Starting phenix.real_space_refine on Thu Jul 25 12:07:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xoa_33342/07_2024/7xoa_33342_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xoa_33342/07_2024/7xoa_33342.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xoa_33342/07_2024/7xoa_33342.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xoa_33342/07_2024/7xoa_33342.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xoa_33342/07_2024/7xoa_33342_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xoa_33342/07_2024/7xoa_33342_neut.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.021 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: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 134 5.16 5 C 18667 2.51 5 N 4812 2.21 5 O 5588 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 34": "NH1" <-> "NH2" Residue "A ARG 44": "NH1" <-> "NH2" Residue "A ARG 102": "NH1" <-> "NH2" Residue "A GLU 169": "OE1" <-> "OE2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A ARG 237": "NH1" <-> "NH2" Residue "A ARG 273": "NH1" <-> "NH2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A ARG 328": "NH1" <-> "NH2" Residue "A PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A ARG 466": "NH1" <-> "NH2" Residue "A ARG 498": "NH1" <-> "NH2" Residue "A PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 567": "NH1" <-> "NH2" Residue "A ARG 577": "NH1" <-> "NH2" Residue "A ARG 765": "NH1" <-> "NH2" Residue "A ARG 815": "NH1" <-> "NH2" Residue "A ARG 905": "NH1" <-> "NH2" Residue "A ARG 983": "NH1" <-> "NH2" Residue "A ARG 995": "NH1" <-> "NH2" Residue "A ARG 1000": "NH1" <-> "NH2" Residue "A ARG 1014": "NH1" <-> "NH2" Residue "A GLU 1017": "OE1" <-> "OE2" Residue "A ARG 1019": "NH1" <-> "NH2" Residue "A ARG 1039": "NH1" <-> "NH2" Residue "A ARG 1091": "NH1" <-> "NH2" Residue "B ARG 34": "NH1" <-> "NH2" Residue "B ARG 44": "NH1" <-> "NH2" Residue "B ARG 102": "NH1" <-> "NH2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B ARG 237": "NH1" <-> "NH2" Residue "B ARG 273": "NH1" <-> "NH2" Residue "B ARG 319": "NH1" <-> "NH2" Residue "B ARG 328": "NH1" <-> "NH2" Residue "B ARG 346": "NH1" <-> "NH2" Residue "B ARG 355": "NH1" <-> "NH2" Residue "B ARG 403": "NH1" <-> "NH2" Residue "B ARG 457": "NH1" <-> "NH2" Residue "B ARG 466": "NH1" <-> "NH2" Residue "B ARG 493": "NH1" <-> "NH2" Residue "B ARG 498": "NH1" <-> "NH2" Residue "B ARG 509": "NH1" <-> "NH2" Residue "B ARG 567": "NH1" <-> "NH2" Residue "B ARG 577": "NH1" <-> "NH2" Residue "B ARG 765": "NH1" <-> "NH2" Residue "B ARG 815": "NH1" <-> "NH2" Residue "B ARG 905": "NH1" <-> "NH2" Residue "B ARG 983": "NH1" <-> "NH2" Residue "B ARG 995": "NH1" <-> "NH2" Residue "B ARG 1000": "NH1" <-> "NH2" Residue "B ARG 1014": "NH1" <-> "NH2" Residue "B ARG 1019": "NH1" <-> "NH2" Residue "B ARG 1039": "NH1" <-> "NH2" Residue "B ARG 1091": "NH1" <-> "NH2" Residue "C TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 34": "NH1" <-> "NH2" Residue "C ARG 44": "NH1" <-> "NH2" Residue "C ARG 102": "NH1" <-> "NH2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C ARG 237": "NH1" <-> "NH2" Residue "C ARG 273": "NH1" <-> "NH2" Residue "C ARG 319": "NH1" <-> "NH2" Residue "C ARG 328": "NH1" <-> "NH2" Residue "C ARG 346": "NH1" <-> "NH2" Residue "C ARG 355": "NH1" <-> "NH2" Residue "C ARG 403": "NH1" <-> "NH2" Residue "C ARG 457": "NH1" <-> "NH2" Residue "C ARG 466": "NH1" <-> "NH2" Residue "C ARG 493": "NH1" <-> "NH2" Residue "C ARG 498": "NH1" <-> "NH2" Residue "C ARG 509": "NH1" <-> "NH2" Residue "C ARG 567": "NH1" <-> "NH2" Residue "C ARG 577": "NH1" <-> "NH2" Residue "C ARG 765": "NH1" <-> "NH2" Residue "C ARG 815": "NH1" <-> "NH2" Residue "C ARG 905": "NH1" <-> "NH2" Residue "C ARG 983": "NH1" <-> "NH2" Residue "C ARG 995": "NH1" <-> "NH2" Residue "C ARG 1000": "NH1" <-> "NH2" Residue "C ARG 1014": "NH1" <-> "NH2" Residue "C ARG 1019": "NH1" <-> "NH2" Residue "C ARG 1039": "NH1" <-> "NH2" Residue "C ARG 1091": "NH1" <-> "NH2" Residue "C PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 95": "NH1" <-> "NH2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D ARG 177": "NH1" <-> "NH2" Residue "D ARG 192": "NH1" <-> "NH2" Residue "D ARG 245": "NH1" <-> "NH2" Residue "D ARG 246": "NH1" <-> "NH2" Residue "D ARG 273": "NH1" <-> "NH2" Residue "D ARG 340": "NH1" <-> "NH2" Residue "D PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 357": "NH1" <-> "NH2" Residue "D ARG 387": "NH1" <-> "NH2" Residue "D ARG 465": "NH1" <-> "NH2" Residue "D GLU 471": "OE1" <-> "OE2" Residue "D ARG 518": "NH1" <-> "NH2" Residue "D ARG 577": "NH1" <-> "NH2" Residue "D ARG 600": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 29202 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 8001 Classifications: {'peptide': 1026} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 56, 'TRANS': 969} Chain breaks: 7 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 7950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 7950 Classifications: {'peptide': 1026} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 56, 'TRANS': 969} Chain breaks: 7 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 3, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 53 Chain: "C" Number of atoms: 7950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 7950 Classifications: {'peptide': 1026} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 56, 'TRANS': 969} Chain breaks: 7 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 3, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 53 Chain: "D" Number of atoms: 4824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4824 Classifications: {'peptide': 592} Link IDs: {'PTRANS': 25, 'TRANS': 566} Chain breaks: 1 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: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' ZN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 15.81, per 1000 atoms: 0.54 Number of scatterers: 29202 At special positions: 0 Unit cell: (132.664, 136.784, 246.376, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 134 16.00 O 5588 8.00 N 4812 7.00 C 18667 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=32, 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=2.01 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.32 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=1.98 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=1.99 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.60 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 B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.76 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.04 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A1074 " " NAG A1302 " - " ASN A1098 " " NAG A1303 " - " ASN A 801 " " NAG A1304 " - " ASN A 709 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 603 " " NAG A1308 " - " ASN A1134 " " NAG A1309 " - " ASN A 61 " " NAG A1310 " - " ASN A 122 " " NAG A1311 " - " ASN A 331 " " NAG B1301 " - " ASN B1074 " " NAG B1302 " - " ASN B1098 " " NAG B1303 " - " ASN B 801 " " NAG B1304 " - " ASN B 709 " " NAG B1305 " - " ASN B 616 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B1134 " " NAG B1308 " - " ASN B 61 " " NAG B1309 " - " ASN B 122 " " NAG B1310 " - " ASN B 331 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C1074 " " NAG C1303 " - " ASN C1098 " " NAG C1304 " - " ASN C 801 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 603 " " NAG C1308 " - " ASN C1134 " " NAG C1309 " - " ASN C 122 " " NAG C1310 " - " ASN C 331 " " NAG C1311 " - " ASN C 709 " " NAG D 902 " - " ASN D 546 " " NAG D 903 " - " ASN D 53 " Time building additional restraints: 10.29 Conformation dependent library (CDL) restraints added in 5.4 seconds 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6888 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 49 sheets defined 30.4% alpha, 17.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.05 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 366 through 370 removed outlier: 3.633A pdb=" N ASN A 370 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 389 removed outlier: 4.188A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.503A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 778 removed outlier: 4.029A pdb=" N LYS A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ARG A 765 " --> pdb=" O THR A 761 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 868 through 884 Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.508A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.787A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 removed outlier: 4.109A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 966 removed outlier: 4.146A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU A 962 " --> pdb=" O ALA A 958 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N VAL A 963 " --> pdb=" O LEU A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.702A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER A 982 " --> pdb=" O ASN A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 5.327A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR A1006 " --> pdb=" O GLN A1002 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N TYR A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 342 Processing helix chain 'B' and resid 364 through 368 Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 