Starting phenix.real_space_refine on Tue Feb 20 11:49:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nda_12281/02_2024/7nda_12281.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nda_12281/02_2024/7nda_12281.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nda_12281/02_2024/7nda_12281.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nda_12281/02_2024/7nda_12281.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nda_12281/02_2024/7nda_12281.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nda_12281/02_2024/7nda_12281.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 121 5.16 5 C 17601 2.51 5 N 4532 2.21 5 O 5467 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 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 27721 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 7845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1005, 7845 Classifications: {'peptide': 1005} Link IDs: {'PTRANS': 49, 'TRANS': 955} Chain breaks: 7 Chain: "B" Number of atoms: 7833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1003, 7833 Classifications: {'peptide': 1003} Link IDs: {'PTRANS': 49, 'TRANS': 953} Chain breaks: 7 Chain: "C" Number of atoms: 7896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1012, 7896 Classifications: {'peptide': 1012} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 49, 'TRANS': 962} Chain breaks: 7 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 1630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1630 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 205} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "L" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1639 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 201} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 15.32, per 1000 atoms: 0.55 Number of scatterers: 27721 At special positions: 0 Unit cell: (138.61, 153.55, 211.65, 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 121 16.00 O 5467 8.00 N 4532 7.00 C 17601 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, 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=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.02 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.02 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 101 " - pdb=" SG CYS H 106 " distance=2.03 Simple disulfide: pdb=" SG CYS H 150 " - pdb=" SG CYS H 206 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 195 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG 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 " BETA1-6 " NAG T 1 " - " FUC T 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1074 " " NAG A1311 " - " ASN A 165 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 343 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B1074 " " NAG B1311 " - " ASN B 165 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 343 " " NAG C1305 " - " ASN C 603 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 657 " " NAG C1308 " - " ASN C 709 " " NAG C1309 " - " ASN C1074 " " NAG C1310 " - " ASN C 165 " " 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 717 " " NAG Q 1 " - " ASN C 801 " " NAG R 1 " - " ASN C1098 " " NAG S 1 " - " ASN C1134 " " NAG T 1 " - " ASN H 102 " Time building additional restraints: 10.77 Conformation dependent library (CDL) restraints added in 4.6 seconds 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6458 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 56 sheets defined 23.3% alpha, 32.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.53 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.379A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 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: 3.598A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.528A 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 removed outlier: 3.627A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 947 through 965 removed outlier: 3.676A 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 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.433A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.194A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.325A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 744 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: 3.621A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (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 removed outlier: 3.564A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 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 966 removed outlier: 3.927A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.552A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.110A 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 337 through 343 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.419A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.590A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.591A 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 853 through 856 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.554A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.516A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (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 966 removed outlier: 3.921A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.524A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.121A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 31 removed outlier: 3.657A pdb=" N THR H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 31' Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.516A pdb=" N GLN H 65 " --> pdb=" O GLN H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 166 through 168 No H-bonds generated for 'chain 'H' and resid 166 through 168' Processing helix chain 'H' and resid 197 through 200 removed outlier: 3.841A pdb=" N GLY H 200 " --> pdb=" O SER H 197 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 197 through 200' Processing helix chain 'H' and resid 211 through 214 Processing helix chain 'L' and resid 30 through 32 No H-bonds generated for 'chain 'L' and resid 30 through 32' Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.680A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing helix chain 'L' and resid 122 through 127 Processing helix chain 'L' and resid 184 through 189 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.050A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.283A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.327A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 43 through 44 removed outlier: 6.334A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.080A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.530A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.509A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.779A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.443A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.790A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N TYR A 396 " --> pdb=" O SER A 514 