Starting phenix.real_space_refine on Sun Mar 24 06:30:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o7r_12754/03_2024/7o7r_12754.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o7r_12754/03_2024/7o7r_12754.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o7r_12754/03_2024/7o7r_12754.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o7r_12754/03_2024/7o7r_12754.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o7r_12754/03_2024/7o7r_12754.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7o7r_12754/03_2024/7o7r_12754.pdb" } resolution = 3.9 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 25734 2.51 5 N 6746 2.21 5 O 7878 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 184": "OE1" <-> "OE2" Residue "A GLU 216": "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 PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 561": "OE1" <-> "OE2" Residue "A GLU 624": "OE1" <-> "OE2" Residue "A ARG 645": "NH1" <-> "NH2" Residue "A PHE 735": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 753": "OE1" <-> "OE2" Residue "A GLU 886": "OE1" <-> "OE2" Residue "A GLU 911": "OE1" <-> "OE2" Residue "A GLU 999": "OE1" <-> "OE2" Residue "A GLU 1096": "OE1" <-> "OE2" Residue "A GLU 1165": "OE1" <-> "OE2" Residue "B GLU 56": "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 439": "OE1" <-> "OE2" Residue "B GLU 612": "OE1" <-> "OE2" Residue "B GLU 624": "OE1" <-> "OE2" Residue "B ARG 645": "NH1" <-> "NH2" Residue "B GLU 753": "OE1" <-> "OE2" Residue "B PHE 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 795": "OE1" <-> "OE2" Residue "B GLU 806": "OE1" <-> "OE2" Residue "B GLU 842": "OE1" <-> "OE2" Residue "B GLU 892": "OE1" <-> "OE2" Residue "B GLU 906": "OE1" <-> "OE2" Residue "B GLU 908": "OE1" <-> "OE2" Residue "B GLU 911": "OE1" <-> "OE2" Residue "B GLU 930": "OE1" <-> "OE2" Residue "B GLU 992": "OE1" <-> "OE2" Residue "B GLU 999": "OE1" <-> "OE2" Residue "B GLU 1030": "OE1" <-> "OE2" Residue "B GLU 1165": "OE1" <-> "OE2" Residue "B GLU 1337": "OE1" <-> "OE2" Residue "C GLU 216": "OE1" <-> "OE2" Residue "C GLU 223": "OE1" <-> "OE2" Residue "C GLU 243": "OE1" <-> "OE2" Residue "C GLU 244": "OE1" <-> "OE2" Residue "C GLU 281": "OE1" <-> "OE2" Residue "C ARG 313": "NH1" <-> "NH2" Residue "C GLU 323": "OE1" <-> "OE2" Residue "C ARG 645": "NH1" <-> "NH2" Residue "C PHE 735": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 737": "OE1" <-> "OE2" Residue "C GLU 753": "OE1" <-> "OE2" Residue "C GLU 795": "OE1" <-> "OE2" Residue "C GLU 840": "OE1" <-> "OE2" Residue "C GLU 908": "OE1" <-> "OE2" Residue "C GLU 999": "OE1" <-> "OE2" Residue "C GLU 1030": "OE1" <-> "OE2" Residue "C GLU 1198": "OE1" <-> "OE2" Residue "C GLU 1337": "OE1" <-> "OE2" Residue "C GLU 1338": "OE1" <-> "OE2" Residue "D GLU 56": "OE1" <-> "OE2" Residue "D GLU 78": "OE1" <-> "OE2" Residue "D GLU 243": "OE1" <-> "OE2" Residue "D GLU 244": "OE1" <-> "OE2" Residue "D ARG 313": "NH1" <-> "NH2" Residue "D GLU 323": "OE1" <-> "OE2" Residue "D GLU 342": "OE1" <-> "OE2" Residue "D GLU 561": "OE1" <-> "OE2" 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 PHE 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 806": "OE1" <-> "OE2" Residue "D GLU 842": "OE1" <-> "OE2" Residue "D GLU 886": "OE1" <-> "OE2" Residue "D GLU 906": "OE1" <-> "OE2" Residue "D GLU 930": "OE1" <-> "OE2" Residue "D GLU 1098": "OE1" <-> "OE2" Residue "D GLU 1137": "OE1" <-> "OE2" Residue "D GLU 1337": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 40530 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 10023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1285, 10023 Classifications: {'peptide': 1285} Link IDs: {'PTRANS': 67, 'TRANS': 1217} Chain breaks: 1 Chain: "B" Number of atoms: 9968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1278, 9968 Classifications: {'peptide': 1278} Link IDs: {'PTRANS': 66, 'TRANS': 1211} Chain breaks: 1 Chain: "C" Number of atoms: 10023 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1285, 10023 Classifications: {'peptide': 1285} Link IDs: {'PTRANS': 67, 'TRANS': 1217} Chain breaks: 1 Chain: "D" Number of atoms: 9968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1278, 9968 Classifications: {'peptide': 