Starting phenix.real_space_refine on Sun Mar 24 05:11:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o7p_12752/03_2024/7o7p_12752.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o7p_12752/03_2024/7o7p_12752.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o7p_12752/03_2024/7o7p_12752.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o7p_12752/03_2024/7o7p_12752.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o7p_12752/03_2024/7o7p_12752.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o7p_12752/03_2024/7o7p_12752.pdb" } resolution = 4.6 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 172 5.16 5 C 25586 2.51 5 N 6717 2.21 5 O 7820 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 216": "OE1" <-> "OE2" Residue "A GLU 223": "OE1" <-> "OE2" Residue "A GLU 243": "OE1" <-> "OE2" Residue "A GLU 281": "OE1" <-> "OE2" Residue "A ARG 313": "NH1" <-> "NH2" Residue "A GLU 323": "OE1" <-> "OE2" Residue "A GLU 342": "OE1" <-> "OE2" Residue "A GLU 467": "OE1" <-> "OE2" Residue "A GLU 612": "OE1" <-> "OE2" Residue "A ARG 645": "NH1" <-> "NH2" Residue "A GLU 753": "OE1" <-> "OE2" Residue "A GLU 795": "OE1" <-> "OE2" Residue "A GLU 908": "OE1" <-> "OE2" Residue "A GLU 999": "OE1" <-> "OE2" Residue "A GLU 1030": "OE1" <-> "OE2" Residue "A GLU 1098": "OE1" <-> "OE2" Residue "A GLU 1137": "OE1" <-> "OE2" Residue "A GLU 1311": "OE1" <-> "OE2" Residue "B GLU 56": "OE1" <-> "OE2" Residue "B GLU 78": "OE1" <-> "OE2" Residue "B GLU 160": "OE1" <-> "OE2" Residue "B GLU 243": "OE1" <-> "OE2" Residue "B ARG 313": "NH1" <-> "NH2" Residue "B GLU 323": "OE1" <-> "OE2" Residue "B GLU 342": "OE1" <-> "OE2" Residue "B PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 612": "OE1" <-> "OE2" Residue "B ARG 645": "NH1" <-> "NH2" Residue "B GLU 737": "OE1" <-> "OE2" Residue "B GLU 753": "OE1" <-> "OE2" Residue "B GLU 795": "OE1" <-> "OE2" Residue "B GLU 842": "OE1" <-> "OE2" Residue "B GLU 886": "OE1" <-> "OE2" Residue "B GLU 908": "OE1" <-> "OE2" Residue "B GLU 911": "OE1" <-> "OE2" Residue "B GLU 930": "OE1" <-> "OE2" Residue "B GLU 941": "OE1" <-> "OE2" Residue "B GLU 992": "OE1" <-> "OE2" Residue "B TYR 1021": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1030": "OE1" <-> "OE2" Residue "B PHE 1044": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1111": "OE1" <-> "OE2" Residue "B GLU 1137": "OE1" <-> "OE2" Residue "B GLU 1172": "OE1" <-> "OE2" Residue "C GLU 216": "OE1" <-> "OE2" Residue "C GLU 223": "OE1" <-> "OE2" Residue "C GLU 243": "OE1" <-> "OE2" Residue "C GLU 281": "OE1" <-> "OE2" Residue "C ARG 313": "NH1" <-> "NH2" Residue "C GLU 323": "OE1" <-> "OE2" Residue "C GLU 342": "OE1" <-> "OE2" Residue "C GLU 467": "OE1" <-> "OE2" Residue "C GLU 612": "OE1" <-> "OE2" Residue "C ARG 645": "NH1" <-> "NH2" Residue "C GLU 753": "OE1" <-> "OE2" Residue "C GLU 795": "OE1" <-> "OE2" Residue "C GLU 908": "OE1" <-> "OE2" Residue "C GLU 999": "OE1" <-> "OE2" Residue "C GLU 1030": "OE1" <-> "OE2" Residue "C GLU 1098": "OE1" <-> "OE2" Residue "C GLU 1137": "OE1" <-> "OE2" Residue "C GLU 1311": "OE1" <-> "OE2" Residue "D GLU 56": "OE1" <-> "OE2" Residue "D GLU 78": "OE1" <-> "OE2" Residue "D GLU 160": "OE1" <-> "OE2" Residue "D GLU 243": "OE1" <-> "OE2" Residue "D ARG 313": "NH1" <-> "NH2" Residue "D GLU 323": "OE1" <-> "OE2" Residue "D GLU 342": "OE1" <-> "OE2" Residue "D PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 612": "OE1" <-> "OE2" Residue "D ARG 645": "NH1" <-> "NH2" Residue "D GLU 737": "OE1" <-> "OE2" Residue "D GLU 753": "OE1" <-> "OE2" Residue "D GLU 795": "OE1" <-> "OE2" Residue "D GLU 842": "OE1" <-> "OE2" Residue "D GLU 886": "OE1" <-> "OE2" Residue "D GLU 908": "OE1" <-> "OE2" Residue "D GLU 911": "OE1" <-> "OE2" Residue "D GLU 930": "OE1" <-> "OE2" Residue "D GLU 941": "OE1" <-> "OE2" Residue "D GLU 992": "OE1" <-> "OE2" Residue "D TYR 1021": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1030": "OE1" <-> "OE2" Residue "D PHE 1044": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1111": "OE1" <-> "OE2" Residue "D GLU 1137": "OE1" <-> "OE2" Residue "D GLU 1172": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 40295 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 9967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1277, 9967 Classifications: {'peptide': 1277} Link IDs: {'PTRANS': 66, 'TRANS': 1210} Chain breaks: 1 Chain: "B" Number of atoms: 9944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1275, 9944 Classifications: {'peptide': 1275} Link IDs: {'PTRANS': 66, 'TRANS': 1208} Chain breaks: 1 Chain: "C" Number of atoms: 9940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1274, 9940 Classifications: {'peptide': 1274} Link IDs: {'PTRANS': 66, 'TRANS': 1207} Chain breaks: 1 Chain: "D" Number of atoms: 9940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1274, 9940 Classifications: {'peptide': 1274} Link IDs: {'PTRANS': 66, 'TRANS': 1207} Chain breaks: 1 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "D" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 20.22, per 1000 atoms: 0.50 Number of scatterers: 40295 At special positions: 0 Unit cell: (214.635, 151.815, 158.097, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 172 16.00 O 7820 8.00 N 6717 7.00 C 25586 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS A 48 " - pdb=" SG CYS A 86 " distance=2.03 Simple disulfide: pdb=" SG CYS A 251 " - pdb=" SG CYS A 299 " distance=2.03 Simple disulfide: pdb=" SG CYS A 269 " - pdb=" SG CYS A 287 " distance=2.03 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS B 431 " distance=2.02 Simple disulfide: pdb=" SG CYS A 431 " - pdb=" SG CYS B 278 " distance=2.03 Simple disulfide: pdb=" SG CYS A 470 " - pdb=" SG CYS A 563 " distance=2.03 Simple disulfide: pdb=" SG CYS A 595 " - pdb=" SG CYS A 771 " distance=2.03 Simple disulfide: pdb=" SG CYS A 642 " - pdb=" SG CYS A 689 " distance=2.02 Simple disulfide: pdb=" SG CYS A 821 " - pdb=" SG CYS A 849 " distance=2.02 Simple disulfide: pdb=" SG CYS A 847 " - pdb=" SG CYS A 883 " distance=2.04 Simple disulfide: pdb=" SG CYS A 921 " - pdb=" SG CYS A1321 " distance=2.03 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1127 " distance=2.02 Simple disulfide: pdb=" SG CYS B 48 " - pdb=" SG CYS B 86 " distance=2.03 Simple disulfide: pdb=" SG CYS B 251 " - pdb=" SG CYS B 299 " distance=2.03 Simple disulfide: pdb=" SG CYS B 269 " - pdb=" SG CYS B 287 " distance=2.03 Simple disulfide: pdb=" SG CYS B 470 " - pdb=" SG CYS B 563 " distance=2.03 Simple disulfide: pdb=" SG CYS B 595 " - pdb=" SG CYS B 771 " distance=2.03 Simple disulfide: pdb=" SG CYS B 642 " - pdb=" SG CYS B 689 " distance=2.03 Simple disulfide: pdb=" SG CYS B 821 " - pdb=" SG CYS B 849 " distance=2.07 Simple disulfide: pdb=" SG CYS B 847 " - pdb=" SG CYS B 883 " distance=2.03 Simple disulfide: pdb=" SG CYS B 921 " - pdb=" SG CYS B1321 " distance=2.03 Simple disulfide: pdb=" SG CYS B1079 " - pdb=" SG CYS B1127 " distance=2.05 Simple disulfide: pdb=" SG CYS C 48 " - pdb=" SG CYS C 86 " distance=2.03 Simple disulfide: pdb=" SG CYS C 251 " - pdb=" SG CYS C 299 " distance=2.03 Simple disulfide: pdb=" SG CYS C 269 " - pdb=" SG CYS C 287 " distance=2.03 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS D 431 " distance=2.02 Simple disulfide: pdb=" SG CYS C 431 " - pdb=" SG CYS D 278 " distance=2.03 Simple disulfide: pdb=" SG CYS C 470 " - pdb=" SG CYS C 563 " distance=2.03 Simple disulfide: pdb=" SG CYS C 595 " - pdb=" SG CYS C 771 " distance=2.03 Simple disulfide: pdb=" SG CYS C 642 " - pdb=" SG CYS C 689 " distance=2.02 Simple disulfide: pdb=" SG CYS C 821 " - pdb=" SG CYS C 849 " distance=2.02 Simple disulfide: pdb=" SG CYS C 847 " - pdb=" SG CYS C 883 " distance=2.04 Simple disulfide: pdb=" SG CYS C 921 " - pdb=" SG CYS C1321 " distance=2.03 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1127 " distance=2.02 Simple disulfide: pdb=" SG CYS D 48 " - pdb=" SG CYS D 86 " distance=2.03 Simple disulfide: pdb=" SG CYS D 251 " - pdb=" SG CYS D 299 " distance=2.03 Simple disulfide: pdb=" SG CYS D 269 " - pdb=" SG CYS D 287 " distance=2.03 Simple disulfide: pdb=" SG CYS D 470 " - pdb=" SG CYS D 563 " distance=2.03 Simple disulfide: pdb=" SG CYS D 595 " - pdb=" SG CYS D 771 " distance=2.03 Simple disulfide: pdb=" SG CYS D 642 " - pdb=" SG CYS D 689 " distance=2.03 Simple disulfide: pdb=" SG CYS D 821 " - pdb=" SG CYS D 849 " distance=2.07 Simple disulfide: pdb=" SG CYS D 847 " - pdb=" SG CYS D 883 " distance=2.03 Simple disulfide: pdb=" SG CYS D 921 " - pdb=" SG CYS D1321 " distance=2.03 Simple disulfide: pdb=" SG CYS D1079 " - pdb=" SG CYS D1127 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG A2001 " - " ASN A 55 " " NAG A2002 " - " ASN A 70 " " NAG A2003 " - " ASN A 247 " " NAG A2004 " - " ASN A 396 " " NAG A2005 " - " ASN A 410 " " NAG B2001 " - " ASN B 55 " " NAG B2002 " - " ASN B 70 " " NAG B2003 " - " ASN B 247 " " NAG B2004 " - " ASN B 396 " " NAG B2005 " - " ASN B 410 " " NAG C2001 " - " ASN C 55 " " NAG C2002 " - " ASN C 70 " " NAG C2003 " - " ASN C 247 " " NAG C2004 " - " ASN C 396 " " NAG C2005 " - " ASN C 410 " " NAG D2001 " - " ASN D 55 " " NAG D2002 " - " ASN D 70 " " NAG D2003 " - " ASN D 247 " " NAG D2004 " - " ASN D 396 " " NAG D2005 " - " ASN D 410 " " NAG E 1 " - " ASN A 869 " " NAG F 1 " - " ASN A 991 " " NAG G 1 " - " ASN B 869 " " NAG H 1 " - " ASN B 991 " " NAG I 1 " - " ASN C 869 " " NAG J 1 " - " ASN C 991 " " NAG K 1 " - " ASN D 869 " " NAG L 1 " - " ASN D 991 " Time building additional restraints: 15.44 Conformation dependent library (CDL) restraints added in 6.5 seconds 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9558 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 0 sheets defined 16.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.63 Creating SS restraints... Processing helix chain 'A' and resid 306 through 309 No H-bonds generated for 'chain 'A' and resid 306 through 309' Processing helix chain 'A' and resid 602 through 607 removed outlier: 4.414A pdb=" N LEU A 606 " --> pdb=" O GLN A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 621 Processing helix chain 'A' and resid 666 through 673 Processing helix chain 'A' and resid 953 through 965 removed outlier: 5.387A pdb=" N SER A 957 " --> pdb=" O ASP A 953 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA A 958 " --> pdb=" O ILE A 954 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N MET A 959 " --> pdb=" O LEU A 955 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N GLN A 960 " --> pdb=" O GLY A 956 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASN A 961 " --> pdb=" O SER A 957 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N THR A 962 " --> pdb=" O ALA A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 993 Proline residue: A 982 - end of helix removed outlier: 4.010A pdb=" N TYR A 985 " --> pdb=" O ALA A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1017 Processing helix chain 'A' and resid 1039 through 1055 Processing helix chain 'A' and resid 1060 through 1073 Processing helix chain 'A' and resid 1098 through 1111 Processing helix chain 'A' and resid 1119 through 1137 Processing helix chain 'A' and resid 1144 through 1157 Processing helix chain 'A' and resid 1160 through 1172 Processing helix chain 'A' and resid 1225 through 1241 Processing helix chain 'A' and resid 1251 through 1268 Processing helix chain 'A' and resid 1294 through 1297 No H-bonds generated for 'chain 'A' and resid 1294 through 1297' Processing helix chain 'B' and resid 306 through 309 No H-bonds generated for 'chain 'B' and resid 306 through 309' Processing helix chain 'B' and resid 602 through 607 removed outlier: 3.924A pdb=" N LEU B 606 " --> pdb=" O GLN B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 621 Processing helix chain 'B' and resid 666 through 673 Processing helix chain 'B' and resid 953 through 965 removed outlier: 6.053A pdb=" N SER B 957 " --> pdb=" O ASP B 953 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA B 958 " --> pdb=" O ILE B 954 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N MET B 959 " --> pdb=" O LEU B 955 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N GLN B 960 " --> pdb=" O GLY B 956 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASN B 961 " --> pdb=" O SER B 957 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N THR B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 973 through 993 Proline residue: B 982 - end of helix removed outlier: 3.933A pdb=" N TYR B 985 " --> pdb=" O ALA B 981 " (cutoff:3.500A) Processing helix chain 'B' and resid 998 through 1017 Processing helix chain 'B' and resid 1039 through 1055 Processing helix chain 'B' and resid 1060 through 1073 Processing helix chain 'B' and resid 1098 through 1111 Processing helix chain 'B' and resid 1119 through 1137 Processing helix chain 'B' and resid 1144 through 1157 Processing helix chain 'B' and resid 1160 through 1172 Processing helix chain 'B' and resid 1225 through 1241 Processing helix chain 'B' and resid 1251 through 1268 Processing helix chain 'B' and resid 1294 through 1297 No H-bonds generated for 'chain 'B' and resid 1294 through 1297' Processing helix chain 'C' and resid 306 through 309 No H-bonds generated for 'chain 'C' and resid 306 through 309' Processing helix chain 'C' and resid 602 through 607 removed outlier: 4.414A pdb=" N LEU C 606 " --> pdb=" O GLN C 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 615 through 621 Processing helix chain 'C' and resid 666 through 673 Processing helix chain 'C' and resid 953 through 965 removed outlier: 5.387A pdb=" N SER C 957 " --> pdb=" O ASP C 953 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA C 958 " --> pdb=" O ILE C 954 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N MET C 959 " --> pdb=" O LEU C 955 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N GLN C 960 " --> pdb=" O GLY C 956 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASN C 961 " --> pdb=" O SER C 957 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N THR C 962 " --> pdb=" O ALA C 958 " (cutoff:3.500A) Processing helix chain 'C' and resid 973 through 993 Proline residue: C 982 - end of helix removed outlier: 4.010A pdb=" N TYR C 985 " --> pdb=" O ALA C 981 " (cutoff:3.500A) Processing helix chain 'C' and resid 998 through 1017 Processing helix chain 'C' and resid 1039 through 1055 Processing helix chain 'C' and resid 1060 through 1073 Processing helix chain 'C' and resid 1098 through 1111 Processing helix chain 'C' and resid 1119 through 1137 Processing helix chain 'C' and resid 1144 through 1157 Processing helix chain 'C' and resid 1160 through 1172 Processing helix chain 'C' and resid 1225 through 1241 Processing helix chain 'C' and resid 1251 through 1268 Processing helix chain 'C' and resid 1294 through 1297 No H-bonds generated for 'chain 'C' and resid 1294 through 1297' Processing helix chain 'D' and resid 306 through 309 No H-bonds generated for 'chain 'D' and resid 306 through 309' Processing helix chain 'D' and resid 602 through 607 removed outlier: 3.924A pdb=" N LEU D 606 " --> pdb=" O GLN D 602 " (cutoff:3.500A) Processing helix chain 'D' and resid 615 through 621 Processing helix chain 'D' and resid 666 through 673 Processing helix chain 'D' and resid 953 through 965 removed outlier: 6.053A pdb=" N SER D 957 " --> pdb=" O ASP D 953 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA D 958 " --> pdb=" O ILE D 954 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N MET D 959 " --> pdb=" O LEU D 955 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N GLN D 960 " --> pdb=" O GLY D 956 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASN D 961 " --> pdb=" O SER D 957 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N THR D 962 " --> pdb=" O ALA D 958 " (cutoff:3.500A) Processing helix chain 'D' and resid 973 through 993 Proline residue: D 982 - end of helix removed outlier: 3.933A pdb=" N TYR D 985 " --> pdb=" O ALA D 981 " (cutoff:3.500A) Processing helix chain 'D' and resid 998 through 1017 Processing helix chain 'D' and resid 1039 through 1055 Processing helix chain 'D' and resid 1060 through 1073 Processing helix chain 'D' and resid 1098 through 1111 Processing helix chain 'D' and resid 1119 through 1137 Processing helix chain 'D' and resid 1144 through 1157 Processing helix chain 'D' and resid 1160 through 1172 Processing helix chain 'D' and resid 1225 through 1241 Processing helix chain 'D' and resid 1251 through 1268 Processing helix chain 'D' and resid 1294 through 1297 No H-bonds generated for 'chain 'D' and resid 1294 through 1297' 536 hydrogen bonds defined for protein. 