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.808A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.711A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.474A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.474A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.392A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.178A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.945A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.266A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.348A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.886A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.061A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.385A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.846A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.498A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.603A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.921A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.696A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.771A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.771A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.592A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.183A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.248A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.236A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.398A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.904A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 5.966A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.446A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.331A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 357 Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.928A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N TYR C 660 " --> pdb=" O SER C 698 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.928A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.424A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.424A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF1, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.103A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AF3, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.695A pdb=" N VAL H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N TRP H 50 " --> pdb=" O VAL H 34 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AF5, first strand: chain 'H' and resid 130 through 134 removed outlier: 6.118A pdb=" N TYR H 186 " --> pdb=" O ASP H 154 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 130 through 134 removed outlier: 6.118A pdb=" N TYR H 186 " --> pdb=" O ASP H 154 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 161 through 164 removed outlier: 4.599A pdb=" N TYR H 204 " --> pdb=" O VAL H 221 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'L' and resid 4 through 7 removed outlier: 5.559A pdb=" N THR L 70 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 10.054A pdb=" N GLN L 27 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 9.964A pdb=" N SER L 68 " --> pdb=" O GLN L 27 " (cutoff:3.500A) removed outlier: 11.904A pdb=" N VAL L 29 " --> pdb=" O SER L 66 " (cutoff:3.500A) removed outlier: 12.400A pdb=" N SER L 66 " --> pdb=" O VAL L 29 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.887A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'L' and resid 115 through 119 removed outlier: 5.905A pdb=" N TYR L 174 " --> pdb=" O ASN L 139 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'L' and resid 154 through 155 1175 hydrogen bonds defined for protein. 3204 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: 14.55 Time building geometry restraints manager: 11.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8806 1.34 - 1.46: 7037 1.46 - 1.58: 12333 1.58 - 1.71: 0 1.71 - 1.83: 149 Bond restraints: 28325 Sorted by residual: bond pdb=" C1 NAG I 2 " pdb=" O5 NAG I 2 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.66e+00 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.51e+00 bond pdb=" C1 NAG J 2 " pdb=" O5 NAG J 2 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.50e+00 bond pdb=" C1 NAG S 2 " pdb=" O5 NAG S 2 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.19e+00 bond pdb=" C1 NAG A1305 " pdb=" O5 NAG A1305 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.16e+00 ... (remaining 28320 not shown) Histogram of bond angle deviations from ideal: 100.01 - 106.80: 870 106.80 - 113.60: 15802 113.60 - 120.40: 10075 120.40 - 127.20: 11548 127.20 - 134.00: 247 Bond angle restraints: 38542 Sorted by residual: angle pdb=" CA CYS A 391 " pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " ideal model delta sigma weight residual 114.40 124.89 -10.49 2.30e+00 1.89e-01 2.08e+01 angle pdb=" CA CYS B 391 " pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " ideal model delta sigma weight residual 114.40 124.06 -9.66 2.30e+00 1.89e-01 1.76e+01 angle pdb=" CA TYR A 904 " pdb=" CB TYR A 904 " pdb=" CG TYR A 904 " ideal model delta sigma weight residual 113.90 120.31 -6.41 1.80e+00 3.09e-01 1.27e+01 angle pdb=" CA TYR B 904 " pdb=" CB TYR B 904 " pdb=" CG TYR B 904 " ideal model delta sigma weight residual 113.90 120.06 -6.16 1.80e+00 3.09e-01 1.17e+01 angle pdb=" CA TYR C 904 " pdb=" CB TYR C 904 " pdb=" CG TYR C 904 " ideal model delta sigma weight residual 113.90 119.88 -5.98 1.80e+00 3.09e-01 1.11e+01 ... (remaining 38537 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 16824 17.98 - 35.97: 644 35.97 - 53.95: 149 53.95 - 71.93: 60 71.93 - 89.92: 23 Dihedral angle restraints: 17700 sinusoidal: 7670 harmonic: 10030 Sorted by residual: dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual -86.00 -162.12 76.12 1 1.00e+01 1.00e-02 7.30e+01 dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual -86.00 -162.11 76.11 1 1.00e+01 1.00e-02 7.30e+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 -86.00 -161.68 75.68 1 1.00e+01 1.00e-02 7.22e+01 ... (remaining 17697 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 3329 0.045 - 0.090: 855 0.090 - 0.135: 376 0.135 - 0.180: 16 0.180 - 0.226: 2 Chirality restraints: 4578 Sorted by residual: chirality pdb=" CB ILE A 332 " pdb=" CA ILE A 332 " pdb=" CG1 ILE A 332 " pdb=" CG2 ILE A 332 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CB ILE B 332 " pdb=" CA ILE B 332 " pdb=" CG1 ILE B 332 " pdb=" CG2 ILE B 332 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CG LEU A 916 " pdb=" CB LEU A 916 " pdb=" CD1 LEU A 916 " pdb=" CD2 LEU A 916 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.78e-01 ... (remaining 4575 not shown) Planarity restraints: 4946 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN B 954 " 0.016 2.00e-02 2.50e+03 3.19e-02 1.02e+01 pdb=" C GLN B 954 " -0.055 2.00e-02 2.50e+03 pdb=" O GLN B 954 " 0.021 2.00e-02 2.50e+03 pdb=" N ASN B 955 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 954 " -0.016 2.00e-02 2.50e+03 3.18e-02 1.01e+01 pdb=" C GLN C 954 " 0.055 2.00e-02 2.50e+03 pdb=" O GLN C 954 " -0.021 2.00e-02 2.50e+03 pdb=" N ASN C 955 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 958 " -0.015 2.00e-02 2.50e+03 3.02e-02 9.13e+00 pdb=" C ALA C 958 " 0.052 2.00e-02 2.50e+03 