404 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.595A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.818A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 778 removed outlier: 3.841A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 868 through 884 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.533A pdb=" N ALA B 890 " --> pdb=" O THR B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.782A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 removed outlier: 4.120A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.541A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 977 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.958A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR B1007 " --> pdb=" O SER B1003 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.536A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 removed outlier: 3.672A pdb=" N PHE C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 3.533A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.560A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 746 through 757 removed outlier: 3.548A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLY C 757 " --> pdb=" O LEU C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 778 removed outlier: 3.690A pdb=" N ARG C 765 " --> pdb=" O THR C 761 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 868 through 884 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.556A pdb=" N ALA C 890 " --> pdb=" O THR C 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.779A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 removed outlier: 4.137A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.152A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 removed outlier: 3.524A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 990 through 1033 removed outlier: 3.581A pdb=" N ASP C 994 " --> pdb=" O GLU C 990 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 Processing helix chain 'D' and resid 20 through 53 removed outlier: 3.781A pdb=" N ASN D 24 " --> pdb=" O LEU D 20 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASP D 38 " --> pdb=" O GLN D 34 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N TYR D 41 " --> pdb=" O GLU D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 81 Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.808A pdb=" N GLN D 102 " --> pdb=" O GLN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 108 removed outlier: 3.798A pdb=" N ALA D 107 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU D 108 " --> pdb=" O SER D 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 104 through 108' Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 147 through 155 Processing helix chain 'D' and resid 157 through 194 removed outlier: 4.147A pdb=" N ALA D 164 " --> pdb=" O SER D 160 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLY D 173 " --> pdb=" O ARG D 169 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS D 174 " --> pdb=" O ALA D 170 " (cutoff:3.500A) Proline residue: D 178 - end of helix removed outlier: 3.732A pdb=" N GLU D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 218 through 233 removed outlier: 3.734A pdb=" N LEU D 222 " --> pdb=" O ASN D 218 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ILE D 223 " --> pdb=" O ARG D 219 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU D 224 " --> pdb=" O ASN D 220 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU D 227 " --> pdb=" O ILE D 223 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU D 232 " --> pdb=" O ARG D 228 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE D 233 " --> pdb=" O THR D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 252 removed outlier: 4.375A pdb=" N ASP D 250 " --> pdb=" O ARG D 246 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N THR D 251 " --> pdb=" O LYS D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 256 removed outlier: 4.204A pdb=" N ILE D 256 " --> pdb=" O PRO D 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 253 through 256' Processing helix chain 'D' and resid 275 through 279 Processing helix chain 'D' and resid 293 through 300 removed outlier: 3.579A pdb=" N GLN D 300 " --> pdb=" O ALA D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 318 removed outlier: 3.528A pdb=" N VAL D 318 " --> pdb=" O PHE D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 330 removed outlier: 3.540A pdb=" N ALA D 329 " --> pdb=" O GLN D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 383 removed outlier: 3.649A pdb=" N HIS D 373 " --> pdb=" O PHE D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 388 removed outlier: 4.153A pdb=" N ARG D 387 " --> pdb=" O ALA D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 397 through 413 removed outlier: 3.824A pdb=" N HIS D 401 " --> pdb=" O ASN D 397 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N GLU D 402 " --> pdb=" O GLU D 398 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA D 403 " --> pdb=" O GLY D 399 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU D 406 " --> pdb=" O GLU D 402 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE D 407 " --> pdb=" O ALA D 403 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 422 Processing helix chain 'D' and resid 431 through 447 removed outlier: 3.747A pdb=" N THR D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 465 Processing helix chain 'D' and resid 472 through 484 Processing helix chain 'D' and resid 499 through 502 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 513 through 532 removed outlier: 3.656A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 removed outlier: 3.557A pdb=" N CYS D 542 " --> pdb=" O LEU D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 559 removed outlier: 3.569A pdb=" N LYS D 553 " --> pdb=" O GLU D 549 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU D 554 " --> pdb=" O ALA D 550 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 572 Processing helix chain 'D' and resid 581 through 588 removed outlier: 3.615A pdb=" N PHE D 588 " --> pdb=" O LEU D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 599 Processing helix chain 'D' and resid 600 through 602 No H-bonds generated for 'chain 'D' and resid 600 through 602' Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.062A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 63 through 65 Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 94 removed outlier: 3.817A pdb=" N LEU A 229 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 170 through 172 removed outlier: 3.985A pdb=" N TYR A 170 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE A 128 " --> pdb=" O TYR A 170 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A 241 " --> pdb=" O GLY A 103 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ILE A 105 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLN A 239 " --> pdb=" O ILE A 105 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 316 removed outlier: 3.622A pdb=" N THR A 315 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA A 609 " --> pdb=" O ILE A 598 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA7, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.599A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 539 through 543 removed outlier: 5.685A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.116A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER A 673 " --> pdb=" O ILE A 693 " (cutoff:3.500A) removed outlier: 6.740A 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: 6.212A pdb=" N ALA A 701 " --> pdb=" O ILE C 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 714 removed outlier: 3.856A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 717 through 728 removed outlier: 3.810A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 789 removed outlier: 5.837A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 29 removed outlier: 3.525A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.198A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 8.446A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.048A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 126 through 132 removed outlier: 3.550A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU B 241 " --> pdb=" O GLY B 103 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 316 removed outlier: 5.319A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 324 through 325 removed outlier: 7.113A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N PHE B 543 " --> pdb=" O LEU B 546 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.513A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 453 through 454 removed outlier: 3.527A pdb=" N ARG B 493 " --> pdb=" O TYR B 453 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.710A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 712 through 714 removed outlier: 3.809A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 717 through 728 removed outlier: 3.831A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.293A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 787 through 788 Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1122 removed outlier: 3.526A pdb=" N CYS B1082 " --> pdb=" O VAL B1133 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.515A pdb=" N SER C 31 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE C 65 " --> pdb=" O TYR C 265 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.099A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 90 through 94 removed outlier: 3.646A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 166 through 169 removed outlier: 3.913A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 316 removed outlier: 5.299A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.911A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 391 through 392 removed outlier: 3.508A pdb=" N VAL C 524 " --> pdb=" O PHE C 392 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 453 through 454 removed outlier: 3.549A pdb=" N TYR C 453 " --> pdb=" O ARG C 493 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG C 493 " --> pdb=" O TYR C 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'C' and resid 538 through 539 removed outlier: 3.534A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 542 through 543 removed outlier: 3.742A pdb=" N PHE C 543 " --> pdb=" O LEU C 546 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 656 removed outlier: 5.621A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 714 removed outlier: 3.832A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 717 through 728 removed outlier: 3.811A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.185A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF2, first strand: chain 'D' and resid 131 through 132 removed outlier: 3.566A pdb=" N VAL D 132 " --> pdb=" O LEU D 142 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU D 142 " --> pdb=" O VAL D 132 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.738A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'D' and resid 347 through 350 1111 hydrogen bonds defined for protein. 3033 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: 13.49 Time building geometry restraints manager: 11.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6036 1.33 - 1.45: 7355 1.45 - 1.57: 16336 1.57 - 1.70: 0 1.70 - 1.82: 179 Bond restraints: 29906 Sorted by residual: bond pdb=" CA ALA C 292 " pdb=" CB ALA C 292 " ideal model delta sigma weight residual 1.527 1.497 0.031 7.60e-03 1.73e+04 1.64e+01 bond pdb=" N VAL C 289 " pdb=" CA VAL C 289 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.19e-02 7.06e+03 1.07e+01 bond pdb=" N ASP A 294 " pdb=" CA ASP A 294 " ideal model delta sigma weight residual 1.455 1.474 -0.019 7.00e-03 2.04e+04 7.61e+00 bond pdb=" N HIS B 519 " pdb=" CA HIS B 519 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.17e-02 7.31e+03 7.49e+00 bond pdb=" CA ALA A 288 " pdb=" CB ALA A 288 " ideal model delta sigma weight residual 1.535 1.483 0.052 1.90e-02 2.77e+03 7.46e+00 ... (remaining 29901 not shown) Histogram of bond angle deviations from ideal: 100.27 - 107.01: 976 107.01 - 113.76: 16289 113.76 - 120.50: 11375 120.50 - 127.25: 11771 127.25 - 133.99: 297 Bond angle restraints: 40708 Sorted by residual: angle pdb=" CA PHE A 374 " pdb=" CB PHE A 374 " pdb=" CG PHE A 374 " ideal model delta sigma weight residual 113.80 120.48 -6.68 1.00e+00 1.00e+00 4.46e+01 angle pdb=" CA PHE A 371 " pdb=" C PHE A 371 " pdb=" O PHE A 371 " ideal model delta sigma weight residual 121.46 114.57 6.89 1.17e+00 7.31e-01 3.47e+01 angle pdb=" CA ALA B 520 " pdb=" C ALA B 520 " pdb=" N PRO B 521 " ideal model delta sigma weight residual 118.44 127.21 -8.77 1.59e+00 3.96e-01 3.04e+01 angle pdb=" CA ALA B 520 " pdb=" C ALA B 520 " pdb=" O ALA B 520 " ideal model delta sigma weight residual 120.16 112.61 7.55 1.37e+00 5.33e-01 3.04e+01 angle pdb=" O ASP A 287 " pdb=" C ASP A 287 " pdb=" N ALA A 288 " ideal model delta sigma weight residual 123.48 117.24 6.24 1.14e+00 7.69e-01 3.00e+01 ... (remaining 40703 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.03: 17786 23.03 - 46.05: 330 46.05 - 69.08: 32 69.08 - 92.10: 19 92.10 - 115.13: 17 Dihedral angle restraints: 18184 sinusoidal: 7482 harmonic: 10702 Sorted by residual: dihedral pdb=" CB CYS D 344 " pdb=" SG CYS D 344 " pdb=" SG CYS D 361 " pdb=" CB CYS D 361 " ideal model delta sinusoidal sigma weight residual -86.00 -160.06 74.06 1 1.00e+01 1.00e-02 6.96e+01 dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual -86.00 -150.16 64.16 1 1.00e+01 1.00e-02 5.42e+01 dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual -86.00 -142.36 56.36 1 1.00e+01 1.00e-02 4.28e+01 ... (remaining 18181 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 4055 0.062 - 0.124: 560 0.124 - 0.186: 26 0.186 - 0.248: 12 0.248 - 0.310: 6 Chirality restraints: 4659 Sorted by residual: chirality pdb=" CA PHE A 371 " pdb=" N PHE A 371 " pdb=" C PHE A 371 " pdb=" CB PHE A 371 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" CA ALA B 292 " pdb=" N ALA B 292 " pdb=" C ALA B 292 " pdb=" CB ALA B 292 " both_signs ideal model delta sigma weight residual False 2.48 2.18 0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" CA CYS B 131 " pdb=" N CYS B 131 " pdb=" C CYS B 131 " pdb=" CB CYS B 131 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.20e+00 ... (remaining 4656 not shown) Planarity restraints: 5252 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1311 " 0.306 2.00e-02 2.50e+03 2.58e-01 8.32e+02 pdb=" C7 NAG C1311 " -0.082 2.00e-02 2.50e+03 pdb=" C8 NAG C1311 " 0.189 2.00e-02 2.50e+03 pdb=" N2 NAG C1311 " -0.443 2.00e-02 2.50e+03 pdb=" O7 NAG C1311 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 366 " -0.023 2.00e-02 2.50e+03 4.53e-02 2.05e+01 pdb=" C SER A 366 " 0.078 2.00e-02 2.50e+03 pdb=" O SER A 366 " -0.029 2.00e-02 2.50e+03 pdb=" N VAL A 367 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 288 " 0.016 2.00e-02 2.50e+03 3.13e-02 9.79e+00 pdb=" C ALA C 288 " -0.054 2.00e-02 2.50e+03 pdb=" O ALA C 288 " 0.020 2.00e-02 2.50e+03 pdb=" N VAL C 289 " 0.018 2.00e-02 2.50e+03 ... (remaining 5249 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 111 2.47 - 3.08: 19550 3.08 - 3.69: 42209 3.69 - 4.29: 62475 4.29 - 4.90: 104598 Nonbonded interactions: 228943 Sorted by model distance: nonbonded pdb=" O CYS B 391 " pdb=" NE2 HIS B 519 " model vdw 1.863 2.520 nonbonded pdb=" NH1 ARG C 577 " pdb=" CD1 LEU C 582 " model vdw 1.900 3.540 nonbonded pdb=" CZ PHE B 375 " pdb=" CE2 TYR B 508 " model vdw 2.058 3.640 nonbonded pdb=" SG CYS B 336 " pdb=" O VAL B 362 " model vdw 2.067 3.400 nonbonded pdb=" OH TYR C 756 " pdb=" OD1 ASP C 994 " model vdw 2.170 2.440 ... (remaining 228938 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 355 or (resid 356 through 357 and (name N or na \ me CA or name C or name O or name CB )) or resid 358 through 387 or (resid 388 a \ nd (name N or name CA or name C or name O or name CB )) or resid 389 through 414 \ or (resid 415 and (name N or name CA or name C or name O or name CB )) or resid \ 416 through 426 or (resid 427 and (name N or name CA or name C or name O or nam \ e CB )) or resid 428 through 447 or (resid 448 and (name N or name CA or name C \ or name O or name CB )) or resid 449 through 453 or (resid 454 and (name N or na \ me CA or name C or name O or name CB )) or resid 455 through 457 or (resid 458 t \ hrough 459 and (name N or name CA or name C or name O or name CB )) or resid 460 \ through 464 or (resid 465 and (name N or name CA or name C or name O or name CB \ )) or resid 466 through 473 or (resid 474 through 475 and (name N or name CA or \ name C or name O or name CB )) or resid 476 through 486 or (resid 487 and (name \ N or name CA or name C or name O or name CB )) or resid 488 through 499 or (res \ id 500 and (name N or name CA or name C or name O or name CB )) or resid 501 thr \ ough 515 or (resid 516 and (name N or name CA or name C or name O or name CB )) \ or resid 517 through 522 or (resid 523 and (name N or name CA or name C or name \ O or name CB )) or resid 524 through 1146 or resid 1301 through 1310)) selection = chain 'B' selection = (chain 'C' and (resid 27 through 1146 or resid 1301 through 1310)) } 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: 5.560 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: 1.140 Check model and map are aligned: 0.210 Set scattering table: 0.260 Process input model: 78.010 Find NCS groups from input model: 1.670 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4609 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 : 0.003 0.053 29906 Z= 0.180 Angle : 0.565 9.543 40708 Z= 0.336 Chirality : 0.044 0.310 4659 Planarity : 0.005 0.258 5219 Dihedral : 9.797 115.126 11200 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.79 % Favored : 97.15 % Rotamer: Outliers : 0.06 % Allowed : 4.85 % Favored : 95.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.12), residues: 3618 helix: -0.33 (0.16), residues: 1009 sheet: -1.39 (0.18), residues: 594 loop : -2.76 (0.11), residues: 2015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 886 HIS 0.002 0.000 HIS B 519 PHE 0.031 0.001 PHE A 374 TYR 0.010 0.001 TYR A 265 ARG 0.003 0.000 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 695 residues out of total 3207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 693 time to evaluate : 2.