.63 (0.14), residues: 1772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 36 HIS 0.008 0.001 HIS A1058 PHE 0.022 0.002 PHE B 400 TYR 0.025 0.002 TYR A 423 ARG 0.006 0.001 ARG C 408 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 314 time to evaluate : 2.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 ASP cc_start: 0.7221 (t70) cc_final: 0.6990 (t0) REVERT: A 568 ASP cc_start: 0.7341 (t0) cc_final: 0.7084 (t0) REVERT: B 265 TYR cc_start: 0.5095 (p90) cc_final: 0.4477 (p90) REVERT: B 465 GLU cc_start: 0.7645 (mm-30) cc_final: 0.7336 (mm-30) REVERT: B 781 VAL cc_start: 0.5437 (t) cc_final: 0.5118 (t) REVERT: B 964 LYS cc_start: 0.8290 (tppp) cc_final: 0.7934 (tptm) REVERT: B 1029 MET cc_start: 0.6694 (tpp) cc_final: 0.6493 (tpp) REVERT: C 194 PHE cc_start: 0.6106 (m-80) cc_final: 0.5844 (m-80) REVERT: C 289 VAL cc_start: 0.7929 (t) cc_final: 0.7597 (p) REVERT: C 614 ASP cc_start: 0.5994 (t0) cc_final: 0.5791 (t0) REVERT: C 825 LYS cc_start: 0.7171 (tppp) cc_final: 0.6883 (tptm) REVERT: C 988 GLU cc_start: 0.6117 (mp0) cc_final: 0.5891 (mp0) REVERT: C 1060 VAL cc_start: 0.8117 (t) cc_final: 0.7818 (p) outliers start: 45 outliers final: 29 residues processed: 338 average time/residue: 0.3784 time to fit residues: 205.8327 Evaluate side-chains 322 residues out of total 2774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 293 time to evaluate : 2.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1134 ASN Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 1133 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 283 optimal weight: 1.9990 chunk 215 optimal weight: 0.0570 chunk 148 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 136 optimal weight: 3.9990 chunk 192 optimal weight: 1.9990 chunk 287 optimal weight: 0.9990 chunk 304 optimal weight: 10.0000 chunk 150 optimal weight: 0.8980 chunk 272 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 overall best weight: 0.7302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN B 536 ASN B1088 HIS ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 703 ASN C 777 ASN C 779 GLN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5910 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 26160 Z= 0.205 Angle : 0.632 13.690 35600 Z= 0.322 Chirality : 0.050 0.685 4236 Planarity : 0.005 0.054 4514 Dihedral : 8.950 99.082 4697 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.91 % Allowed : 9.05 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.14), residues: 3096 helix: 1.71 (0.21), residues: 671 sheet: 0.46 (0.19), residues: 636 loop : -0.72 (0.14), residues: 1789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP H 47 HIS 0.005 0.001 HIS A1058 PHE 0.022 0.002 PHE C 823 TYR 0.034 0.001 TYR A 423 ARG 0.008 0.000 ARG B 190 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 300 time to evaluate : 2.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 389 ASP cc_start: 0.7098 (t70) cc_final: 0.6876 (t0) REVERT: A 402 ILE cc_start: 0.3815 (OUTLIER) cc_final: 0.3437 (mm) REVERT: A 976 VAL cc_start: 0.8136 (t) cc_final: 0.7707 (p) REVERT: B 423 TYR cc_start: 0.3893 (m-10) cc_final: 0.3552 (m-10) REVERT: B 424 LYS cc_start: 0.7619 (tptt) cc_final: 0.6732 (ptpp) REVERT: B 523 THR cc_start: 0.7446 (OUTLIER) cc_final: 0.7202 (m) REVERT: B 781 VAL cc_start: 0.5379 (t) cc_final: 0.5033 (t) REVERT: B 988 GLU cc_start: 0.5780 (mp0) cc_final: 0.5520 (mp0) REVERT: C 289 VAL cc_start: 0.8007 (t) cc_final: 0.7656 (p) REVERT: C 614 ASP cc_start: 0.6018 (t0) cc_final: 0.5726 (t0) REVERT: C 674 TYR cc_start: 0.7923 (t80) cc_final: 0.7465 (t80) REVERT: C 1060 VAL cc_start: 0.8126 (t) cc_final: 0.7911 (p) REVERT: H 103 ASP cc_start: 0.8065 (m-30) cc_final: 0.7803 (m-30) outliers start: 53 outliers final: 33 residues processed: 334 average time/residue: 0.3692 time to fit residues: 195.7077 Evaluate side-chains 328 residues out of total 2774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 293 time to evaluate : 2.