1278} Link IDs: {'PTRANS': 66, 'TRANS': 1211} 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 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: 20.02, per 1000 atoms: 0.49 Number of scatterers: 40530 At special positions: 0 Unit cell: (213.556, 152.54, 158.852, 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 7878 8.00 N 6746 7.00 C 25734 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=2.04 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=2.01 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS B 431 " distance=2.03 Simple disulfide: pdb=" SG CYS A 431 " - pdb=" SG CYS B 278 " distance=2.02 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS B 251 " - pdb=" SG CYS B 299 " distance=2.02 Simple disulfide: pdb=" SG CYS B 269 " - pdb=" SG CYS B 287 " distance=2.02 Simple disulfide: pdb=" SG CYS B 470 " - pdb=" SG CYS B 563 " distance=2.04 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=2.03 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=2.02 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=2.02 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS D 431 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS C 642 " - pdb=" SG CYS C 689 " distance=2.04 Simple disulfide: pdb=" SG CYS C 821 " - pdb=" SG CYS C 849 " distance=2.03 Simple disulfide: pdb=" SG CYS C 847 " - pdb=" SG CYS C 883 " distance=2.03 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=2.01 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=2.04 Simple disulfide: pdb=" SG CYS D 595 " - pdb=" SG CYS D 771 " distance=2.04 Simple disulfide: pdb=" SG CYS D 642 " - pdb=" SG CYS D 689 " distance=2.02 Simple disulfide: pdb=" SG CYS D 821 " - pdb=" SG CYS D 849 " distance=2.04 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=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " 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: 15.76 Conformation dependent library (CDL) restraints added in 7.3 seconds 10220 Ramachandran restraints generated. 5110 Oldfield, 0 Emsley, 5110 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9600 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 0 sheets defined 16.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.52 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 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: 6.241A pdb=" N SER A 957 " --> pdb=" O ASP A 953 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA A 958 " --> pdb=" O ILE A 954 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N MET A 959 " --> pdb=" O LEU A 955 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N GLN A 960 " --> pdb=" O GLY A 956 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ASN A 961 " --> pdb=" O SER A 957 " (cutoff:3.500A) removed outlier: 4.456A 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: 4.023A 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: 3.541A 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: 6.830A pdb=" N SER B 957 " --> pdb=" O ASP B 953 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ALA B 958 " --> pdb=" O ILE B 954 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N MET B 959 " --> pdb=" O LEU B 955 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N GLN B 960 " --> pdb=" O GLY B 956 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ASN B 961 " --> pdb=" O SER B 957 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N THR B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN B 963 " --> pdb=" O MET B 959 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU B 965 " --> pdb=" O ASN B 961 " (cutoff:3.500A) Processing helix chain 'B' and resid 973 through 993 removed outlier: 3.502A pdb=" N MET B 977 " --> pdb=" O GLY B 973 " (cutoff:3.500A) Proline residue: B 982 - end of helix removed outlier: 4.345A pdb=" N TYR B 985 " --> pdb=" O ALA B 981 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL B 986 " --> pdb=" O PRO B 982 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU B 987 " --> pdb=" O ASN B 983 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASP B 988 " --> pdb=" O ILE B 984 " (cutoff:3.500A) Processing helix chain 'B' and resid 998 through 1017 removed outlier: 4.061A pdb=" N TYR B1007 " --> pdb=" O