1608 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: 8.97 Time building geometry restraints manager: 16.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 6742 1.31 - 1.44: 10711 1.44 - 1.56: 23464 1.56 - 1.69: 10 1.69 - 1.82: 252 Bond restraints: 41179 Sorted by residual: bond pdb=" C7 NAG B2001 " pdb=" N2 NAG B2001 " ideal model delta sigma weight residual 1.346 1.464 -0.118 2.00e-02 2.50e+03 3.49e+01 bond pdb=" C7 NAG D2001 " pdb=" N2 NAG D2001 " ideal model delta sigma weight residual 1.346 1.464 -0.118 2.00e-02 2.50e+03 3.49e+01 bond pdb=" C7 NAG C2003 " pdb=" N2 NAG C2003 " ideal model delta sigma weight residual 1.346 1.461 -0.115 2.00e-02 2.50e+03 3.30e+01 bond pdb=" C7 NAG A2003 " pdb=" N2 NAG A2003 " ideal model delta sigma weight residual 1.346 1.461 -0.115 2.00e-02 2.50e+03 3.30e+01 bond pdb=" C7 NAG A2004 " pdb=" N2 NAG A2004 " ideal model delta sigma weight residual 1.346 1.457 -0.111 2.00e-02 2.50e+03 3.10e+01 ... (remaining 41174 not shown) Histogram of bond angle deviations from ideal: 98.69 - 105.78: 1032 105.78 - 112.88: 21897 112.88 - 119.98: 14114 119.98 - 127.08: 18383 127.08 - 134.17: 522 Bond angle restraints: 55948 Sorted by residual: angle pdb=" CA CYS B 821 " pdb=" C CYS B 821 " pdb=" N ILE B 822 " ideal model delta sigma weight residual 116.39 106.28 10.11 1.17e+00 7.31e-01 7.47e+01 angle pdb=" CA CYS D 821 " pdb=" C CYS D 821 " pdb=" N ILE D 822 " ideal model delta sigma weight residual 116.39 106.28 10.11 1.17e+00 7.31e-01 7.47e+01 angle pdb=" CA CYS D 821 " pdb=" CB CYS D 821 " pdb=" SG CYS D 821 " ideal model delta sigma weight residual 114.40 130.74 -16.34 2.30e+00 1.89e-01 5.05e+01 angle pdb=" CA CYS B 821 " pdb=" CB CYS B 821 " pdb=" SG CYS B 821 " ideal model delta sigma weight residual 114.40 130.74 -16.34 2.30e+00 1.89e-01 5.05e+01 angle pdb=" N ILE C1112 " pdb=" CA ILE C1112 " pdb=" C ILE C1112 " ideal model delta sigma weight residual 109.02 103.41 5.61 9.30e-01 1.16e+00 3.64e+01 ... (remaining 55943 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.34: 23638 23.34 - 46.68: 1458 46.68 - 70.02: 233 70.02 - 93.35: 40 93.35 - 116.69: 3 Dihedral angle restraints: 25372 sinusoidal: 10526 harmonic: 14846 Sorted by residual: dihedral pdb=" CB CYS A 431 " pdb=" SG CYS A 431 " pdb=" SG CYS B 278 " pdb=" CB CYS B 278 " ideal model delta sinusoidal sigma weight residual 93.00 152.34 -59.34 1 1.00e+01 1.00e-02 4.70e+01 dihedral pdb=" CB CYS C 431 " pdb=" SG CYS C 431 " pdb=" SG CYS D 278 " pdb=" CB CYS D 278 " ideal model delta sinusoidal sigma weight residual 93.00 152.34 -59.34 1 1.00e+01 1.00e-02 4.70e+01 dihedral pdb=" CB CYS C 470 " pdb=" SG CYS C 470 " pdb=" SG CYS C 563 " pdb=" CB CYS C 563 " ideal model delta sinusoidal sigma weight residual 93.00 149.60 -56.60 1 1.00e+01 1.00e-02 4.32e+01 ... (remaining 25369 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.793: 6470 0.793 - 1.586: 0 1.586 - 2.379: 0 2.379 - 3.173: 0 3.173 - 3.966: 1 Chirality restraints: 6471 Sorted by residual: chirality pdb=" C1 NAG L 1 " pdb=" ND2 ASN D 991 " pdb=" C2 NAG L 1 " pdb=" O5 NAG L 1 " both_signs ideal model delta sigma weight residual False -2.40 1.57 -3.97 2.00e-01 2.50e+01 3.93e+02 chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-02 2.50e+03 2.46e+02 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-02 2.50e+03 2.25e+02 ... (remaining 6468 not shown) Planarity restraints: 7194 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG I 1 " -0.354 2.00e-02 2.50e+03 3.05e-01 1.17e+03 pdb=" C7 NAG I 1 " 0.083 2.00e-02 2.50e+03 pdb=" C8 NAG I 1 " -0.090 2.00e-02 2.50e+03 pdb=" N2 NAG I 1 " 0.542 2.00e-02 2.50e+03 pdb=" O7 NAG I 1 " -0.181 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 1 " 0.353 2.00e-02 2.50e+03 3.03e-01 1.15e+03 pdb=" C7 NAG H 1 " -0.083 2.00e-02 2.50e+03 pdb=" C8 NAG H 1 " 0.058 2.00e-02 2.50e+03 pdb=" N2 NAG H 1 " -0.532 2.00e-02 2.50e+03 pdb=" O7 NAG H 1 " 0.204 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG K 1 " -0.350 2.00e-02 2.50e+03 3.02e-01 1.14e+03 pdb=" C7 NAG K 1 " 0.086 2.00e-02 2.50e+03 pdb=" C8 NAG K 1 " -0.138 2.00e-02 2.50e+03 pdb=" N2 NAG K 1 " 0.537 2.00e-02 2.50e+03 pdb=" O7 NAG K 1 " -0.134 2.00e-02 2.50e+03 ... (remaining 7191 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 528 2.51 - 3.10: 34727 3.10 - 3.70: 65138 3.70 - 4.30: 88768 4.30 - 4.90: 140952 Nonbonded interactions: 330113 Sorted by model distance: nonbonded pdb=" O PRO B 657 " pdb=" OG1 THR C 656 " model vdw 1.908 2.440 nonbonded pdb=" OG1 THR A 656 " pdb=" O PRO D 657 " model vdw 1.908 2.440 nonbonded pdb=" OG1 THR B 656 " pdb=" O PRO C 657 " model vdw 2.017 2.440 nonbonded pdb=" O PRO A 657 " pdb=" OG1 THR D 656 " model vdw 2.017 2.440 nonbonded pdb=" OD1 ASP A 134 " pdb=" OG1 THR A 738 " model vdw 2.023 2.440 ... (remaining 330108 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 28 through 1335 or resid 2001 through 2005)) selection = (chain 'B' and (resid 28 through 1335 or resid 2001 through 2005)) selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.010 Normalize map: mean=0, sd=1: 2.060 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: 9.380 Check model and map are aligned: 0.600 Set scattering table: 0.340 Process input model: 93.370 Find NCS groups from input model: 3.400 Set up NCS constraints: 0.400 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:3.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 112.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 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 : 0.009 0.118 41179 Z= 0.620 Angle : 1.149 16.343 55948 Z= 0.640 Chirality : 0.075 3.966 6471 Planarity : 0.014 0.305 7166 Dihedral : 15.253 116.693 15682 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.31 % Allowed : 12.65 % Favored : 87.04 % Rotamer: Outliers : 0.13 % Allowed : 5.06 % Favored : 94.81 % Cbeta Deviations : 0.04 % 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: -4.55 (0.10), residues: 5084 helix: -1.90 (0.14), residues: 856 sheet: -2.58 (0.10), residues: 1802 loop : -3.81 (0.11), residues: 2426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP D 765 HIS 0.016 0.002 HIS D1182 PHE 0.030 0.003 PHE B 735 TYR 0.026 0.003 TYR A 558 ARG 0.012 0.001 ARG D 360 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1156 residues out of total 4451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1150 time to evaluate : 4.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 32 MET cc_start: 0.9105 (ttt) cc_final: 0.8688 (ttm) REVERT: A 97 ASN cc_start: 0.8976 (t0) cc_final: 0.8689 (t0) REVERT: A 99 GLU cc_start: 0.9152 (tt0) cc_final: 0.8603 (mp0) REVERT: A 146 PHE cc_start: 0.9413 (p90) cc_final: 0.9071 (p90) REVERT: A 183 LEU cc_start: 0.8401 (mt) cc_final: 0.8190 (mt) REVERT: A 204 LYS cc_start: 0.6764 (mtpt) cc_final: 0.6508 (tppt) REVERT: A 209 LYS cc_start: 0.9418 (mtmt) cc_final: 0.8290 (mmtm) REVERT: A 229 PHE cc_start: 0.8951 (p90) cc_final: 0.8676 (p90) REVERT: A 270 ARG cc_start: 0.7569 (tpt-90) cc_final: 0.7008 (mtt90) REVERT: A 290 PHE cc_start: 0.9432 (m-80) cc_final: 0.9034 (m-80) REVERT: A 321 HIS cc_start: 0.8922 (m-70) cc_final: 0.8706 (m-70) REVERT: A 428 ARG cc_start: 0.5669 (mpt180) cc_final: 0.5029 (mtm180) REVERT: A 496 TYR cc_start: 0.7716 (m-80) cc_final: 0.7200 (m-80) REVERT: A 550 ASP cc_start: 0.8700 (m-30) cc_final: 0.8076 (m-30) REVERT: A 569 ASP cc_start: 0.8769 (m-30) cc_final: 0.8540 (m-30) REVERT: A 573 SER cc_start: 0.9158 (t) cc_final: 0.8929 (p) REVERT: A 650 ILE cc_start: 0.6290 (mm) cc_final: 0.5885 (mm) REVERT: A 669 PHE cc_start: 0.8455 (m-10) cc_final: 0.7982 (m-10) REVERT: A 670 LEU cc_start: 0.9592 (mp) cc_final: 0.9286 (pp) REVERT: A 688 MET cc_start: 0.8506 (ppp) cc_final: 0.8077 (ppp) REVERT: A 809 THR cc_start: 0.9337 (t) cc_final: 0.9009 (t) REVERT: A 870 PHE cc_start: 0.8554 (m-80) cc_final: 0.8328 (m-80) REVERT: A 933 LEU cc_start: 0.8932 (mt) cc_final: 0.8557 (mt) REVERT: A 965 LEU cc_start: 0.9156 (tt) cc_final: 0.8771 (tt) REVERT: A 975 GLN cc_start: 0.8814 (mm-40) cc_final: 0.8399 (tp-100) REVERT: A 978 VAL cc_start: 0.8728 (t) cc_final: 0.8350 (t) REVERT: A 983 ASN cc_start: 0.9348 (m-40) cc_final: 0.9045 (m110) REVERT: A 988 ASP cc_start: 0.9094 (m-30) cc_final: 0.8799 (m-30) REVERT: A 1020 HIS cc_start: 0.8480 (m-70) cc_final: 0.7289 (m-70) REVERT: A 1028 PHE cc_start: 0.8454 (m-80) cc_final: 0.8184 (m-80) REVERT: A 1057 PHE cc_start: 0.8651 (t80) cc_final: 0.8359 (t80) REVERT: A 1076 ASP cc_start: 0.8506 (p0) cc_final: 0.7940 (m-30) REVERT: A 1154 PHE cc_start: 0.8566 (m-80) cc_final: 0.8051 (m-80) REVERT: A 1163 ARG cc_start: 0.8758 (ttt180) cc_final: 0.8328 (mtp180) REVERT: A 1241 GLN cc_start: 0.8389 (mm-40) cc_final: 0.8152 (mm110) REVERT: A 1312 TYR cc_start: 0.9527 (m-80) cc_final: 0.9018 (m-80) REVERT: B 32 MET cc_start: 0.9325 (ttt) cc_final: 0.8891 (ttp) REVERT: B 50 LEU cc_start: 0.9071 (tt) cc_final: 0.7740 (tt) REVERT: B 121 MET cc_start: 0.7761 (tpp) cc_final: 0.6968 (tpp) REVERT: B 146 PHE cc_start: 0.9250 (p90) cc_final: 0.8765 (p90) REVERT: B 222 GLU cc_start: 0.9429 (pt0) cc_final: 0.9185 (pm20) REVERT: B 316 TYR cc_start: 0.6131 (m-80) cc_final: 0.5554 (t80) REVERT: B 354 LYS cc_start: 0.8631 (tttp) cc_final: 0.7506 (mttt) REVERT: B 356 ASP cc_start: 0.8820 (m-30) cc_final: 0.8338 (p0) REVERT: B 406 GLN cc_start: 0.8929 (mp10) cc_final: 0.8715 (mp-120) REVERT: B 461 LEU cc_start: 0.9234 (mp) cc_final: 0.9026 (mm) REVERT: B 479 HIS cc_start: 0.8925 (m170) cc_final: 0.8502 (m170) REVERT: B 496 TYR cc_start: 0.7943 (m-80) cc_final: 0.7163 (m-80) REVERT: B 543 TYR cc_start: 0.8506 (p90) cc_final: 0.7480 (p90) REVERT: B 552 ILE cc_start: 0.8804 (pt) cc_final: 0.8534 (pt) REVERT: B 569 ASP cc_start: 0.9166 (t0) cc_final: 0.8761 (t70) REVERT: B 570 LEU cc_start: 0.9119 (tt) cc_final: 0.8419 (pt) REVERT: B 571 SER cc_start: 0.9163 (t) cc_final: 0.8474 (p) REVERT: B 572 PHE cc_start: 0.8072 (p90) cc_final: 0.7355 (p90) REVERT: B 635 ASN cc_start: 0.9118 (p0) cc_final: 0.8909 (p0) REVERT: B 638 ASP cc_start: 0.9121 (t70) cc_final: 0.8543 (p0) REVERT: B 666 MET cc_start: 0.7847 (tpp) cc_final: 0.7305 (ttm) REVERT: B 669 PHE cc_start: 0.8691 (m-80) cc_final: 0.8189 (m-80) REVERT: B 828 LEU cc_start: 0.8480 (pt) cc_final: 0.8270 (mm) REVERT: B 870 PHE cc_start: 0.9178 (t80) cc_final: 0.8772 (t80) REVERT: B 901 LYS cc_start: 0.9132 (mmmm) cc_final: 0.8725 (mmtt) REVERT: B 935 LEU cc_start: 0.6858 (mt) cc_final: 0.6277 (mt) REVERT: B 985 TYR cc_start: 0.9029 (m-80) cc_final: 0.8641 (m-80) REVERT: B 1067 LEU cc_start: 0.7428 (tp) cc_final: 0.7146 (mt) REVERT: B 1089 ASN cc_start: 0.8244 (m-40) cc_final: 0.7848 (p0) REVERT: B 1224 THR cc_start: 0.8307 (p) cc_final: 0.7852 (t) REVERT: B 1227 ASP cc_start: 0.8531 (m-30) cc_final: 0.7736 (p0) REVERT: B 1237 TRP cc_start: 0.8534 (t60) cc_final: 0.7964 (t60) REVERT: B 1238 ILE cc_start: 0.7785 (mm) cc_final: 0.7248 (mm) REVERT: B 1331 ASN cc_start: 0.7073 (m110) cc_final: 0.6310 (t0) REVERT: C 32 MET cc_start: 0.9106 (ttt) cc_final: 0.8669 (ttm) REVERT: C 97 ASN cc_start: 0.8976 (t0) cc_final: 0.8689 (t0) REVERT: C 99 GLU cc_start: 0.9152 (tt0) cc_final: 0.8602 (mp0) REVERT: C 146 PHE cc_start: 0.9412 (p90) cc_final: 0.9071 (p90) REVERT: C 183 LEU cc_start: 0.8396 (mt) cc_final: 0.8186 (mt) REVERT: C 204 LYS cc_start: 0.6759 (mtpt) cc_final: 0.6501 (tppt) REVERT: C 209 LYS cc_start: 0.9415 (mtmt) cc_final: 0.8290 (mmtm) REVERT: C 229 PHE cc_start: 0.8954 (p90) cc_final: 0.8679 (p90) REVERT: C 270 ARG cc_start: 0.7580 (tpt-90) cc_final: 0.7022 (mtt90) REVERT: C 290 PHE cc_start: 0.9428 (m-80) cc_final: 0.9030 (m-80) REVERT: C 321 HIS cc_start: 0.8925 (m-70) cc_final: 0.8708 (m-70) REVERT: C 428 ARG cc_start: 0.5671 (mpt180) cc_final: 0.5052 (mtm180) REVERT: C 496 TYR cc_start: 0.7718 (m-80) cc_final: 0.7193 (m-80) REVERT: C 550 ASP cc_start: 0.8685 (m-30) cc_final: 0.8089 (m-30) REVERT: C 569 ASP cc_start: 0.8767 (m-30) cc_final: 0.8537 (m-30) REVERT: C 573 SER cc_start: 0.9161 (t) cc_final: 0.8930 (p) REVERT: C 650 ILE cc_start: 0.6303 (mm) cc_final: 0.5892 (mm) REVERT: C 669 PHE cc_start: 0.8458 (m-10) cc_final: 0.7983 (m-10) REVERT: C 670 LEU cc_start: 0.9591 (mp) cc_final: 0.9285 (pp) REVERT: C 688 MET cc_start: 0.8508 (ppp) cc_final: 0.8078 (ppp) REVERT: C 809 THR cc_start: 0.9334 (t) cc_final: 0.9007 (t) REVERT: C 933 LEU cc_start: 0.8932 (mt) cc_final: 0.8558 (mt) REVERT: C 938 ASN cc_start: 0.8529 (OUTLIER) cc_final: 0.8025 (p0) REVERT: C 965 LEU cc_start: 0.9157 (tt) cc_final: 0.8771 (tt) REVERT: C 975 GLN cc_start: 0.8816 (mm-40) cc_final: 0.8402 (tp-100) REVERT: C 978 VAL cc_start: 0.8727 (t) cc_final: 0.8350 (t) REVERT: C 983 ASN cc_start: 0.9354 (m-40) cc_final: 0.9132 (m110) REVERT: C 1020 HIS cc_start: 0.8479 (m-70) cc_final: 0.7291 (m-70) REVERT: C 1028 PHE cc_start: 0.8456 (m-80) cc_final: 0.8187 (m-80) REVERT: C 1057 PHE cc_start: 0.8672 (t80) cc_final: 0.8377 (t80) REVERT: C 1076 ASP cc_start: 0.8503 (p0) cc_final: 0.7935 (m-30) REVERT: C 1150 LEU cc_start: 0.9431 (mm) cc_final: 0.9220 (mm) REVERT: C 1154 PHE cc_start: 0.8564 (m-80) cc_final: 0.8008 (m-80) REVERT: C 1163 ARG cc_start: 0.8758 (ttt180) cc_final: 0.8326 (mtp180) REVERT: C 1241 GLN cc_start: 0.8390 (mm-40) cc_final: 0.8152 (mm110) REVERT: C 1312 TYR cc_start: 0.9526 (m-80) cc_final: 0.9020 (m-80) REVERT: C 1335 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8095 (mp0) REVERT: D 32 MET cc_start: 0.9327 (ttt) cc_final: 0.8891 (ttp) REVERT: D 50 LEU cc_start: 0.9070 (tt) cc_final: 0.7738 (tt) REVERT: D 121 MET cc_start: 0.7759 (tpp) cc_final: 0.6985 (tpp) REVERT: D 146 PHE cc_start: 0.9249 (p90) cc_final: 0.8762 (p90) REVERT: D 222 GLU cc_start: 0.9430 (pt0) cc_final: 0.9187 (pm20) REVERT: D 316 TYR cc_start: 0.6135 (m-80) cc_final: 0.5560 (t80) REVERT: D 354 LYS cc_start: 0.8632 (tttp) cc_final: 0.7511 (mttt) REVERT: D 356 ASP cc_start: 0.8819 (m-30) cc_final: 0.8338 (p0) REVERT: D 406 GLN cc_start: 0.8929 (mp10) cc_final: 0.8715 (mp-120) REVERT: D 461 LEU cc_start: 0.9236 (mp) cc_final: 0.9029 (mm) REVERT: D 479 HIS cc_start: 0.8928 (m170) cc_final: 0.8506 (m170) REVERT: D 496 TYR cc_start: 0.7947 (m-80) cc_final: 0.7166 (m-80) REVERT: D 543 TYR cc_start: 0.8503 (p90) cc_final: 0.7482 (p90) REVERT: D 552 ILE cc_start: 0.8807 (pt) cc_final: 0.8540 (pt) REVERT: D 569 ASP cc_start: 0.9168 (t0) cc_final: 0.8762 (t70) REVERT: D 570 LEU cc_start: 0.9121 (tt) cc_final: 0.8419 (pt) REVERT: D 571 SER cc_start: 0.9162 (t) cc_final: 0.8471 (p) REVERT: D 572 PHE cc_start: 0.8074 (p90) cc_final: 0.7355 (p90) REVERT: D 635 ASN cc_start: 0.9122 (p0) cc_final: 0.8851 (p0) REVERT: D 666 MET cc_start: 0.7837 (tpp) cc_final: 0.7314 (ttm) REVERT: D 669 PHE cc_start: 0.8693 (m-80) cc_final: 0.8191 (m-80) REVERT: D 828 LEU cc_start: 0.8475 (pt) cc_final: 0.8267 (mm) REVERT: D 870 PHE cc_start: 0.9232 (t80) cc_final: 0.8806 (t80) REVERT: D 901 LYS cc_start: 0.9137 (mmmm) cc_final: 0.8733 (mmtt) REVERT: D 935 LEU cc_start: 0.6859 (mt) cc_final: 0.6243 (mt) REVERT: D 985 TYR cc_start: 0.8992 (m-80) cc_final: 0.8608 (m-80) REVERT: D 1067 LEU cc_start: 0.7426 (tp) cc_final: 0.7142 (mt) REVERT: D 1089 ASN cc_start: 0.8246 (m-40) cc_final: 0.7847 (p0) REVERT: D 1224 THR cc_start: 0.8307 (p) cc_final: 0.7851 (t) REVERT: D 1227 ASP cc_start: 0.8528 (m-30) cc_final: 0.7734 (p0) REVERT: D 1237 TRP cc_start: 0.8535 (t60) cc_final: 0.7966 (t60) REVERT: D 1238 ILE cc_start: 0.7789 (mm) cc_final: 0.7252 (mm) REVERT: D 1331 ASN cc_start: 0.6770 (m110) cc_final: 0.6139 (t0) outliers start: 6 outliers final: 2 residues processed: 1156 average time/residue: 0.5624 time to fit residues: 1051.3874 Evaluate side-chains 755 residues out of total 4451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 751 time to evaluate : 4.