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1134 ASN Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 954 GLN Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain L residue 50 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 253 optimal weight: 1.9990 chunk 172 optimal weight: 0.4980 chunk 4 optimal weight: 0.6980 chunk 226 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 259 optimal weight: 1.9990 chunk 210 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 155 optimal weight: 3.9990 chunk 273 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 784 GLN A 901 GLN ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1011 GLN ** L 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6058 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.127 26160 Z= 0.327 Angle : 0.724 14.407 35600 Z= 0.376 Chirality : 0.052 0.552 4236 Planarity : 0.006 0.059 4514 Dihedral : 8.905 115.488 4697 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.92 % Allowed : 9.81 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: -0.52 (0.14), residues: 3096 helix: 1.19 (0.20), residues: 673 sheet: 0.05 (0.20), residues: 631 loop : -1.12 (0.13), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP H 47 HIS 0.010 0.002 HIS B1058 PHE 0.031 0.002 PHE A 543 TYR 0.035 0.002 TYR A 423 ARG 0.005 0.001 ARG B 815 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 332 time to evaluate : 2.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8089 (mttp) cc_final: 0.7695 (mmmt) REVERT: A 402 ILE cc_start: 0.4374 (OUTLIER) cc_final: 0.3894 (mm) REVERT: A 750 SER cc_start: 0.7503 (t) cc_final: 0.7160 (p) REVERT: A 1047 TYR cc_start: 0.5773 (OUTLIER) cc_final: 0.4745 (m-80) REVERT: B 47 VAL cc_start: 0.8479 (OUTLIER) cc_final: 0.8130 (m) REVERT: B 287 ASP cc_start: 0.6547 (t0) cc_final: 0.6052 (t0) REVERT: B 303 LEU cc_start: 0.7318 (tp) cc_final: 0.7086 (tt) REVERT: B 423 TYR cc_start: 0.4263 (m-10) cc_final: 0.3876 (m-10) REVERT: B 748 GLU cc_start: 0.7014 (mp0) cc_final: 0.6652 (mp0) REVERT: B 781 VAL cc_start: 0.5700 (t) cc_final: 0.5361 (t) REVERT: B 964 LYS cc_start: 0.8418 (tppp) cc_final: 0.8040 (tppp) REVERT: B 988 GLU cc_start: 0.5908 (mp0) cc_final: 0.5549 (mp0) REVERT: B 994 ASP cc_start: 0.6003 (p0) cc_final: 0.5772 (p0) REVERT: B 1019 ARG cc_start: 0.6927 (ttm110) cc_final: 0.6613 (ttm170) REVERT: C 266 TYR cc_start: 0.4821 (OUTLIER) cc_final: 0.4538 (m-80) REVERT: C 289 VAL cc_start: 0.8096 (t) cc_final: 0.7760 (p) REVERT: C 422 ASN cc_start: 0.4243 (OUTLIER) cc_final: 0.2977 (p0) REVERT: C 614 ASP cc_start: 0.6248 (t0) cc_final: 0.5950 (t0) REVERT: C 730 SER cc_start: 0.7847 (m) cc_final: 0.7567 (p) REVERT: C 921 LYS cc_start: 0.5561 (OUTLIER) cc_final: 0.5225 (ptpp) REVERT: C 1017 GLU cc_start: 0.7285 (tp30) cc_final: 0.6854 (tp30) outliers start: 81 outliers final: 47 residues processed: 383 average time/residue: 0.3695 time to fit residues: 222.7440 Evaluate side-chains 359 residues out of total 2774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 306 time to evaluate : 2.