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 TYR cc_start: 0.7093 (m-80) cc_final: 0.6783 (m-80) REVERT: A 595 VAL cc_start: 0.8339 (m) cc_final: 0.8052 (t) REVERT: A 698 SER cc_start: 0.8489 (t) cc_final: 0.8222 (p) REVERT: A 737 ASP cc_start: 0.6712 (t70) cc_final: 0.6393 (t0) REVERT: A 821 LEU cc_start: 0.8349 (tt) cc_final: 0.8079 (tp) REVERT: A 822 LEU cc_start: 0.7926 (mt) cc_final: 0.7654 (mp) REVERT: A 875 SER cc_start: 0.8408 (t) cc_final: 0.7922 (m) REVERT: A 881 THR cc_start: 0.7849 (t) cc_final: 0.7628 (t) REVERT: A 929 SER cc_start: 0.8070 (t) cc_final: 0.7828 (p) REVERT: A 1002 GLN cc_start: 0.7169 (tt0) cc_final: 0.6939 (tt0) REVERT: B 290 ASP cc_start: 0.7514 (t0) cc_final: 0.7260 (t0) REVERT: B 340 GLU cc_start: 0.6294 (tp30) cc_final: 0.6035 (tp30) REVERT: B 354 ASN cc_start: 0.7342 (m-40) cc_final: 0.6914 (m-40) REVERT: B 398 ASP cc_start: 0.6368 (m-30) cc_final: 0.6061 (m-30) REVERT: B 420 ASP cc_start: 0.6550 (m-30) cc_final: 0.6325 (m-30) REVERT: B 494 SER cc_start: 0.7248 (m) cc_final: 0.6918 (t) REVERT: B 513 LEU cc_start: 0.7845 (mt) cc_final: 0.7414 (mp) REVERT: B 663 ASP cc_start: 0.6974 (p0) cc_final: 0.6699 (p0) REVERT: B 864 LEU cc_start: 0.7792 (tp) cc_final: 0.7442 (tp) REVERT: B 905 ARG cc_start: 0.6905 (mtt-85) cc_final: 0.6701 (mtp85) REVERT: B 1017 GLU cc_start: 0.6604 (tp30) cc_final: 0.5980 (tp30) REVERT: B 1084 ASP cc_start: 0.6946 (t0) cc_final: 0.6394 (t0) REVERT: B 1123 SER cc_start: 0.7979 (t) cc_final: 0.7694 (t) REVERT: C 45 SER cc_start: 0.8024 (p) cc_final: 0.7740 (p) REVERT: C 303 LEU cc_start: 0.8484 (tp) cc_final: 0.8168 (tt) REVERT: C 305 SER cc_start: 0.8409 (m) cc_final: 0.8184 (m) REVERT: C 595 VAL cc_start: 0.8225 (m) cc_final: 0.7920 (t) REVERT: C 774 GLN cc_start: 0.7531 (mm-40) cc_final: 0.7271 (mm110) REVERT: C 800 PHE cc_start: 0.7373 (m-80) cc_final: 0.5535 (m-80) REVERT: C 822 LEU cc_start: 0.7633 (mt) cc_final: 0.7432 (mt) REVERT: C 907 ASN cc_start: 0.7266 (t0) cc_final: 0.6856 (t0) REVERT: C 1038 LYS cc_start: 0.7764 (mmmm) cc_final: 0.7544 (mmmm) REVERT: D 499 ASP cc_start: -0.1173 (m-30) cc_final: -0.2538 (p0) REVERT: D 557 MET cc_start: -0.1026 (tmm) cc_final: -0.1288 (tmm) outliers start: 2 outliers final: 2 residues processed: 695 average time/residue: 0.4001 time to fit residues: 437.2052 Evaluate side-chains 519 residues out of total 3207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 517 time to evaluate : 2.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 374 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 308 optimal weight: 6.9990 chunk 276 optimal weight: 0.5980 chunk 153 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 186 optimal weight: 0.6980 chunk 147 optimal weight: 3.9990 chunk 286 optimal weight: 0.6980 chunk 110 optimal weight: 0.9990 chunk 173 optimal weight: 3.9990 chunk 212 optimal weight: 2.9990 chunk 331 optimal weight: 7.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN A 394 ASN A 405 ASN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN A 563 GLN A 607 GLN A 755 GLN A 774 GLN A 784 GLN A 804 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN A 949 GLN A 955 ASN A 965 GLN ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN B 30 ASN B 52 GLN B 81 ASN B 282 ASN B 394 ASN ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B 965 GLN ** B1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1135 ASN C 81 ASN ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN C 606 ASN C 613 GLN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN C 901 GLN C 907 ASN C 955 ASN C1010 GLN C1023 ASN C1106 GLN D 42 GLN D 60 GLN D 86 GLN D 98 GLN D 221 GLN D 325 GLN D 345 HIS D 380 GLN ** D 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 442 GLN D 472 GLN D 522 GLN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5028 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 29906 Z= 0.346 Angle : 0.682 12.660 40708 Z= 0.344 Chirality : 0.049 0.535 4659 Planarity : 0.005 0.057 5219 Dihedral : 6.274 99.383 4653 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.85 % Allowed : 9.70 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.13), residues: 3618 helix: 0.37 (0.17), residues: 1004 sheet: -0.81 (0.19), residues: 586 loop : -2.38 (0.12), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 436 HIS 0.015 0.002 HIS A1064 PHE 0.030 0.002 PHE D 308 TYR 0.027 0.002 TYR C 279 ARG 0.011 0.001 ARG C 34 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 3207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 595 time to evaluate : 2.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 LYS cc_start: 0.7223 (tppt) cc_final: 0.6965 (tptm) REVERT: A 313 TYR cc_start: 0.7822 (m-80) cc_final: 0.7564 (m-80) REVERT: A 552 LEU cc_start: 0.7693 (OUTLIER) cc_final: 0.7463 (mp) REVERT: A 698 SER cc_start: 0.8499 (t) cc_final: 0.8158 (p) REVERT: A 737 ASP cc_start: 0.7119 (t70) cc_final: 0.6624 (t0) REVERT: A 739 THR cc_start: 0.7491 (m) cc_final: 0.7210 (t) REVERT: A 820 ASP cc_start: 0.7380 (t70) cc_final: 0.6645 (t70) REVERT: A 822 LEU cc_start: 0.8377 (mt) cc_final: 0.8116 (mp) REVERT: A 935 GLN cc_start: 0.6986 (mt0) cc_final: 0.6713 (mt0) REVERT: A 1010 GLN cc_start: 0.7612 (mm-40) cc_final: 0.7190 (mp10) REVERT: A 1130 ILE cc_start: 0.8337 (OUTLIER) cc_final: 0.8066 (mt) REVERT: A 1139 ASP cc_start: 0.7921 (t0) cc_final: 0.7287 (t0) REVERT: B 364 ASP cc_start: 0.6664 (t0) cc_final: 0.6265 (t70) REVERT: B 599 THR cc_start: 0.8542 (t) cc_final: 0.8264 (p) REVERT: B 907 ASN cc_start: 0.7649 (t0) cc_final: 0.7147 (t0) REVERT: B 1084 ASP cc_start: 0.7191 (t0) cc_final: 0.6641 (t0) REVERT: B 1123 SER cc_start: 0.8039 (t) cc_final: 0.7751 (t) REVERT: C 44 ARG cc_start: 0.8524 (mpt180) cc_final: 0.7985 (mtt180) REVERT: C 129 LYS cc_start: 0.7796 (mtmm) cc_final: 0.7570 (ptpp) REVERT: C 170 TYR cc_start: 0.7228 (m-80) cc_final: 0.7012 (m-80) REVERT: C 303 LEU cc_start: 0.8634 (tp) cc_final: 0.8418 (mt) REVERT: C 304 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7981 (mttm) REVERT: C 644 GLN cc_start: 0.7177 (tp40) cc_final: 0.6755 (tp40) REVERT: C 704 SER cc_start: 0.7557 (m) cc_final: 0.7291 (p) REVERT: C 739 THR cc_start: 0.7096 (m) cc_final: 0.6867 (p) REVERT: C 907 ASN cc_start: 0.7749 (t0) cc_final: 0.7275 (t0) REVERT: C 921 LYS cc_start: 0.7911 (OUTLIER) cc_final: 0.7699 (mttp) REVERT: C 1005 GLN cc_start: 0.7182 (tp40) cc_final: 0.6929 (tp40) REVERT: C 1038 LYS cc_start: 0.8355 (mmmm) cc_final: 0.8052 (mmtm) REVERT: C 1128 VAL cc_start: 0.8321 (m) cc_final: 0.8086 (p) REVERT: D 499 ASP cc_start: -0.0698 (m-30) cc_final: -0.2641 (p0) outliers start: 90 outliers final: 33 residues processed: 647 average time/residue: 0.4208 time to fit residues: 426.2271 Evaluate side-chains 567 residues out of total 3207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 530 time to evaluate : 2.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 552 LEU Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 810 SER Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain D residue 49 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 184 optimal weight: 0.0870 chunk 102 optimal weight: 4.9990 chunk 275 optimal weight: 3.9990 chunk 225 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 332 optimal weight: 40.0000 chunk 358 optimal weight: 20.0000 chunk 295 optimal weight: 0.9990 chunk 329 optimal weight: 8.9990 chunk 113 optimal weight: 0.7980 chunk 266 optimal weight: 0.9990 overall best weight: 0.7362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 388 ASN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN A 774 GLN A 949 GLN ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 ASN B 354 ASN B 613 GLN B 935 GLN B1005 GLN B1125 ASN C 173 GLN C 394 ASN C 606 ASN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 774 GLN ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN C 925 ASN ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 380 GLN D 505 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5078 moved from start: 0.3586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.117 29906 Z= 0.265 Angle : 0.571 14.104 40708 Z= 0.289 Chirality : 0.045 0.256 4659 Planarity : 0.004 0.062 5219 Dihedral : 5.148 91.567 4651 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.85 % Allowed : 12.23 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.13), residues: 3618 helix: 0.82 (0.17), residues: 1001 sheet: -0.58 (0.19), residues: 591 loop : -2.13 (0.12), residues: 2026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 275 HIS 0.008 0.001 HIS A1064 PHE 0.046 0.002 PHE D 308 TYR 0.017 0.002 TYR B 380 ARG 0.006 0.000 ARG B 646 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 3207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 553 time to evaluate : 3.