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 428 optimal weight: 0.9990 chunk 385 optimal weight: 7.9990 chunk 213 optimal weight: 5.9990 chunk 131 optimal weight: 5.9990 chunk 259 optimal weight: 1.9990 chunk 205 optimal weight: 0.1980 chunk 398 optimal weight: 6.9990 chunk 154 optimal weight: 6.9990 chunk 242 optimal weight: 7.9990 chunk 296 optimal weight: 8.9990 chunk 461 optimal weight: 7.9990 overall best weight: 3.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 132 GLN ** A 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 413 ASN ** A 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 582 HIS A 691 GLN ** A 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 960 GLN A 976 ASN A1065 GLN A1241 GLN ** A1291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 GLN B 302 GLN ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 GLN B 424 ASN B 441 HIS B 511 HIS B 637 GLN ** B 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 967 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1017 ASN ** B1281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 GLN ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 413 ASN ** C 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 582 HIS ** C 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 960 GLN C 976 ASN C1065 GLN C1241 GLN ** C1277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 GLN D 302 GLN ** D 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 GLN D 424 ASN D 441 HIS D 511 HIS D 637 GLN ** D 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 967 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1017 ASN ** D1281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 41179 Z= 0.282 Angle : 0.841 15.872 55948 Z= 0.421 Chirality : 0.051 0.510 6471 Planarity : 0.006 0.077 7166 Dihedral : 8.906 85.622 6200 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 18.82 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.52 % Favored : 90.36 % Rotamer: Outliers : 0.54 % Allowed : 7.41 % Favored : 92.05 % 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: -3.61 (0.11), residues: 5084 helix: -0.58 (0.16), residues: 859 sheet: -2.14 (0.11), residues: 1877 loop : -3.32 (0.12), residues: 2348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B1132 HIS 0.009 0.001 HIS C 358 PHE 0.027 0.002 PHE D 114 TYR 0.026 0.002 TYR D 256 ARG 0.010 0.001 ARG A 370 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 961 residues out of total 4451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 937 time to evaluate : 4.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 MET cc_start: 0.9211 (ttt) cc_final: 0.8935 (ttm) REVERT: A 97 ASN cc_start: 0.8944 (t0) cc_final: 0.8500 (t0) REVERT: A 121 MET cc_start: 0.8507 (mmt) cc_final: 0.8068 (mpp) REVERT: A 151 MET cc_start: 0.4846 (ttp) cc_final: 0.4481 (tpp) REVERT: A 209 LYS cc_start: 0.9520 (mtmt) cc_final: 0.8746 (ptpt) REVERT: A 270 ARG cc_start: 0.7984 (tpt-90) cc_final: 0.6890 (tpt170) REVERT: A 290 PHE cc_start: 0.9479 (m-80) cc_final: 0.9074 (m-80) REVERT: A 389 ASN cc_start: 0.7852 (m-40) cc_final: 0.7447 (t0) REVERT: A 428 ARG cc_start: 0.5848 (mpt180) cc_final: 0.5182 (mtm180) REVERT: A 496 TYR cc_start: 0.7611 (m-80) cc_final: 0.7273 (m-80) REVERT: A 564 LEU cc_start: 0.8799 (tp) cc_final: 0.8157 (tt) REVERT: A 567 LYS cc_start: 0.9476 (mmpt) cc_final: 0.9204 (mmmt) REVERT: A 628 THR cc_start: 0.7159 (t) cc_final: 0.6698 (m) REVERT: A 650 ILE cc_start: 0.6813 (mm) cc_final: 0.6413 (mm) REVERT: A 666 MET cc_start: 0.8951 (ttm) cc_final: 0.8304 (ptm) REVERT: A 669 PHE cc_start: 0.8190 (m-10) cc_final: 0.7830 (m-10) REVERT: A 670 LEU cc_start: 0.9597 (mp) cc_final: 0.9294 (pp) REVERT: A 800 TYR cc_start: 0.9020 (p90) cc_final: 0.8620 (p90) REVERT: A 868 VAL cc_start: 0.9698 (m) cc_final: 0.9497 (m) REVERT: A 870 PHE cc_start: 0.8674 (m-80) cc_final: 0.8387 (m-80) REVERT: A 931 LEU cc_start: 0.9259 (tp) cc_final: 0.8895 (tp) REVERT: A 965 LEU cc_start: 0.9079 (tt) cc_final: 0.8204 (mm) REVERT: A 975 GLN cc_start: 0.8855 (mm-40) cc_final: 0.8439 (tp-100) REVERT: A 983 ASN cc_start: 0.9396 (m-40) cc_final: 0.8988 (m110) REVERT: A 985 TYR cc_start: 0.8296 (m-80) cc_final: 0.8086 (m-10) REVERT: A 988 ASP cc_start: 0.9143 (m-30) cc_final: 0.8610 (m-30) REVERT: A 1028 PHE cc_start: 0.8483 (m-80) cc_final: 0.8281 (m-80) REVERT: A 1047 LYS cc_start: 0.9399 (ttmt) cc_final: 0.9157 (ptmm) REVERT: A 1057 PHE cc_start: 0.8725 (t80) cc_final: 0.8296 (t80) REVERT: A 1076 ASP cc_start: 0.8674 (p0) cc_final: 0.7959 (m-30) REVERT: A 1125 LEU cc_start: 0.9519 (mt) cc_final: 0.9252 (pp) REVERT: A 1128 LEU cc_start: 0.9433 (mt) cc_final: 0.9147 (mt) REVERT: A 1132 TRP cc_start: 0.9097 (t60) cc_final: 0.8535 (t60) REVERT: A 1133 LYS cc_start: 0.9414 (ttmt) cc_final: 0.9203 (tptt) REVERT: A 1150 LEU cc_start: 0.9367 (mm) cc_final: 0.9046 (mm) REVERT: A 1154 PHE cc_start: 0.8588 (m-80) cc_final: 0.7141 (m-80) REVERT: A 1314 MET cc_start: 0.9116 (mpp) cc_final: 0.8898 (ptp) REVERT: A 1323 TYR cc_start: 0.7851 (t80) cc_final: 0.7625 (t80) REVERT: B 50 LEU cc_start: 0.9132 (tt) cc_final: 0.8752 (tt) REVERT: B 121 MET cc_start: 0.8125 (tpp) cc_final: 0.7163 (tpp) REVERT: B 126 ASP cc_start: 0.9133 (p0) cc_final: 0.8888 (p0) REVERT: B 209 LYS cc_start: 0.9214 (mtmt) cc_final: 0.8822 (mmtm) REVERT: B 216 GLU cc_start: 0.8850 (pp20) cc_final: 0.8433 (pp20) REVERT: B 316 TYR cc_start: 0.6494 (m-80) cc_final: 0.6071 (t80) REVERT: B 356 ASP cc_start: 0.9110 (m-30) cc_final: 0.8423 (p0) REVERT: B 394 TYR cc_start: 0.8097 (t80) cc_final: 0.7467 (t80) REVERT: B 415 MET cc_start: 0.7556 (ppp) cc_final: 0.7181 (pmm) REVERT: B 496 TYR cc_start: 0.8023 (m-80) cc_final: 0.7672 (m-80) REVERT: B 543 TYR cc_start: 0.8530 (p90) cc_final: 0.8315 (p90) REVERT: B 545 VAL cc_start: 0.9110 (t) cc_final: 0.8256 (t) REVERT: B 552 ILE cc_start: 0.8704 (pt) cc_final: 0.8390 (pt) REVERT: B 569 ASP cc_start: 0.9169 (t0) cc_final: 0.8943 (t70) REVERT: B 571 SER cc_start: 0.9111 (t) cc_final: 0.8804 (p) REVERT: B 586 ARG cc_start: 0.9134 (ttt90) cc_final: 0.8448 (tpp-160) REVERT: B 635 ASN cc_start: 0.9017 (p0) cc_final: 0.8379 (p0) REVERT: B 669 PHE cc_start: 0.8628 (m-80) cc_final: 0.8408 (m-80) REVERT: B 734 TYR cc_start: 0.7884 (t80) cc_final: 0.7462 (t80) REVERT: B 858 TRP cc_start: 0.8169 (m-90) cc_final: 0.7521 (m-90) REVERT: B 870 PHE cc_start: 0.9463 (t80) cc_final: 0.8664 (t80) REVERT: B 901 LYS cc_start: 0.9179 (mmmm) cc_final: 0.8744 (mmtt) REVERT: B 935 LEU cc_start: 0.7220 (mt) cc_final: 0.6706 (mt) REVERT: B 985 TYR cc_start: 0.9144 (m-80) cc_final: 0.8572 (m-80) REVERT: B 1072 GLN cc_start: 0.9161 (mt0) cc_final: 0.8450 (tt0) REVERT: B 1208 MET cc_start: 0.9550 (ppp) cc_final: 0.9330 (ppp) REVERT: B 1224 THR cc_start: 0.8434 (p) cc_final: 0.7906 (t) REVERT: B 1227 ASP cc_start: 0.8544 (m-30) cc_final: 0.7718 (p0) REVERT: B 1238 ILE cc_start: 0.7990 (mm) cc_final: 0.7723 (mm) REVERT: B 1241 GLN cc_start: 0.7470 (mp-120) cc_final: 0.7169 (mp10) REVERT: B 1323 TYR cc_start: 0.7543 (t80) cc_final: 0.7281 (t80) REVERT: B 1331 ASN cc_start: 0.6800 (m110) cc_final: 0.3793 (m110) REVERT: C 32 MET cc_start: 0.9212 (ttt) cc_final: 0.8942 (ttm) REVERT: C 97 ASN cc_start: 0.8944 (t0) cc_final: 0.8503 (t0) REVERT: C 121 MET cc_start: 0.8519 (mmt) cc_final: 0.8075 (mpp) REVERT: C 151 MET cc_start: 0.4842 (ttp) cc_final: 0.4478 (tpp) REVERT: C 209 LYS cc_start: 0.9522 (mtmt) cc_final: 0.8745 (ptpt) REVERT: C 270 ARG cc_start: 0.7977 (tpt-90) cc_final: 0.6884 (tpt170) REVERT: C 290 PHE cc_start: 0.9476 (m-80) cc_final: 0.9072 (m-80) REVERT: C 389 ASN cc_start: 0.7853 (m-40) cc_final: 0.7449 (t0) REVERT: C 428 ARG cc_start: 0.5856 (mpt180) cc_final: 0.5197 (mtm180) REVERT: C 496 TYR cc_start: 0.7609 (m-80) cc_final: 0.7269 (m-80) REVERT: C 564 LEU cc_start: 0.8796 (tp) cc_final: 0.8161 (tt) REVERT: C 567 LYS cc_start: 0.9475 (mmpt) cc_final: 0.9203 (mmmt) REVERT: C 627 LEU cc_start: 0.7579 (tp) cc_final: 0.7110 (tp) REVERT: C 650 ILE cc_start: 0.6836 (mm) cc_final: 0.6433 (mm) REVERT: C 666 MET cc_start: 0.8956 (ttm) cc_final: 0.8312 (ptm) REVERT: C 669 PHE cc_start: 0.8195 (m-10) cc_final: 0.7833 (m-10) REVERT: C 670 LEU cc_start: 0.9596 (mp) cc_final: 0.9295 (pp) REVERT: C 800 TYR cc_start: 0.8991 (p90) cc_final: 0.8608 (p90) REVERT: C 931 LEU cc_start: 0.9262 (tp) cc_final: 0.8887 (tp) REVERT: C 965 LEU cc_start: 0.9079 (tt) cc_final: 0.8868 (tt) REVERT: C 975 GLN cc_start: 0.8856 (mm-40) cc_final: 0.8439 (tp-100) REVERT: C 983 ASN cc_start: 0.9385 (m-40) cc_final: 0.9064 (m110) REVERT: C 985 TYR cc_start: 0.8378 (m-80) cc_final: 0.8065 (m-10) REVERT: C 988 ASP cc_start: 0.9330 (m-30) cc_final: 0.8910 (m-30) REVERT: C 1028 PHE cc_start: 0.8486 (m-80) cc_final: 0.8260 (m-80) REVERT: C 1047 LYS cc_start: 0.9396 (ttmt) cc_final: 0.9162 (ptmm) REVERT: C 1057 PHE cc_start: 0.8751 (t80) cc_final: 0.8325 (t80) REVERT: C 1076 ASP cc_start: 0.8674 (p0) cc_final: 0.7963 (m-30) REVERT: C 1125 LEU cc_start: 0.9525 (mt) cc_final: 0.9247 (pp) REVERT: C 1128 LEU cc_start: 0.9427 (mt) cc_final: 0.9106 (mt) REVERT: C 1132 TRP cc_start: 0.9097 (t60) cc_final: 0.8531 (t60) REVERT: C 1133 LYS cc_start: 0.9405 (ttmt) cc_final: 0.9193 (tptt) REVERT: C 1150 LEU cc_start: 0.9367 (mm) cc_final: 0.9028 (mm) REVERT: C 1154 PHE cc_start: 0.8586 (m-80) cc_final: 0.7147 (m-80) REVERT: C 1314 MET cc_start: 0.9120 (mpp) cc_final: 0.8897 (ptp) REVERT: C 1323 TYR cc_start: 0.7862 (t80) cc_final: 0.7632 (t80) REVERT: D 50 LEU cc_start: 0.9131 (tt) cc_final: 0.8739 (tt) REVERT: D 121 MET cc_start: 0.8120 (tpp) cc_final: 0.7156 (tpp) REVERT: D 126 ASP cc_start: 0.9136 (p0) cc_final: 0.8891 (p0) REVERT: D 209 LYS cc_start: 0.9214 (mtmt) cc_final: 0.8823 (mmtm) REVERT: D 216 GLU cc_start: 0.8848 (pp20) cc_final: 0.8432 (pp20) REVERT: D 316 TYR cc_start: 0.6495 (m-80) cc_final: 0.6074 (t80) REVERT: D 356 ASP cc_start: 0.9115 (m-30) cc_final: 0.8426 (p0) REVERT: D 394 TYR cc_start: 0.8057 (t80) cc_final: 0.7283 (t80) REVERT: D 415 MET cc_start: 0.7553 (ppp) cc_final: 0.7179 (pmm) REVERT: D 493 LEU cc_start: 0.9177 (tp) cc_final: 0.8870 (tp) REVERT: D 496 TYR cc_start: 0.8028 (m-80) cc_final: 0.7680 (m-80) REVERT: D 543 TYR cc_start: 0.8531 (p90) cc_final: 0.8320 (p90) REVERT: D 545 VAL cc_start: 0.9111 (t) cc_final: 0.7953 (t) REVERT: D 552 ILE cc_start: 0.8708 (pt) cc_final: 0.8393 (pt) REVERT: D 569 ASP cc_start: 0.9172 (t0) cc_final: 0.8944 (t70) REVERT: D 571 SER cc_start: 0.9107 (t) cc_final: 0.8803 (p) REVERT: D 586 ARG cc_start: 0.9130 (ttt90) cc_final: 0.8443 (tpp-160) REVERT: D 635 ASN cc_start: 0.8982 (p0) cc_final: 0.8427 (p0) REVERT: D 669 PHE cc_start: 0.8631 (m-80) cc_final: 0.8408 (m-80) REVERT: D 734 TYR cc_start: 0.7887 (t80) cc_final: 0.7466 (t80) REVERT: D 858 TRP cc_start: 0.8172 (m-90) cc_final: 0.7520 (m-90) REVERT: D 870 PHE cc_start: 0.9485 (t80) cc_final: 0.8714 (t80) REVERT: D 901 LYS cc_start: 0.9166 (mmmm) cc_final: 0.8749 (mmtt) REVERT: D 935 LEU cc_start: 0.7180 (mt) cc_final: 0.6497 (mt) REVERT: D 985 TYR cc_start: 0.9174 (m-80) cc_final: 0.8614 (m-80) REVERT: D 1072 GLN cc_start: 0.9185 (mt0) cc_final: 0.8300 (tt0) REVERT: D 1224 THR cc_start: 0.8432 (p) cc_final: 0.7908 (t) REVERT: D 1227 ASP cc_start: 0.8542 (m-30) cc_final: 0.7715 (p0) REVERT: D 1323 TYR cc_start: 0.7545 (t80) cc_final: 0.7280 (t80) REVERT: D 1328 LEU cc_start: 0.9456 (tp) cc_final: 0.9135 (tp) REVERT: D 1331 ASN cc_start: 0.6482 (m110) cc_final: 0.3681 (m110) outliers start: 24 outliers final: 4 residues processed: 949 average time/residue: 0.5152 time to fit residues: 799.2314 Evaluate side-chains 692 residues out of total 4451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 688 time to evaluate : 3.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 256 optimal weight: 0.1980 chunk 143 optimal weight: 10.0000 chunk 383 optimal weight: 6.9990 chunk 314 optimal weight: 9.9990 chunk 127 optimal weight: 3.9990 chunk 462 optimal weight: 20.0000 chunk 499 optimal weight: 0.5980 chunk 411 optimal weight: 5.9990 chunk 458 optimal weight: 10.0000 chunk 157 optimal weight: 9.9990 chunk 370 optimal weight: 0.0370 overall best weight: 2.1662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 854 GLN ** A 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 938 ASN A 976 ASN ** A1233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 GLN B 441 HIS ** B 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 967 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 483 ASN ** C 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 691 GLN C 854 GLN ** C 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 976 ASN ** C1233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 406 GLN D 441 HIS ** D 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 967 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 41179 Z= 0.238 Angle : 0.767 14.377 55948 Z= 0.382 Chirality : 0.049 0.306 6471 Planarity : 0.005 0.070 7166 Dihedral : 8.195 73.285 6200 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 20.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.97 % Favored : 89.95 % Rotamer: Outliers : 0.36 % Allowed : 4.94 % Favored : 94.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -3.12 (0.11), residues: 5084 helix: 0.04 (0.17), residues: 860 sheet: -1.72 (0.11), residues: 1840 loop : -3.20 (0.11), residues: 2384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 436 HIS 0.009 0.001 HIS C 466 PHE 0.047 0.002 PHE B1049 TYR 0.027 0.002 TYR D 256 ARG 0.010 0.001 ARG C 370 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 931 residues out of total 4451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 915 time to evaluate : 4.