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1047 TYR Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 775 ASP Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1134 ASN Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 422 ASN Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 721 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 954 GLN Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain L residue 50 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 102 optimal weight: 3.9990 chunk 274 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 178 optimal weight: 2.9990 chunk 75 optimal weight: 0.1980 chunk 304 optimal weight: 10.0000 chunk 253 optimal weight: 0.9980 chunk 141 optimal weight: 0.2980 chunk 25 optimal weight: 0.6980 chunk 100 optimal weight: 6.9990 chunk 160 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 784 GLN ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 HIS ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 703 ASN C 777 ASN C 779 GLN ** C 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN ** L 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6004 moved from start: 0.3609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 26160 Z= 0.201 Angle : 0.641 13.938 35600 Z= 0.329 Chirality : 0.049 0.559 4236 Planarity : 0.005 0.058 4514 Dihedral : 8.383 103.110 4697 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.09 % Allowed : 11.68 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: -0.42 (0.15), residues: 3096 helix: 1.50 (0.21), residues: 668 sheet: -0.07 (0.20), residues: 651 loop : -1.08 (0.14), residues: 1777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 36 HIS 0.006 0.001 HIS B 655 PHE 0.024 0.001 PHE B 888 TYR 0.029 0.001 TYR A 423 ARG 0.010 0.000 ARG B 190 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 323 time to evaluate : 2.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8131 (mttp) cc_final: 0.7683 (mmmt) REVERT: A 402 ILE cc_start: 0.4097 (OUTLIER) cc_final: 0.3643 (mm) REVERT: A 415 THR cc_start: 0.7657 (m) cc_final: 0.7441 (t) REVERT: A 750 SER cc_start: 0.7437 (t) cc_final: 0.7066 (p) REVERT: B 47 VAL cc_start: 0.8455 (OUTLIER) cc_final: 0.8138 (m) REVERT: B 287 ASP cc_start: 0.6442 (t0) cc_final: 0.5938 (t0) REVERT: B 423 TYR cc_start: 0.4130 (m-10) cc_final: 0.3822 (m-10) REVERT: B 781 VAL cc_start: 0.5488 (t) cc_final: 0.5162 (t) REVERT: B 964 LYS cc_start: 0.8355 (tppp) cc_final: 0.7937 (tppp) REVERT: C 266 TYR cc_start: 0.4976 (OUTLIER) cc_final: 0.4590 (m-80) REVERT: C 289 VAL cc_start: 0.8100 (t) cc_final: 0.7716 (p) REVERT: C 614 ASP cc_start: 0.6162 (t0) cc_final: 0.5862 (t0) REVERT: C 674 TYR cc_start: 0.7898 (t80) cc_final: 0.7125 (t80) REVERT: C 730 SER cc_start: 0.7821 (m) cc_final: 0.7533 (p) REVERT: C 918 GLU cc_start: 0.5195 (OUTLIER) cc_final: 0.2998 (tp30) REVERT: C 988 GLU cc_start: 0.6291 (mp0) cc_final: 0.5971 (mp0) outliers start: 58 outliers final: 48 residues processed: 356 average time/residue: 0.3708 time to fit residues: 208.5658 Evaluate side-chains 364 residues out of total 2774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 312 time to evaluate : 2.