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 328 ARG cc_start: 0.7647 (mmm-85) cc_final: 0.7443 (mmm-85) REVERT: A 586 ASP cc_start: 0.6863 (m-30) cc_final: 0.6641 (t0) REVERT: A 698 SER cc_start: 0.8479 (t) cc_final: 0.8183 (p) REVERT: A 708 SER cc_start: 0.7843 (m) cc_final: 0.7592 (p) REVERT: A 718 PHE cc_start: 0.8297 (p90) cc_final: 0.7993 (p90) REVERT: A 784 GLN cc_start: 0.8178 (OUTLIER) cc_final: 0.7607 (mt0) REVERT: A 820 ASP cc_start: 0.7260 (t70) cc_final: 0.6924 (t70) REVERT: A 875 SER cc_start: 0.8459 (t) cc_final: 0.8122 (m) REVERT: A 1010 GLN cc_start: 0.7608 (mm-40) cc_final: 0.7225 (mp10) REVERT: A 1130 ILE cc_start: 0.8397 (OUTLIER) cc_final: 0.8166 (mt) REVERT: A 1139 ASP cc_start: 0.7920 (t0) cc_final: 0.7366 (t0) REVERT: B 34 ARG cc_start: 0.7384 (mtp85) cc_final: 0.6839 (mtp85) REVERT: B 276 LEU cc_start: 0.7166 (tt) cc_final: 0.6949 (tt) REVERT: B 380 TYR cc_start: 0.7634 (m-80) cc_final: 0.7379 (m-80) REVERT: B 542 ASN cc_start: 0.7969 (t0) cc_final: 0.7742 (t0) REVERT: B 599 THR cc_start: 0.8450 (t) cc_final: 0.8175 (p) REVERT: B 900 MET cc_start: 0.8001 (mtp) cc_final: 0.7758 (mtp) REVERT: B 907 ASN cc_start: 0.7532 (t0) cc_final: 0.7129 (t0) REVERT: B 1084 ASP cc_start: 0.7204 (t0) cc_final: 0.6653 (t0) REVERT: B 1123 SER cc_start: 0.8046 (t) cc_final: 0.7716 (t) REVERT: C 129 LYS cc_start: 0.7847 (mtmm) cc_final: 0.7610 (ptpp) REVERT: C 142 ASP cc_start: 0.4954 (OUTLIER) cc_final: 0.4203 (p0) REVERT: C 304 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7948 (mttm) REVERT: C 644 GLN cc_start: 0.7208 (tp40) cc_final: 0.6783 (tp-100) REVERT: C 650 LEU cc_start: 0.8142 (tp) cc_final: 0.7839 (tp) REVERT: C 659 SER cc_start: 0.7915 (OUTLIER) cc_final: 0.7670 (m) REVERT: C 707 TYR cc_start: 0.8299 (t80) cc_final: 0.7779 (t80) REVERT: C 756 TYR cc_start: 0.7924 (OUTLIER) cc_final: 0.6859 (t80) REVERT: C 907 ASN cc_start: 0.7647 (t0) cc_final: 0.7235 (t0) REVERT: C 1017 GLU cc_start: 0.6759 (tp30) cc_final: 0.6286 (tp30) REVERT: C 1038 LYS cc_start: 0.8368 (mmmm) cc_final: 0.8074 (mmtm) REVERT: C 1107 ARG cc_start: 0.6685 (mtt90) cc_final: 0.6441 (mtt-85) REVERT: C 1128 VAL cc_start: 0.8454 (m) cc_final: 0.8208 (p) REVERT: D 298 MET cc_start: 0.4478 (tpp) cc_final: 0.3928 (tpp) REVERT: D 332 MET cc_start: -0.0362 (tmm) cc_final: -0.3386 (ttm) REVERT: D 499 ASP cc_start: -0.0649 (m-30) cc_final: -0.3166 (t0) outliers start: 90 outliers final: 44 residues processed: 604 average time/residue: 0.4270 time to fit residues: 403.6733 Evaluate side-chains 579 residues out of total 3207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 529 time to evaluate : 3.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 659 SER Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 810 SER Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain D residue 49 ASN Chi-restraints excluded: chain D residue 69 TRP Chi-restraints excluded: chain D residue 90 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 328 optimal weight: 10.0000 chunk 249 optimal weight: 3.9990 chunk 172 optimal weight: 0.9980 chunk 36 optimal weight: 9.9990 chunk 158 optimal weight: 0.6980 chunk 222 optimal weight: 0.0470 chunk 333 optimal weight: 9.9990 chunk 352 optimal weight: 30.0000 chunk 174 optimal weight: 0.6980 chunk 315 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 774 GLN ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 GLN B 282 ASN B 784 GLN B 925 ASN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN C 606 ASN C 607 GLN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 774 GLN C 784 GLN D 76 GLN ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 380 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5106 moved from start: 0.3974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 29906 Z= 0.243 Angle : 0.555 9.742 40708 Z= 0.280 Chirality : 0.044 0.288 4659 Planarity : 0.004 0.061 5219 Dihedral : 5.027 89.263 4651 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.69 % Allowed : 13.62 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.13), residues: 3618 helix: 0.96 (0.17), residues: 994 sheet: -0.34 (0.20), residues: 584 loop : -2.01 (0.12), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP D 275 HIS 0.007 0.001 HIS A1088 PHE 0.045 0.002 PHE D 308 TYR 0.028 0.001 TYR C 904 ARG 0.009 0.000 ARG A1107 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 639 residues out of total 3207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 554 time to evaluate : 2.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.7970 (t) cc_final: 0.7726 (t) REVERT: A 586 ASP cc_start: 0.6848 (m-30) cc_final: 0.6640 (t0) REVERT: A 708 SER cc_start: 0.7882 (m) cc_final: 0.7596 (p) REVERT: A 784 GLN cc_start: 0.8200 (OUTLIER) cc_final: 0.7607 (mt0) REVERT: A 811 LYS cc_start: 0.8201 (mtpp) cc_final: 0.7990 (mtpt) REVERT: A 875 SER cc_start: 0.8447 (t) cc_final: 0.8114 (m) REVERT: A 1130 ILE cc_start: 0.8388 (OUTLIER) cc_final: 0.8158 (mt) REVERT: A 1139 ASP cc_start: 0.7940 (t0) cc_final: 0.7583 (t70) REVERT: B 542 ASN cc_start: 0.8090 (t0) cc_final: 0.7808 (t0) REVERT: B 599 THR cc_start: 0.8423 (OUTLIER) cc_final: 0.8129 (p) REVERT: B 821 LEU cc_start: 0.8041 (mp) cc_final: 0.7818 (mp) REVERT: B 900 MET cc_start: 0.7911 (mtp) cc_final: 0.7705 (mtp) REVERT: B 907 ASN cc_start: 0.7558 (t0) cc_final: 0.7140 (t0) REVERT: B 934 ILE cc_start: 0.8102 (tt) cc_final: 0.7868 (tp) REVERT: B 935 GLN cc_start: 0.7942 (tt0) cc_final: 0.7708 (tt0) REVERT: B 1084 ASP cc_start: 0.7223 (t0) cc_final: 0.6670 (t0) REVERT: B 1123 SER cc_start: 0.8011 (t) cc_final: 0.7723 (t) REVERT: C 44 ARG cc_start: 0.8509 (mpt180) cc_final: 0.8103 (mtt180) REVERT: C 273 ARG cc_start: 0.7451 (mmt90) cc_final: 0.7209 (mtp85) REVERT: C 304 LYS cc_start: 0.8233 (ttmm) cc_final: 0.7937 (mttm) REVERT: C 644 GLN cc_start: 0.7220 (tp40) cc_final: 0.6800 (tp-100) REVERT: C 707 TYR cc_start: 0.8227 (t80) cc_final: 0.7994 (t80) REVERT: C 756 TYR cc_start: 0.7954 (OUTLIER) cc_final: 0.6953 (t80) REVERT: C 907 ASN cc_start: 0.7690 (t0) cc_final: 0.7297 (t0) REVERT: C 1017 GLU cc_start: 0.6773 (tp30) cc_final: 0.6352 (tp30) REVERT: C 1038 LYS cc_start: 0.8408 (mmmm) cc_final: 0.8116 (mmtm) REVERT: C 1128 VAL cc_start: 0.8556 (m) cc_final: 0.8289 (p) REVERT: D 249 MET cc_start: 0.1579 (OUTLIER) cc_final: 0.1366 (mmm) REVERT: D 332 MET cc_start: -0.0644 (tmm) cc_final: -0.3573 (ttm) outliers start: 85 outliers final: 47 residues processed: 601 average time/residue: 0.4391 time to fit residues: 410.8448 Evaluate side-chains 583 residues out of total 3207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 531 time to evaluate : 2.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain D residue 49 ASN Chi-restraints excluded: chain D residue 69 TRP Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 560 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 293 optimal weight: 0.9990 chunk 200 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 262 optimal weight: 0.0670 chunk 145 optimal weight: 5.9990 chunk 301 optimal weight: 1.9990 chunk 243 optimal weight: 50.0000 chunk 0 optimal weight: 3.9990 chunk 180 optimal weight: 0.8980 chunk 316 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN A 774 GLN ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 ASN B 409 GLN B 935 GLN B1005 GLN C 606 ASN C 607 GLN C 613 GLN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 GLN D 24 ASN D 322 HIS D 417 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5139 moved from start: 0.4395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 29906 Z= 0.262 Angle : 0.570 11.489 40708 Z= 0.289 Chirality : 0.045 0.314 4659 Planarity : 0.004 0.062 5219 Dihedral : 4.991 87.162 4651 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.23 % Allowed : 13.59 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.13), residues: 3618 helix: 0.89 (0.17), residues: 1002 sheet: -0.27 (0.20), residues: 590 loop : -1.96 (0.13), residues: 2026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP D 328 HIS 0.008 0.001 HIS A1088 PHE 0.048 0.002 PHE D 308 TYR 0.025 0.002 TYR C 904 ARG 0.006 0.000 ARG B 646 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 654 residues out of total 3207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 552 time to evaluate : 2.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 602 THR cc_start: 0.7634 (p) cc_final: 0.7268 (m) REVERT: A 708 SER cc_start: 0.7872 (m) cc_final: 0.7602 (p) REVERT: A 748 GLU cc_start: 0.7000 (OUTLIER) cc_final: 0.6605 (pm20) REVERT: A 784 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.7607 (mt0) REVERT: A 811 LYS cc_start: 0.8263 (mtpp) cc_final: 0.7938 (mtpt) REVERT: A 875 SER cc_start: 0.8430 (t) cc_final: 0.8108 (m) REVERT: A 981 LEU cc_start: 0.8020 (mm) cc_final: 0.7786 (mt) REVERT: A 1130 ILE cc_start: 0.8423 (OUTLIER) cc_final: 0.8175 (mt) REVERT: B 48 LEU cc_start: 0.7436 (mm) cc_final: 0.7149 (mp) REVERT: B 420 ASP cc_start: 0.6548 (m-30) cc_final: 0.6057 (m-30) REVERT: B 421 TYR cc_start: 0.7364 (m-80) cc_final: 0.7083 (m-10) REVERT: B 542 ASN cc_start: 0.8194 (t0) cc_final: 0.7883 (t0) REVERT: B 599 THR cc_start: 0.8379 (OUTLIER) cc_final: 0.8090 (p) REVERT: B 821 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7816 (mp) REVERT: B 900 MET cc_start: 0.7908 (mtp) cc_final: 0.7577 (mtp) REVERT: B 907 ASN cc_start: 0.7527 (t0) cc_final: 0.7179 (t0) REVERT: B 934 ILE cc_start: 0.8377 (tt) cc_final: 0.8004 (tp) REVERT: B 935 GLN cc_start: 0.7871 (OUTLIER) cc_final: 0.7653 (tt0) REVERT: B 1084 ASP cc_start: 0.7251 (t0) cc_final: 0.6706 (t0) REVERT: B 1123 SER cc_start: 0.8024 (t) cc_final: 0.7734 (t) REVERT: B 1136 THR cc_start: 0.8473 (OUTLIER) cc_final: 0.8205 (p) REVERT: C 142 ASP cc_start: 0.5161 (OUTLIER) cc_final: 0.4509 (p0) REVERT: C 273 ARG cc_start: 0.7486 (mmt90) cc_final: 0.7227 (mmm160) REVERT: C 304 LYS cc_start: 0.8230 (ttmm) cc_final: 0.7943 (mttm) REVERT: C 644 GLN cc_start: 0.7220 (tp40) cc_final: 0.6830 (tp40) REVERT: C 707 TYR cc_start: 0.8303 (t80) cc_final: 0.8018 (t80) REVERT: C 756 TYR cc_start: 0.7941 (OUTLIER) cc_final: 0.6959 (t80) REVERT: C 774 GLN cc_start: 0.7473 (mm-40) cc_final: 0.7074 (mp10) REVERT: C 855 PHE cc_start: 0.6164 (m-10) cc_final: 0.5940 (m-80) REVERT: C 907 ASN cc_start: 0.7690 (t0) cc_final: 0.7346 (t0) REVERT: C 921 LYS cc_start: 0.7937 (ttmm) cc_final: 0.7611 (mtpp) REVERT: C 1017 GLU cc_start: 0.6711 (tp30) cc_final: 0.6339 (tp30) REVERT: C 1038 LYS cc_start: 0.8439 (mmmm) cc_final: 0.8166 (mmtm) REVERT: C 1107 ARG cc_start: 0.6737 (mtt90) cc_final: 0.6516 (mtt180) REVERT: C 1128 VAL cc_start: 0.8604 (m) cc_final: 0.8321 (p) REVERT: C 1141 LEU cc_start: 0.7790 (tt) cc_final: 0.7577 (tp) REVERT: D 249 MET cc_start: 0.1767 (OUTLIER) cc_final: 0.1508 (mmm) REVERT: D 322 HIS cc_start: 0.1467 (OUTLIER) cc_final: 0.0064 (t70) REVERT: D 332 MET cc_start: -0.0555 (tmm) cc_final: -0.3483 (ttm) outliers start: 102 outliers final: 64 residues processed: 607 average time/residue: 0.4346 time to fit residues: 416.7760 Evaluate side-chains 607 residues out of total 3207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 532 time to evaluate : 3.