pdb=" O ALA C 958 " -0.020 2.00e-02 2.50e+03 pdb=" N LEU C 959 " -0.018 2.00e-02 2.50e+03 ... (remaining 4943 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 233 2.62 - 3.19: 23850 3.19 - 3.76: 41821 3.76 - 4.33: 60278 4.33 - 4.90: 99195 Nonbonded interactions: 225377 Sorted by model distance: nonbonded pdb=" OE1 GLU L 106 " pdb=" OH TYR L 174 " model vdw 2.051 2.440 nonbonded pdb=" O ASN A 439 " pdb=" OG SER A 443 " model vdw 2.189 2.440 nonbonded pdb=" O ASN C 439 " pdb=" OG SER C 443 " model vdw 2.190 2.440 nonbonded pdb=" O ASN B 439 " pdb=" OG SER B 443 " model vdw 2.191 2.440 nonbonded pdb=" OD2 ASP L 171 " pdb=" OG1 THR L 173 " model vdw 2.201 2.440 ... (remaining 225372 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 620 or resid 641 through 1147 or resid 1301 thr \ ough 1310)) selection = (chain 'B' and (resid 27 through 827 or resid 853 through 1147 or resid 1301 thr \ ough 1310)) selection = (chain 'C' and (resid 27 through 620 or resid 641 through 827 or resid 853 throu \ gh 1147 or resid 1301 through 1310)) } 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' } 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: 5.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 15.250 Check model and map are aligned: 0.400 Set scattering table: 0.230 Process input model: 77.480 Find NCS groups from input model: 2.040 Set up NCS constraints: 0.300 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 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 0.043 28325 Z= 0.252 Angle : 0.629 10.697 38542 Z= 0.330 Chirality : 0.046 0.226 4578 Planarity : 0.004 0.064 4899 Dihedral : 11.131 89.915 11110 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.38 % Favored : 95.29 % Rotamer: Outliers : 0.30 % Allowed : 2.69 % Favored : 97.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % 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: -0.16 (0.14), residues: 3398 helix: 0.66 (0.19), residues: 679 sheet: 0.42 (0.16), residues: 902 loop : -0.63 (0.14), residues: 1817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 886 HIS 0.008 0.001 HIS C 519 PHE 0.018 0.001 PHE C 515 TYR 0.022 0.001 TYR A 789 ARG 0.004 0.000 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 3016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 556 time to evaluate : 3.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 PHE cc_start: 0.8606 (m-80) cc_final: 0.8316 (m-80) REVERT: A 270 LEU cc_start: 0.8594 (mt) cc_final: 0.8377 (mp) REVERT: A 398 ASP cc_start: 0.7812 (m-30) cc_final: 0.7517 (m-30) REVERT: A 549 THR cc_start: 0.8440 (m) cc_final: 0.8214 (m) REVERT: A 745 ASP cc_start: 0.7220 (m-30) cc_final: 0.6753 (t0) REVERT: A 779 GLN cc_start: 0.8605 (OUTLIER) cc_final: 0.8258 (tp40) REVERT: A 979 ASP cc_start: 0.7763 (m-30) cc_final: 0.7487 (t0) REVERT: B 41 LYS cc_start: 0.8102 (mttp) cc_final: 0.7530 (mtpt) REVERT: C 42 VAL cc_start: 0.9330 (t) cc_final: 0.9056 (t) REVERT: C 49 HIS cc_start: 0.7591 (t70) cc_final: 0.7326 (t70) REVERT: C 104 TRP cc_start: 0.5850 (m-90) cc_final: 0.5132 (m-90) REVERT: C 223 LEU cc_start: 0.8519 (mp) cc_final: 0.8047 (mp) REVERT: C 266 TYR cc_start: 0.7086 (m-80) cc_final: 0.6139 (m-80) REVERT: C 354 ASN cc_start: 0.8621 (t0) cc_final: 0.8198 (t0) REVERT: C 490 PHE cc_start: 0.8830 (t80) cc_final: 0.8574 (t80) REVERT: C 1101 HIS cc_start: 0.7196 (m90) cc_final: 0.6957 (m-70) REVERT: H 36 TRP cc_start: 0.5795 (m100) cc_final: 0.5594 (m100) REVERT: H 87 ARG cc_start: 0.7899 (ptt-90) cc_final: 0.7672 (ptp-170) REVERT: L 50 TYR cc_start: 0.7859 (p90) cc_final: 0.6878 (p90) REVERT: L 55 ARG cc_start: 0.8567 (mtm-85) cc_final: 0.8366 (ttm110) REVERT: L 83 ASP cc_start: 0.2105 (m-30) cc_final: 0.1683 (m-30) outliers start: 9 outliers final: 5 residues processed: 565 average time/residue: 0.4361 time to fit residues: 378.7844 Evaluate side-chains 322 residues out of total 3016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 316 time to evaluate : 3.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain C residue 637 SER Chi-restraints excluded: chain C residue 849 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 289 optimal weight: 1.9990 chunk 259 optimal weight: 1.9990 chunk 144 optimal weight: 10.0000 chunk 88 optimal weight: 1.9990 chunk 175 optimal weight: 0.6980 chunk 138 optimal weight: 10.0000 chunk 268 optimal weight: 0.0770 chunk 104 optimal weight: 3.9990 chunk 163 optimal weight: 6.9990 chunk 200 optimal weight: 20.0000 chunk 311 optimal weight: 30.0000 overall best weight: 1.3544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN A 913 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 536 ASN B 613 GLN B 675 GLN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 ASN C 907 ASN C 955 ASN H 59 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 28325 Z= 0.264 Angle : 0.606 12.168 38542 Z= 0.315 Chirality : 0.045 0.204 4578 Planarity : 0.004 0.100 4899 Dihedral : 6.397 59.870 5012 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.47 % Favored : 97.44 % Rotamer: Outliers : 1.66 % Allowed : 8.07 % Favored : 90.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.14), residues: 3398 helix: 1.28 (0.20), residues: 695 sheet: 0.58 (0.16), residues: 908 loop : -0.45 (0.14), residues: 1795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 353 HIS 0.006 0.001 HIS B1058 PHE 0.026 0.002 PHE B 338 TYR 0.025 0.002 TYR C 453 ARG 0.015 0.001 ARG C 34 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 3016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 340 time to evaluate : 3.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 LEU cc_start: 0.8608 (mt) cc_final: 0.8261 (mp) REVERT: A 271 GLN cc_start: 0.8423 (mm-40) cc_final: 0.8123 (mm110) REVERT: A 342 PHE cc_start: 0.9219 (m-80) cc_final: 0.8965 (m-80) REVERT: A 451 TYR cc_start: 0.6334 (m-80) cc_final: 0.5847 (m-80) REVERT: A 745 ASP cc_start: 0.7358 (m-30) cc_final: 0.6904 (t0) REVERT: A 779 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.8303 (tp40) REVERT: A 995 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.8040 (ttp80) REVERT: B 41 LYS cc_start: 0.8081 (mttp) cc_final: 0.7530 (mtpt) REVERT: B 191 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7714 (mt-10) REVERT: B 398 ASP cc_start: 0.7606 (m-30) cc_final: 0.6773 (p0) REVERT: B 755 GLN cc_start: 0.7440 (mm-40) cc_final: 0.7234 (mm-40) REVERT: C 40 ASP cc_start: 0.8160 (p0) cc_final: 0.7955 (p0) REVERT: C 49 HIS cc_start: 0.7718 (t70) cc_final: 0.7334 (t-170) REVERT: C 86 PHE cc_start: 0.7766 (t80) cc_final: 0.7036 (t80) REVERT: C 91 TYR cc_start: 0.8539 (t80) cc_final: 0.8336 (t80) REVERT: C 104 TRP cc_start: 0.5590 (m-90) cc_final: 0.5198 (m-90) REVERT: C 223 LEU cc_start: 0.8548 (mp) cc_final: 0.8026 (mp) REVERT: C 266 TYR cc_start: 0.7067 (m-80) cc_final: 0.6351 (m-80) REVERT: C 269 TYR cc_start: 0.5937 (m-80) cc_final: 0.5579 (m-80) REVERT: C 347 PHE cc_start: 0.6812 (m-80) cc_final: 0.5569 (m-10) REVERT: C 354 ASN cc_start: 0.8522 (t0) cc_final: 0.8041 (t0) REVERT: C 454 ARG cc_start: 0.7389 (mtt-85) cc_final: 0.6793 (mtp85) REVERT: C 461 LEU cc_start: 0.8602 (mm) cc_final: 0.8104 (mm) REVERT: C 490 PHE cc_start: 0.8784 (t80) cc_final: 0.8532 (t80) REVERT: C 759 PHE cc_start: 0.6825 (OUTLIER) cc_final: 0.6391 (t80) REVERT: C 912 THR cc_start: 0.8244 (m) cc_final: 0.8009 (p) REVERT: C 977 LEU cc_start: 0.8873 (tp) cc_final: 0.8671 (tt) REVERT: C 1101 HIS cc_start: 0.7243 (m90) cc_final: 0.7022 (m-70) REVERT: H 48 ILE cc_start: 0.7961 (mt) cc_final: 0.7673 (mp) REVERT: H 108 ASP cc_start: 0.8488 (p0) cc_final: 0.7924 (p0) REVERT: L 4 MET cc_start: 0.3355 (mtp) cc_final: 0.2862 (mtp) REVERT: L 55 ARG cc_start: 0.8619 (mtm-85) cc_final: 0.8274 (ttm-80) REVERT: L 63 PHE cc_start: 0.8426 (m-10) cc_final: 0.7919 (m-80) REVERT: L 106 GLU cc_start: 0.5170 (pt0) cc_final: 0.4703 (pt0) outliers start: 50 outliers final: 32 residues processed: 381 average time/residue: 0.4172 time to fit residues: 246.1365 Evaluate side-chains 323 residues out of total 3016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 288 time to evaluate : 3.