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 MET cc_start: 0.9248 (ttt) cc_final: 0.8985 (ttt) REVERT: A 98 GLU cc_start: 0.8925 (pm20) cc_final: 0.8553 (pm20) REVERT: A 121 MET cc_start: 0.8711 (mmt) cc_final: 0.8170 (mpp) REVERT: A 209 LYS cc_start: 0.9508 (mtmt) cc_final: 0.8300 (mmtm) REVERT: A 251 CYS cc_start: 0.8388 (m) cc_final: 0.7873 (t) REVERT: A 289 LYS cc_start: 0.9472 (mppt) cc_final: 0.9219 (mmmt) REVERT: A 290 PHE cc_start: 0.9450 (m-80) cc_final: 0.8982 (m-80) REVERT: A 389 ASN cc_start: 0.8083 (m-40) cc_final: 0.7682 (t0) REVERT: A 428 ARG cc_start: 0.5884 (mpt180) cc_final: 0.5187 (mtp180) REVERT: A 496 TYR cc_start: 0.7666 (m-80) cc_final: 0.7386 (m-80) REVERT: A 552 ILE cc_start: 0.8541 (tp) cc_final: 0.8309 (tp) REVERT: A 564 LEU cc_start: 0.8656 (tp) cc_final: 0.7746 (tt) REVERT: A 567 LYS cc_start: 0.9497 (mmpt) cc_final: 0.9258 (mmmt) REVERT: A 620 ASN cc_start: 0.9144 (p0) cc_final: 0.8937 (p0) REVERT: A 627 LEU cc_start: 0.8142 (mm) cc_final: 0.7564 (mt) REVERT: A 650 ILE cc_start: 0.6872 (mm) cc_final: 0.6462 (mm) REVERT: A 666 MET cc_start: 0.8987 (ttm) cc_final: 0.8286 (ptm) REVERT: A 669 PHE cc_start: 0.8197 (m-10) cc_final: 0.7949 (m-10) REVERT: A 670 LEU cc_start: 0.9579 (mp) cc_final: 0.9244 (pp) REVERT: A 800 TYR cc_start: 0.8979 (p90) cc_final: 0.8627 (p90) REVERT: A 870 PHE cc_start: 0.8588 (m-80) cc_final: 0.8320 (m-80) REVERT: A 975 GLN cc_start: 0.8911 (mm-40) cc_final: 0.8475 (tp-100) REVERT: A 983 ASN cc_start: 0.9377 (m-40) cc_final: 0.9063 (m110) REVERT: A 988 ASP cc_start: 0.9116 (m-30) cc_final: 0.8542 (m-30) REVERT: A 1028 PHE cc_start: 0.8555 (m-80) cc_final: 0.8321 (m-80) REVERT: A 1057 PHE cc_start: 0.8726 (t80) cc_final: 0.8324 (t80) REVERT: A 1076 ASP cc_start: 0.8616 (p0) cc_final: 0.7904 (m-30) REVERT: A 1128 LEU cc_start: 0.9409 (mt) cc_final: 0.9184 (mt) REVERT: A 1144 VAL cc_start: 0.8423 (p) cc_final: 0.8133 (m) REVERT: A 1150 LEU cc_start: 0.9420 (mm) cc_final: 0.9096 (mm) REVERT: A 1154 PHE cc_start: 0.8504 (m-80) cc_final: 0.7360 (m-80) REVERT: A 1165 GLU cc_start: 0.8230 (tm-30) cc_final: 0.7797 (tm-30) REVERT: A 1314 MET cc_start: 0.9138 (mpp) cc_final: 0.8891 (ptp) REVERT: B 50 LEU cc_start: 0.9163 (tt) cc_final: 0.8669 (tt) REVERT: B 121 MET cc_start: 0.8182 (tpp) cc_final: 0.7297 (tpp) REVERT: B 126 ASP cc_start: 0.9193 (p0) cc_final: 0.8834 (p0) REVERT: B 151 MET cc_start: 0.6423 (mtt) cc_final: 0.6038 (ttp) REVERT: B 194 LEU cc_start: 0.8351 (mm) cc_final: 0.8044 (mm) REVERT: B 216 GLU cc_start: 0.8908 (pp20) cc_final: 0.8500 (pp20) REVERT: B 354 LYS cc_start: 0.8475 (tttp) cc_final: 0.7535 (mttt) REVERT: B 356 ASP cc_start: 0.9125 (m-30) cc_final: 0.8389 (p0) REVERT: B 373 ASP cc_start: 0.8136 (t0) cc_final: 0.7884 (t0) REVERT: B 394 TYR cc_start: 0.8049 (t80) cc_final: 0.7747 (t80) REVERT: B 496 TYR cc_start: 0.8008 (m-80) cc_final: 0.7673 (m-80) REVERT: B 543 TYR cc_start: 0.8763 (p90) cc_final: 0.8186 (p90) REVERT: B 552 ILE cc_start: 0.8945 (pt) cc_final: 0.8466 (pt) REVERT: B 572 PHE cc_start: 0.8145 (p90) cc_final: 0.7811 (p90) REVERT: B 669 PHE cc_start: 0.8414 (m-80) cc_final: 0.8114 (m-80) REVERT: B 798 MET cc_start: 0.8177 (mpp) cc_final: 0.7857 (mpp) REVERT: B 858 TRP cc_start: 0.7980 (m-90) cc_final: 0.7522 (m-90) REVERT: B 870 PHE cc_start: 0.9424 (t80) cc_final: 0.9132 (t80) REVERT: B 901 LYS cc_start: 0.9030 (mmmm) cc_final: 0.8607 (mmtt) REVERT: B 933 LEU cc_start: 0.9504 (mt) cc_final: 0.9297 (mt) REVERT: B 935 LEU cc_start: 0.7518 (mt) cc_final: 0.7103 (mt) REVERT: B 985 TYR cc_start: 0.9067 (m-80) cc_final: 0.8683 (m-80) REVERT: B 1072 GLN cc_start: 0.9204 (mt0) cc_final: 0.8526 (tt0) REVERT: B 1223 PRO cc_start: 0.5463 (Cg_exo) cc_final: 0.4960 (Cg_endo) REVERT: B 1224 THR cc_start: 0.8336 (p) cc_final: 0.7925 (t) REVERT: B 1227 ASP cc_start: 0.8978 (m-30) cc_final: 0.8646 (p0) REVERT: B 1323 TYR cc_start: 0.7542 (t80) cc_final: 0.7294 (t80) REVERT: B 1331 ASN cc_start: 0.6358 (m110) cc_final: 0.3968 (m110) REVERT: C 32 MET cc_start: 0.9265 (ttt) cc_final: 0.8859 (ttm) REVERT: C 98 GLU cc_start: 0.8916 (pm20) cc_final: 0.8546 (pm20) REVERT: C 121 MET cc_start: 0.8728 (mmt) cc_final: 0.8190 (mpp) REVERT: C 209 LYS cc_start: 0.9506 (mtmt) cc_final: 0.8297 (mmtm) REVERT: C 251 CYS cc_start: 0.8387 (m) cc_final: 0.7874 (t) REVERT: C 289 LYS cc_start: 0.9472 (mppt) cc_final: 0.9218 (mmmt) REVERT: C 290 PHE cc_start: 0.9447 (m-80) cc_final: 0.8981 (m-80) REVERT: C 389 ASN cc_start: 0.8086 (m-40) cc_final: 0.7681 (t0) REVERT: C 428 ARG cc_start: 0.5878 (mpt180) cc_final: 0.5167 (mtm180) REVERT: C 496 TYR cc_start: 0.7663 (m-80) cc_final: 0.7375 (m-80) REVERT: C 552 ILE cc_start: 0.8526 (tp) cc_final: 0.8299 (tp) REVERT: C 564 LEU cc_start: 0.8654 (tp) cc_final: 0.7744 (tt) REVERT: C 567 LYS cc_start: 0.9499 (mmpt) cc_final: 0.9259 (mmmt) REVERT: C 620 ASN cc_start: 0.9144 (p0) cc_final: 0.8939 (p0) REVERT: C 628 THR cc_start: 0.7306 (m) cc_final: 0.7017 (m) REVERT: C 650 ILE cc_start: 0.6879 (mm) cc_final: 0.6470 (mm) REVERT: C 666 MET cc_start: 0.8997 (ttm) cc_final: 0.8284 (ptm) REVERT: C 669 PHE cc_start: 0.8181 (m-10) cc_final: 0.7930 (m-10) REVERT: C 670 LEU cc_start: 0.9579 (mp) cc_final: 0.9257 (pp) REVERT: C 800 TYR cc_start: 0.8959 (p90) cc_final: 0.8681 (p90) REVERT: C 975 GLN cc_start: 0.8915 (mm-40) cc_final: 0.8479 (tp-100) REVERT: C 983 ASN cc_start: 0.9353 (m-40) cc_final: 0.8958 (m110) REVERT: C 1028 PHE cc_start: 0.8557 (m-80) cc_final: 0.8327 (m-80) REVERT: C 1057 PHE cc_start: 0.8915 (t80) cc_final: 0.8427 (t80) REVERT: C 1076 ASP cc_start: 0.8616 (p0) cc_final: 0.7905 (m-30) REVERT: C 1128 LEU cc_start: 0.9412 (mt) cc_final: 0.9164 (mt) REVERT: C 1144 VAL cc_start: 0.8386 (p) cc_final: 0.8089 (m) REVERT: C 1150 LEU cc_start: 0.9419 (mm) cc_final: 0.9095 (mm) REVERT: C 1154 PHE cc_start: 0.8487 (m-80) cc_final: 0.7336 (m-80) REVERT: C 1165 GLU cc_start: 0.8232 (tm-30) cc_final: 0.7798 (tm-30) REVERT: C 1314 MET cc_start: 0.9140 (mpp) cc_final: 0.8887 (ptp) REVERT: D 50 LEU cc_start: 0.9124 (tt) cc_final: 0.8578 (tt) REVERT: D 121 MET cc_start: 0.8174 (tpp) cc_final: 0.7291 (tpp) REVERT: D 126 ASP cc_start: 0.9198 (p0) cc_final: 0.8838 (p0) REVERT: D 151 MET cc_start: 0.6418 (mtt) cc_final: 0.6036 (ttp) REVERT: D 194 LEU cc_start: 0.8391 (mm) cc_final: 0.8094 (mm) REVERT: D 216 GLU cc_start: 0.8907 (pp20) cc_final: 0.8499 (pp20) REVERT: D 220 THR cc_start: 0.9227 (m) cc_final: 0.9026 (t) REVERT: D 290 PHE cc_start: 0.8955 (m-80) cc_final: 0.8753 (m-80) REVERT: D 354 LYS cc_start: 0.8479 (tttp) cc_final: 0.7541 (mttt) REVERT: D 356 ASP cc_start: 0.9131 (m-30) cc_final: 0.8392 (p0) REVERT: D 373 ASP cc_start: 0.8140 (t0) cc_final: 0.7886 (t0) REVERT: D 394 TYR cc_start: 0.7957 (t80) cc_final: 0.7495 (t80) REVERT: D 496 TYR cc_start: 0.8010 (m-80) cc_final: 0.7653 (m-80) REVERT: D 543 TYR cc_start: 0.8753 (p90) cc_final: 0.8200 (p90) REVERT: D 552 ILE cc_start: 0.8932 (pt) cc_final: 0.8454 (pt) REVERT: D 554 ASP cc_start: 0.6782 (t0) cc_final: 0.6430 (t0) REVERT: D 572 PHE cc_start: 0.8143 (p90) cc_final: 0.7811 (p90) REVERT: D 669 PHE cc_start: 0.8416 (m-80) cc_final: 0.8114 (m-80) REVERT: D 798 MET cc_start: 0.8215 (mpp) cc_final: 0.7851 (mpp) REVERT: D 858 TRP cc_start: 0.7984 (m-90) cc_final: 0.7525 (m-90) REVERT: D 870 PHE cc_start: 0.9454 (t80) cc_final: 0.9165 (t80) REVERT: D 901 LYS cc_start: 0.9002 (mmmm) cc_final: 0.8583 (mmtt) REVERT: D 933 LEU cc_start: 0.9501 (mt) cc_final: 0.9299 (mt) REVERT: D 935 LEU cc_start: 0.7439 (mt) cc_final: 0.7094 (mt) REVERT: D 985 TYR cc_start: 0.9141 (m-80) cc_final: 0.8820 (m-80) REVERT: D 1072 GLN cc_start: 0.9195 (mt0) cc_final: 0.8530 (tt0) REVERT: D 1223 PRO cc_start: 0.5512 (Cg_exo) cc_final: 0.5038 (Cg_endo) REVERT: D 1224 THR cc_start: 0.8330 (p) cc_final: 0.7918 (t) REVERT: D 1227 ASP cc_start: 0.8941 (m-30) cc_final: 0.8645 (p0) REVERT: D 1323 TYR cc_start: 0.7540 (t80) cc_final: 0.7289 (t80) REVERT: D 1331 ASN cc_start: 0.6070 (m110) cc_final: 0.5210 (t0) outliers start: 16 outliers final: 2 residues processed: 925 average time/residue: 0.5090 time to fit residues: 772.6318 Evaluate side-chains 691 residues out of total 4451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 689 time to evaluate : 4.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 456 optimal weight: 8.9990 chunk 347 optimal weight: 4.9990 chunk 239 optimal weight: 10.0000 chunk 51 optimal weight: 7.9990 chunk 220 optimal weight: 0.9990 chunk 310 optimal weight: 3.9990 chunk 463 optimal weight: 20.0000 chunk 491 optimal weight: 5.9990 chunk 242 optimal weight: 0.9990 chunk 439 optimal weight: 8.9990 chunk 132 optimal weight: 8.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 976 ASN A1051 GLN A1252 GLN ** A1277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 976 ASN C1252 GLN ** C1277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 ASN ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.4340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 41179 Z= 0.280 Angle : 0.782 11.237 55948 Z= 0.395 Chirality : 0.049 0.399 6471 Planarity : 0.006 0.071 7166 Dihedral : 7.997 60.267 6200 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 26.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.68 % Favored : 89.24 % Rotamer: Outliers : 0.09 % Allowed : 5.55 % Favored : 94.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -3.02 (0.11), residues: 5084 helix: -0.02 (0.17), residues: 858 sheet: -1.61 (0.12), residues: 1793 loop : -3.11 (0.11), residues: 2433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP B1132 HIS 0.009 0.001 HIS C 321 PHE 0.037 0.002 PHE B1049 TYR 0.028 0.002 TYR D 53 ARG 0.007 0.001 ARG B 945 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 870 residues out of total 4451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 866 time to evaluate : 4.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 GLU cc_start: 0.8883 (pm20) cc_final: 0.8572 (pm20) REVERT: A 121 MET cc_start: 0.8975 (mmt) cc_final: 0.8428 (mpp) REVERT: A 183 LEU cc_start: 0.7994 (tp) cc_final: 0.7766 (tp) REVERT: A 290 PHE cc_start: 0.9510 (m-80) cc_final: 0.9147 (m-80) REVERT: A 301 TYR cc_start: 0.6771 (t80) cc_final: 0.6481 (t80) REVERT: A 373 ASP cc_start: 0.7924 (t0) cc_final: 0.7499 (t0) REVERT: A 389 ASN cc_start: 0.8596 (m-40) cc_final: 0.8123 (t0) REVERT: A 415 MET cc_start: 0.5086 (ppp) cc_final: 0.4864 (ppp) REVERT: A 428 ARG cc_start: 0.5972 (mpt180) cc_final: 0.5239 (mtm180) REVERT: A 491 LYS cc_start: 0.9460 (mmpt) cc_final: 0.9257 (mmmt) REVERT: A 542 ILE cc_start: 0.9415 (mt) cc_final: 0.9134 (tp) REVERT: A 567 LYS cc_start: 0.9547 (mmpt) cc_final: 0.9250 (mmmt) REVERT: A 620 ASN cc_start: 0.9186 (p0) cc_final: 0.8984 (p0) REVERT: A 627 LEU cc_start: 0.8666 (mm) cc_final: 0.8227 (mt) REVERT: A 638 ASP cc_start: 0.8875 (t70) cc_final: 0.8409 (t0) REVERT: A 650 ILE cc_start: 0.6952 (mm) cc_final: 0.6526 (mm) REVERT: A 666 MET cc_start: 0.9075 (ttm) cc_final: 0.8502 (ptm) REVERT: A 669 PHE cc_start: 0.8203 (m-10) cc_final: 0.7900 (m-10) REVERT: A 670 LEU cc_start: 0.9589 (mp) cc_final: 0.9259 (pp) REVERT: A 787 ARG cc_start: 0.8632 (ppt170) cc_final: 0.8289 (pmt-80) REVERT: A 800 TYR cc_start: 0.9028 (p90) cc_final: 0.8724 (p90) REVERT: A 870 PHE cc_start: 0.8799 (m-80) cc_final: 0.8474 (m-80) REVERT: A 933 LEU cc_start: 0.9264 (mt) cc_final: 0.9034 (mt) REVERT: A 965 LEU cc_start: 0.9031 (tt) cc_final: 0.8757 (tt) REVERT: A 968 MET cc_start: 0.7892 (tpt) cc_final: 0.7295 (pmm) REVERT: A 975 GLN cc_start: 0.8971 (mm-40) cc_final: 0.8527 (tp-100) REVERT: A 983 ASN cc_start: 0.9406 (m-40) cc_final: 0.9139 (m110) REVERT: A 988 ASP cc_start: 0.8963 (m-30) cc_final: 0.8520 (m-30) REVERT: A 1028 PHE cc_start: 0.8585 (m-80) cc_final: 0.8336 (m-80) REVERT: A 1057 PHE cc_start: 0.8871 (t80) cc_final: 0.8397 (t80) REVERT: A 1150 LEU cc_start: 0.9429 (mm) cc_final: 0.9129 (pp) REVERT: A 1154 PHE cc_start: 0.8898 (m-80) cc_final: 0.7807 (m-80) REVERT: A 1165 GLU cc_start: 0.8380 (tm-30) cc_final: 0.7958 (tm-30) REVERT: A 1323 TYR cc_start: 0.8027 (t80) cc_final: 0.7781 (t80) REVERT: B 121 MET cc_start: 0.8417 (tpp) cc_final: 0.7659 (tpp) REVERT: B 126 ASP cc_start: 0.9317 (p0) cc_final: 0.9104 (p0) REVERT: B 151 MET cc_start: 0.6395 (mtt) cc_final: 0.5769 (ttp) REVERT: B 209 LYS cc_start: 0.9191 (mtmt) cc_final: 0.8760 (mmtm) REVERT: B 216 GLU cc_start: 0.9039 (pp20) cc_final: 0.8640 (pp20) REVERT: B 290 PHE cc_start: 0.8982 (m-80) cc_final: 0.8676 (m-80) REVERT: B 354 LYS cc_start: 0.8582 (tttp) cc_final: 0.7531 (mttt) REVERT: B 356 ASP cc_start: 0.9147 (m-30) cc_final: 0.8827 (t0) REVERT: B 360 ARG cc_start: 0.8714 (mpt180) cc_final: 0.8457 (mpt-90) REVERT: B 394 TYR cc_start: 0.8052 (t80) cc_final: 0.7435 (t80) REVERT: B 461 LEU cc_start: 0.9267 (mp) cc_final: 0.8962 (mm) REVERT: B 496 TYR cc_start: 0.8153 (m-80) cc_final: 0.7774 (m-80) REVERT: B 543 TYR cc_start: 0.8754 (p90) cc_final: 0.8285 (p90) REVERT: B 545 VAL cc_start: 0.8870 (t) cc_final: 0.8309 (t) REVERT: B 552 ILE cc_start: 0.8927 (pt) cc_final: 0.8595 (pt) REVERT: B 572 PHE cc_start: 0.8342 (p90) cc_final: 0.8080 (p90) REVERT: B 796 LEU cc_start: 0.9007 (pp) cc_final: 0.8438 (pp) REVERT: B 863 LYS cc_start: 0.9426 (ttpt) cc_final: 0.9221 (mtpt) REVERT: B 870 PHE cc_start: 0.9479 (t80) cc_final: 0.9183 (t80) REVERT: B 901 LYS cc_start: 0.9067 (mmmm) cc_final: 0.8644 (mmtt) REVERT: B 935 LEU cc_start: 0.7842 (mt) cc_final: 0.7471 (mp) REVERT: B 945 ARG cc_start: 0.8775 (tpm170) cc_final: 0.8503 (tpp-160) REVERT: B 985 TYR cc_start: 0.9076 (m-80) cc_final: 0.8617 (m-80) REVERT: B 1072 GLN cc_start: 0.9390 (mt0) cc_final: 0.8780 (tm-30) REVERT: B 1205 GLU cc_start: 0.8343 (pt0) cc_final: 0.8066 (tt0) REVERT: B 1207 GLU cc_start: 0.9240 (tp30) cc_final: 0.8987 (mm-30) REVERT: B 1223 PRO cc_start: 0.6242 (Cg_exo) cc_final: 0.5936 (Cg_endo) REVERT: B 1224 THR cc_start: 0.8562 (p) cc_final: 0.8099 (t) REVERT: B 1227 ASP cc_start: 0.9166 (m-30) cc_final: 0.8912 (p0) REVERT: B 1241 GLN cc_start: 0.7411 (mp-120) cc_final: 0.7205 (mm-40) REVERT: B 1323 TYR cc_start: 0.7746 (t80) cc_final: 0.7506 (t80) REVERT: B 1329 LYS cc_start: 0.8807 (pttt) cc_final: 0.8535 (mppt) REVERT: B 1331 ASN cc_start: 0.6630 (m110) cc_final: 0.4448 (m110) REVERT: C 32 MET cc_start: 0.9360 (ttt) cc_final: 0.9106 (ttt) REVERT: C 98 GLU cc_start: 0.8872 (pm20) cc_final: 0.8563 (pm20) REVERT: C 121 MET cc_start: 0.8958 (mmt) cc_final: 0.8418 (mpp) REVERT: C 151 MET cc_start: 0.3747 (ttm) cc_final: 0.2980 (ttm) REVERT: C 290 PHE cc_start: 0.9509 (m-80) cc_final: 0.9149 (m-80) REVERT: C 301 TYR cc_start: 0.6763 (t80) cc_final: 0.6479 (t80) REVERT: C 373 ASP cc_start: 0.7931 (t0) cc_final: 0.7509 (t0) REVERT: C 389 ASN cc_start: 0.8581 (m-40) cc_final: 0.8110 (t0) REVERT: C 428 ARG cc_start: 0.5908 (mpt180) cc_final: 0.5209 (mtm180) REVERT: C 491 LYS cc_start: 0.9461 (mmpt) cc_final: 0.9258 (mmmt) REVERT: C 542 ILE cc_start: 0.9428 (mt) cc_final: 0.9151 (tp) REVERT: C 567 LYS cc_start: 0.9546 (mmpt) cc_final: 0.9250 (mmmt) REVERT: C 620 ASN cc_start: 0.9195 (p0) cc_final: 0.8992 (p0) REVERT: C 627 LEU cc_start: 0.8656 (mm) cc_final: 0.8256 (mt) REVERT: C 650 ILE cc_start: 0.6967 (mm) cc_final: 0.6540 (mm) REVERT: C 666 MET cc_start: 0.9056 (ttm) cc_final: 0.8591 (ptm) REVERT: C 669 PHE cc_start: 0.8251 (m-10) cc_final: 0.7998 (m-10) REVERT: C 787 ARG cc_start: 0.8630 (ppt170) cc_final: 0.8291 (pmt-80) REVERT: C 798 MET cc_start: 0.8635 (ppp) cc_final: 0.8198 (ppp) REVERT: C 800 TYR cc_start: 0.8907 (p90) cc_final: 0.8643 (p90) REVERT: C 931 LEU cc_start: 0.9096 (tp) cc_final: 0.8894 (tp) REVERT: C 933 LEU cc_start: 0.9265 (mt) cc_final: 0.9032 (mt) REVERT: C 968 MET cc_start: 0.7883 (tpt) cc_final: 0.7289 (pmm) REVERT: C 975 GLN cc_start: 0.8972 (mm-40) cc_final: 0.8529 (tp-100) REVERT: C 983 ASN cc_start: 0.9315 (m-40) cc_final: 0.9037 (m110) REVERT: C 988 ASP cc_start: 0.9244 (m-30) cc_final: 0.8914 (m-30) REVERT: C 1028 PHE cc_start: 0.8589 (m-80) cc_final: 0.8337 (m-80) REVERT: C 1057 PHE cc_start: 0.8791 (t80) cc_final: 0.8339 (t80) REVERT: C 1150 LEU cc_start: 0.9424 (mm) cc_final: 0.9076 (mm) REVERT: C 1154 PHE cc_start: 0.8916 (m-80) cc_final: 0.7830 (m-80) REVERT: C 1165 GLU cc_start: 0.8382 (tm-30) cc_final: 0.7976 (tm-30) REVERT: C 1323 TYR cc_start: 0.8046 (t80) cc_final: 0.7796 (t80) REVERT: D 32 MET cc_start: 0.9259 (tpt) cc_final: 0.9013 (tpt) REVERT: D 54 LEU cc_start: 0.8012 (tp) cc_final: 0.7607 (pp) REVERT: D 121 MET cc_start: 0.8419 (tpp) cc_final: 0.7651 (tpp) REVERT: D 126 ASP cc_start: 0.9321 (p0) cc_final: 0.9110 (p0) REVERT: D 151 MET cc_start: 0.6394 (mtt) cc_final: 0.5772 (ttp) REVERT: D 209 LYS cc_start: 0.9194 (mtmt) cc_final: 0.8763 (mmtm) REVERT: D 216 GLU cc_start: 0.9039 (pp20) cc_final: 0.8640 (pp20) REVERT: D 290 PHE cc_start: 0.9040 (m-80) cc_final: 0.8720 (m-80) REVERT: D 354 LYS cc_start: 0.8591 (tttp) cc_final: 0.7541 (mttt) REVERT: D 356 ASP cc_start: 0.9152 (m-30) cc_final: 0.8828 (t0) REVERT: D 360 ARG cc_start: 0.8699 (mpt180) cc_final: 0.8453 (mpt-90) REVERT: D 394 TYR cc_start: 0.7907 (t80) cc_final: 0.7365 (t80) REVERT: D 461 LEU cc_start: 0.9283 (mp) cc_final: 0.9030 (mp) REVERT: D 496 TYR cc_start: 0.8126 (m-80) cc_final: 0.7782 (m-80) REVERT: D 543 TYR cc_start: 0.8742 (p90) cc_final: 0.8280 (p90) REVERT: D 545 VAL cc_start: 0.8704 (t) cc_final: 0.7838 (t) REVERT: D 552 ILE cc_start: 0.8924 (pt) cc_final: 0.8589 (pt) REVERT: D 572 PHE cc_start: 0.8340 (p90) cc_final: 0.8082 (p90) REVERT: D 796 LEU cc_start: 0.9030 (pp) cc_final: 0.8475 (pp) REVERT: D 870 PHE cc_start: 0.9494 (t80) cc_final: 0.9181 (t80) REVERT: D 901 LYS cc_start: 0.9050 (mmmm) cc_final: 0.8615 (mmtt) REVERT: D 935 LEU cc_start: 0.7688 (mt) cc_final: 0.7319 (mp) REVERT: D 985 TYR cc_start: 0.9210 (m-80) cc_final: 0.8819 (m-80) REVERT: D 1072 GLN cc_start: 0.9250 (mt0) cc_final: 0.8556 (tt0) REVERT: D 1205 GLU cc_start: 0.8099 (pt0) cc_final: 0.7812 (tt0) REVERT: D 1223 PRO cc_start: 0.6252 (Cg_exo) cc_final: 0.5968 (Cg_endo) REVERT: D 1224 THR cc_start: 0.8549 (p) cc_final: 0.8089 (t) REVERT: D 1227 ASP cc_start: 0.9151 (m-30) cc_final: 0.8910 (p0) REVERT: D 1330 TYR cc_start: 0.9192 (p90) cc_final: 0.8956 (p90) REVERT: D 1331 ASN cc_start: 0.6304 (m110) cc_final: 0.5109 (t0) REVERT: D 1333 LEU cc_start: 0.9135 (tp) cc_final: 0.8929 (tp) outliers start: 4 outliers final: 0 residues processed: 868 average time/residue: 0.5206 time to fit residues: 738.5570 Evaluate side-chains 697 residues out of total 4451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 697 time to evaluate : 4.