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 748 GLU Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 921 LYS Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1068 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 810 SER Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 49 ASN Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 322 HIS Chi-restraints excluded: chain D residue 455 MET Chi-restraints excluded: chain D residue 560 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 118 optimal weight: 1.9990 chunk 317 optimal weight: 20.0000 chunk 69 optimal weight: 0.4980 chunk 207 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 353 optimal weight: 30.0000 chunk 293 optimal weight: 0.8980 chunk 163 optimal weight: 0.7980 chunk 29 optimal weight: 7.9990 chunk 116 optimal weight: 4.9990 chunk 185 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 ASN A 657 ASN ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 774 GLN ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 ASN B 804 GLN B 901 GLN C 606 ASN C 607 GLN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 299 ASN D 322 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5167 moved from start: 0.4716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 29906 Z= 0.275 Angle : 0.579 14.181 40708 Z= 0.292 Chirality : 0.045 0.271 4659 Planarity : 0.004 0.061 5219 Dihedral : 4.980 85.715 4651 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.33 % Allowed : 14.96 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.13), residues: 3618 helix: 0.93 (0.17), residues: 1004 sheet: -0.25 (0.20), residues: 586 loop : -1.87 (0.13), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 477 HIS 0.022 0.001 HIS D 322 PHE 0.048 0.002 PHE D 308 TYR 0.021 0.002 TYR B 453 ARG 0.008 0.000 ARG D 177 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 3207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 538 time to evaluate : 3.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 328 ARG cc_start: 0.7549 (mmm-85) cc_final: 0.7321 (mmm-85) REVERT: A 602 THR cc_start: 0.7724 (p) cc_final: 0.7409 (m) REVERT: A 708 SER cc_start: 0.7905 (m) cc_final: 0.7644 (p) REVERT: A 748 GLU cc_start: 0.6962 (OUTLIER) cc_final: 0.6641 (pm20) REVERT: A 784 GLN cc_start: 0.8194 (OUTLIER) cc_final: 0.7570 (mt0) REVERT: A 875 SER cc_start: 0.8424 (t) cc_final: 0.8118 (m) REVERT: A 981 LEU cc_start: 0.8053 (mm) cc_final: 0.7773 (mt) REVERT: A 1127 ASP cc_start: 0.6849 (t0) cc_final: 0.6594 (t70) REVERT: A 1130 ILE cc_start: 0.8455 (OUTLIER) cc_final: 0.8208 (mt) REVERT: A 1136 THR cc_start: 0.8411 (OUTLIER) cc_final: 0.8196 (p) REVERT: B 48 LEU cc_start: 0.7543 (mm) cc_final: 0.7249 (mp) REVERT: B 420 ASP cc_start: 0.6583 (m-30) cc_final: 0.6155 (m-30) REVERT: B 542 ASN cc_start: 0.8256 (t0) cc_final: 0.7952 (t0) REVERT: B 599 THR cc_start: 0.8351 (OUTLIER) cc_final: 0.8069 (p) REVERT: B 651 ILE cc_start: 0.8334 (pt) cc_final: 0.7924 (mt) REVERT: B 781 VAL cc_start: 0.8207 (OUTLIER) cc_final: 0.7974 (t) REVERT: B 821 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7925 (mp) REVERT: B 900 MET cc_start: 0.7792 (mtp) cc_final: 0.7521 (mtp) REVERT: B 907 ASN cc_start: 0.7550 (t0) cc_final: 0.7198 (t0) REVERT: B 934 ILE cc_start: 0.8451 (tt) cc_final: 0.8056 (tp) REVERT: B 1005 GLN cc_start: 0.7587 (tt0) cc_final: 0.7289 (mt0) REVERT: B 1084 ASP cc_start: 0.7263 (t0) cc_final: 0.6722 (t0) REVERT: B 1123 SER cc_start: 0.8033 (t) cc_final: 0.7748 (t) REVERT: C 142 ASP cc_start: 0.5133 (OUTLIER) cc_final: 0.4550 (p0) REVERT: C 239 GLN cc_start: 0.7051 (tp40) cc_final: 0.6792 (tp40) REVERT: C 273 ARG cc_start: 0.7495 (mmt90) cc_final: 0.7252 (mmm160) REVERT: C 307 THR cc_start: 0.7973 (p) cc_final: 0.7454 (p) REVERT: C 644 GLN cc_start: 0.7259 (tp40) cc_final: 0.6891 (tp40) REVERT: C 651 ILE cc_start: 0.8404 (pt) cc_final: 0.8044 (mt) REVERT: C 707 TYR cc_start: 0.8300 (t80) cc_final: 0.8034 (t80) REVERT: C 756 TYR cc_start: 0.7966 (OUTLIER) cc_final: 0.6971 (t80) REVERT: C 774 GLN cc_start: 0.7493 (mm-40) cc_final: 0.7067 (mp10) REVERT: C 855 PHE cc_start: 0.6328 (m-10) cc_final: 0.6090 (m-80) REVERT: C 907 ASN cc_start: 0.7714 (t0) cc_final: 0.7369 (t0) REVERT: C 921 LYS cc_start: 0.7940 (ttmm) cc_final: 0.7613 (mtpp) REVERT: C 1017 GLU cc_start: 0.6622 (tp30) cc_final: 0.6296 (tp30) REVERT: C 1038 LYS cc_start: 0.8443 (mmmm) cc_final: 0.8179 (mmtm) REVERT: C 1107 ARG cc_start: 0.6764 (mtt90) cc_final: 0.6501 (mtt180) REVERT: C 1128 VAL cc_start: 0.8628 (m) cc_final: 0.8328 (p) REVERT: C 1141 LEU cc_start: 0.7829 (tt) cc_final: 0.7590 (tp) REVERT: D 31 ASN cc_start: 0.3524 (t0) cc_final: 0.2135 (t0) REVERT: D 332 MET cc_start: -0.0606 (tmm) cc_final: -0.3265 (ttm) outliers start: 105 outliers final: 69 residues processed: 600 average time/residue: 0.4307 time to fit residues: 403.3652 Evaluate side-chains 602 residues out of total 3207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 524 time to evaluate : 2.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 748 GLU Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 921 LYS Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1068 VAL Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 810 SER Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 49 ASN Chi-restraints excluded: chain D residue 69 TRP Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 455 MET Chi-restraints excluded: chain D residue 560 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 340 optimal weight: 0.5980 chunk 39 optimal weight: 4.9990 chunk 201 optimal weight: 0.0570 chunk 257 optimal weight: 1.9990 chunk 199 optimal weight: 0.9990 chunk 297 optimal weight: 0.5980 chunk 197 optimal weight: 0.5980 chunk 351 optimal weight: 10.0000 chunk 220 optimal weight: 0.5980 chunk 214 optimal weight: 1.9990 chunk 162 optimal weight: 0.3980 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 ASN A 774 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 HIS ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 ASN B 804 GLN B 901 GLN B 935 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 GLN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 ASN D 121 ASN ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 397 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5150 moved from start: 0.4850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 29906 Z= 0.193 Angle : 0.555 14.130 40708 Z= 0.278 Chirality : 0.044 0.402 4659 Planarity : 0.004 0.060 5219 Dihedral : 4.827 84.318 4651 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.72 % Allowed : 15.84 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.14), residues: 3618 helix: 1.03 (0.17), residues: 1018 sheet: -0.14 (0.20), residues: 580 loop : -1.76 (0.13), residues: 2020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP D 203 HIS 0.005 0.001 HIS A1088 PHE 0.058 0.001 PHE D 308 TYR 0.021 0.001 TYR B 453 ARG 0.008 0.000 ARG B 646 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 3207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 529 time to evaluate : 3.