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 919 ASN Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain C residue 202 LYS Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 80 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 173 optimal weight: 0.5980 chunk 96 optimal weight: 1.9990 chunk 259 optimal weight: 1.9990 chunk 212 optimal weight: 20.0000 chunk 85 optimal weight: 0.6980 chunk 312 optimal weight: 20.0000 chunk 337 optimal weight: 50.0000 chunk 277 optimal weight: 0.6980 chunk 309 optimal weight: 50.0000 chunk 106 optimal weight: 8.9990 chunk 250 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 907 ASN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN B 207 HIS B 613 GLN B1002 GLN C 448 ASN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 28325 Z= 0.210 Angle : 0.568 10.869 38542 Z= 0.294 Chirality : 0.044 0.204 4578 Planarity : 0.004 0.046 4899 Dihedral : 5.696 59.936 5007 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.83 % Favored : 97.09 % Rotamer: Outliers : 1.89 % Allowed : 9.33 % Favored : 88.78 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.92 % 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: 0.38 (0.14), residues: 3398 helix: 1.52 (0.20), residues: 681 sheet: 0.62 (0.17), residues: 907 loop : -0.39 (0.14), residues: 1810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 436 HIS 0.004 0.001 HIS B1058 PHE 0.034 0.001 PHE B 342 TYR 0.024 0.001 TYR A 904 ARG 0.007 0.000 ARG C 34 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 3016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 317 time to evaluate : 3.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 PHE cc_start: 0.7334 (m-10) cc_final: 0.7089 (m-10) REVERT: A 270 LEU cc_start: 0.8641 (mt) cc_final: 0.8123 (mp) REVERT: A 271 GLN cc_start: 0.8505 (mm-40) cc_final: 0.8215 (mm110) REVERT: A 342 PHE cc_start: 0.9234 (m-80) cc_final: 0.9012 (m-80) REVERT: A 380 TYR cc_start: 0.8551 (m-10) cc_final: 0.8277 (m-10) REVERT: A 511 VAL cc_start: 0.9165 (OUTLIER) cc_final: 0.8940 (p) REVERT: A 515 PHE cc_start: 0.8198 (m-80) cc_final: 0.7982 (m-80) REVERT: A 581 THR cc_start: 0.8847 (OUTLIER) cc_final: 0.8583 (p) REVERT: A 779 GLN cc_start: 0.8647 (OUTLIER) cc_final: 0.8362 (tp40) REVERT: A 984 LEU cc_start: 0.8743 (mt) cc_final: 0.7891 (tp) REVERT: A 995 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.8197 (ttm110) REVERT: B 41 LYS cc_start: 0.8037 (mttp) cc_final: 0.7486 (mtpt) REVERT: C 49 HIS cc_start: 0.7737 (t70) cc_final: 0.7367 (t-170) REVERT: C 86 PHE cc_start: 0.7800 (t80) cc_final: 0.7335 (t80) REVERT: C 91 TYR cc_start: 0.8535 (t80) cc_final: 0.8289 (t80) REVERT: C 104 TRP cc_start: 0.5730 (m-90) cc_final: 0.5334 (m-90) REVERT: C 223 LEU cc_start: 0.8528 (mp) cc_final: 0.8015 (mp) REVERT: C 266 TYR cc_start: 0.6899 (m-80) cc_final: 0.6340 (m-80) REVERT: C 269 TYR cc_start: 0.6185 (m-80) cc_final: 0.5883 (m-80) REVERT: C 347 PHE cc_start: 0.6794 (m-80) cc_final: 0.5616 (m-10) REVERT: C 354 ASN cc_start: 0.8537 (t0) cc_final: 0.8187 (t0) REVERT: C 414 GLN cc_start: 0.8139 (mm-40) cc_final: 0.7800 (tp-100) REVERT: C 454 ARG cc_start: 0.7681 (mtt-85) cc_final: 0.7070 (mtt-85) REVERT: C 473 TYR cc_start: 0.7702 (t80) cc_final: 0.7430 (t80) REVERT: C 486 PHE cc_start: 0.7724 (t80) cc_final: 0.6088 (t80) REVERT: C 490 PHE cc_start: 0.8803 (t80) cc_final: 0.8514 (t80) REVERT: C 1094 VAL cc_start: 0.8209 (m) cc_final: 0.7252 (t) REVERT: C 1101 HIS cc_start: 0.7192 (m90) cc_final: 0.6988 (m-70) REVERT: H 23 LYS cc_start: 0.9503 (tptp) cc_final: 0.9200 (tptp) REVERT: H 74 MET cc_start: 0.7787 (mpp) cc_final: 0.7264 (mpp) REVERT: H 108 ASP cc_start: 0.8526 (p0) cc_final: 0.7900 (m-30) REVERT: L 4 MET cc_start: 0.3548 (mtp) cc_final: 0.3019 (mtp) REVERT: L 55 ARG cc_start: 0.8715 (mtm-85) cc_final: 0.8260 (ttm-80) REVERT: L 63 PHE cc_start: 0.8394 (m-10) cc_final: 0.8064 (m-80) REVERT: L 92 TYR cc_start: 0.8131 (p90) cc_final: 0.7267 (p90) REVERT: L 188 GLU cc_start: 0.7216 (mm-30) cc_final: 0.5786 (pp20) outliers start: 57 outliers final: 36 residues processed: 356 average time/residue: 0.4111 time to fit residues: 230.1504 Evaluate side-chains 313 residues out of total 3016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 273 time to evaluate : 3.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 919 ASN Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 995 ARG Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 118 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 308 optimal weight: 5.9990 chunk 234 optimal weight: 4.9990 chunk 161 optimal weight: 1.9990 chunk 34 optimal weight: 9.9990 chunk 148 optimal weight: 7.9990 chunk 209 optimal weight: 5.9990 chunk 313 optimal weight: 9.9990 chunk 331 optimal weight: 30.0000 chunk 163 optimal weight: 0.9980 chunk 296 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN B 957 GLN C 125 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN C 804 GLN C 853 GLN C 935 GLN H 3 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 28325 Z= 0.359 Angle : 0.600 12.224 38542 Z= 0.310 Chirality : 0.045 0.209 4578 Planarity : 0.004 0.058 4899 Dihedral : 5.317 59.591 5007 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.33 % Favored : 96.59 % Rotamer: Outliers : 2.26 % Allowed : 10.39 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % 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: 0.18 (0.14), residues: 3398 helix: 1.16 (0.20), residues: 687 sheet: 0.59 (0.17), residues: 907 loop : -0.51 (0.14), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 436 HIS 0.011 0.001 HIS B1058 PHE 0.032 0.002 PHE L 119 TYR 0.038 0.002 TYR A 904 ARG 0.011 0.001 ARG A1107 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 3016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 300 time to evaluate : 3.