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 540 ASN Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 721 SER Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 655 HIS Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1134 ASN Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 954 GLN Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain L residue 50 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 293 optimal weight: 7.9990 chunk 34 optimal weight: 0.9990 chunk 173 optimal weight: 1.9990 chunk 222 optimal weight: 3.9990 chunk 172 optimal weight: 0.6980 chunk 256 optimal weight: 0.2980 chunk 170 optimal weight: 0.6980 chunk 303 optimal weight: 5.9990 chunk 190 optimal weight: 0.0000 chunk 185 optimal weight: 0.6980 chunk 140 optimal weight: 0.8980 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 HIS ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN ** C 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN C 957 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5985 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 26160 Z= 0.185 Angle : 0.627 10.828 35600 Z= 0.319 Chirality : 0.048 0.538 4236 Planarity : 0.005 0.057 4514 Dihedral : 8.116 96.974 4697 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.20 % Allowed : 12.55 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: -0.33 (0.15), residues: 3096 helix: 1.60 (0.21), residues: 677 sheet: -0.02 (0.20), residues: 645 loop : -1.04 (0.14), residues: 1774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 36 HIS 0.025 0.001 HIS B 655 PHE 0.032 0.001 PHE A 201 TYR 0.022 0.001 TYR A 423 ARG 0.012 0.000 ARG B 190 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 309 time to evaluate : 2.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8142 (mttp) cc_final: 0.7706 (mmmt) REVERT: A 402 ILE cc_start: 0.3982 (OUTLIER) cc_final: 0.3545 (mm) REVERT: A 415 THR cc_start: 0.7691 (m) cc_final: 0.7470 (t) REVERT: A 595 VAL cc_start: 0.8447 (t) cc_final: 0.8239 (p) REVERT: A 750 SER cc_start: 0.7399 (t) cc_final: 0.7033 (p) REVERT: B 47 VAL cc_start: 0.8495 (OUTLIER) cc_final: 0.8225 (m) REVERT: B 287 ASP cc_start: 0.6425 (t0) cc_final: 0.5940 (t0) REVERT: B 423 TYR cc_start: 0.3881 (m-10) cc_final: 0.3630 (m-10) REVERT: B 781 VAL cc_start: 0.5260 (t) cc_final: 0.4938 (t) REVERT: B 964 LYS cc_start: 0.8316 (tppp) cc_final: 0.7919 (tptm) REVERT: C 52 GLN cc_start: 0.7889 (tm-30) cc_final: 0.7575 (tm-30) REVERT: C 266 TYR cc_start: 0.4944 (OUTLIER) cc_final: 0.4532 (m-80) REVERT: C 289 VAL cc_start: 0.8133 (t) cc_final: 0.7723 (p) REVERT: C 465 GLU cc_start: 0.6799 (OUTLIER) cc_final: 0.6562 (mp0) REVERT: C 614 ASP cc_start: 0.6042 (t0) cc_final: 0.5709 (t0) REVERT: C 674 TYR cc_start: 0.7898 (t80) cc_final: 0.7162 (t80) REVERT: C 675 GLN cc_start: 0.7674 (tm-30) cc_final: 0.7192 (tm-30) REVERT: C 730 SER cc_start: 0.7801 (m) cc_final: 0.7518 (p) REVERT: C 918 GLU cc_start: 0.5285 (OUTLIER) cc_final: 0.3622 (mm-30) REVERT: C 957 GLN cc_start: 0.7728 (tt0) cc_final: 0.7243 (tt0) REVERT: C 988 GLU cc_start: 0.6272 (mp0) cc_final: 0.5935 (mp0) outliers start: 61 outliers final: 43 residues processed: 343 average time/residue: 0.3607 time to fit residues: 196.6224 Evaluate side-chains 346 residues out of total 2774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 298 time to evaluate : 2.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 655 HIS Chi-restraints excluded: chain B residue 657 ASN Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1134 ASN Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 954 GLN Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain L residue 50 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 187 optimal weight: 0.3980 chunk 121 optimal weight: 2.9990 chunk 181 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 193 optimal weight: 0.6980 chunk 206 optimal weight: 1.9990 chunk 150 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 238 optimal weight: 4.