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 GLN cc_start: 0.6324 (pm20) cc_final: 0.5867 (pp30) REVERT: A 602 THR cc_start: 0.7739 (p) cc_final: 0.7451 (m) REVERT: A 708 SER cc_start: 0.7872 (m) cc_final: 0.7593 (p) REVERT: A 748 GLU cc_start: 0.6950 (OUTLIER) cc_final: 0.6633 (pm20) REVERT: A 784 GLN cc_start: 0.8171 (OUTLIER) cc_final: 0.7543 (mt0) REVERT: A 875 SER cc_start: 0.8428 (t) cc_final: 0.8111 (m) REVERT: A 981 LEU cc_start: 0.8007 (mm) cc_final: 0.7731 (mt) REVERT: A 1127 ASP cc_start: 0.6881 (t0) cc_final: 0.6574 (t0) REVERT: A 1130 ILE cc_start: 0.8456 (OUTLIER) cc_final: 0.8218 (mt) REVERT: A 1136 THR cc_start: 0.8392 (t) cc_final: 0.8190 (p) REVERT: B 48 LEU cc_start: 0.7560 (mm) cc_final: 0.7290 (mp) REVERT: B 420 ASP cc_start: 0.6733 (m-30) cc_final: 0.5977 (m-30) REVERT: B 542 ASN cc_start: 0.8197 (t0) cc_final: 0.7910 (t0) REVERT: B 599 THR cc_start: 0.8342 (OUTLIER) cc_final: 0.8043 (p) REVERT: B 651 ILE cc_start: 0.8328 (pt) cc_final: 0.7914 (mt) REVERT: B 781 VAL cc_start: 0.8173 (OUTLIER) cc_final: 0.7905 (t) REVERT: B 900 MET cc_start: 0.7780 (mtp) cc_final: 0.7441 (mtp) REVERT: B 907 ASN cc_start: 0.7519 (t0) cc_final: 0.7129 (t0) REVERT: B 934 ILE cc_start: 0.8468 (tt) cc_final: 0.8089 (tp) REVERT: B 970 PHE cc_start: 0.8259 (m-80) cc_final: 0.7961 (m-80) REVERT: B 1084 ASP cc_start: 0.7255 (t0) cc_final: 0.6701 (t0) REVERT: B 1123 SER cc_start: 0.8035 (t) cc_final: 0.7767 (t) REVERT: B 1136 THR cc_start: 0.8515 (OUTLIER) cc_final: 0.8265 (p) REVERT: C 44 ARG cc_start: 0.8513 (mpt180) cc_final: 0.7999 (mtt180) REVERT: C 142 ASP cc_start: 0.5128 (OUTLIER) cc_final: 0.4579 (p0) REVERT: C 273 ARG cc_start: 0.7457 (mmt90) cc_final: 0.7194 (mmm160) REVERT: C 307 THR cc_start: 0.8077 (p) cc_final: 0.7785 (p) REVERT: C 644 GLN cc_start: 0.7268 (tp40) cc_final: 0.6917 (tp40) REVERT: C 651 ILE cc_start: 0.8353 (pt) cc_final: 0.8008 (mt) REVERT: C 707 TYR cc_start: 0.8325 (t80) cc_final: 0.7955 (t80) REVERT: C 756 TYR cc_start: 0.7862 (OUTLIER) cc_final: 0.6916 (t80) REVERT: C 774 GLN cc_start: 0.7478 (mm-40) cc_final: 0.7082 (mp10) REVERT: C 907 ASN cc_start: 0.7672 (t0) cc_final: 0.7301 (t0) REVERT: C 921 LYS cc_start: 0.7890 (ttmm) cc_final: 0.7569 (mtpp) REVERT: C 1017 GLU cc_start: 0.6665 (tp30) cc_final: 0.6331 (tp30) REVERT: C 1038 LYS cc_start: 0.8439 (mmmm) cc_final: 0.8175 (mmtm) REVERT: C 1128 VAL cc_start: 0.8637 (m) cc_final: 0.8339 (p) REVERT: C 1136 THR cc_start: 0.8507 (OUTLIER) cc_final: 0.8249 (p) REVERT: C 1141 LEU cc_start: 0.7836 (tt) cc_final: 0.7611 (tp) REVERT: D 332 MET cc_start: -0.0778 (tmm) cc_final: -0.3452 (ttm) outliers start: 86 outliers final: 62 residues processed: 580 average time/residue: 0.4278 time to fit residues: 385.2167 Evaluate side-chains 586 residues out of total 3207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 515 time to evaluate : 2.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 748 GLU Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 810 SER Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 49 ASN Chi-restraints excluded: chain D residue 69 TRP Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 368 ASN Chi-restraints excluded: chain D residue 440 LEU Chi-restraints excluded: chain D residue 455 MET Chi-restraints excluded: chain D residue 560 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 217 optimal weight: 1.9990 chunk 140 optimal weight: 0.4980 chunk 210 optimal weight: 0.0040 chunk 105 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 223 optimal weight: 5.9990 chunk 239 optimal weight: 10.0000 chunk 173 optimal weight: 0.0570 chunk 32 optimal weight: 0.8980 chunk 276 optimal weight: 0.5980 overall best weight: 0.3710 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 ASN A 774 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN C 607 GLN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5149 moved from start: 0.4958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 29906 Z= 0.179 Angle : 0.547 13.301 40708 Z= 0.274 Chirality : 0.044 0.298 4659 Planarity : 0.004 0.059 5219 Dihedral : 4.691 82.170 4649 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.53 % Allowed : 16.22 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.14), residues: 3618 helix: 1.10 (0.17), residues: 1013 sheet: -0.18 (0.20), residues: 594 loop : -1.69 (0.13), residues: 2011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D 203 HIS 0.003 0.001 HIS C1064 PHE 0.056 0.001 PHE D 308 TYR 0.022 0.001 TYR B 453 ARG 0.011 0.000 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 3207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 514 time to evaluate : 2.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 GLN cc_start: 0.6296 (pm20) cc_final: 0.5805 (pp30) REVERT: A 602 THR cc_start: 0.7758 (p) cc_final: 0.7484 (m) REVERT: A 708 SER cc_start: 0.7867 (m) cc_final: 0.7579 (p) REVERT: A 748 GLU cc_start: 0.6940 (OUTLIER) cc_final: 0.6615 (pm20) REVERT: A 784 GLN cc_start: 0.8142 (OUTLIER) cc_final: 0.7462 (mt0) REVERT: A 875 SER cc_start: 0.8410 (t) cc_final: 0.8115 (m) REVERT: A 981 LEU cc_start: 0.7998 (mm) cc_final: 0.7709 (mt) REVERT: A 1127 ASP cc_start: 0.6931 (t0) cc_final: 0.6616 (t0) REVERT: A 1130 ILE cc_start: 0.8479 (OUTLIER) cc_final: 0.8222 (mt) REVERT: A 1136 THR cc_start: 0.8374 (t) cc_final: 0.8167 (p) REVERT: B 48 LEU cc_start: 0.7644 (mm) cc_final: 0.7372 (mp) REVERT: B 420 ASP cc_start: 0.6560 (m-30) cc_final: 0.5946 (m-30) REVERT: B 542 ASN cc_start: 0.8196 (t0) cc_final: 0.7894 (t0) REVERT: B 599 THR cc_start: 0.8328 (OUTLIER) cc_final: 0.8052 (p) REVERT: B 651 ILE cc_start: 0.8263 (pt) cc_final: 0.7934 (mt) REVERT: B 781 VAL cc_start: 0.8147 (OUTLIER) cc_final: 0.7863 (t) REVERT: B 900 MET cc_start: 0.7767 (mtp) cc_final: 0.7444 (mtp) REVERT: B 907 ASN cc_start: 0.7531 (t0) cc_final: 0.7147 (t0) REVERT: B 934 ILE cc_start: 0.8351 (tt) cc_final: 0.8123 (tp) REVERT: B 970 PHE cc_start: 0.8254 (m-80) cc_final: 0.7958 (m-80) REVERT: B 1084 ASP cc_start: 0.7257 (t0) cc_final: 0.6696 (t0) REVERT: B 1136 THR cc_start: 0.8516 (OUTLIER) cc_final: 0.8274 (p) REVERT: C 44 ARG cc_start: 0.8513 (mpt180) cc_final: 0.8309 (mpt180) REVERT: C 142 ASP cc_start: 0.5090 (OUTLIER) cc_final: 0.4505 (p0) REVERT: C 273 ARG cc_start: 0.7448 (mmt90) cc_final: 0.7172 (mmm160) REVERT: C 307 THR cc_start: 0.8144 (p) cc_final: 0.7928 (p) REVERT: C 644 GLN cc_start: 0.7273 (tp40) cc_final: 0.6914 (tp-100) REVERT: C 651 ILE cc_start: 0.8324 (pt) cc_final: 0.8035 (mt) REVERT: C 707 TYR cc_start: 0.8313 (t80) cc_final: 0.7917 (t80) REVERT: C 756 TYR cc_start: 0.7846 (OUTLIER) cc_final: 0.6776 (t80) REVERT: C 774 GLN cc_start: 0.7518 (mm-40) cc_final: 0.7147 (mp10) REVERT: C 907 ASN cc_start: 0.7654 (t0) cc_final: 0.7293 (t0) REVERT: C 921 LYS cc_start: 0.7875 (ttmm) cc_final: 0.7557 (mtpp) REVERT: C 1017 GLU cc_start: 0.6709 (tp30) cc_final: 0.6385 (tp30) REVERT: C 1038 LYS cc_start: 0.8428 (mmmm) cc_final: 0.8169 (mmtm) REVERT: C 1107 ARG cc_start: 0.6719 (mtt90) cc_final: 0.6462 (mtt-85) REVERT: C 1128 VAL cc_start: 0.8658 (m) cc_final: 0.8371 (p) REVERT: C 1136 THR cc_start: 0.8501 (OUTLIER) cc_final: 0.8254 (p) REVERT: C 1141 LEU cc_start: 0.7852 (tt) cc_final: 0.7608 (tp) REVERT: D 322 HIS cc_start: 0.1101 (OUTLIER) cc_final: -0.0171 (t70) REVERT: D 332 MET cc_start: -0.0644 (tmm) cc_final: -0.3228 (ttm) REVERT: D 359 LYS cc_start: 0.2614 (mttt) cc_final: 0.2335 (mttt) outliers start: 80 outliers final: 58 residues processed: 558 average time/residue: 0.4398 time to fit residues: 378.3269 Evaluate side-chains 569 residues out of total 3207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 501 time to evaluate : 2.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 748 GLU Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 493 ARG Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 810 SER Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 49 ASN Chi-restraints excluded: chain D residue 69 TRP Chi-restraints excluded: chain D residue 322 HIS Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 455 MET Chi-restraints excluded: chain D residue 560 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 320 optimal weight: 0.9980 chunk 337 optimal weight: 10.0000 chunk 307 optimal weight: 5.9990 chunk 327 optimal weight: 4.9990 chunk 336 optimal weight: 2.9990 chunk 197 optimal weight: 1.9990 chunk 142 optimal weight: 0.9990 chunk 257 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 296 optimal weight: 0.9980 chunk 310 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 388 ASN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 ASN A 774 GLN A 901 GLN ** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 ASN ** C 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 GLN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 ASN D 394 ASN ** D 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5253 moved from start: 0.5536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 29906 Z= 0.436 Angle : 0.670 13.537 40708 Z= 0.341 Chirality : 0.049 0.267 4659 Planarity : 0.005 0.058 5219 Dihedral : 5.217 82.165 4649 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.88 % Allowed : 16.57 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.13), residues: 3618 helix: 0.78 (0.17), residues: 1029 sheet: -0.15 (0.20), residues: 587 loop : -1.81 (0.13), residues: 2002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP D 168 HIS 0.010 0.001 HIS C1064 PHE 0.048 0.002 PHE D 308 TYR 0.028 0.002 TYR B 453 ARG 0.022 0.001 ARG A1014 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 3207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 550 time to evaluate : 3.