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 PHE cc_start: 0.7561 (m-10) cc_final: 0.7299 (m-10) REVERT: A 270 LEU cc_start: 0.8801 (mt) cc_final: 0.8126 (mp) REVERT: A 271 GLN cc_start: 0.8568 (mm-40) cc_final: 0.8209 (mm110) REVERT: A 342 PHE cc_start: 0.9286 (m-80) cc_final: 0.9019 (m-80) REVERT: A 354 ASN cc_start: 0.9368 (t0) cc_final: 0.9100 (t0) REVERT: A 511 VAL cc_start: 0.9186 (OUTLIER) cc_final: 0.8983 (p) REVERT: A 745 ASP cc_start: 0.7208 (m-30) cc_final: 0.6430 (t0) REVERT: A 984 LEU cc_start: 0.8795 (mt) cc_final: 0.7851 (tp) REVERT: B 41 LYS cc_start: 0.8101 (mttp) cc_final: 0.7513 (mtpt) REVERT: C 49 HIS cc_start: 0.7779 (t70) cc_final: 0.7509 (t-170) REVERT: C 86 PHE cc_start: 0.7999 (t80) cc_final: 0.7528 (t80) REVERT: C 91 TYR cc_start: 0.8572 (t80) cc_final: 0.8332 (t80) REVERT: C 104 TRP cc_start: 0.5962 (m-90) cc_final: 0.5538 (m-90) REVERT: C 223 LEU cc_start: 0.8517 (mp) cc_final: 0.8042 (mp) REVERT: C 266 TYR cc_start: 0.6870 (m-80) cc_final: 0.6460 (m-80) REVERT: C 269 TYR cc_start: 0.6266 (m-80) cc_final: 0.5952 (m-80) REVERT: C 347 PHE cc_start: 0.6815 (m-80) cc_final: 0.5713 (m-10) REVERT: C 354 ASN cc_start: 0.8540 (t0) cc_final: 0.8189 (t0) REVERT: C 414 GLN cc_start: 0.8326 (mm-40) cc_final: 0.7966 (tp-100) REVERT: C 454 ARG cc_start: 0.7823 (mtt-85) cc_final: 0.7199 (mtt-85) REVERT: C 456 PHE cc_start: 0.8629 (m-10) cc_final: 0.8340 (m-10) REVERT: C 473 TYR cc_start: 0.7887 (t80) cc_final: 0.7588 (t80) REVERT: C 486 PHE cc_start: 0.7594 (t80) cc_final: 0.6725 (t80) REVERT: C 490 PHE cc_start: 0.8850 (t80) cc_final: 0.8530 (t80) REVERT: C 576 VAL cc_start: 0.8112 (m) cc_final: 0.7880 (t) REVERT: H 36 TRP cc_start: 0.5411 (m100) cc_final: 0.4817 (m100) REVERT: L 4 MET cc_start: 0.3659 (mtp) cc_final: 0.3032 (mtp) REVERT: L 55 ARG cc_start: 0.8721 (mtm-85) cc_final: 0.8242 (ttm-80) REVERT: L 63 PHE cc_start: 0.8556 (m-10) cc_final: 0.7886 (m-80) REVERT: L 188 GLU cc_start: 0.7281 (mm-30) cc_final: 0.5993 (pp20) outliers start: 68 outliers final: 53 residues processed: 351 average time/residue: 0.4130 time to fit residues: 227.1738 Evaluate side-chains 335 residues out of total 3016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 281 time to evaluate : 3.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 919 ASN Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 758 SER Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 118 MET Chi-restraints excluded: chain L residue 106 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 276 optimal weight: 0.0870 chunk 188 optimal weight: 0.5980 chunk 4 optimal weight: 4.9990 chunk 246 optimal weight: 20.0000 chunk 136 optimal weight: 30.0000 chunk 282 optimal weight: 2.9990 chunk 229 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 169 optimal weight: 2.9990 chunk 297 optimal weight: 0.6980 chunk 83 optimal weight: 4.9990 overall best weight: 1.4762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1135 ASN ** C 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN C 762 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 28325 Z= 0.260 Angle : 0.553 9.835 38542 Z= 0.286 Chirality : 0.044 0.194 4578 Planarity : 0.004 0.044 4899 Dihedral : 4.990 57.195 5005 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.06 % Favored : 96.85 % Rotamer: Outliers : 2.36 % Allowed : 11.39 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % 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: 0.18 (0.14), residues: 3398 helix: 1.17 (0.20), residues: 690 sheet: 0.51 (0.17), residues: 949 loop : -0.48 (0.15), residues: 1759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 436 HIS 0.006 0.001 HIS B1058 PHE 0.031 0.001 PHE B 92 TYR 0.038 0.001 TYR B 904 ARG 0.007 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 3016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 302 time to evaluate : 2.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 PHE cc_start: 0.7545 (m-10) cc_final: 0.7343 (m-10) REVERT: A 235 ILE cc_start: 0.8246 (mm) cc_final: 0.8031 (mm) REVERT: A 270 LEU cc_start: 0.8795 (mt) cc_final: 0.8084 (mp) REVERT: A 271 GLN cc_start: 0.8590 (mm-40) cc_final: 0.8225 (mm-40) REVERT: A 342 PHE cc_start: 0.9301 (m-80) cc_final: 0.9047 (m-80) REVERT: A 354 ASN cc_start: 0.9394 (t0) cc_final: 0.9126 (t0) REVERT: A 984 LEU cc_start: 0.8782 (mt) cc_final: 0.7854 (tp) REVERT: B 41 LYS cc_start: 0.8048 (mttp) cc_final: 0.7446 (mtpt) REVERT: C 49 HIS cc_start: 0.7844 (t70) cc_final: 0.7557 (t70) REVERT: C 86 PHE cc_start: 0.7999 (t80) cc_final: 0.7523 (t80) REVERT: C 91 TYR cc_start: 0.8557 (t80) cc_final: 0.8305 (t80) REVERT: C 104 TRP cc_start: 0.5957 (m-90) cc_final: 0.5556 (m-90) REVERT: C 223 LEU cc_start: 0.8481 (mp) cc_final: 0.7996 (mp) REVERT: C 266 TYR cc_start: 0.6829 (m-80) cc_final: 0.6505 (m-80) REVERT: C 269 TYR cc_start: 0.6351 (m-80) cc_final: 0.6127 (m-80) REVERT: C 347 PHE cc_start: 0.6848 (m-80) cc_final: 0.5834 (m-10) REVERT: C 354 ASN cc_start: 0.8516 (t0) cc_final: 0.8165 (t0) REVERT: C 414 GLN cc_start: 0.8323 (mm-40) cc_final: 0.7996 (tp-100) REVERT: C 452 LEU cc_start: 0.9244 (mm) cc_final: 0.8725 (tp) REVERT: C 454 ARG cc_start: 0.7792 (mtt-85) cc_final: 0.7133 (mtt-85) REVERT: C 456 PHE cc_start: 0.8615 (m-80) cc_final: 0.8308 (m-10) REVERT: C 466 ARG cc_start: 0.7820 (OUTLIER) cc_final: 0.7602 (mtm110) REVERT: C 473 TYR cc_start: 0.7905 (t80) cc_final: 0.7604 (t80) REVERT: C 490 PHE cc_start: 0.8835 (t80) cc_final: 0.8490 (t80) REVERT: C 636 TYR cc_start: 0.7254 (OUTLIER) cc_final: 0.6981 (t80) REVERT: H 108 ASP cc_start: 0.8139 (p0) cc_final: 0.7859 (p0) REVERT: L 4 MET cc_start: 0.3899 (mtp) cc_final: 0.3225 (mtp) REVERT: L 92 TYR cc_start: 0.8059 (OUTLIER) cc_final: 0.7040 (p90) REVERT: L 188 GLU cc_start: 0.7296 (mm-30) cc_final: 0.6103 (pp20) outliers start: 71 outliers final: 53 residues processed: 356 average time/residue: 0.3958 time to fit residues: 225.6999 Evaluate side-chains 331 residues out of total 3016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 275 time to evaluate : 3.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 919 ASN Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 466 ARG Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 505 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 636 TYR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 118 MET Chi-restraints excluded: chain L residue 92 TYR Chi-restraints excluded: chain L residue 146 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 111 optimal weight: 20.0000 chunk 298 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 194 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 331 optimal weight: 20.0000 chunk 275 optimal weight: 0.9990 chunk 153 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 chunk 109 optimal weight: 5.9990 chunk 174 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN A 755 GLN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN C 317 ASN C 762 GLN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 148 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 28325 Z= 0.203 Angle : 0.542 9.865 38542 Z= 0.280 Chirality : 0.044 0.212 4578 Planarity : 0.004 0.133 4899 Dihedral : 4.769 56.635 5005 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.09 % Favored : 96.82 % Rotamer: Outliers : 2.16 % Allowed : 12.28 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % 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: 0.25 (0.14), residues: 3398 helix: 1.32 (0.20), residues: 689 sheet: 0.57 (0.17), residues: 932 loop : -0.48 (0.15), residues: 1777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 436 HIS 0.006 0.001 HIS A 49 PHE 0.030 0.001 PHE B 92 TYR 0.023 0.001 TYR A 380 ARG 0.005 0.000 ARG L 62 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 3016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 296 time to evaluate : 3.