LYS B1003 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU B1016 " --> pdb=" O TYR B1012 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASN B1017 " --> pdb=" O GLN B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1039 through 1055 removed outlier: 3.860A pdb=" N TYR B1055 " --> pdb=" O GLN B1051 " (cutoff:3.500A) Processing helix chain 'B' and resid 1060 through 1073 removed outlier: 4.472A pdb=" N ALA B1066 " --> pdb=" O HIS B1062 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N TRP B1069 " --> pdb=" O GLN B1065 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU B1070 " --> pdb=" O ALA B1066 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER B1071 " --> pdb=" O LEU B1067 " (cutoff:3.500A) Processing helix chain 'B' and resid 1098 through 1111 removed outlier: 3.520A pdb=" N ILE B1107 " --> pdb=" O ALA B1103 " (cutoff:3.500A) Processing helix chain 'B' and resid 1119 through 1137 removed outlier: 4.088A pdb=" N PHE B1126 " --> pdb=" O ARG B1122 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA B1135 " --> pdb=" O ALA B1131 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU B1137 " --> pdb=" O LYS B1133 " (cutoff:3.500A) Processing helix chain 'B' and resid 1144 through 1157 removed outlier: 3.542A pdb=" N TYR B1152 " --> pdb=" O ALA B1148 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA B1153 " --> pdb=" O LEU B1149 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA B1157 " --> pdb=" O ALA B1153 " (cutoff:3.500A) Processing helix chain 'B' and resid 1160 through 1172 removed outlier: 4.680A pdb=" N LYS B1164 " --> pdb=" O GLN B1160 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU B1165 " --> pdb=" O ASP B1161 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL B1166 " --> pdb=" O LYS B1162 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N SER B1169 " --> pdb=" O GLU B1165 " (cutoff:3.500A) Processing helix chain 'B' and resid 1225 through 1241 removed outlier: 3.568A pdb=" N SER B1230 " --> pdb=" O GLU B1226 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL B1235 " --> pdb=" O ALA B1231 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TRP B1237 " --> pdb=" O ASN B1233 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LYS B1240 " --> pdb=" O LYS B1236 " (cutoff:3.500A) Processing helix chain 'B' and resid 1251 through 1268 removed outlier: 4.422A pdb=" N LEU B1258 " --> pdb=" O THR B1254 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N HIS B1259 " --> pdb=" O VAL B1255 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA B1267 " --> pdb=" O LYS B1263 " (cutoff:3.500A) 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 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: 6.323A pdb=" N SER C 957 " --> pdb=" O ASP C 953 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ALA C 958 " --> pdb=" O ILE C 954 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N MET C 959 " --> pdb=" O LEU C 955 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N GLN C 960 " --> pdb=" O GLY C 956 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ASN C 961 " --> pdb=" O SER C 957 " (cutoff:3.500A) removed outlier: 3.731A 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: 4.043A 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 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: 6.995A pdb=" N SER D 957 " --> pdb=" O ASP D 953 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA D 958 " --> pdb=" O ILE D 954 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N MET D 959 " --> pdb=" O LEU D 955 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N GLN D 960 " --> pdb=" O GLY D 956 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ASN D 961 " --> pdb=" O SER D 957 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N THR D 962 " --> pdb=" O ALA D 958 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLN D 963 " --> pdb=" O MET D 959 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU D 965 " --> pdb=" O ASN D 961 " (cutoff:3.500A) Processing helix chain 'D' and resid 973 through 993 removed outlier: 3.696A pdb=" N MET D 977 " --> pdb=" O GLY D 973 " (cutoff:3.500A) Proline residue: D 982 - end of helix removed outlier: 3.931A pdb=" N TYR