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 PHE cc_start: 0.8067 (OUTLIER) cc_final: 0.7007 (m-80) REVERT: A 303 LEU cc_start: 0.8409 (mp) cc_final: 0.8184 (mp) REVERT: A 602 THR cc_start: 0.7879 (p) cc_final: 0.7598 (m) REVERT: A 660 TYR cc_start: 0.7944 (m-10) cc_final: 0.7653 (m-80) REVERT: A 708 SER cc_start: 0.7991 (m) cc_final: 0.7733 (p) REVERT: A 784 GLN cc_start: 0.8191 (OUTLIER) cc_final: 0.7491 (mt0) REVERT: A 875 SER cc_start: 0.8426 (t) cc_final: 0.8160 (m) REVERT: A 977 LEU cc_start: 0.8206 (mp) cc_final: 0.7961 (mp) REVERT: A 1118 ASP cc_start: 0.7091 (t0) cc_final: 0.6840 (t0) REVERT: A 1127 ASP cc_start: 0.6959 (t0) cc_final: 0.6688 (t0) REVERT: A 1128 VAL cc_start: 0.8540 (OUTLIER) cc_final: 0.8264 (p) REVERT: A 1130 ILE cc_start: 0.8524 (OUTLIER) cc_final: 0.8306 (mt) REVERT: B 48 LEU cc_start: 0.7749 (mm) cc_final: 0.7498 (mp) REVERT: B 402 ILE cc_start: 0.7251 (pt) cc_final: 0.7004 (pt) REVERT: B 420 ASP cc_start: 0.6712 (m-30) cc_final: 0.6215 (m-30) REVERT: B 542 ASN cc_start: 0.8286 (t0) cc_final: 0.7868 (t0) REVERT: B 599 THR cc_start: 0.8355 (OUTLIER) cc_final: 0.8062 (p) REVERT: B 651 ILE cc_start: 0.8206 (pt) cc_final: 0.7996 (mt) REVERT: B 658 ASN cc_start: 0.8142 (OUTLIER) cc_final: 0.7818 (p0) REVERT: B 740 MET cc_start: 0.6538 (mtp) cc_final: 0.6157 (mtp) REVERT: B 781 VAL cc_start: 0.8270 (OUTLIER) cc_final: 0.8053 (t) REVERT: B 907 ASN cc_start: 0.7586 (t0) cc_final: 0.7220 (t0) REVERT: B 970 PHE cc_start: 0.8386 (m-80) cc_final: 0.8027 (m-80) REVERT: B 1084 ASP cc_start: 0.7298 (t0) cc_final: 0.6800 (t0) REVERT: B 1136 THR cc_start: 0.8531 (OUTLIER) cc_final: 0.8243 (p) REVERT: C 142 ASP cc_start: 0.4979 (OUTLIER) cc_final: 0.4186 (p0) REVERT: C 287 ASP cc_start: 0.6957 (m-30) cc_final: 0.6721 (m-30) REVERT: C 307 THR cc_start: 0.8321 (p) cc_final: 0.8069 (p) REVERT: C 644 GLN cc_start: 0.7329 (tp40) cc_final: 0.6970 (tp40) REVERT: C 651 ILE cc_start: 0.8397 (pt) cc_final: 0.8072 (mt) REVERT: C 707 TYR cc_start: 0.8331 (t80) cc_final: 0.7930 (t80) REVERT: C 756 TYR cc_start: 0.8004 (OUTLIER) cc_final: 0.6902 (t80) REVERT: C 907 ASN cc_start: 0.7773 (t0) cc_final: 0.7435 (t0) REVERT: C 964 LYS cc_start: 0.8024 (tttp) cc_final: 0.7803 (tttm) REVERT: C 994 ASP cc_start: 0.7735 (t70) cc_final: 0.7494 (t0) REVERT: C 1017 GLU cc_start: 0.6585 (tp30) cc_final: 0.6309 (tp30) REVERT: C 1141 LEU cc_start: 0.7980 (tt) cc_final: 0.7758 (tp) REVERT: D 322 HIS cc_start: 0.1016 (OUTLIER) cc_final: -0.0070 (t70) REVERT: D 567 THR cc_start: 0.3187 (p) cc_final: 0.0895 (m) outliers start: 91 outliers final: 67 residues processed: 601 average time/residue: 0.4819 time to fit residues: 460.7838 Evaluate side-chains 616 residues out of total 3207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 538 time to evaluate : 3.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 PHE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 493 ARG Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1068 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 659 SER Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1073 LYS Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 34 GLN Chi-restraints excluded: chain D residue 49 ASN Chi-restraints excluded: chain D residue 69 TRP Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 322 HIS Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 455 MET Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 560 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 326 optimal weight: 0.9980 chunk 215 optimal weight: 6.9990 chunk 346 optimal weight: 0.5980 chunk 211 optimal weight: 0.3980 chunk 164 optimal weight: 0.7980 chunk 240 optimal weight: 5.9990 chunk 363 optimal weight: 10.0000 chunk 334 optimal weight: 6.9990 chunk 289 optimal weight: 0.0060 chunk 30 optimal weight: 4.9990 chunk 223 optimal weight: 10.0000 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 ASN A 657 ASN A 901 GLN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 GLN C 703 ASN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5208 moved from start: 0.5587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 29906 Z= 0.226 Angle : 0.604 13.314 40708 Z= 0.302 Chirality : 0.045 0.245 4659 Planarity : 0.004 0.064 5219 Dihedral : 6.187 126.433 4649 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.50 % Allowed : 17.24 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.14), residues: 3618 helix: 0.94 (0.17), residues: 1022 sheet: -0.11 (0.21), residues: 568 loop : -1.71 (0.13), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D 168 HIS 0.004 0.001 HIS B1064 PHE 0.061 0.002 PHE D 308 TYR 0.043 0.001 TYR C 904 ARG 0.011 0.001 ARG A 328 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7236 Ramachandran restraints generated. 3618 Oldfield, 0 Emsley, 3618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 3207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 530 time to evaluate : 3.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 602 THR cc_start: 0.7865 (p) cc_final: 0.7573 (m) REVERT: A 606 ASN cc_start: 0.7637 (m-40) cc_final: 0.7377 (m-40) REVERT: A 660 TYR cc_start: 0.7917 (m-10) cc_final: 0.7393 (m-80) REVERT: A 708 SER cc_start: 0.7929 (m) cc_final: 0.7686 (p) REVERT: A 784 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.7466 (mt0) REVERT: A 875 SER cc_start: 0.8413 (t) cc_final: 0.8137 (m) REVERT: A 981 LEU cc_start: 0.8067 (mm) cc_final: 0.7840 (mt) REVERT: A 1118 ASP cc_start: 0.7036 (t0) cc_final: 0.6799 (t0) REVERT: A 1127 ASP cc_start: 0.6982 (t0) cc_final: 0.6670 (t0) REVERT: A 1128 VAL cc_start: 0.8535 (OUTLIER) cc_final: 0.8268 (p) REVERT: A 1130 ILE cc_start: 0.8498 (OUTLIER) cc_final: 0.8282 (mt) REVERT: B 34 ARG cc_start: 0.7265 (mtp85) cc_final: 0.6992 (mtp85) REVERT: B 48 LEU cc_start: 0.7711 (mm) cc_final: 0.7466 (mp) REVERT: B 402 ILE cc_start: 0.7195 (pt) cc_final: 0.6960 (pt) REVERT: B 420 ASP cc_start: 0.6755 (m-30) cc_final: 0.6014 (m-30) REVERT: B 542 ASN cc_start: 0.8189 (t0) cc_final: 0.7778 (t0) REVERT: B 599 THR cc_start: 0.8299 (OUTLIER) cc_final: 0.8025 (p) REVERT: B 658 ASN cc_start: 0.8079 (OUTLIER) cc_final: 0.7805 (p0) REVERT: B 781 VAL cc_start: 0.8232 (OUTLIER) cc_final: 0.7953 (t) REVERT: B 907 ASN cc_start: 0.7555 (t0) cc_final: 0.7182 (t0) REVERT: B 970 PHE cc_start: 0.8310 (m-80) cc_final: 0.7984 (m-80) REVERT: B 1084 ASP cc_start: 0.7267 (t0) cc_final: 0.6779 (t0) REVERT: B 1136 THR cc_start: 0.8503 (OUTLIER) cc_final: 0.8232 (p) REVERT: C 44 ARG cc_start: 0.8496 (mpt180) cc_final: 0.8273 (mpt180) REVERT: C 142 ASP cc_start: 0.4860 (OUTLIER) cc_final: 0.4062 (p0) REVERT: C 273 ARG cc_start: 0.7506 (mmt90) cc_final: 0.7218 (mmm160) REVERT: C 307 THR cc_start: 0.8339 (p) cc_final: 0.8100 (p) REVERT: C 644 GLN cc_start: 0.7335 (tp40) cc_final: 0.7022 (tp-100) REVERT: C 651 ILE cc_start: 0.8297 (pt) cc_final: 0.8007 (mt) REVERT: C 707 TYR cc_start: 0.8289 (t80) cc_final: 0.7857 (t80) REVERT: C 756 TYR cc_start: 0.7910 (OUTLIER) cc_final: 0.6928 (t80) REVERT: C 907 ASN cc_start: 0.7723 (t0) cc_final: 0.7386 (t0) REVERT: C 921 LYS cc_start: 0.7924 (ttmm) cc_final: 0.7583 (mtpp) REVERT: C 964 LYS cc_start: 0.8008 (tttp) cc_final: 0.7787 (tttm) REVERT: C 994 ASP cc_start: 0.7590 (t70) cc_final: 0.7359 (t0) REVERT: C 1017 GLU cc_start: 0.6651 (tp30) cc_final: 0.6355 (tp30) REVERT: C 1136 THR cc_start: 0.8553 (OUTLIER) cc_final: 0.8352 (p) REVERT: C 1141 LEU cc_start: 0.7937 (tt) cc_final: 0.7678 (tp) REVERT: D 297 MET cc_start: 0.3086 (mpp) cc_final: 0.2419 (mmt) REVERT: D 322 HIS cc_start: 0.0936 (OUTLIER) cc_final: -0.0120 (t70) REVERT: D 474 MET cc_start: 0.3338 (mpp) cc_final: 0.2973 (mtm) REVERT: D 499 ASP cc_start: 0.0161 (m-30) cc_final: -0.0707 (m-30) REVERT: D 567 THR cc_start: 0.3117 (p) cc_final: 0.0749 (m) outliers start: 79 outliers final: 61 residues processed: 572 average time/residue: 0.4488 time to fit residues: 401.7469 Evaluate side-chains 595 residues out of total 3207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 523 time to evaluate : 3.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 166 CYS Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 784 GLN Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 493 ARG Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 776 LYS Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1068 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain D residue 34 GLN Chi-restraints excluded: chain D residue 49 ASN Chi-restraints excluded: chain D residue 69 TRP Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 322 HIS Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain D residue 455 MET Chi-restraints excluded: chain D residue 487 VAL Chi-restraints excluded: chain D residue 560 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 365 random chunks: chunk 177 optimal weight: 0.9980 chunk 230 optimal weight: 0.0570 chunk 308 optimal weight: 6.9990 chunk 88 optimal weight: 0.4980 chunk 266 optimal weight: 0.6980 chunk 42 optimal weight: 9.9990 chunk 80 optimal weight: 0.6980 chunk 290 optimal weight: 2.9990 chunk 121 optimal weight: 6.9990 chunk 297 optimal weight: 0.6980 chunk 36 optimal weight: 7.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN ** C 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 GLN C 703 ASN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.203083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.149033 restraints weight = 43986.782| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 2.76 r_work: 0.3618 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3451 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.5681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 29906 Z= 0.218 Angle : 0.584 13.420 40708 Z= 0.293 Chirality : 0.045 0.227 4659 Planarity : 0.004 0.064 5219 Dihedral : 6.192 121.878 4649 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.53 % Allowed : 17.40 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.14), residues: 3618 helix: 0.94 (0.17), residues: 1022 sheet: -0.03 (0.20), residues: 601 loop : -1.66 (0.13), residues: 1995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D 168 HIS 0.005 0.001 HIS C 954 PHE 0.059 0.002 PHE D 308 TYR 0.037 0.001 TYR C 904 ARG 0.009 0.001 ARG A 328 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8776.23 seconds wall clock time: 155 minutes 33.96 seconds (9333.96 seconds total)