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN B 655 HIS ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6012 moved from start: 0.3928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 26160 Z= 0.216 Angle : 0.638 9.614 35600 Z= 0.325 Chirality : 0.049 0.515 4236 Planarity : 0.005 0.056 4514 Dihedral : 7.872 105.628 4697 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.20 % Allowed : 13.12 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: -0.43 (0.15), residues: 3096 helix: 1.53 (0.20), residues: 683 sheet: -0.11 (0.20), residues: 627 loop : -1.10 (0.14), residues: 1786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 36 HIS 0.028 0.001 HIS B 655 PHE 0.022 0.001 PHE A 201 TYR 0.024 0.001 TYR A 423 ARG 0.010 0.000 ARG B 190 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 306 time to evaluate : 2.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8178 (mttp) cc_final: 0.7717 (mmmt) REVERT: A 402 ILE cc_start: 0.4057 (OUTLIER) cc_final: 0.3597 (mm) REVERT: A 750 SER cc_start: 0.7453 (t) cc_final: 0.7101 (p) REVERT: A 790 LYS cc_start: 0.7034 (mmmt) cc_final: 0.6832 (mmmt) REVERT: B 47 VAL cc_start: 0.8553 (OUTLIER) cc_final: 0.8274 (m) REVERT: B 287 ASP cc_start: 0.6432 (t0) cc_final: 0.5925 (t0) REVERT: B 423 TYR cc_start: 0.3921 (m-10) cc_final: 0.3707 (m-10) REVERT: B 781 VAL cc_start: 0.5357 (t) cc_final: 0.5025 (t) REVERT: B 964 LYS cc_start: 0.8342 (tppp) cc_final: 0.7975 (tptm) REVERT: C 52 GLN cc_start: 0.7929 (tm-30) cc_final: 0.7534 (tm-30) REVERT: C 266 TYR cc_start: 0.5179 (OUTLIER) cc_final: 0.4838 (m-80) REVERT: C 465 GLU cc_start: 0.6814 (OUTLIER) cc_final: 0.6581 (mp0) REVERT: C 614 ASP cc_start: 0.6068 (t0) cc_final: 0.5727 (t0) REVERT: C 675 GLN cc_start: 0.7761 (tm-30) cc_final: 0.7321 (tm-30) REVERT: C 730 SER cc_start: 0.7817 (m) cc_final: 0.7552 (p) REVERT: C 918 GLU cc_start: 0.5584 (OUTLIER) cc_final: 0.3895 (mm-30) REVERT: C 988 GLU cc_start: 0.6517 (mp0) cc_final: 0.6182 (mp0) REVERT: L 21 MET cc_start: 0.1547 (pmm) cc_final: -0.2095 (ptt) outliers start: 61 outliers final: 51 residues processed: 342 average time/residue: 0.3552 time to fit residues: 194.2859 Evaluate side-chains 350 residues out of total 2774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 294 time to evaluate : 2.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 657 ASN Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1134 ASN Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 954 GLN Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain L residue 50 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 276 optimal weight: 0.0060 chunk 290 optimal weight: 1.9990 chunk 265 optimal weight: 8.9990 chunk 282 optimal weight: 1.9990 chunk 170 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 222 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 255 optimal weight: 1.9990 chunk 267 optimal weight: 0.9980 chunk 281 optimal weight: 0.9980 overall best weight: 1.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6082 moved from start: 0.4317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 26160 Z= 0.286 Angle : 0.693 10.963 35600 Z= 0.357 Chirality : 0.051 0.504 4236 Planarity : 0.005 0.057 4514 Dihedral : 8.164 100.789 4697 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.34 % Allowed : 13.45 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: -0.68 (0.15), residues: 3096 helix: 1.37 (0.20), residues: 674 sheet: -0.13 (0.21), residues: 605 loop : -1.33 (0.13), residues: 1817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 52 HIS 0.006 0.001 HIS B1058 PHE 0.026 0.002 PHE A 543 TYR 0.029 0.002 TYR A 423 ARG 0.009 0.001 ARG B 190 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 320 time to evaluate : 2.