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 PHE cc_start: 0.7558 (m-10) cc_final: 0.7315 (m-10) REVERT: A 270 LEU cc_start: 0.8797 (mt) cc_final: 0.8074 (mp) REVERT: A 271 GLN cc_start: 0.8568 (mm-40) cc_final: 0.8245 (mm-40) REVERT: A 342 PHE cc_start: 0.9293 (m-80) cc_final: 0.9031 (m-80) REVERT: A 354 ASN cc_start: 0.9376 (t0) cc_final: 0.9105 (t0) REVERT: A 779 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.8368 (tp40) REVERT: A 976 VAL cc_start: 0.8846 (t) cc_final: 0.8523 (m) REVERT: B 41 LYS cc_start: 0.8035 (mttp) cc_final: 0.7433 (mtpt) REVERT: C 49 HIS cc_start: 0.7832 (t70) cc_final: 0.7558 (t70) REVERT: C 86 PHE cc_start: 0.7987 (t80) cc_final: 0.7509 (t80) REVERT: C 104 TRP cc_start: 0.5956 (m-90) cc_final: 0.5579 (m-90) REVERT: C 223 LEU cc_start: 0.8452 (mp) cc_final: 0.8010 (mp) REVERT: C 266 TYR cc_start: 0.6777 (m-80) cc_final: 0.6503 (m-80) REVERT: C 269 TYR cc_start: 0.6358 (m-80) cc_final: 0.6096 (m-80) REVERT: C 347 PHE cc_start: 0.6912 (m-80) cc_final: 0.5960 (m-10) REVERT: C 354 ASN cc_start: 0.8500 (t0) cc_final: 0.7884 (t0) REVERT: C 414 GLN cc_start: 0.8310 (mm-40) cc_final: 0.8041 (tp-100) REVERT: C 456 PHE cc_start: 0.8632 (m-80) cc_final: 0.8352 (m-80) REVERT: C 466 ARG cc_start: 0.7691 (OUTLIER) cc_final: 0.6870 (mtm110) REVERT: C 473 TYR cc_start: 0.7896 (t80) cc_final: 0.7558 (t80) REVERT: C 486 PHE cc_start: 0.7469 (t80) cc_final: 0.6822 (t80) REVERT: C 490 PHE cc_start: 0.8822 (t80) cc_final: 0.8473 (t80) REVERT: C 636 TYR cc_start: 0.7278 (OUTLIER) cc_final: 0.6977 (t80) REVERT: H 23 LYS cc_start: 0.9460 (tptp) cc_final: 0.9120 (tptp) REVERT: L 4 MET cc_start: 0.3735 (mtp) cc_final: 0.3076 (mtp) REVERT: L 92 TYR cc_start: 0.8013 (p90) cc_final: 0.7044 (p90) REVERT: L 188 GLU cc_start: 0.7531 (mm-30) cc_final: 0.6376 (pp20) outliers start: 65 outliers final: 52 residues processed: 345 average time/residue: 0.3979 time to fit residues: 219.6625 Evaluate side-chains 326 residues out of total 3016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 271 time to evaluate : 2.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 919 ASN Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 466 ARG Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 636 TYR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 118 MET Chi-restraints excluded: chain L residue 33 TYR Chi-restraints excluded: chain L residue 174 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 319 optimal weight: 50.0000 chunk 37 optimal weight: 2.9990 chunk 189 optimal weight: 0.4980 chunk 242 optimal weight: 8.9990 chunk 187 optimal weight: 0.9980 chunk 279 optimal weight: 2.9990 chunk 185 optimal weight: 0.6980 chunk 330 optimal weight: 0.6980 chunk 206 optimal weight: 0.9990 chunk 201 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN B 762 GLN C 360 ASN C 658 ASN ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 28325 Z= 0.179 Angle : 0.530 9.439 38542 Z= 0.274 Chirality : 0.044 0.200 4578 Planarity : 0.004 0.082 4899 Dihedral : 4.579 56.447 5005 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.94 % Favored : 96.97 % Rotamer: Outliers : 2.03 % Allowed : 12.85 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % 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: 0.32 (0.14), residues: 3398 helix: 1.45 (0.21), residues: 685 sheet: 0.60 (0.17), residues: 930 loop : -0.46 (0.15), residues: 1783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 436 HIS 0.005 0.001 HIS A 49 PHE 0.027 0.001 PHE B 92 TYR 0.018 0.001 TYR C1067 ARG 0.009 0.000 ARG B 577 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 3016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 292 time to evaluate : 3.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 PHE cc_start: 0.7629 (m-10) cc_final: 0.7384 (m-10) REVERT: A 270 LEU cc_start: 0.8755 (mt) cc_final: 0.8054 (mp) REVERT: A 271 GLN cc_start: 0.8574 (mm-40) cc_final: 0.8239 (mm-40) REVERT: A 342 PHE cc_start: 0.9289 (m-80) cc_final: 0.9040 (m-80) REVERT: A 351 TYR cc_start: 0.8498 (p90) cc_final: 0.8080 (p90) REVERT: A 354 ASN cc_start: 0.9351 (t0) cc_final: 0.9091 (t0) REVERT: A 779 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.8354 (tp40) REVERT: A 984 LEU cc_start: 0.8770 (mt) cc_final: 0.7902 (tp) REVERT: B 41 LYS cc_start: 0.8013 (mttp) cc_final: 0.7412 (mtpt) REVERT: B 973 ILE cc_start: 0.9191 (OUTLIER) cc_final: 0.8968 (mt) REVERT: C 49 HIS cc_start: 0.7836 (t70) cc_final: 0.7447 (t-90) REVERT: C 86 PHE cc_start: 0.8019 (t80) cc_final: 0.7529 (t80) REVERT: C 104 TRP cc_start: 0.5973 (m-90) cc_final: 0.5567 (m-90) REVERT: C 223 LEU cc_start: 0.8417 (mp) cc_final: 0.7949 (mp) REVERT: C 269 TYR cc_start: 0.6412 (m-80) cc_final: 0.6163 (m-80) REVERT: C 329 PHE cc_start: 0.8321 (m-10) cc_final: 0.8119 (m-80) REVERT: C 347 PHE cc_start: 0.6882 (m-80) cc_final: 0.5981 (m-10) REVERT: C 354 ASN cc_start: 0.8464 (t0) cc_final: 0.7839 (t0) REVERT: C 408 ARG cc_start: 0.8817 (ptm-80) cc_final: 0.8551 (ptm-80) REVERT: C 414 GLN cc_start: 0.8316 (mm-40) cc_final: 0.8113 (tp-100) REVERT: C 452 LEU cc_start: 0.9151 (mm) cc_final: 0.8615 (tp) REVERT: C 454 ARG cc_start: 0.8077 (mtp180) cc_final: 0.7854 (mtp85) REVERT: C 466 ARG cc_start: 0.7656 (OUTLIER) cc_final: 0.7125 (mtm180) REVERT: C 473 TYR cc_start: 0.7857 (t80) cc_final: 0.7543 (t80) REVERT: C 486 PHE cc_start: 0.7628 (t80) cc_final: 0.6740 (t80) REVERT: C 490 PHE cc_start: 0.8813 (t80) cc_final: 0.8476 (t80) REVERT: C 636 TYR cc_start: 0.7213 (OUTLIER) cc_final: 0.6943 (t80) REVERT: H 23 LYS cc_start: 0.9450 (tptp) cc_final: 0.9081 (tptp) REVERT: H 108 ASP cc_start: 0.8238 (p0) cc_final: 0.8030 (p0) REVERT: L 92 TYR cc_start: 0.8018 (p90) cc_final: 0.6932 (p90) REVERT: L 188 GLU cc_start: 0.7454 (mm-30) cc_final: 0.6364 (pp20) outliers start: 61 outliers final: 50 residues processed: 339 average time/residue: 0.4216 time to fit residues: 228.7122 Evaluate side-chains 327 residues out of total 3016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 273 time to evaluate : 2.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 919 ASN Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 466 ARG Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 636 TYR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 118 MET Chi-restraints excluded: chain L residue 33 TYR Chi-restraints excluded: chain L residue 174 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 204 optimal weight: 1.9990 chunk 132 optimal weight: 20.0000 chunk 197 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 210 optimal weight: 9.9990 chunk 225 optimal weight: 9.9990 chunk 163 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 chunk 259 optimal weight: 2.9990 chunk 300 optimal weight: 0.0060 overall best weight: 2.