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 408 optimal weight: 7.9990 chunk 278 optimal weight: 8.9990 chunk 7 optimal weight: 10.0000 chunk 365 optimal weight: 10.0000 chunk 202 optimal weight: 9.9990 chunk 419 optimal weight: 4.9990 chunk 339 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 250 optimal weight: 3.9990 chunk 440 optimal weight: 0.7980 chunk 123 optimal weight: 7.9990 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 647 ASN ** A 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 ASN ** B 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 GLN ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 584 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 647 ASN ** C 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1051 GLN ** C1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 302 GLN ** D 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.5337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 41179 Z= 0.368 Angle : 0.863 10.258 55948 Z= 0.445 Chirality : 0.051 0.357 6471 Planarity : 0.006 0.072 7166 Dihedral : 8.225 59.827 6200 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 34.18 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.84 % Favored : 88.08 % Rotamer: Outliers : 0.04 % Allowed : 5.44 % Favored : 94.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -3.30 (0.11), residues: 5084 helix: -0.65 (0.16), residues: 867 sheet: -1.75 (0.11), residues: 1773 loop : -3.15 (0.11), residues: 2444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.004 TRP B 436 HIS 0.013 0.002 HIS C 321 PHE 0.028 0.003 PHE D1049 TYR 0.052 0.003 TYR B1152 ARG 0.011 0.001 ARG B 945 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 825 residues out of total 4451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 823 time to evaluate : 4.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 32 MET cc_start: 0.9565 (ttt) cc_final: 0.9354 (ttm) REVERT: A 50 LEU cc_start: 0.9617 (tt) cc_final: 0.8970 (mm) REVERT: A 121 MET cc_start: 0.9070 (mmt) cc_final: 0.8622 (mpp) REVERT: A 137 ILE cc_start: 0.9021 (tt) cc_final: 0.8798 (tt) REVERT: A 151 MET cc_start: 0.4534 (ttm) cc_final: 0.4082 (tpp) REVERT: A 216 GLU cc_start: 0.9095 (pm20) cc_final: 0.8892 (mp0) REVERT: A 289 LYS cc_start: 0.9452 (mppt) cc_final: 0.9157 (mmmt) REVERT: A 290 PHE cc_start: 0.9396 (m-80) cc_final: 0.9145 (m-80) REVERT: A 309 PHE cc_start: 0.9101 (m-80) cc_final: 0.8827 (m-10) REVERT: A 351 SER cc_start: 0.9383 (m) cc_final: 0.8984 (t) REVERT: A 373 ASP cc_start: 0.8299 (t0) cc_final: 0.7902 (t0) REVERT: A 462 GLU cc_start: 0.7765 (pt0) cc_final: 0.7524 (pm20) REVERT: A 464 MET cc_start: 0.9452 (ttm) cc_final: 0.9222 (ttm) REVERT: A 523 HIS cc_start: 0.9115 (m-70) cc_final: 0.8825 (m-70) REVERT: A 573 SER cc_start: 0.9296 (t) cc_final: 0.9062 (p) REVERT: A 627 LEU cc_start: 0.8849 (mm) cc_final: 0.8464 (mt) REVERT: A 650 ILE cc_start: 0.7262 (mm) cc_final: 0.6847 (mm) REVERT: A 666 MET cc_start: 0.9177 (ttm) cc_final: 0.8909 (ttm) REVERT: A 669 PHE cc_start: 0.8520 (m-10) cc_final: 0.8242 (m-10) REVERT: A 764 GLU cc_start: 0.6353 (mp0) cc_final: 0.5972 (mp0) REVERT: A 800 TYR cc_start: 0.9038 (p90) cc_final: 0.8718 (p90) REVERT: A 870 PHE cc_start: 0.8892 (m-80) cc_final: 0.8505 (m-80) REVERT: A 931 LEU cc_start: 0.8951 (tp) cc_final: 0.8686 (tp) REVERT: A 933 LEU cc_start: 0.9171 (mt) cc_final: 0.8956 (mt) REVERT: A 968 MET cc_start: 0.7796 (tpt) cc_final: 0.7087 (pmm) REVERT: A 975 GLN cc_start: 0.9002 (mm-40) cc_final: 0.8520 (tp-100) REVERT: A 988 ASP cc_start: 0.9102 (m-30) cc_final: 0.8664 (m-30) REVERT: A 1028 PHE cc_start: 0.8679 (m-80) cc_final: 0.8416 (m-80) REVERT: A 1057 PHE cc_start: 0.8816 (t80) cc_final: 0.8532 (t80) REVERT: A 1076 ASP cc_start: 0.8745 (p0) cc_final: 0.8098 (m-30) REVERT: A 1132 TRP cc_start: 0.8771 (t60) cc_final: 0.8149 (t60) REVERT: A 1133 LYS cc_start: 0.9485 (ttmt) cc_final: 0.9250 (tppt) REVERT: A 1144 VAL cc_start: 0.8620 (p) cc_final: 0.8315 (m) REVERT: A 1150 LEU cc_start: 0.9526 (mm) cc_final: 0.9232 (pp) REVERT: A 1154 PHE cc_start: 0.9206 (m-80) cc_final: 0.8227 (m-80) REVERT: A 1165 GLU cc_start: 0.8585 (tm-30) cc_final: 0.8359 (tm-30) REVERT: A 1323 TYR cc_start: 0.8228 (t80) cc_final: 0.7792 (t80) REVERT: B 121 MET cc_start: 0.8661 (tpp) cc_final: 0.8211 (tpt) REVERT: B 126 ASP cc_start: 0.9457 (p0) cc_final: 0.9133 (p0) REVERT: B 151 MET cc_start: 0.6678 (mtt) cc_final: 0.5885 (ttp) REVERT: B 290 PHE cc_start: 0.9109 (m-80) cc_final: 0.8775 (m-80) REVERT: B 354 LYS cc_start: 0.8652 (tttp) cc_final: 0.7592 (mttt) REVERT: B 356 ASP cc_start: 0.9220 (m-30) cc_final: 0.8905 (t0) REVERT: B 370 ARG cc_start: 0.8682 (ptm160) cc_final: 0.8038 (ttm110) REVERT: B 418 SER cc_start: 0.9250 (t) cc_final: 0.9001 (t) REVERT: B 422 ARG cc_start: 0.9056 (mtt90) cc_final: 0.8504 (mtm-85) REVERT: B 461 LEU cc_start: 0.9329 (mp) cc_final: 0.9126 (mm) REVERT: B 496 TYR cc_start: 0.8158 (m-80) cc_final: 0.7884 (m-80) REVERT: B 543 TYR cc_start: 0.8702 (p90) cc_final: 0.8186 (p90) REVERT: B 545 VAL cc_start: 0.8665 (t) cc_final: 0.8131 (t) REVERT: B 550 ASP cc_start: 0.9306 (m-30) cc_final: 0.9103 (m-30) REVERT: B 552 ILE cc_start: 0.9368 (pt) cc_final: 0.8909 (pt) REVERT: B 688 MET cc_start: 0.8201 (ppp) cc_final: 0.7919 (ppp) REVERT: B 796 LEU cc_start: 0.8596 (pp) cc_final: 0.8386 (pp) REVERT: B 870 PHE cc_start: 0.9497 (t80) cc_final: 0.9204 (t80) REVERT: B 901 LYS cc_start: 0.9050 (mmmm) cc_final: 0.8603 (mmmt) REVERT: B 985 TYR cc_start: 0.9114 (m-80) cc_final: 0.8885 (m-80) REVERT: B 1072 GLN cc_start: 0.9441 (mt0) cc_final: 0.9004 (tm-30) REVERT: B 1156 LEU cc_start: 0.7880 (mm) cc_final: 0.7502 (mm) REVERT: B 1205 GLU cc_start: 0.8268 (pt0) cc_final: 0.7967 (tt0) REVERT: B 1207 GLU cc_start: 0.9331 (tp30) cc_final: 0.9081 (tp30) REVERT: B 1223 PRO cc_start: 0.6823 (Cg_exo) cc_final: 0.6510 (Cg_endo) REVERT: B 1224 THR cc_start: 0.8813 (p) cc_final: 0.8414 (t) REVERT: B 1227 ASP cc_start: 0.9294 (m-30) cc_final: 0.9083 (p0) REVERT: B 1328 LEU cc_start: 0.9447 (tp) cc_final: 0.8974 (tp) REVERT: B 1330 TYR cc_start: 0.9188 (p90) cc_final: 0.8904 (p90) REVERT: B 1331 ASN cc_start: 0.6528 (m110) cc_final: 0.4519 (m110) REVERT: C 32 MET cc_start: 0.9525 (ttt) cc_final: 0.9299 (ttt) REVERT: C 50 LEU cc_start: 0.9605 (tt) cc_final: 0.9007 (mm) REVERT: C 121 MET cc_start: 0.9079 (mmt) cc_final: 0.8621 (mpp) REVERT: C 137 ILE cc_start: 0.9022 (tt) cc_final: 0.8799 (tt) REVERT: C 200 GLN cc_start: 0.8750 (mt0) cc_final: 0.8509 (tt0) REVERT: C 289 LYS cc_start: 0.9443 (mppt) cc_final: 0.9188 (mmmt) REVERT: C 290 PHE cc_start: 0.9385 (m-80) cc_final: 0.9154 (m-80) REVERT: C 309 PHE cc_start: 0.9107 (m-80) cc_final: 0.8768 (m-10) REVERT: C 351 SER cc_start: 0.9382 (m) cc_final: 0.8990 (t) REVERT: C 373 ASP cc_start: 0.8319 (t0) cc_final: 0.7933 (t0) REVERT: C 428 ARG cc_start: 0.6187 (mpt180) cc_final: 0.5495 (mtp180) REVERT: C 462 GLU cc_start: 0.7735 (pt0) cc_final: 0.7508 (pm20) REVERT: C 464 MET cc_start: 0.9454 (ttm) cc_final: 0.9235 (ttm) REVERT: C 523 HIS cc_start: 0.9119 (m-70) cc_final: 0.8824 (m-70) REVERT: C 567 LYS cc_start: 0.9619 (mmpt) cc_final: 0.9375 (mmmt) REVERT: C 573 SER cc_start: 0.9294 (t) cc_final: 0.9061 (p) REVERT: C 627 LEU cc_start: 0.8881 (mm) cc_final: 0.8530 (mt) REVERT: C 650 ILE cc_start: 0.7274 (mm) cc_final: 0.6858 (mm) REVERT: C 666 MET cc_start: 0.9171 (ttm) cc_final: 0.8902 (ttm) REVERT: C 669 PHE cc_start: 0.8510 (m-10) cc_final: 0.8233 (m-10) REVERT: C 764 GLU cc_start: 0.6325 (mp0) cc_final: 0.5944 (mp0) REVERT: C 800 TYR cc_start: 0.8917 (p90) cc_final: 0.8666 (p90) REVERT: C 931 LEU cc_start: 0.9040 (tp) cc_final: 0.8815 (tp) REVERT: C 933 LEU cc_start: 0.9150 (mt) cc_final: 0.8949 (mt) REVERT: C 968 MET cc_start: 0.7775 (tpt) cc_final: 0.7102 (pmm) REVERT: C 975 GLN cc_start: 0.9003 (mm-40) cc_final: 0.8524 (tp-100) REVERT: C 988 ASP cc_start: 0.9188 (m-30) cc_final: 0.8935 (m-30) REVERT: C 1028 PHE cc_start: 0.8680 (m-80) cc_final: 0.8416 (m-80) REVERT: C 1057 PHE cc_start: 0.8894 (t80) cc_final: 0.8501 (t80) REVERT: C 1076 ASP cc_start: 0.8746 (p0) cc_final: 0.8105 (m-30) REVERT: C 1144 VAL cc_start: 0.8611 (p) cc_final: 0.8278 (m) REVERT: C 1150 LEU cc_start: 0.9527 (mm) cc_final: 0.9201 (pp) REVERT: C 1154 PHE cc_start: 0.9221 (m-80) cc_final: 0.8178 (m-80) REVERT: C 1165 GLU cc_start: 0.8587 (tm-30) cc_final: 0.8135 (tm-30) REVERT: C 1323 TYR cc_start: 0.8241 (t80) cc_final: 0.7803 (t80) REVERT: D 54 LEU cc_start: 0.8114 (tp) cc_final: 0.7847 (tp) REVERT: D 121 MET cc_start: 0.8664 (tpp) cc_final: 0.8208 (tpt) REVERT: D 126 ASP cc_start: 0.9458 (p0) cc_final: 0.9141 (p0) REVERT: D 151 MET cc_start: 0.6670 (mtt) cc_final: 0.5886 (ttp) REVERT: D 290 PHE cc_start: 0.9136 (m-80) cc_final: 0.8799 (m-80) REVERT: D 354 LYS cc_start: 0.8657 (tttp) cc_final: 0.7592 (mttt) REVERT: D 356 ASP cc_start: 0.9222 (m-30) cc_final: 0.8906 (t0) REVERT: D 461 LEU cc_start: 0.9332 (mp) cc_final: 0.9122 (mm) REVERT: D 496 TYR cc_start: 0.8121 (m-80) cc_final: 0.7794 (m-80) REVERT: D 543 TYR cc_start: 0.8659 (p90) cc_final: 0.8092 (p90) REVERT: D 552 ILE cc_start: 0.9364 (pt) cc_final: 0.8897 (pt) REVERT: D 688 MET cc_start: 0.8156 (ppp) cc_final: 0.7899 (ppp) REVERT: D 796 LEU cc_start: 0.8593 (pp) cc_final: 0.8357 (pp) REVERT: D 870 PHE cc_start: 0.9519 (t80) cc_final: 0.9229 (t80) REVERT: D 901 LYS cc_start: 0.9035 (mmmm) cc_final: 0.8560 (mmmt) REVERT: D 985 TYR cc_start: 0.9013 (m-80) cc_final: 0.8702 (m-80) REVERT: D 1072 GLN cc_start: 0.9204 (mt0) cc_final: 0.8499 (tt0) REVERT: D 1156 LEU cc_start: 0.7918 (mm) cc_final: 0.7551 (mm) REVERT: D 1205 GLU cc_start: 0.8176 (pt0) cc_final: 0.7814 (tt0) REVERT: D 1223 PRO cc_start: 0.6739 (Cg_exo) cc_final: 0.6417 (Cg_endo) REVERT: D 1224 THR cc_start: 0.8752 (p) cc_final: 0.8360 (t) REVERT: D 1241 GLN cc_start: 0.7451 (mp-120) cc_final: 0.6895 (mp-120) REVERT: D 1330 TYR cc_start: 0.9317 (p90) cc_final: 0.9095 (p90) REVERT: D 1331 ASN cc_start: 0.6175 (m110) cc_final: 0.5209 (t0) REVERT: D 1333 LEU cc_start: 0.9247 (tp) cc_final: 0.9030 (tp) outliers start: 2 outliers final: 0 residues processed: 825 average time/residue: 0.5204 time to fit residues: 710.3995 Evaluate side-chains 639 residues out of total 4451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 639 time to evaluate : 4.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 165 optimal weight: 8.9990 chunk 442 optimal weight: 8.9990 chunk 97 optimal weight: 2.9990 chunk 288 optimal weight: 6.9990 chunk 121 optimal weight: 20.0000 chunk 491 optimal weight: 6.9990 chunk 408 optimal weight: 8.9990 chunk 227 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 162 optimal weight: 9.9990 chunk 258 optimal weight: 5.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 584 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 639 ASN A 647 ASN ** A 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1017 ASN ** B1277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 584 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 647 ASN ** C 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1017 ASN ** D1277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.5936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 41179 Z= 0.320 Angle : 0.813 12.348 55948 Z= 0.416 Chirality : 0.050 0.374 6471 Planarity : 0.006 0.057 7166 Dihedral : 8.124 58.398 6200 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 32.27 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.23 % Favored : 88.69 % Rotamer: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -3.26 (0.11), residues: 5084 helix: -0.56 (0.16), residues: 858 sheet: -1.80 (0.11), residues: 1807 loop : -3.07 (0.11), residues: 2419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP B 436 HIS 0.012 0.002 HIS A 321 PHE 0.051 0.003 PHE C1126 TYR 0.029 0.002 TYR D1152 ARG 0.008 0.001 ARG C 539 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 809 residues out of total 4451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 809 time to evaluate : 4.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 32 MET cc_start: 0.9519 (ttt) cc_final: 0.9234 (ttt) REVERT: A 121 MET cc_start: 0.9055 (mmt) cc_final: 0.8572 (mpp) REVERT: A 137 ILE cc_start: 0.9005 (tt) cc_final: 0.8693 (tt) REVERT: A 209 LYS cc_start: 0.9138 (mttt) cc_final: 0.7937 (mmtm) REVERT: A 216 GLU cc_start: 0.9123 (pm20) cc_final: 0.8859 (mp0) REVERT: A 251 CYS cc_start: 0.8681 (m) cc_final: 0.8242 (t) REVERT: A 290 PHE cc_start: 0.9348 (m-80) cc_final: 0.9014 (m-80) REVERT: A 309 PHE cc_start: 0.9336 (m-80) cc_final: 0.8814 (m-80) REVERT: A 351 SER cc_start: 0.9382 (m) cc_final: 0.8989 (t) REVERT: A 373 ASP cc_start: 0.8511 (t0) cc_final: 0.8101 (t0) REVERT: A 385 PHE cc_start: 0.9081 (m-80) cc_final: 0.8698 (m-80) REVERT: A 464 MET cc_start: 0.9451 (ttm) cc_final: 0.9177 (ttm) REVERT: A 500 MET cc_start: 0.7500 (tmm) cc_final: 0.7082 (ttt) REVERT: A 523 HIS cc_start: 0.9187 (m-70) cc_final: 0.8921 (m-70) REVERT: A 564 LEU cc_start: 0.8765 (tp) cc_final: 0.8188 (tt) REVERT: A 582 HIS cc_start: 0.9215 (t70) cc_final: 0.8915 (p-80) REVERT: A 627 LEU cc_start: 0.9013 (mm) cc_final: 0.8530 (mp) REVERT: A 669 PHE cc_start: 0.8534 (m-10) cc_final: 0.8243 (m-10) REVERT: A 688 MET cc_start: 0.8784 (ppp) cc_final: 0.8363 (ppp) REVERT: A 800 TYR cc_start: 0.9036 (p90) cc_final: 0.8671 (p90) REVERT: A 931 LEU cc_start: 0.9023 (tp) cc_final: 0.8750 (tp) REVERT: A 933 LEU cc_start: 0.9183 (mt) cc_final: 0.8964 (mt) REVERT: A 968 MET cc_start: 0.7833 (tpt) cc_final: 0.7074 (pmm) REVERT: A 975 GLN cc_start: 0.9062 (mm-40) cc_final: 0.8602 (tp-100) REVERT: A 988 ASP cc_start: 0.9117 (m-30) cc_final: 0.8666 (m-30) REVERT: A 1028 PHE cc_start: 0.8631 (m-80) cc_final: 0.8375 (m-80) REVERT: A 1076 ASP cc_start: 0.8704 (p0) cc_final: 0.8117 (m-30) REVERT: A 1132 TRP cc_start: 0.8698 (t60) cc_final: 0.7973 (t60) REVERT: A 1133 LYS cc_start: 0.9479 (ttmt) cc_final: 0.9232 (tppt) REVERT: A 1150 LEU cc_start: 0.9535 (mm) cc_final: 0.9254 (pp) REVERT: A 1154 PHE cc_start: 0.9255 (m-80) cc_final: 0.8289 (m-80) REVERT: A 1214 LEU cc_start: 0.9251 (mt) cc_final: 0.9022 (mt) REVERT: A 1323 TYR cc_start: 0.8253 (t80) cc_final: 0.7601 (t80) REVERT: B 54 LEU cc_start: 0.7838 (tp) cc_final: 0.7614 (tp) REVERT: B 121 MET cc_start: 0.8684 (tpp) cc_final: 0.8265 (tpt) REVERT: B 126 ASP cc_start: 0.9472 (p0) cc_final: 0.9094 (p0) REVERT: B 290 PHE cc_start: 0.9151 (m-80) cc_final: 0.8785 (m-80) REVERT: B 354 LYS cc_start: 0.8672 (tttp) cc_final: 0.7579 (mttt) REVERT: B 356 ASP cc_start: 0.9275 (m-30) cc_final: 0.8938 (t0) REVERT: B 360 ARG cc_start: 0.9003 (mpt180) cc_final: 0.8671 (mpt-90) REVERT: B 370 ARG cc_start: 0.8697 (ptm160) cc_final: 0.8032 (ttm110) REVERT: B 461 LEU cc_start: 0.9267 (mp) cc_final: 0.8812 (mm) REVERT: B 496 TYR cc_start: 0.7974 (m-80) cc_final: 0.7683 (m-80) REVERT: B 543 TYR cc_start: 0.8700 (p90) cc_final: 0.8130 (p90) REVERT: B 552 ILE cc_start: 0.9362 (pt) cc_final: 0.8977 (pt) REVERT: B 688 MET cc_start: 0.8176 (ppp) cc_final: 0.7974 (ppp) REVERT: B 870 PHE cc_start: 0.9443 (t80) cc_final: 0.9153 (t80) REVERT: B 877 LEU cc_start: 0.8772 (mm) cc_final: 0.8231 (tt) REVERT: B 901 LYS cc_start: 0.9053 (mmmm) cc_final: 0.8568 (mmmt) REVERT: B 977 MET cc_start: 0.9444 (mmp) cc_final: 0.9227 (mmp) REVERT: B 985 TYR cc_start: 0.9046 (m-80) cc_final: 0.8845 (m-80) REVERT: B 1072 GLN cc_start: 0.9449 (mt0) cc_final: 0.9037 (tm-30) REVERT: B 1156 LEU cc_start: 0.7789 (mm) cc_final: 0.7403 (mm) REVERT: B 1205 GLU cc_start: 0.8146 (pt0) cc_final: 0.7905 (tt0) REVERT: B 1207 GLU cc_start: 0.9310 (tp30) cc_final: 0.9054 (tp30) REVERT: B 1223 PRO cc_start: 0.6988 (Cg_exo) cc_final: 0.6619 (Cg_endo) REVERT: B 1224 THR cc_start: 0.8759 (p) cc_final: 0.8431 (t) REVERT: B 1328 LEU cc_start: 0.9414 (tp) cc_final: 0.9012 (tp) REVERT: B 1330 TYR cc_start: 0.9151 (p90) cc_final: 0.8902 (p90) REVERT: C 121 MET cc_start: 0.9074 (mmt) cc_final: 0.8586 (mpp) REVERT: C 137 ILE cc_start: 0.8989 (tt) cc_final: 0.8669 (tt) REVERT: C 151 MET cc_start: 0.4416 (ttm) cc_final: 0.4156 (ttm) REVERT: C 209 LYS cc_start: 0.9152 (mttt) cc_final: 0.7920 (mmtm) REVERT: C 251 CYS cc_start: 0.8677 (m) cc_final: 0.8241 (t) REVERT: C 290 PHE cc_start: 0.9350 (m-80) cc_final: 0.9047 (m-80) REVERT: C 309 PHE cc_start: 0.9320 (m-80) cc_final: 0.9016 (m-80) REVERT: C 351 SER cc_start: 0.9397 (m) cc_final: 0.9038 (t) REVERT: C 373 ASP cc_start: 0.8512 (t0) cc_final: 0.8114 (t0) REVERT: C 385 PHE cc_start: 0.9080 (m-80) cc_final: 0.8698 (m-80) REVERT: C 415 MET cc_start: 0.5605 (ppp) cc_final: 0.5380 (ppp) REVERT: C 464 MET cc_start: 0.9444 (ttm) cc_final: 0.9157 (ttm) REVERT: C 523 HIS cc_start: 0.9187 (m-70) cc_final: 0.8921 (m-70) REVERT: C 564 LEU cc_start: 0.8826 (tp) cc_final: 0.8268 (tt) REVERT: C 573 SER cc_start: 0.9310 (t) cc_final: 0.9108 (p) REVERT: C 582 HIS cc_start: 0.9216 (t70) cc_final: 0.8913 (p-80) REVERT: C 627 LEU cc_start: 0.9132 (mm) cc_final: 0.8732 (mp) REVERT: C 669 PHE cc_start: 0.8440 (m-10) cc_final: 0.8184 (m-10) REVERT: C 688 MET cc_start: 0.8779 (ppp) cc_final: 0.8360 (ppp) REVERT: C 798 MET cc_start: 0.8739 (ppp) cc_final: 0.8523 (ppp) REVERT: C 800 TYR cc_start: 0.8937 (p90) cc_final: 0.8709 (p90) REVERT: C 931 LEU cc_start: 0.9067 (tp) cc_final: 0.8851 (tp) REVERT: C 968 MET cc_start: 0.7787 (tpt) cc_final: 0.7011 (pmm) REVERT: C 975 GLN cc_start: 0.9065 (mm-40) cc_final: 0.8531 (tp-100) REVERT: C 988 ASP cc_start: 0.9077 (m-30) cc_final: 0.8804 (m-30) REVERT: C 1028 PHE cc_start: 0.8632 (m-80) cc_final: 0.8378 (m-80) REVERT: C 1057 PHE cc_start: 0.8785 (t80) cc_final: 0.8468 (t80) REVERT: C 1076 ASP cc_start: 0.8702 (p0) cc_final: 0.8119 (m-30) REVERT: C 1132 TRP cc_start: 0.8839 (t60) cc_final: 0.7938 (t60) REVERT: C 1133 LYS cc_start: 0.9321 (mmpt) cc_final: 0.8873 (mmmt) REVERT: C 1150 LEU cc_start: 0.9535 (mm) cc_final: 0.9228 (pp) REVERT: C 1154 PHE cc_start: 0.9287 (m-80) cc_final: 0.8328 (m-80) REVERT: C 1214 LEU cc_start: 0.9246 (mt) cc_final: 0.9017 (mt) REVERT: C 1323 TYR cc_start: 0.8257 (t80) cc_final: 0.7612 (t80) REVERT: D 121 MET cc_start: 0.8689 (tpp) cc_final: 0.8262 (tpt) REVERT: D 126 ASP cc_start: 0.9472 (p0) cc_final: 0.9090 (p0) REVERT: D 290 PHE cc_start: 0.9170 (m-80) cc_final: 0.8819 (m-80) REVERT: D 354 LYS cc_start: 0.8694 (tttp) cc_final: 0.7615 (mttt) REVERT: D 356 ASP cc_start: 0.9280 (m-30) cc_final: 0.8935 (t0) REVERT: D 360 ARG cc_start: 0.9007 (mpt180) cc_final: 0.8699 (mpt-90) REVERT: D 461 LEU cc_start: 0.9268 (mp) cc_final: 0.8810 (mm) REVERT: D 496 TYR cc_start: 0.7987 (m-80) cc_final: 0.7747 (m-80) REVERT: D 543 TYR cc_start: 0.8717 (p90) cc_final: 0.8125 (p90) REVERT: D 545 VAL cc_start: 0.8769 (t) cc_final: 0.8134 (t) REVERT: D 552 ILE cc_start: 0.9358 (pt) cc_final: 0.8972 (pt) REVERT: D 688 MET cc_start: 0.8128 (ppp) cc_final: 0.7925 (ppp) REVERT: D 870 PHE cc_start: 0.9447 (t80) cc_final: 0.9202 (t80) REVERT: D 877 LEU cc_start: 0.8775 (mm) cc_final: 0.8235 (tt) REVERT: D 901 LYS cc_start: 0.9050 (mmmm) cc_final: 0.8557 (mmmt) REVERT: D 977 MET cc_start: 0.9440 (mmp) cc_final: 0.9233 (mmp) REVERT: D 985 TYR cc_start: 0.9063 (m-80) cc_final: 0.8793 (m-80) REVERT: D 1072 GLN cc_start: 0.9256 (mt0) cc_final: 0.8536 (tt0) REVERT: D 1126 PHE cc_start: 0.8920 (m-10) cc_final: 0.8658 (m-80) REVERT: D 1156 LEU cc_start: 0.7766 (mm) cc_final: 0.7389 (mm) REVERT: D 1205 GLU cc_start: 0.8272 (pt0) cc_final: 0.7902 (tt0) REVERT: D 1238 ILE cc_start: 0.8166 (mt) cc_final: 0.7902 (mm) REVERT: D 1241 GLN cc_start: 0.7058 (mp-120) cc_final: 0.6653 (mp-120) REVERT: D 1316 VAL cc_start: 0.8777 (t) cc_final: 0.8571 (p) REVERT: D 1323 TYR cc_start: 0.8155 (t80) cc_final: 0.7920 (t80) REVERT: D 1331 ASN cc_start: 0.6037 (m110) cc_final: 0.5360 (t0) outliers start: 0 outliers final: 0 residues processed: 809 average time/residue: 0.4959 time to fit residues: 661.3679 Evaluate side-chains 634 residues out of total 4451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 634 time to evaluate : 4.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 473 optimal weight: 0.6980 chunk 55 optimal weight: 10.0000 chunk 280 optimal weight: 7.9990 chunk 358 optimal weight: 6.9990 chunk 278 optimal weight: 6.9990 chunk 413 optimal weight: 10.0000 chunk 274 optimal weight: 0.9980 chunk 489 optimal weight: 10.0000 chunk 306 optimal weight: 0.9980 chunk 298 optimal weight: 10.0000 chunk 226 optimal weight: 10.0000 overall best weight: 3.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 200 GLN ** A 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN A 523 HIS ** A 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 584 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 647 ASN ** A 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1013 GLN ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1017 ASN ** B1277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 GLN ** C 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 GLN C 523 HIS ** C 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 584 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1017 ASN ** D1277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.6261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 41179 Z= 0.267 Angle : 0.778 13.288 55948 Z= 0.393 Chirality : 0.049 0.353 6471 Planarity : 0.006 0.084 7166 Dihedral : 8.005 59.353 6200 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 28.74 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.51 % Favored : 88.45 % Rotamer: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -3.11 (0.11), residues: 5084 helix: -0.35 (0.16), residues: 862 sheet: -1.75 (0.11), residues: 1823 loop : -2.99 (0.12), residues: 2399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP D 436 HIS 0.011 0.001 HIS D 441 PHE 0.056 0.002 PHE C1049 TYR 0.031 0.002 TYR D1152 ARG 0.006 0.001 ARG C1271 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 832 residues out of total 4451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 832 time to evaluate : 4.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 50 LEU cc_start: 0.9673 (tp) cc_final: 0.9413 (tp) REVERT: A 121 MET cc_start: 0.9111 (mmt) cc_final: 0.8603 (mpp) REVERT: A 137 ILE cc_start: 0.8991 (tt) cc_final: 0.8724 (tt) REVERT: A 151 MET cc_start: 0.4839 (ttm) cc_final: 0.4348 (tpp) REVERT: A 216 GLU cc_start: 0.9049 (pm20) cc_final: 0.8767 (mp0) REVERT: A 251 CYS cc_start: 0.8660 (m) cc_final: 0.8257 (t) REVERT: A 289 LYS cc_start: 0.9473 (mppt) cc_final: 0.8989 (mmmt) REVERT: A 290 PHE cc_start: 0.9365 (m-80) cc_final: 0.9049 (m-80) REVERT: A 309 PHE cc_start: 0.9238 (m-80) cc_final: 0.8943 (m-80) REVERT: A 351 SER cc_start: 0.9350 (m) cc_final: 0.9009 (t) REVERT: A 373 ASP cc_start: 0.8532 (t0) cc_final: 0.8088 (t0) REVERT: A 385 PHE cc_start: 0.9061 (m-80) cc_final: 0.8660 (m-80) REVERT: A 415 MET cc_start: 0.5741 (ppp) cc_final: 0.5377 (ppp) REVERT: A 428 ARG cc_start: 0.6044 (mpt180) cc_final: 0.5383 (mtp180) REVERT: A 523 HIS cc_start: 0.9226 (m90) cc_final: 0.8939 (m-70) REVERT: A 530 VAL cc_start: 0.9335 (t) cc_final: 0.9128 (p) REVERT: A 552 ILE cc_start: 0.8846 (tp) cc_final: 0.8596 (tp) REVERT: A 582 HIS cc_start: 0.9205 (t70) cc_final: 0.8872 (p-80) REVERT: A 626 ASP cc_start: 0.9121 (p0) cc_final: 0.8498 (t0) REVERT: A 627 LEU cc_start: 0.9082 (mm) cc_final: 0.8655 (mp) REVERT: A 666 MET cc_start: 0.9120 (ttm) cc_final: 0.8742 (ttp) REVERT: A 669 PHE cc_start: 0.8459 (m-10) cc_final: 0.8218 (m-80) REVERT: A 764 GLU cc_start: 0.6350 (mp0) cc_final: 0.5974 (mp0) REVERT: A 800 TYR cc_start: 0.9003 (p90) cc_final: 0.8620 (p90) REVERT: A 931 LEU cc_start: 0.9037 (tp) cc_final: 0.8790 (tp) REVERT: A 968 MET cc_start: 0.7792 (tpt) cc_final: 0.6954 (pmm) REVERT: A 975 GLN cc_start: 0.9060 (mm-40) cc_final: 0.8530 (tp-100) REVERT: A 988 ASP cc_start: 0.8652 (m-30) cc_final: 0.8186 (m-30) REVERT: A 1020 HIS cc_start: 0.9258 (t-90) cc_final: 0.8987 (t-90) REVERT: A 1028 PHE cc_start: 0.8655 (m-80) cc_final: 0.8401 (m-80) REVERT: A 1057 PHE cc_start: 0.8611 (t80) cc_final: 0.8357 (t80) REVERT: A 1076 ASP cc_start: 0.8635 (p0) cc_final: 0.8050 (m-30) REVERT: A 1132 TRP cc_start: 0.8746 (t60) cc_final: 0.8092 (t60) REVERT: A 1133 LYS cc_start: 0.9475 (ttmt) cc_final: 0.9238 (tppt) REVERT: A 1144 VAL cc_start: 0.8567 (p) cc_final: 0.8227 (m) REVERT: A 1150 LEU cc_start: 0.9549 (mm) cc_final: 0.9227 (pp) REVERT: A 1154 PHE cc_start: 0.9348 (m-80) cc_final: 0.8479 (m-80) REVERT: A 1214 LEU cc_start: 0.9324 (mt) cc_final: 0.9102 (mt) REVERT: A 1323 TYR cc_start: 0.8111 (t80) cc_final: 0.7582 (t80) REVERT: B 54 LEU cc_start: 0.7814 (tp) cc_final: 0.7561 (tp) REVERT: B 121 MET cc_start: 0.8700 (tpp) cc_final: 0.8301 (tpt) REVERT: B 126 ASP cc_start: 0.9515 (p0) cc_final: 0.9312 (p0) REVERT: B 290 PHE cc_start: 0.9147 (m-80) cc_final: 0.8794 (m-80) REVERT: B 354 LYS cc_start: 0.8624 (tttp) cc_final: 0.7598 (mttt) REVERT: B 356 ASP cc_start: 0.9284 (m-30) cc_final: 0.8973 (t0) REVERT: B 360 ARG cc_start: 0.8998 (mpt180) cc_final: 0.8343 (mpt-90) REVERT: B 363 ILE cc_start: 0.9299 (tp) cc_final: 0.8692 (tp) REVERT: B 370 ARG cc_start: 0.8668 (ptm160) cc_final: 0.8000 (ttm110) REVERT: B 461 LEU cc_start: 0.9312 (mp) cc_final: 0.8876 (mm) REVERT: B 543 TYR cc_start: 0.8658 (p90) cc_final: 0.8300 (p90) REVERT: B 550 ASP cc_start: 0.9322 (m-30) cc_final: 0.9108 (m-30) REVERT: B 552 ILE cc_start: 0.9376 (pt) cc_final: 0.8931 (pt) REVERT: B 554 ASP cc_start: 0.7343 (t0) cc_final: 0.7109 (t0) REVERT: B 870 PHE cc_start: 0.9410 (t80) cc_final: 0.9160 (t80) REVERT: B 877 LEU cc_start: 0.8836 (mm) cc_final: 0.8296 (tt) REVERT: B 901 LYS cc_start: 0.9024 (mmmm) cc_final: 0.8535 (mmmt) REVERT: B 977 MET cc_start: 0.9475 (mmp) cc_final: 0.9261 (mmp) REVERT: B 1072 GLN cc_start: 0.9451 (mt0) cc_final: 0.9053 (tm-30) REVERT: B 1156 LEU cc_start: 0.7829 (mm) cc_final: 0.7430 (mm) REVERT: B 1207 GLU cc_start: 0.9309 (tp30) cc_final: 0.9054 (tp30) REVERT: B 1238 ILE cc_start: 0.7334 (pt) cc_final: 0.7019 (pt) REVERT: B 1330 TYR cc_start: 0.9141 (p90) cc_final: 0.8875 (p90) REVERT: C 50 LEU cc_start: 0.9704 (tp) cc_final: 0.9478 (tp) REVERT: C 121 MET cc_start: 0.9091 (mmt) cc_final: 0.8600 (mpp) REVERT: C 137 ILE cc_start: 0.8983 (tt) cc_final: 0.8718 (tt) REVERT: C 251 CYS cc_start: 0.8666 (m) cc_final: 0.8257 (t) REVERT: C 289 LYS cc_start: 0.9466 (mppt) cc_final: 0.8935 (mmmt) REVERT: C 290 PHE cc_start: 0.9342 (m-80) cc_final: 0.9051 (m-80) REVERT: C 318 MET cc_start: 0.8574 (tpp) cc_final: 0.8248 (tpp) REVERT: C 351 SER cc_start: 0.9357 (m) cc_final: 0.9024 (t) REVERT: C 373 ASP cc_start: 0.8511 (t0) cc_final: 0.8064 (t0) REVERT: C 385 PHE cc_start: 0.9061 (m-80) cc_final: 0.8660 (m-80) REVERT: C 415 MET cc_start: 0.5762 (ppp) cc_final: 0.5526 (ppp) REVERT: C 428 ARG cc_start: 0.6038 (mpt180) cc_final: 0.5338 (mtt180) REVERT: C 464 MET cc_start: 0.9462 (ttm) cc_final: 0.9259 (ttm) REVERT: C 523 HIS cc_start: 0.9226 (m90) cc_final: 0.8939 (m-70) REVERT: C 530 VAL cc_start: 0.9381 (t) cc_final: 0.9168 (p) REVERT: C 552 ILE cc_start: 0.8828 (tp) cc_final: 0.8576 (tp) REVERT: C 564 LEU cc_start: 0.8842 (tp) cc_final: 0.8273 (tt) REVERT: C 582 HIS cc_start: 0.9216 (t70) cc_final: 0.8879 (p-80) REVERT: C 626 ASP cc_start: 0.9174 (p0) cc_final: 0.8526 (t0) REVERT: C 627 LEU cc_start: 0.9139 (mm) cc_final: 0.8805 (mp) REVERT: C 666 MET cc_start: 0.9143 (ttm) cc_final: 0.8735 (ttp) REVERT: C 669 PHE cc_start: 0.8381 (m-10) cc_final: 0.8151 (m-80) REVERT: C 764 GLU cc_start: 0.6379 (mp0) cc_final: 0.6002 (mp0) REVERT: C 800 TYR cc_start: 0.8946 (p90) cc_final: 0.8699 (p90) REVERT: C 931 LEU cc_start: 0.9076 (tp) cc_final: 0.8813 (tp) REVERT: C 933 LEU cc_start: 0.9198 (mt) cc_final: 0.8989 (mt) REVERT: C 968 MET cc_start: 0.7772 (tpt) cc_final: 0.7034 (pmm) REVERT: C 975 GLN cc_start: 0.9062 (mm-40) cc_final: 0.8536 (tp-100) REVERT: C 988 ASP cc_start: 0.9101 (m-30) cc_final: 0.8762 (m-30) REVERT: C 1028 PHE cc_start: 0.8664 (m-80) cc_final: 0.8409 (m-80) REVERT: C 1057 PHE cc_start: 0.8779 (t80) cc_final: 0.8412 (t80) REVERT: C 1076 ASP cc_start: 0.8626 (p0) cc_final: 0.8038 (m-30) REVERT: C 1112 ILE cc_start: 0.8737 (mt) cc_final: 0.8537 (mt) REVERT: C 1132 TRP cc_start: 0.8794 (t60) cc_final: 0.7997 (t60) REVERT: C 1133 LYS cc_start: 0.9388 (mmmt) cc_final: 0.9060 (mmmt) REVERT: C 1144 VAL cc_start: 0.8536 (p) cc_final: 0.8154 (m) REVERT: C 1150 LEU cc_start: 0.9556 (mm) cc_final: 0.9209 (pp) REVERT: C 1154 PHE cc_start: 0.9368 (m-80) cc_final: 0.8495 (m-80) REVERT: C 1214 LEU cc_start: 0.9319 (mt) cc_final: 0.9096 (mt) REVERT: C 1323 TYR cc_start: 0.8129 (t80) cc_final: 0.7604 (t80) REVERT: D 121 MET cc_start: 0.8693 (tpp) cc_final: 0.8290 (tpt) REVERT: D 290 PHE cc_start: 0.9167 (m-80) cc_final: 0.8804 (m-80) REVERT: D 354 LYS cc_start: 0.8689 (tttp) cc_final: 0.7569 (mttt) REVERT: D 356 ASP cc_start: 0.9294 (m-30) cc_final: 0.8986 (t0) REVERT: D 360 ARG cc_start: 0.8976 (mpt180) cc_final: 0.8656 (mpt-90) REVERT: D 363 ILE cc_start: 0.9298 (tp) cc_final: 0.9097 (tp) REVERT: D 461 LEU cc_start: 0.9324 (mp) cc_final: 0.8856 (mm) REVERT: D 543 TYR cc_start: 0.8674 (p90) cc_final: 0.8295 (p90) REVERT: D 552 ILE cc_start: 0.9380 (pt) cc_final: 0.8917 (pt) REVERT: D 554 ASP cc_start: 0.7259 (t0) cc_final: 0.6922 (t0) REVERT: D 858 TRP cc_start: 0.8740 (m100) cc_final: 0.8366 (m100) REVERT: D 870 PHE cc_start: 0.9416 (t80) cc_final: 0.9145 (t80) REVERT: D 877 LEU cc_start: 0.8844 (mm) cc_final: 0.8303 (tt) REVERT: D 901 LYS cc_start: 0.9031 (mmmm) cc_final: 0.8521 (mmtt) REVERT: D 977 MET cc_start: 0.9477 (mmp) cc_final: 0.9255 (mmp) REVERT: D 985 TYR cc_start: 0.8984 (m-80) cc_final: 0.8776 (m-80) REVERT: D 1072 GLN cc_start: 0.9284 (mt0) cc_final: 0.8570 (tt0) REVERT: D 1156 LEU cc_start: 0.7808 (mm) cc_final: 0.7401 (mm) REVERT: D 1205 GLU cc_start: 0.8320 (pt0) cc_final: 0.8030 (tt0) REVERT: D 1316 VAL cc_start: 0.8799 (t) cc_final: 0.8565 (p) REVERT: D 1328 LEU cc_start: 0.9475 (tp) cc_final: 0.9186 (tp) REVERT: D 1331 ASN cc_start: 0.5777 (m110) cc_final: 0.5124 (t0) outliers start: 0 outliers final: 0 residues processed: 832 average time/residue: 0.4771 time to fit residues: 661.6004 Evaluate side-chains 660 residues out of total 4451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 660 time to evaluate : 4.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 302 optimal weight: 20.0000 chunk 195 optimal weight: 0.0050 chunk 292 optimal weight: 1.9990 chunk 147 optimal weight: 7.9990 chunk 96 optimal weight: 8.9990 chunk 94 optimal weight: 0.7980 chunk 311 optimal weight: 10.0000 chunk 333 optimal weight: 30.0000 chunk 242 optimal weight: 6.9990 chunk 45 optimal weight: 9.9990 chunk 384 optimal weight: 20.0000 overall best weight: 3.