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8298 (mttp) cc_final: 0.7739 (mmmt) REVERT: A 402 ILE cc_start: 0.4301 (OUTLIER) cc_final: 0.3800 (mm) REVERT: A 750 SER cc_start: 0.7554 (t) cc_final: 0.7103 (p) REVERT: A 1017 GLU cc_start: 0.7587 (tp30) cc_final: 0.7370 (tp30) REVERT: B 47 VAL cc_start: 0.8642 (OUTLIER) cc_final: 0.8358 (m) REVERT: B 265 TYR cc_start: 0.5509 (p90) cc_final: 0.4559 (p90) REVERT: B 275 PHE cc_start: 0.2287 (OUTLIER) cc_final: 0.1432 (m-80) REVERT: B 287 ASP cc_start: 0.6440 (t0) cc_final: 0.5964 (t0) REVERT: B 423 TYR cc_start: 0.4273 (m-10) cc_final: 0.4012 (m-10) REVERT: B 781 VAL cc_start: 0.5665 (t) cc_final: 0.5349 (t) REVERT: B 964 LYS cc_start: 0.8428 (tppp) cc_final: 0.8058 (tppp) REVERT: C 52 GLN cc_start: 0.7953 (tm-30) cc_final: 0.7540 (tm-30) REVERT: C 204 TYR cc_start: 0.3561 (OUTLIER) cc_final: 0.3322 (m-80) REVERT: C 265 TYR cc_start: 0.6051 (p90) cc_final: 0.5510 (p90) REVERT: C 266 TYR cc_start: 0.5177 (OUTLIER) cc_final: 0.4764 (m-80) REVERT: C 614 ASP cc_start: 0.6105 (t0) cc_final: 0.5765 (t0) REVERT: C 675 GLN cc_start: 0.7827 (tm-30) cc_final: 0.7324 (tm-30) REVERT: C 730 SER cc_start: 0.7800 (m) cc_final: 0.7575 (p) REVERT: C 918 GLU cc_start: 0.5815 (OUTLIER) cc_final: 0.3832 (tp30) REVERT: C 988 GLU cc_start: 0.6372 (mp0) cc_final: 0.6072 (mp0) outliers start: 65 outliers final: 50 residues processed: 359 average time/residue: 0.3625 time to fit residues: 205.9220 Evaluate side-chains 370 residues out of total 2774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 314 time to evaluate : 2.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 657 ASN Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1134 ASN Chi-restraints excluded: chain C residue 204 TYR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 954 GLN Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1133 VAL Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain L residue 50 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 185 optimal weight: 0.7980 chunk 299 optimal weight: 4.9990 chunk 182 optimal weight: 0.8980 chunk 141 optimal weight: 0.9980 chunk 207 optimal weight: 0.3980 chunk 313 optimal weight: 0.6980 chunk 288 optimal weight: 2.9990 chunk 249 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 193 optimal weight: 0.5980 chunk 153 optimal weight: 4.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 777 ASN ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 ASN C 409 GLN C 777 ASN ** C 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6031 moved from start: 0.4378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 26160 Z= 0.206 Angle : 0.638 9.447 35600 Z= 0.327 Chirality : 0.049 0.564 4236 Planarity : 0.005 0.059 4514 Dihedral : 7.716 101.923 4697 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.95 % Allowed : 14.06 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: -0.53 (0.15), residues: 3096 helix: 1.61 (0.21), residues: 672 sheet: -0.07 (0.21), residues: 592 loop : -1.25 (0.14), residues: 1832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 36 HIS 0.003 0.001 HIS A 519 PHE 0.025 0.001 PHE B 888 TYR 0.021 0.001 TYR A 423 ARG 0.008 0.000 ARG B 190 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 312 time to evaluate : 2.