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 762 GLN L 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 28325 Z= 0.328 Angle : 0.577 8.512 38542 Z= 0.298 Chirality : 0.045 0.198 4578 Planarity : 0.004 0.059 4899 Dihedral : 4.637 56.556 5005 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.44 % Favored : 96.50 % Rotamer: Outliers : 2.36 % Allowed : 13.18 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % 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: 0.16 (0.14), residues: 3398 helix: 1.21 (0.20), residues: 684 sheet: 0.52 (0.17), residues: 931 loop : -0.52 (0.15), residues: 1783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP A 436 HIS 0.007 0.001 HIS B1058 PHE 0.029 0.002 PHE B 92 TYR 0.022 0.002 TYR A 451 ARG 0.005 0.000 ARG B 567 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 3016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 287 time to evaluate : 3.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 PHE cc_start: 0.7642 (m-10) cc_final: 0.7307 (m-10) REVERT: A 235 ILE cc_start: 0.8273 (mm) cc_final: 0.7967 (mm) REVERT: A 270 LEU cc_start: 0.8820 (mt) cc_final: 0.8051 (mp) REVERT: A 271 GLN cc_start: 0.8596 (mm-40) cc_final: 0.8177 (mm110) REVERT: A 342 PHE cc_start: 0.9317 (m-80) cc_final: 0.9048 (m-80) REVERT: A 351 TYR cc_start: 0.8476 (p90) cc_final: 0.8023 (p90) REVERT: A 354 ASN cc_start: 0.9347 (t0) cc_final: 0.9075 (t0) REVERT: A 779 GLN cc_start: 0.8728 (OUTLIER) cc_final: 0.8405 (tp40) REVERT: A 976 VAL cc_start: 0.8878 (t) cc_final: 0.8591 (m) REVERT: A 984 LEU cc_start: 0.8795 (mt) cc_final: 0.7909 (tp) REVERT: B 41 LYS cc_start: 0.8078 (mttp) cc_final: 0.7492 (mtpt) REVERT: B 1127 ASP cc_start: 0.7539 (t0) cc_final: 0.7318 (t0) REVERT: C 49 HIS cc_start: 0.7831 (t70) cc_final: 0.7459 (t-90) REVERT: C 86 PHE cc_start: 0.8086 (t80) cc_final: 0.7407 (t80) REVERT: C 104 TRP cc_start: 0.6065 (m-90) cc_final: 0.5641 (m-90) REVERT: C 223 LEU cc_start: 0.8426 (mp) cc_final: 0.7969 (mp) REVERT: C 266 TYR cc_start: 0.7224 (m-80) cc_final: 0.6005 (m-10) REVERT: C 269 TYR cc_start: 0.6470 (m-80) cc_final: 0.6220 (m-80) REVERT: C 347 PHE cc_start: 0.6948 (m-80) cc_final: 0.6062 (m-10) REVERT: C 354 ASN cc_start: 0.8498 (t0) cc_final: 0.7911 (t0) REVERT: C 369 TYR cc_start: 0.7721 (t80) cc_final: 0.7310 (t80) REVERT: C 414 GLN cc_start: 0.8365 (mm-40) cc_final: 0.8080 (tp-100) REVERT: C 452 LEU cc_start: 0.9200 (mm) cc_final: 0.8671 (tp) REVERT: C 454 ARG cc_start: 0.8181 (mtp180) cc_final: 0.7951 (mtp85) REVERT: C 466 ARG cc_start: 0.7797 (OUTLIER) cc_final: 0.6930 (mtm110) REVERT: C 473 TYR cc_start: 0.7873 (t80) cc_final: 0.7608 (t80) REVERT: C 486 PHE cc_start: 0.7723 (t80) cc_final: 0.6780 (t80) REVERT: C 490 PHE cc_start: 0.8882 (t80) cc_final: 0.8595 (t80) REVERT: C 636 TYR cc_start: 0.7223 (OUTLIER) cc_final: 0.6988 (t80) REVERT: C 976 VAL cc_start: 0.8924 (t) cc_final: 0.8668 (m) REVERT: H 23 LYS cc_start: 0.9489 (tptp) cc_final: 0.9104 (tptp) REVERT: H 80 TYR cc_start: 0.7753 (OUTLIER) cc_final: 0.7473 (m-80) REVERT: H 108 ASP cc_start: 0.8418 (p0) cc_final: 0.8201 (p0) REVERT: L 4 MET cc_start: 0.3286 (mtp) cc_final: 0.2113 (tpt) REVERT: L 92 TYR cc_start: 0.8155 (p90) cc_final: 0.7035 (p90) REVERT: L 188 GLU cc_start: 0.7557 (mm-30) cc_final: 0.6477 (pp20) outliers start: 71 outliers final: 59 residues processed: 337 average time/residue: 0.4022 time to fit residues: 217.3062 Evaluate side-chains 339 residues out of total 3016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 276 time to evaluate : 3.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 919 ASN Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 466 ARG Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 636 TYR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 118 MET Chi-restraints excluded: chain L residue 33 TYR Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain L residue 174 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 316 optimal weight: 8.9990 chunk 288 optimal weight: 1.9990 chunk 308 optimal weight: 2.9990 chunk 185 optimal weight: 0.7980 chunk 134 optimal weight: 20.0000 chunk 241 optimal weight: 8.9990 chunk 94 optimal weight: 1.9990 chunk 278 optimal weight: 0.8980 chunk 291 optimal weight: 0.6980 chunk 306 optimal weight: 20.0000 chunk 202 optimal weight: 10.0000 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 ASN A 787 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 28325 Z= 0.236 Angle : 0.557 12.052 38542 Z= 0.287 Chirality : 0.044 0.254 4578 Planarity : 0.004 0.053 4899 Dihedral : 4.512 56.015 5005 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.33 % Favored : 96.62 % Rotamer: Outliers : 2.12 % Allowed : 13.78 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % 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: 0.22 (0.14), residues: 3398 helix: 1.41 (0.20), residues: 685 sheet: 0.50 (0.17), residues: 916 loop : -0.51 (0.15), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP A 436 HIS 0.004 0.001 HIS B1058 PHE 0.030 0.001 PHE L 119 TYR 0.032 0.001 TYR A 451 ARG 0.007 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 3016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 284 time to evaluate : 3.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 PHE cc_start: 0.7614 (m-10) cc_final: 0.7321 (m-10) REVERT: A 235 ILE cc_start: 0.8275 (mm) cc_final: 0.8004 (mm) REVERT: A 270 LEU cc_start: 0.8788 (mt) cc_final: 0.8021 (mp) REVERT: A 271 GLN cc_start: 0.8607 (mm-40) cc_final: 0.8177 (mm-40) REVERT: A 342 PHE cc_start: 0.9325 (m-80) cc_final: 0.9039 (m-80) REVERT: A 351 TYR cc_start: 0.8471 (p90) cc_final: 0.8029 (p90) REVERT: A 354 ASN cc_start: 0.9332 (t0) cc_final: 0.9076 (t0) REVERT: A 779 GLN cc_start: 0.8711 (OUTLIER) cc_final: 0.8375 (tp40) REVERT: A 976 VAL cc_start: 0.8877 (t) cc_final: 0.8564 (m) REVERT: A 984 LEU cc_start: 0.8756 (mt) cc_final: 0.7982 (tp) REVERT: B 41 LYS cc_start: 0.8021 (mttp) cc_final: 0.7414 (mtpt) REVERT: B 231 ILE cc_start: 0.9149 (mt) cc_final: 0.8943 (tt) REVERT: B 387 LEU cc_start: 0.8497 (mt) cc_final: 0.8230 (mt) REVERT: C 49 HIS cc_start: 0.7839 (t70) cc_final: 0.7486 (t-90) REVERT: C 86 PHE cc_start: 0.8057 (t80) cc_final: 0.7386 (t80) REVERT: C 104 TRP cc_start: 0.5970 (m-90) cc_final: 0.5522 (m-90) REVERT: C 266 TYR cc_start: 0.7211 (m-80) cc_final: 0.6053 (m-10) REVERT: C 269 TYR cc_start: 0.6563 (m-80) cc_final: 0.6312 (m-80) REVERT: C 354 ASN cc_start: 0.8464 (t0) cc_final: 0.7923 (t0) REVERT: C 369 TYR cc_start: 0.7740 (t80) cc_final: 0.7339 (t80) REVERT: C 414 GLN cc_start: 0.8334 (mm-40) cc_final: 0.8049 (tp-100) REVERT: C 452 LEU cc_start: 0.9188 (mm) cc_final: 0.8677 (tp) REVERT: C 454 ARG cc_start: 0.8152 (mtp180) cc_final: 0.7917 (mtp85) REVERT: C 466 ARG cc_start: 0.7733 (OUTLIER) cc_final: 0.6921 (mtm110) REVERT: C 473 TYR cc_start: 0.7830 (t80) cc_final: 0.7584 (t80) REVERT: C 486 PHE cc_start: 0.7760 (t80) cc_final: 0.6746 (t80) REVERT: C 490 PHE cc_start: 0.8887 (t80) cc_final: 0.8618 (t80) REVERT: C 636 TYR cc_start: 0.7157 (OUTLIER) cc_final: 0.6857 (t80) REVERT: C 994 ASP cc_start: 0.7214 (m-30) cc_final: 0.6926 (m-30) REVERT: H 23 LYS cc_start: 0.9468 (tptp) cc_final: 0.9096 (tptp) REVERT: H 80 TYR cc_start: 0.7766 (OUTLIER) cc_final: 0.7335 (m-80) REVERT: H 108 ASP cc_start: 0.8486 (p0) cc_final: 0.8280 (p0) REVERT: L 4 MET cc_start: 0.3214 (mtp) cc_final: 0.2150 (tpt) REVERT: L 92 TYR cc_start: 0.8192 (p90) cc_final: 0.6996 (p90) REVERT: L 188 GLU cc_start: 0.7515 (mm-30) cc_final: 0.6471 (pp20) outliers start: 64 outliers final: 52 residues processed: 331 average time/residue: 0.4179 time to fit residues: 224.9616 Evaluate side-chains 330 residues out of total 3016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 274 time to evaluate : 3.