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 584 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 647 ASN ** A 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1017 ASN ** B1182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 584 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1017 ASN ** D1277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.6662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 41179 Z= 0.272 Angle : 0.784 11.777 55948 Z= 0.397 Chirality : 0.049 0.329 6471 Planarity : 0.006 0.073 7166 Dihedral : 7.982 59.746 6200 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 30.36 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.86 % Favored : 88.06 % Rotamer: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -3.08 (0.11), residues: 5084 helix: -0.37 (0.16), residues: 861 sheet: -1.71 (0.12), residues: 1719 loop : -2.93 (0.11), residues: 2504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP D 436 HIS 0.010 0.001 HIS B 441 PHE 0.045 0.003 PHE C1126 TYR 0.026 0.002 TYR D1152 ARG 0.006 0.001 ARG A 270 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 830 residues out of total 4451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 830 time to evaluate : 5.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 38 LEU cc_start: 0.8251 (tt) cc_final: 0.7965 (tt) REVERT: A 50 LEU cc_start: 0.9695 (tp) cc_final: 0.9434 (tp) REVERT: A 121 MET cc_start: 0.9144 (mmt) cc_final: 0.8725 (mpp) REVERT: A 137 ILE cc_start: 0.9011 (tt) cc_final: 0.8738 (tt) REVERT: A 151 MET cc_start: 0.4620 (ttm) cc_final: 0.4108 (tpp) REVERT: A 200 GLN cc_start: 0.8952 (mt0) cc_final: 0.8719 (tp40) REVERT: A 216 GLU cc_start: 0.9117 (pm20) cc_final: 0.8824 (mp0) REVERT: A 251 CYS cc_start: 0.8616 (m) cc_final: 0.8288 (t) REVERT: A 289 LYS cc_start: 0.9327 (mppt) cc_final: 0.9063 (mmmt) REVERT: A 290 PHE cc_start: 0.9400 (m-80) cc_final: 0.9104 (m-80) REVERT: A 373 ASP cc_start: 0.8571 (t0) cc_final: 0.8119 (t0) REVERT: A 415 MET cc_start: 0.5605 (ppp) cc_final: 0.5304 (ppp) REVERT: A 428 ARG cc_start: 0.6132 (mpt180) cc_final: 0.5499 (mtp180) REVERT: A 523 HIS cc_start: 0.9230 (m90) cc_final: 0.8931 (m-70) REVERT: A 530 VAL cc_start: 0.9320 (t) cc_final: 0.9067 (p) REVERT: A 582 HIS cc_start: 0.9290 (t70) cc_final: 0.8878 (p-80) REVERT: A 626 ASP cc_start: 0.9168 (p0) cc_final: 0.8543 (t0) REVERT: A 627 LEU cc_start: 0.9129 (mm) cc_final: 0.8765 (mp) REVERT: A 666 MET cc_start: 0.9164 (ttm) cc_final: 0.8831 (ttp) REVERT: A 764 GLU cc_start: 0.6364 (mp0) cc_final: 0.5976 (mp0) REVERT: A 800 TYR cc_start: 0.9019 (p90) cc_final: 0.8613 (p90) REVERT: A 931 LEU cc_start: 0.9028 (tp) cc_final: 0.8738 (tp) REVERT: A 933 LEU cc_start: 0.9183 (mt) cc_final: 0.8971 (mt) REVERT: A 975 GLN cc_start: 0.9074 (mm-40) cc_final: 0.8541 (tp-100) REVERT: A 988 ASP cc_start: 0.8857 (m-30) cc_final: 0.8357 (m-30) REVERT: A 1020 HIS cc_start: 0.9260 (t-90) cc_final: 0.9001 (t-90) REVERT: A 1028 PHE cc_start: 0.8618 (m-80) cc_final: 0.8356 (m-80) REVERT: A 1076 ASP cc_start: 0.8659 (p0) cc_final: 0.8078 (m-30) REVERT: A 1144 VAL cc_start: 0.8496 (p) cc_final: 0.8134 (m) REVERT: A 1150 LEU cc_start: 0.9570 (mm) cc_final: 0.9212 (pp) REVERT: A 1154 PHE cc_start: 0.9363 (m-80) cc_final: 0.8394 (m-80) REVERT: A 1323 TYR cc_start: 0.8146 (t80) cc_final: 0.7526 (t80) REVERT: B 54 LEU cc_start: 0.7824 (tp) cc_final: 0.7588 (tp) REVERT: B 121 MET cc_start: 0.8730 (tpp) cc_final: 0.8358 (tpt) REVERT: B 126 ASP cc_start: 0.9505 (p0) cc_final: 0.9298 (p0) REVERT: B 290 PHE cc_start: 0.9124 (m-80) cc_final: 0.8794 (m-80) REVERT: B 309 PHE cc_start: 0.9226 (m-80) cc_final: 0.9025 (m-80) REVERT: B 354 LYS cc_start: 0.8668 (tttp) cc_final: 0.7594 (mttt) REVERT: B 356 ASP cc_start: 0.9311 (m-30) cc_final: 0.9002 (t0) REVERT: B 360 ARG cc_start: 0.9036 (mpt180) cc_final: 0.8714 (mpt-90) REVERT: B 363 ILE cc_start: 0.9362 (tp) cc_final: 0.9148 (tp) REVERT: B 370 ARG cc_start: 0.8661 (ptm160) cc_final: 0.7981 (ttm110) REVERT: B 461 LEU cc_start: 0.9320 (mp) cc_final: 0.8835 (mm) REVERT: B 550 ASP cc_start: 0.9298 (m-30) cc_final: 0.9032 (m-30) REVERT: B 552 ILE cc_start: 0.9407 (pt) cc_final: 0.8959 (pt) REVERT: B 554 ASP cc_start: 0.7326 (t0) cc_final: 0.6986 (t0) REVERT: B 770 PHE cc_start: 0.9122 (t80) cc_final: 0.8594 (t80) REVERT: B 870 PHE cc_start: 0.9385 (t80) cc_final: 0.9112 (t80) REVERT: B 877 LEU cc_start: 0.8845 (mm) cc_final: 0.8296 (tt) REVERT: B 901 LYS cc_start: 0.9049 (mmmm) cc_final: 0.8562 (mmmt) REVERT: B 985 TYR cc_start: 0.9056 (m-80) cc_final: 0.8781 (m-80) REVERT: B 1072 GLN cc_start: 0.9456 (mt0) cc_final: 0.9159 (tm-30) REVERT: B 1156 LEU cc_start: 0.7741 (mm) cc_final: 0.7421 (mm) REVERT: B 1207 GLU cc_start: 0.9331 (tp30) cc_final: 0.9078 (tp30) REVERT: B 1237 TRP cc_start: 0.8749 (t60) cc_final: 0.8007 (t60) REVERT: B 1238 ILE cc_start: 0.7139 (pt) cc_final: 0.6463 (pt) REVERT: B 1328 LEU cc_start: 0.9418 (tp) cc_final: 0.8872 (tp) REVERT: B 1330 TYR cc_start: 0.9093 (p90) cc_final: 0.8835 (p90) REVERT: C 32 MET cc_start: 0.9596 (ttt) cc_final: 0.9168 (ttt) REVERT: C 38 LEU cc_start: 0.8262 (tt) cc_final: 0.7980 (tt) REVERT: C 50 LEU cc_start: 0.9718 (tp) cc_final: 0.9461 (tp) REVERT: C 121 MET cc_start: 0.9133 (mmt) cc_final: 0.8691 (mpp) REVERT: C 137 ILE cc_start: 0.9005 (tt) cc_final: 0.8734 (tt) REVERT: C 151 MET cc_start: 0.4748 (ttm) cc_final: 0.4487 (ttm) REVERT: C 251 CYS cc_start: 0.8638 (m) cc_final: 0.8308 (t) REVERT: C 289 LYS cc_start: 0.9338 (mppt) cc_final: 0.9060 (mmmt) REVERT: C 290 PHE cc_start: 0.9350 (m-80) cc_final: 0.8988 (m-80) REVERT: C 373 ASP cc_start: 0.8556 (t0) cc_final: 0.8103 (t0) REVERT: C 428 ARG cc_start: 0.6108 (mpt180) cc_final: 0.5468 (mtp180) REVERT: C 464 MET cc_start: 0.9453 (ttm) cc_final: 0.9219 (ttm) REVERT: C 523 HIS cc_start: 0.9248 (m90) cc_final: 0.8963 (m-70) REVERT: C 530 VAL cc_start: 0.9335 (t) cc_final: 0.9090 (p) REVERT: C 564 LEU cc_start: 0.8768 (tp) cc_final: 0.8168 (tt) REVERT: C 582 HIS cc_start: 0.9290 (t70) cc_final: 0.8877 (p-80) REVERT: C 626 ASP cc_start: 0.9184 (p0) cc_final: 0.8603 (t0) REVERT: C 627 LEU cc_start: 0.9202 (mm) cc_final: 0.8867 (mp) REVERT: C 666 MET cc_start: 0.9145 (ttm) cc_final: 0.8740 (ttp) REVERT: C 764 GLU cc_start: 0.6381 (mp0) cc_final: 0.5997 (mp0) REVERT: C 800 TYR cc_start: 0.8964 (p90) cc_final: 0.8689 (p90) REVERT: C 931 LEU cc_start: 0.9061 (tp) cc_final: 0.8743 (tp) REVERT: C 933 LEU cc_start: 0.9167 (mt) cc_final: 0.8960 (mt) REVERT: C 968 MET cc_start: 0.7740 (tpt) cc_final: 0.7004 (pmm) REVERT: C 975 GLN cc_start: 0.9066 (mm-40) cc_final: 0.8594 (tp-100) REVERT: C 988 ASP cc_start: 0.9138 (m-30) cc_final: 0.8816 (m-30) REVERT: C 1020 HIS cc_start: 0.9267 (t-90) cc_final: 0.9002 (t-90) REVERT: C 1028 PHE cc_start: 0.8631 (m-80) cc_final: 0.8366 (m-80) REVERT: C 1057 PHE cc_start: 0.8794 (t80) cc_final: 0.8493 (t80) REVERT: C 1076 ASP cc_start: 0.8647 (p0) cc_final: 0.8063 (m-30) REVERT: C 1112 ILE cc_start: 0.8723 (mt) cc_final: 0.8523 (mt) REVERT: C 1132 TRP cc_start: 0.8812 (t60) cc_final: 0.7955 (t60) REVERT: C 1133 LYS cc_start: 0.9431 (mmmt) cc_final: 0.9066 (mmmt) REVERT: C 1144 VAL cc_start: 0.8481 (p) cc_final: 0.8085 (m) REVERT: C 1150 LEU cc_start: 0.9579 (mm) cc_final: 0.9239 (pp) REVERT: C 1154 PHE cc_start: 0.9402 (m-80) cc_final: 0.8543 (m-80) REVERT: C 1323 TYR cc_start: 0.8168 (t80) cc_final: 0.7022 (t80) REVERT: C 1324 LEU cc_start: 0.7899 (mp) cc_final: 0.7648 (tt) REVERT: D 121 MET cc_start: 0.8715 (tpp) cc_final: 0.8343 (tpt) REVERT: D 126 ASP cc_start: 0.9499 (p0) cc_final: 0.9262 (p0) REVERT: D 290 PHE cc_start: 0.9088 (m-80) cc_final: 0.8775 (m-80) REVERT: D 309 PHE cc_start: 0.9220 (m-80) cc_final: 0.9007 (m-80) REVERT: D 354 LYS cc_start: 0.8718 (tttp) cc_final: 0.7618 (mttt) REVERT: D 356 ASP cc_start: 0.9323 (m-30) cc_final: 0.9037 (t0) REVERT: D 360 ARG cc_start: 0.9016 (mpt180) cc_final: 0.8696 (mpt-90) REVERT: D 363 ILE cc_start: 0.9361 (tp) cc_final: 0.9142 (tp) REVERT: D 422 ARG cc_start: 0.9197 (mtt90) cc_final: 0.8609 (mtm-85) REVERT: D 461 LEU cc_start: 0.9320 (mp) cc_final: 0.8829 (mm) REVERT: D 550 ASP cc_start: 0.9312 (m-30) cc_final: 0.9094 (m-30) REVERT: D 552 ILE cc_start: 0.9390 (pt) cc_final: 0.8909 (pt) REVERT: D 554 ASP cc_start: 0.7252 (t0) cc_final: 0.6917 (t0) REVERT: D 870 PHE cc_start: 0.9403 (t80) cc_final: 0.9111 (t80) REVERT: D 877 LEU cc_start: 0.8870 (mm) cc_final: 0.8340 (tt) REVERT: D 901 LYS cc_start: 0.9037 (mmmm) cc_final: 0.8520 (mmtt) REVERT: D 1072 GLN cc_start: 0.9317 (mt0) cc_final: 0.8613 (tt0) REVERT: D 1076 ASP cc_start: 0.8911 (p0) cc_final: 0.8533 (p0) REVERT: D 1156 LEU cc_start: 0.7905 (mm) cc_final: 0.7512 (mm) REVERT: D 1165 GLU cc_start: 0.9083 (mp0) cc_final: 0.8777 (pm20) REVERT: D 1205 GLU cc_start: 0.8402 (pt0) cc_final: 0.8110 (tt0) REVERT: D 1241 GLN cc_start: 0.7218 (mp-120) cc_final: 0.6970 (mp-120) REVERT: D 1331 ASN cc_start: 0.5749 (m110) cc_final: 0.5073 (t0) outliers start: 0 outliers final: 0 residues processed: 830 average time/residue: 0.4977 time to fit residues: 681.2993 Evaluate side-chains 668 residues out of total 4451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 668 time to evaluate : 3.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 445 optimal weight: 2.9990 chunk 469 optimal weight: 8.9990 chunk 427 optimal weight: 0.0870 chunk 456 optimal weight: 30.0000 chunk 468 optimal weight: 5.9990 chunk 274 optimal weight: 0.8980 chunk 198 optimal weight: 4.9990 chunk 358 optimal weight: 10.0000 chunk 140 optimal weight: 5.9990 chunk 412 optimal weight: 8.9990 chunk 431 optimal weight: 5.9990 overall best weight: 2.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 ASN ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 441 HIS ** A 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 584 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1243 ASN ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 994 GLN B1017 ASN ** B1277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 ASN ** C 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 584 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 402 HIS ** D 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1017 ASN ** D1277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.6926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 41179 Z= 0.250 Angle : 0.765 13.080 55948 Z= 0.386 Chirality : 0.049 0.467 6471 Planarity : 0.005 0.066 7166 Dihedral : 7.869 59.490 6200 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 28.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.33 % Favored : 88.63 % Rotamer: Outliers : 0.02 % Allowed : 0.74 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -3.02 (0.11), residues: 5084 helix: -0.28 (0.16), residues: 866 sheet: -1.67 (0.12), residues: 1769 loop : -2.94 (0.12), residues: 2449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP B 436 HIS 0.011 0.001 HIS D1259 PHE 0.030 0.002 PHE A1049 TYR 0.025 0.002 TYR D1152 ARG 0.007 0.001 ARG A 270 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 828 residues out of total 4451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 827 time to evaluate : 4.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 38 LEU cc_start: 0.8280 (tt) cc_final: 0.7992 (tt) REVERT: A 50 LEU cc_start: 0.9702 (tp) cc_final: 0.9445 (tp) REVERT: A 121 MET cc_start: 0.9159 (mmt) cc_final: 0.8793 (mpp) REVERT: A 137 ILE cc_start: 0.8974 (tt) cc_final: 0.8735 (tt) REVERT: A 151 MET cc_start: 0.4696 (ttm) cc_final: 0.4293 (tpp) REVERT: A 216 GLU cc_start: 0.9088 (pm20) cc_final: 0.8834 (mp0) REVERT: A 251 CYS cc_start: 0.8600 (m) cc_final: 0.8277 (t) REVERT: A 271 LYS cc_start: 0.8427 (mppt) cc_final: 0.8174 (tmtt) REVERT: A 290 PHE cc_start: 0.9388 (m-80) cc_final: 0.9136 (m-80) REVERT: A 373 ASP cc_start: 0.8598 (t0) cc_final: 0.8193 (t0) REVERT: A 385 PHE cc_start: 0.9016 (m-80) cc_final: 0.8570 (m-80) REVERT: A 464 MET cc_start: 0.9480 (ttm) cc_final: 0.9246 (ttm) REVERT: A 523 HIS cc_start: 0.9211 (m90) cc_final: 0.8924 (m-70) REVERT: A 582 HIS cc_start: 0.9293 (t70) cc_final: 0.8865 (p-80) REVERT: A 626 ASP cc_start: 0.9187 (p0) cc_final: 0.8556 (t0) REVERT: A 627 LEU cc_start: 0.9146 (mm) cc_final: 0.8804 (mp) REVERT: A 688 MET cc_start: 0.8796 (ppp) cc_final: 0.8439 (ppp) REVERT: A 764 GLU cc_start: 0.6415 (mp0) cc_final: 0.6023 (mp0) REVERT: A 800 TYR cc_start: 0.8946 (p90) cc_final: 0.8493 (p90) REVERT: A 931 LEU cc_start: 0.9023 (tp) cc_final: 0.8729 (tp) REVERT: A 975 GLN cc_start: 0.9068 (mm-40) cc_final: 0.8613 (tp-100) REVERT: A 977 MET cc_start: 0.9383 (mmm) cc_final: 0.9162 (mmm) REVERT: A 988 ASP cc_start: 0.8925 (m-30) cc_final: 0.8414 (m-30) REVERT: A 1020 HIS cc_start: 0.9254 (t-90) cc_final: 0.8992 (t-90) REVERT: A 1028 PHE cc_start: 0.8645 (m-80) cc_final: 0.8379 (m-80) REVERT: A 1057 PHE cc_start: 0.8558 (t80) cc_final: 0.8269 (t80) REVERT: A 1076 ASP cc_start: 0.8641 (p0) cc_final: 0.8061 (m-30) REVERT: A 1133 LYS cc_start: 0.9480 (ttmt) cc_final: 0.9150 (tppt) REVERT: A 1144 VAL cc_start: 0.8490 (p) cc_final: 0.8145 (m) REVERT: A 1150 LEU cc_start: 0.9577 (mm) cc_final: 0.9233 (pp) REVERT: A 1154 PHE cc_start: 0.9387 (m-80) cc_final: 0.8442 (m-80) REVERT: A 1323 TYR cc_start: 0.8111 (t80) cc_final: 0.7017 (t80) REVERT: A 1324 LEU cc_start: 0.7969 (mp) cc_final: 0.7709 (tt) REVERT: B 51 LEU cc_start: 0.8992 (mt) cc_final: 0.8773 (mt) REVERT: B 54 LEU cc_start: 0.7764 (tp) cc_final: 0.7537 (tp) REVERT: B 121 MET cc_start: 0.8741 (tpp) cc_final: 0.8342 (tpt) REVERT: B 126 ASP cc_start: 0.9504 (p0) cc_final: 0.9292 (p0) REVERT: B 290 PHE cc_start: 0.9092 (m-80) cc_final: 0.8819 (m-80) REVERT: B 321 HIS cc_start: 0.8983 (m90) cc_final: 0.8696 (m-70) REVERT: B 354 LYS cc_start: 0.8626 (tttp) cc_final: 0.8362 (tttp) REVERT: B 356 ASP cc_start: 0.9300 (m-30) cc_final: 0.8980 (t0) REVERT: B 360 ARG cc_start: 0.9024 (mpt180) cc_final: 0.8716 (mpt-90) REVERT: B 363 ILE cc_start: 0.9381 (tp) cc_final: 0.9165 (tp) REVERT: B 370 ARG cc_start: 0.8641 (ptm160) cc_final: 0.7955 (ttm110) REVERT: B 415 MET cc_start: 0.6630 (pmm) cc_final: 0.4990 (pmm) REVERT: B 461 LEU cc_start: 0.9247 (mp) cc_final: 0.8803 (mm) REVERT: B 543 TYR cc_start: 0.8753 (p90) cc_final: 0.8488 (p90) REVERT: B 550 ASP cc_start: 0.9264 (m-30) cc_final: 0.9059 (m-30) REVERT: B 552 ILE cc_start: 0.9386 (pt) cc_final: 0.8925 (pt) REVERT: B 554 ASP cc_start: 0.7347 (t0) cc_final: 0.7010 (t0) REVERT: B 688 MET cc_start: 0.8043 (ppp) cc_final: 0.7682 (ppp) REVERT: B 870 PHE cc_start: 0.9404 (t80) cc_final: 0.9098 (t80) REVERT: B 877 LEU cc_start: 0.8817 (mm) cc_final: 0.8258 (tt) REVERT: B 901 LYS cc_start: 0.9022 (mmmm) cc_final: 0.8588 (mmmt) REVERT: B 968 MET cc_start: 0.8542 (tpt) cc_final: 0.8200 (tpt) REVERT: B 994 GLN cc_start: 0.9265 (tp40) cc_final: 0.9059 (tp-100) REVERT: B 1072 GLN cc_start: 0.9448 (mt0) cc_final: 0.9219 (tm-30) REVERT: B 1156 LEU cc_start: 0.7693 (mm) cc_final: 0.7367 (mm) REVERT: B 1207 GLU cc_start: 0.9345 (tp30) cc_final: 0.9079 (tp30) REVERT: B 1328 LEU cc_start: 0.9441 (tp) cc_final: 0.8950 (tp) REVERT: B 1330 TYR cc_start: 0.9086 (p90) cc_final: 0.8853 (p90) REVERT: C 32 MET cc_start: 0.9580 (ttt) cc_final: 0.9293 (tpp) REVERT: C 38 LEU cc_start: 0.8306 (tt) cc_final: 0.8021 (tt) REVERT: C 121 MET cc_start: 0.9156 (mmt) cc_final: 0.8770 (mpp) REVERT: C 137 ILE cc_start: 0.9023 (tt) cc_final: 0.8808 (tt) REVERT: C 151 MET cc_start: 0.4736 (ttm) cc_final: 0.4476 (ttm) REVERT: C 251 CYS cc_start: 0.8615 (m) cc_final: 0.8285 (t) REVERT: C 289 LYS cc_start: 0.9285 (mppt) cc_final: 0.9069 (mmmt) REVERT: C 290 PHE cc_start: 0.9376 (m-80) cc_final: 0.8987 (m-80) REVERT: C 373 ASP cc_start: 0.8584 (t0) cc_final: 0.8360 (t0) REVERT: C 428 ARG cc_start: 0.6125 (mpt180) cc_final: 0.5486 (mtp180) REVERT: C 464 MET cc_start: 0.9451 (ttm) cc_final: 0.9199 (ttm) REVERT: C 523 HIS cc_start: 0.9194 (m90) cc_final: 0.8896 (m-70) REVERT: C 564 LEU cc_start: 0.8735 (tp) cc_final: 0.8134 (tt) REVERT: C 582 HIS cc_start: 0.9291 (t70) cc_final: 0.8867 (p-80) REVERT: C 607 MET cc_start: 0.8550 (tmm) cc_final: 0.8335 (ttp) REVERT: C 626 ASP cc_start: 0.9187 (p0) cc_final: 0.8617 (t0) REVERT: C 627 LEU cc_start: 0.9226 (mm) cc_final: 0.8936 (mp) REVERT: C 688 MET cc_start: 0.8782 (ppp) cc_final: 0.8426 (ppp) REVERT: C 764 GLU cc_start: 0.6384 (mp0) cc_final: 0.5997 (mp0) REVERT: C 800 TYR cc_start: 0.8962 (p90) cc_final: 0.8675 (p90) REVERT: C 916 PHE cc_start: 0.8292 (t80) cc_final: 0.8057 (t80) REVERT: C 975 GLN cc_start: 0.9075 (mm-40) cc_final: 0.8591 (tp-100) REVERT: C 1020 HIS cc_start: 0.9252 (t-90) cc_final: 0.8987 (t-90) REVERT: C 1028 PHE cc_start: 0.8661 (m-80) cc_final: 0.8394 (m-80) REVERT: C 1057 PHE cc_start: 0.8827 (t80) cc_final: 0.8513 (t80) REVERT: C 1076 ASP cc_start: 0.8628 (p0) cc_final: 0.8052 (m-30) REVERT: C 1132 TRP cc_start: 0.8796 (t60) cc_final: 0.8573 (t60) REVERT: C 1144 VAL cc_start: 0.8438 (p) cc_final: 0.8045 (m) REVERT: C 1150 LEU cc_start: 0.9588 (mm) cc_final: 0.9246 (pp) REVERT: C 1154 PHE cc_start: 0.9421 (m-80) cc_final: 0.8473 (m-80) REVERT: C 1323 TYR cc_start: 0.8156 (t80) cc_final: 0.7716 (t80) REVERT: D 121 MET cc_start: 0.8723 (tpp) cc_final: 0.8324 (tpt) REVERT: D 126 ASP cc_start: 0.9481 (p0) cc_final: 0.9241 (p0) REVERT: D 290 PHE cc_start: 0.9081 (m-80) cc_final: 0.8769 (m-80) REVERT: D 309 PHE cc_start: 0.9195 (m-80) cc_final: 0.8986 (m-80) REVERT: D 321 HIS cc_start: 0.9007 (m90) cc_final: 0.8684 (m-70) REVERT: D 354 LYS cc_start: 0.8707 (tttp) cc_final: 0.7601 (mttt) REVERT: D 356 ASP cc_start: 0.9315 (m-30) cc_final: 0.8957 (t0) REVERT: D 360 ARG cc_start: 0.9032 (mpt180) cc_final: 0.8707 (mpt-90) REVERT: D 363 ILE cc_start: 0.9367 (tp) cc_final: 0.9143 (tp) REVERT: D 415 MET cc_start: 0.6618 (pmm) cc_final: 0.4965 (pmm) REVERT: D 422 ARG cc_start: 0.9224 (mtt90) cc_final: 0.8627 (mtm-85) REVERT: D 461 LEU cc_start: 0.9240 (mp) cc_final: 0.8784 (mm) REVERT: D 543 TYR cc_start: 0.8741 (p90) cc_final: 0.8486 (p90) REVERT: D 552 ILE cc_start: 0.9372 (pt) cc_final: 0.8881 (pt) REVERT: D 554 ASP cc_start: 0.7302 (t0) cc_final: 0.6977 (t0) REVERT: D 572 PHE cc_start: 0.8452 (p90) cc_final: 0.8105 (p90) REVERT: D 688 MET cc_start: 0.8067 (ppp) cc_final: 0.7679 (ppp) REVERT: D 786 LEU cc_start: 0.8950 (mp) cc_final: 0.8728 (mp) REVERT: D 877 LEU cc_start: 0.8828 (mm) cc_final: 0.8268 (tt) REVERT: D 901 LYS cc_start: 0.9024 (mmmm) cc_final: 0.8505 (mmtt) REVERT: D 968 MET cc_start: 0.8555 (tpt) cc_final: 0.8225 (tpt) REVERT: D 985 TYR cc_start: 0.9085 (m-80) cc_final: 0.8803 (m-80) REVERT: D 1072 GLN cc_start: 0.9318 (mt0) cc_final: 0.8647 (tt0) REVERT: D 1076 ASP cc_start: 0.8928 (p0) cc_final: 0.8658 (p0) REVERT: D 1156 LEU cc_start: 0.7705 (mm) cc_final: 0.7421 (mm) REVERT: D 1205 GLU cc_start: 0.8394 (pt0) cc_final: 0.8124 (tt0) REVERT: D 1331 ASN cc_start: 0.5614 (m110) cc_final: 0.4927 (t0) outliers start: 1 outliers final: 0 residues processed: 828 average time/residue: 0.5009 time to fit residues: 684.6706 Evaluate side-chains 665 residues out of total 4451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 665 time to evaluate : 4.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 454 optimal weight: 6.9990 chunk 299 optimal weight: 0.9980 chunk 482 optimal weight: 8.9990 chunk 294 optimal weight: 0.0000 chunk 228 optimal weight: 0.8980 chunk 335 optimal weight: 10.0000 chunk 506 optimal weight: 4.9990 chunk 465 optimal weight: 5.9990 chunk 403 optimal weight: 0.9990 chunk 41 optimal weight: 9.9990 chunk 311 optimal weight: 7.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 200 GLN ** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 441 HIS ** A 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 584 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 647 ASN A 917 ASN A1233 ASN ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1017 ASN ** B1277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 441 HIS ** C 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 584 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 647 ASN C 917 ASN ** C1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1233 ASN ** C1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1243 ASN ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1017 ASN ** D1277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.7077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.101 41179 Z= 0.216 Angle : 0.765 18.120 55948 Z= 0.380 Chirality : 0.050 0.366 6471 Planarity : 0.005 0.093 7166 Dihedral : 7.682 58.858 6200 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 23.65 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.70 % Favored : 89.26 % Rotamer: Outliers : 0.07 % Allowed : 0.31 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.85 (0.11), residues: 5084 helix: -0.08 (0.17), residues: 850 sheet: -1.53 (0.12), residues: 1784 loop : -2.86 (0.12), residues: 2450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.003 TRP B1132 HIS 0.010 0.001 HIS C 358 PHE 0.045 0.002 PHE C1049 TYR 0.025 0.002 TYR B1152 ARG 0.009 0.001 ARG D 598 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10168 Ramachandran restraints generated. 5084 Oldfield, 0 Emsley, 5084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 818 residues out of total 4451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 815 time to evaluate : 4.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LEU cc_start: 0.8257 (tt) cc_final: 0.7977 (tt) REVERT: A 50 LEU cc_start: 0.9673 (tp) cc_final: 0.9380 (tp) REVERT: A 121 MET cc_start: 0.9145 (mmt) cc_final: 0.8702 (mpp) REVERT: A 151 MET cc_start: 0.4473 (ttm) cc_final: 0.4159 (tpp) REVERT: A 216 GLU cc_start: 0.9077 (pm20) cc_final: 0.8802 (mp0) REVERT: A 251 CYS cc_start: 0.8512 (m) cc_final: 0.8222 (t) REVERT: A 290 PHE cc_start: 0.9335 (m-80) cc_final: 0.9034 (m-80) REVERT: A 318 MET cc_start: 0.8542 (tpp) cc_final: 0.8128 (tpp) REVERT: A 373 ASP cc_start: 0.8657 (t0) cc_final: 0.8266 (t0) REVERT: A 385 PHE cc_start: 0.8949 (m-80) cc_final: 0.8484 (m-80) REVERT: A 428 ARG cc_start: 0.6251 (mpt180) cc_final: 0.5541 (mtp85) REVERT: A 464 MET cc_start: 0.9457 (ttm) cc_final: 0.9218 (ttm) REVERT: A 500 MET cc_start: 0.7520 (tmm) cc_final: 0.6881 (ttt) REVERT: A 523 HIS cc_start: 0.9196 (m90) cc_final: 0.8908 (m-70) REVERT: A 530 VAL cc_start: 0.9128 (m) cc_final: 0.8755 (p) REVERT: A 552 ILE cc_start: 0.9054 (tp) cc_final: 0.8758 (tp) REVERT: A 582 HIS cc_start: 0.9292 (t70) cc_final: 0.8885 (p-80) REVERT: A 626 ASP cc_start: 0.9174 (p0) cc_final: 0.8542 (t0) REVERT: A 627 LEU cc_start: 0.9171 (mm) cc_final: 0.8859 (mp) REVERT: A 688 MET cc_start: 0.8802 (ppp) cc_final: 0.8454 (ppp) REVERT: A 764 GLU cc_start: 0.6225 (mp0) cc_final: 0.5831 (mp0) REVERT: A 800 TYR cc_start: 0.8946 (p90) cc_final: 0.8511 (p90) REVERT: A 931 LEU cc_start: 0.8974 (tp) cc_final: 0.8663 (tp) REVERT: A 975 GLN cc_start: 0.9063 (mm-40) cc_final: 0.8582 (tp-100) REVERT: A 988 ASP cc_start: 0.8935 (m-30) cc_final: 0.8421 (m-30) REVERT: A 1020 HIS cc_start: 0.9209 (t-90) cc_final: 0.8941 (t-90) REVERT: A 1028 PHE cc_start: 0.8625 (m-80) cc_final: 0.8361 (m-80) REVERT: A 1057 PHE cc_start: 0.8654 (t80) cc_final: 0.8449 (t80) REVERT: A 1076 ASP cc_start: 0.8558 (p0) cc_final: 0.8004 (m-30) REVERT: A 1133 LYS cc_start: 0.9501 (ttmt) cc_final: 0.9191 (tppt) REVERT: A 1144 VAL cc_start: 0.8394 (p) cc_final: 0.8045 (m) REVERT: A 1150 LEU cc_start: 0.9576 (mm) cc_final: 0.9215 (pp) REVERT: A 1154 PHE cc_start: 0.9333 (m-80) cc_final: 0.8378 (m-80) REVERT: A 1214 LEU cc_start: 0.9287 (mt) cc_final: 0.9052 (mt) REVERT: A 1323 TYR cc_start: 0.7949 (t80) cc_final: 0.6896 (t80) REVERT: A 1324 LEU cc_start: 0.7887 (mp) cc_final: 0.7567 (tt) REVERT: B 54 LEU cc_start: 0.7706 (tp) cc_final: 0.7483 (tp) REVERT: B 121 MET cc_start: 0.8765 (tpp) cc_final: 0.8342 (tpt) REVERT: B 126 ASP cc_start: 0.9480 (p0) cc_final: 0.9262 (p0) REVERT: B 290 PHE cc_start: 0.9041 (m-80) cc_final: 0.8758 (m-80) REVERT: B 321 HIS cc_start: 0.8868 (m90) cc_final: 0.8452 (m90) REVERT: B 356 ASP cc_start: 0.9276 (m-30) cc_final: 0.8989 (t0) REVERT: B 360 ARG cc_start: 0.8934 (mpt180) cc_final: 0.8624 (mpt-90) REVERT: B 363 ILE cc_start: 0.9359 (tp) cc_final: 0.9138 (tp) REVERT: B 415 MET cc_start: 0.6956 (pmm) cc_final: 0.5411 (pmm) REVERT: B 419 LEU cc_start: 0.9346 (mp) cc_final: 0.9134 (mp) REVERT: B 461 LEU cc_start: 0.9310 (mp) cc_final: 0.8887 (mm) REVERT: B 543 TYR cc_start: 0.8709 (p90) cc_final: 0.8494 (p90) REVERT: B 550 ASP cc_start: 0.9236 (m-30) cc_final: 0.9014 (m-30) REVERT: B 552 ILE cc_start: 0.9377 (pt) cc_final: 0.8948 (pt) REVERT: B 554 ASP cc_start: 0.7227 (t0) cc_final: 0.6999 (t0) REVERT: B 572 PHE cc_start: 0.8254 (p90) cc_final: 0.7888 (p90) REVERT: B 650 ILE cc_start: 0.6927 (mm) cc_final: 0.6726 (mm) REVERT: B 688 MET cc_start: 0.8033 (ppp) cc_final: 0.7715 (ppp) REVERT: B 870 PHE cc_start: 0.9368 (t80) cc_final: 0.9123 (t80) REVERT: B 877 LEU cc_start: 0.8830 (mm) cc_final: 0.8288 (tt) REVERT: B 1072 GLN cc_start: 0.9438 (mt0) cc_final: 0.9199 (tm-30) REVERT: B 1156 LEU cc_start: 0.7644 (mm) cc_final: 0.7323 (mm) REVERT: B 1207 GLU cc_start: 0.9303 (tp30) cc_final: 0.9052 (tp30) REVERT: B 1328 LEU cc_start: 0.9439 (tp) cc_final: 0.8922 (tp) REVERT: B 1330 TYR cc_start: 0.9028 (p90) cc_final: 0.8779 (p90) REVERT: C 32 MET cc_start: 0.9555 (ttt) cc_final: 0.9290 (tpp) REVERT: C 38 LEU cc_start: 0.8259 (tt) cc_final: 0.7980 (tt) REVERT: C 121 MET cc_start: 0.9152 (mmt) cc_final: 0.8701 (mpp) REVERT: C 137 ILE cc_start: 0.8980 (tt) cc_final: 0.8759 (tt) REVERT: C 151 MET cc_start: 0.4568 (ttm) cc_final: 0.3824 (tpp) REVERT: C 251 CYS cc_start: 0.8581 (m) cc_final: 0.8290 (t) REVERT: C 289 LYS cc_start: 0.9117 (mppt) cc_final: 0.8879 (tptt) REVERT: C 373 ASP cc_start: 0.8604 (t0) cc_final: 0.8200 (t0) REVERT: C 428 ARG cc_start: 0.6197 (mpt180) cc_final: 0.5447 (mtp85) REVERT: C 464 MET cc_start: 0.9458 (ttm) cc_final: 0.9207 (ttm) REVERT: C 523 HIS cc_start: 0.9190 (m90) cc_final: 0.8885 (m-70) REVERT: C 530 VAL cc_start: 0.9140 (m) cc_final: 0.8770 (p) REVERT: C 552 ILE cc_start: 0.9031 (tp) cc_final: 0.8706 (tp) REVERT: C 564 LEU cc_start: 0.8654 (tp) cc_final: 0.8069 (tt) REVERT: C 582 HIS cc_start: 0.9288 (t70) cc_final: 0.8883 (p-80) REVERT: C 626 ASP cc_start: 0.9144 (p0) cc_final: 0.8511 (t0) REVERT: C 627 LEU cc_start: 0.9223 (mm) cc_final: 0.8960 (mp) REVERT: C 669 PHE cc_start: 0.8557 (m-10) cc_final: 0.8241 (m-80) REVERT: C 688 MET cc_start: 0.8784 (ppp) cc_final: 0.8439 (ppp) REVERT: C 764 GLU cc_start: 0.6212 (mp0) cc_final: 0.5809 (mp0) REVERT: C 800 TYR cc_start: 0.8925 (p90) cc_final: 0.8669 (p90) REVERT: C 916 PHE cc_start: 0.8207 (t80) cc_final: 0.7985 (t80) REVERT: C 968 MET cc_start: 0.7806 (tpt) cc_final: 0.6842 (pmm) REVERT: C 975 GLN cc_start: 0.9067 (mm-40) cc_final: 0.8581 (tp-100) REVERT: C 1020 HIS cc_start: 0.9198 (t-90) cc_final: 0.8921 (t-90) REVERT: C 1028 PHE cc_start: 0.8647 (m-80) cc_final: 0.8373 (m-80) REVERT: C 1057 PHE cc_start: 0.8835 (t80) cc_final: 0.8516 (t80) REVERT: C 1076 ASP cc_start: 0.8545 (p0) cc_final: 0.7981 (m-30) REVERT: C 1132 TRP cc_start: 0.8776 (t60) cc_final: 0.8559 (t60) REVERT: C 1144 VAL cc_start: 0.8366 (p) cc_final: 0.7990 (m) REVERT: C 1150 LEU cc_start: 0.9594 (mm) cc_final: 0.9237 (pp) REVERT: C 1154 PHE cc_start: 0.9414 (m-80) cc_final: 0.8449 (m-80) REVERT: C 1214 LEU cc_start: 0.9282 (mt) cc_final: 0.9049 (mt) REVERT: C 1323 TYR cc_start: 0.7488 (t80) cc_final: 0.6994 (t80) REVERT: D 121 MET cc_start: 0.8726 (tpp) cc_final: 0.8314 (tpt) REVERT: D 126 ASP cc_start: 0.9468 (p0) cc_final: 0.9218 (p0) REVERT: D 290 PHE cc_start: 0.9050 (m-80) cc_final: 0.8721 (m-80) REVERT: D 291 SER cc_start: 0.9070 (p) cc_final: 0.8860 (p) REVERT: D 321 HIS cc_start: 0.8874 (m90) cc_final: 0.8467 (m90) REVERT: D 354 LYS cc_start: 0.8622 (tttp) cc_final: 0.7478 (mttt) REVERT: D 356 ASP cc_start: 0.9293 (m-30) cc_final: 0.8924 (t0) REVERT: D 360 ARG cc_start: 0.8935 (mpt180) cc_final: 0.8565 (mpt-90) REVERT: D 363 ILE cc_start: 0.9355 (tp) cc_final: 0.9133 (tp) REVERT: D 415 MET cc_start: 0.6931 (pmm) cc_final: 0.5396 (pmm) REVERT: D 422 ARG cc_start: 0.9199 (mtt90) cc_final: 0.8607 (mtm-85) REVERT: D 543 TYR cc_start: 0.8760 (p90) cc_final: 0.8507 (p90) REVERT: D 552 ILE cc_start: 0.9355 (pt) cc_final: 0.8855 (pt) REVERT: D 572 PHE cc_start: 0.8375 (p90) cc_final: 0.8047 (p90) REVERT: D 688 MET cc_start: 0.8028 (ppp) cc_final: 0.7721 (ppp) REVERT: D 870 PHE cc_start: 0.9329 (t80) cc_final: 0.9032 (t80) REVERT: D 877 LEU cc_start: 0.8836 (mm) cc_final: 0.8294 (tt) REVERT: D 901 LYS cc_start: 0.8970 (mmmm) cc_final: 0.8464 (mmtt) REVERT: D 1072 GLN cc_start: 0.9342 (mt0) cc_final: 0.8677 (tt0) REVERT: D 1076 ASP cc_start: 0.8907 (p0) cc_final: 0.8647 (p0) REVERT: D 1133 LYS cc_start: 0.9437 (mmtm) cc_final: 0.9183 (mmmt) REVERT: D 1154 PHE cc_start: 0.8727 (m-80) cc_final: 0.7591 (m-80) REVERT: D 1156 LEU cc_start: 0.7570 (mm) cc_final: 0.7260 (mm) REVERT: D 1165 GLU cc_start: 0.9087 (mp0) cc_final: 0.8835 (pm20) REVERT: D 1205 GLU cc_start: 0.8404 (pt0) cc_final: 0.8172 (tt0) REVERT: D 1323 TYR cc_start: 0.8149 (t80) cc_final: 0.7724 (t80) REVERT: D 1331 ASN cc_start: 0.5482 (m110) cc_final: 0.4782 (t0) outliers start: 3 outliers final: 0 residues processed: 818 average time/residue: 0.4963 time to fit residues: 670.9524 Evaluate side-chains 655 residues out of total 4451 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 655 time to evaluate : 4.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 247 optimal weight: 8.9990 chunk 320 optimal weight: 0.0670 chunk 429 optimal weight: 10.0000 chunk 123 optimal weight: 5.9990 chunk 371 optimal weight: 3.9990 chunk 59 optimal weight: 8.9990 chunk 111 optimal weight: 20.0000 chunk 403 optimal weight: 9.9990 chunk 168 optimal weight: 8.9990 chunk 414 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 overall best weight: 2.9924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 HIS ** A 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 584 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 647 ASN A 917 ASN A1233 ASN ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1017 ASN ** B1277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 441 HIS ** C 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 584 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 647 ASN C 917 ASN ** C1013 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1233 ASN ** C1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 321 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 479 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 994 GLN D1015 GLN D1017 ASN ** D1277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.082946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.062850 restraints weight = 185113.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.065261 restraints weight = 128759.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.067163 restraints weight = 96901.116| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.7298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 41179 Z= 0.252 Angle : 0.769 16.484 55948 Z= 0.386 Chirality : 0.049 0.379 6471 Planarity : 0.005 0.061 7166 Dihedral : 7.672 58.722 6200 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 27.64 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.41 % Favored : 88.51 % Rotamer: Outliers : 0.04 % Allowed : 0.40 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.92 (0.11), residues: 5084 helix: -0.18 (0.16), residues: 861 sheet: -1.58 (0.12), residues: 1793 loop : -2.90 (0.12), residues: 2430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.004 TRP A1183 HIS 0.015 0.001 HIS B 402 PHE 0.038 0.002 PHE C1049 TYR 0.028 0.002 TYR D1152 ARG 0.015 0.001 ARG B 732 =============================================================================== Job complete usr+sys time: 11529.35 seconds wall clock time: 211 minutes 16.29 seconds (12676.29 seconds total)