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8311 (mttp) cc_final: 0.7729 (mmmt) REVERT: A 402 ILE cc_start: 0.3999 (OUTLIER) cc_final: 0.3560 (mm) REVERT: A 750 SER cc_start: 0.7501 (t) cc_final: 0.7050 (p) REVERT: B 47 VAL cc_start: 0.8701 (OUTLIER) cc_final: 0.8407 (m) REVERT: B 265 TYR cc_start: 0.5399 (p90) cc_final: 0.4491 (p90) REVERT: B 275 PHE cc_start: 0.2434 (OUTLIER) cc_final: 0.1490 (m-80) REVERT: B 287 ASP cc_start: 0.6321 (t0) cc_final: 0.5849 (t0) REVERT: B 450 ASN cc_start: 0.7868 (m110) cc_final: 0.7597 (m110) REVERT: B 781 VAL cc_start: 0.5425 (t) cc_final: 0.5099 (t) REVERT: B 964 LYS cc_start: 0.8346 (tppp) cc_final: 0.7960 (tppp) REVERT: C 52 GLN cc_start: 0.7926 (tm-30) cc_final: 0.7559 (tm-30) REVERT: C 265 TYR cc_start: 0.6015 (p90) cc_final: 0.5526 (p90) REVERT: C 266 TYR cc_start: 0.4954 (OUTLIER) cc_final: 0.4511 (m-80) REVERT: C 465 GLU cc_start: 0.6817 (OUTLIER) cc_final: 0.6599 (mp0) REVERT: C 614 ASP cc_start: 0.6101 (t0) cc_final: 0.5760 (t0) REVERT: C 675 GLN cc_start: 0.7745 (tm-30) cc_final: 0.7257 (tm-30) REVERT: C 730 SER cc_start: 0.7779 (m) cc_final: 0.7544 (p) REVERT: C 918 GLU cc_start: 0.5837 (OUTLIER) cc_final: 0.3846 (mm-30) REVERT: C 957 GLN cc_start: 0.7518 (tt0) cc_final: 0.7247 (tt0) REVERT: C 988 GLU cc_start: 0.6448 (mp0) cc_final: 0.6110 (mp0) outliers start: 54 outliers final: 45 residues processed: 345 average time/residue: 0.3707 time to fit residues: 204.2210 Evaluate side-chains 357 residues out of total 2774 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 306 time to evaluate : 2.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 598 ILE Chi-restraints excluded: chain B residue 657 ASN Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1134 ASN Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 954 GLN Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain L residue 50 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 315 random chunks: chunk 198 optimal weight: 1.9990 chunk 266 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 230 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 250 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 chunk 257 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 46 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN C 777 ASN ** C 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1108 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4658 r_free = 0.4658 target = 0.209004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.173053 restraints weight = 42059.390| |-----------------------------------------------------------------------------| r_work (start): 0.4271 rms_B_bonded: 3.36 r_work: 0.4160 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.4160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6314 moved from start: 0.4559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 26160 Z= 0.234 Angle : 0.655 9.504 35600 Z= 0.338 Chirality : 0.049 0.478 4236 Planarity : 0.005 0.058 4514 Dihedral : 7.462 104.610 4697 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.24 % Allowed : 13.88 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: -0.59 (0.15), residues: 3096 helix: 1.52 (0.20), residues: 676 sheet: -0.19 (0.21), residues: 612 loop : -1.27 (0.14), residues: 1808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 36 HIS 0.007 0.001 HIS B 655 PHE 0.026 0.002 PHE B 888 TYR 0.039 0.002 TYR B 423 ARG 0.008 0.000 ARG B 190 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5444.05 seconds wall clock time: 99 minutes 52.67 seconds (5992.67 seconds total)