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 450 ASN Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 919 ASN Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 466 ARG Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 636 TYR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 118 MET Chi-restraints excluded: chain L residue 33 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 325 optimal weight: 20.0000 chunk 198 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 226 optimal weight: 6.9990 chunk 341 optimal weight: 50.0000 chunk 314 optimal weight: 2.9990 chunk 272 optimal weight: 0.5980 chunk 28 optimal weight: 10.0000 chunk 210 optimal weight: 5.9990 chunk 166 optimal weight: 0.5980 chunk 216 optimal weight: 6.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 ASN B 914 ASN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 28325 Z= 0.307 Angle : 0.588 12.509 38542 Z= 0.302 Chirality : 0.045 0.207 4578 Planarity : 0.004 0.047 4899 Dihedral : 4.545 56.110 5005 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.99 % Allowed : 14.08 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % 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: 0.15 (0.14), residues: 3398 helix: 1.33 (0.20), residues: 684 sheet: 0.45 (0.17), residues: 929 loop : -0.54 (0.15), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP A 436 HIS 0.007 0.001 HIS B1058 PHE 0.030 0.002 PHE B 92 TYR 0.030 0.002 TYR L 174 ARG 0.008 0.000 ARG B 214 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6796 Ramachandran restraints generated. 3398 Oldfield, 0 Emsley, 3398 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 3016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 274 time to evaluate : 3.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 PHE cc_start: 0.7630 (m-10) cc_final: 0.7286 (m-10) REVERT: A 235 ILE cc_start: 0.8286 (mm) cc_final: 0.8011 (mm) REVERT: A 342 PHE cc_start: 0.9322 (m-80) cc_final: 0.9025 (m-80) REVERT: A 351 TYR cc_start: 0.8498 (p90) cc_final: 0.8038 (p90) REVERT: A 354 ASN cc_start: 0.9335 (t0) cc_final: 0.9084 (t0) REVERT: A 779 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.8400 (tp40) REVERT: A 976 VAL cc_start: 0.8865 (t) cc_final: 0.8562 (m) REVERT: B 41 LYS cc_start: 0.8040 (mttp) cc_final: 0.7429 (mtpt) REVERT: B 387 LEU cc_start: 0.8518 (mt) cc_final: 0.8245 (mt) REVERT: B 1127 ASP cc_start: 0.7558 (t0) cc_final: 0.7313 (t0) REVERT: C 49 HIS cc_start: 0.7842 (t70) cc_final: 0.7489 (t-90) REVERT: C 86 PHE cc_start: 0.8089 (t80) cc_final: 0.7380 (t80) REVERT: C 104 TRP cc_start: 0.6015 (m-90) cc_final: 0.5557 (m-90) REVERT: C 223 LEU cc_start: 0.8235 (mp) cc_final: 0.7341 (mp) REVERT: C 266 TYR cc_start: 0.7294 (m-80) cc_final: 0.6006 (m-10) REVERT: C 269 TYR cc_start: 0.6595 (m-80) cc_final: 0.6344 (m-80) REVERT: C 347 PHE cc_start: 0.7354 (m-80) cc_final: 0.6489 (m-10) REVERT: C 354 ASN cc_start: 0.8484 (t0) cc_final: 0.8095 (t0) REVERT: C 369 TYR cc_start: 0.7808 (t80) cc_final: 0.7404 (t80) REVERT: C 414 GLN cc_start: 0.8374 (mm-40) cc_final: 0.8083 (tp-100) REVERT: C 452 LEU cc_start: 0.9197 (mm) cc_final: 0.8689 (tp) REVERT: C 454 ARG cc_start: 0.8174 (mtp180) cc_final: 0.7474 (mtt-85) REVERT: C 466 ARG cc_start: 0.7764 (OUTLIER) cc_final: 0.6947 (mtm110) REVERT: C 473 TYR cc_start: 0.7833 (t80) cc_final: 0.7607 (t80) REVERT: C 486 PHE cc_start: 0.7795 (t80) cc_final: 0.6805 (t80) REVERT: C 490 PHE cc_start: 0.8915 (t80) cc_final: 0.8654 (t80) REVERT: C 636 TYR cc_start: 0.7129 (OUTLIER) cc_final: 0.6843 (t80) REVERT: C 976 VAL cc_start: 0.8961 (t) cc_final: 0.8721 (m) REVERT: C 994 ASP cc_start: 0.7313 (m-30) cc_final: 0.7002 (m-30) REVERT: H 23 LYS cc_start: 0.9440 (tptp) cc_final: 0.9076 (tptp) REVERT: H 80 TYR cc_start: 0.7856 (OUTLIER) cc_final: 0.7495 (m-80) REVERT: H 108 ASP cc_start: 0.8538 (p0) cc_final: 0.8335 (p0) REVERT: L 4 MET cc_start: 0.3265 (OUTLIER) cc_final: 0.2310 (mmt) REVERT: L 92 TYR cc_start: 0.8205 (p90) cc_final: 0.7028 (p90) REVERT: L 188 GLU cc_start: 0.7488 (mm-30) cc_final: 0.6454 (pp20) outliers start: 60 outliers final: 54 residues processed: 314 average time/residue: 0.4048 time to fit residues: 205.6590 Evaluate side-chains 328 residues out of total 3016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 269 time to evaluate : 2.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 919 ASN Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 982 SER Chi-restraints excluded: chain A residue 1037 SER Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 951 VAL Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 466 ARG Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 636 TYR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 967 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain H residue 118 MET Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 33 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 289 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 chunk 250 optimal weight: 0.8980 chunk 40 optimal weight: 8.9990 chunk 75 optimal weight: 0.5980 chunk 272 optimal weight: 0.9980 chunk 114 optimal weight: 7.9990 chunk 279 optimal weight: 0.3980 chunk 34 optimal weight: 10.0000 chunk 50 optimal weight: 4.9990 chunk 239 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1011 GLN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.169888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.105514 restraints weight = 52595.294| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 3.64 r_work: 0.3129 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 28325 Z= 0.182 Angle : 0.560 13.077 38542 Z= 0.286 Chirality : 0.044 0.233 4578 Planarity : 0.004 0.049 4899 Dihedral : 4.351 55.659 5005 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.76 % Allowed : 14.38 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.92 % 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: 0.27 (0.14), residues: 3398 helix: 1.54 (0.20), residues: 684 sheet: 0.52 (0.17), residues: 918 loop : -0.51 (0.15), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP A 436 HIS 0.003 0.001 HIS A 49 PHE 0.025 0.001 PHE B 92 TYR 0.021 0.001 TYR A 451 ARG 0.008 0.000 ARG B 214 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6536.16 seconds wall clock time: 119 minutes 24.41 seconds (7164.41 seconds total)