D 985 " --> pdb=" O ALA D 981 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL D 986 " --> pdb=" O PRO D 982 " (cutoff:3.500A) Processing helix chain 'D' and resid 998 through 1017 removed outlier: 3.669A pdb=" N THR D1010 " --> pdb=" O GLY D1006 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN D1017 " --> pdb=" O GLN D1013 " (cutoff:3.500A) Processing helix chain 'D' and resid 1039 through 1055 removed outlier: 3.595A pdb=" N GLN D1051 " --> pdb=" O LYS D1047 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA D1054 " --> pdb=" O ALA D1050 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N TYR D1055 " --> pdb=" O GLN D1051 " (cutoff:3.500A) Processing helix chain 'D' and resid 1060 through 1073 removed outlier: 3.670A pdb=" N THR D1064 " --> pdb=" O GLU D1060 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N TRP D1069 " --> pdb=" O GLN D1065 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU D1070 " --> pdb=" O ALA D1066 " (cutoff:3.500A) Processing helix chain 'D' and resid 1098 through 1111 Processing helix chain 'D' and resid 1119 through 1137 removed outlier: 3.850A pdb=" N PHE D1126 " --> pdb=" O ARG D1122 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N CYS D1127 " --> pdb=" O ASN D1123 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA D1135 " --> pdb=" O ALA D1131 " (cutoff:3.500A) Processing helix chain 'D' and resid 1144 through 1157 removed outlier: 4.007A pdb=" N LEU D1156 " --> pdb=" O TYR D1152 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ALA D1157 " --> pdb=" O ALA D1153 " (cutoff:3.500A) Processing helix chain 'D' and resid 1160 through 1172 removed outlier: 4.689A pdb=" N LYS D1164 " --> pdb=" O GLN D1160 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLU D1165 " --> pdb=" O ASP D1161 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL D1166 " --> pdb=" O LYS D1162 " (cutoff:3.500A) Processing helix chain 'D' and resid 1225 through 1241 removed outlier: 3.619A pdb=" N THR D1229 " --> pdb=" O SER D1225 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER D1230 " --> pdb=" O GLU D1226 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TRP D1237 " --> pdb=" O ASN D1233 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS D1240 " --> pdb=" O LYS D1236 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN D1241 " --> pdb=" O TRP D1237 " (cutoff:3.500A) Processing helix chain 'D' and resid 1251 through 1268 removed outlier: 3.614A pdb=" N LYS D1263 " --> pdb=" O HIS D1259 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA D1267 " --> pdb=" O LYS D1263 " (cutoff:3.500A) Processing helix chain 'D' and resid 1294 through 1297 No H-bonds generated for 'chain 'D' and resid 1294 through 1297' 480 hydrogen bonds defined for protein. 1440 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: 8.52 Time building geometry restraints manager: 17.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 6761 1.30 - 1.43: 10901 1.43 - 1.57: 23502 1.57 - 1.71: 3 1.71 - 1.84: 253 Bond restraints: 41420 Sorted by residual: bond pdb=" N PRO C 902 " pdb=" CA PRO C 902 " ideal model delta sigma weight residual 1.470 1.700 -0.230 1.01e-02 9.80e+03 5.18e+02 bond pdb=" N PRO B 29 " pdb=" CA PRO B 29 " ideal model delta sigma weight residual 1.469 1.710 -0.241 1.28e-02 6.10e+03 3.55e+02 bond pdb=" N PRO D 29 " pdb=" CA PRO D 29 " ideal model delta sigma weight residual 1.469 1.706 -0.237 1.28e-02 6.10e+03 3.44e+02 bond pdb=" C GLN D 168 " pdb=" N ASP D 169 " ideal model delta sigma weight residual 1.331 1.162 0.169 1.59e-02 3.96e+03 1.14e+02 bond pdb=" C GLN C 967 " pdb=" N MET C 968 " ideal model delta sigma weight residual 1.330 1.209 0.121 1.47e-02 4.63e+03 6.82e+01 ... (remaining 41415 not shown) Histogram of bond angle deviations from ideal: 98.35 - 106.68: 1542 106.68 - 115.02: 25230 115.02 - 123.35: 25899 123.35 - 131.68: 3540 131.68 - 140.01: 59 Bond angle restraints: 56270 Sorted by residual: angle pdb=" C LYS B 28 " pdb=" N PRO B 29 " pdb=" CA PRO B 29 " ideal model delta sigma weight residual 119.84 138.75 -18.91 1.25e+00 6.40e-01 2.29e+02 angle pdb=" C LYS D 28 " pdb=" N PRO D 29 " pdb=" CA PRO D 29 " ideal model delta sigma weight residual 119.84 138.61 -18.77 1.25e+00 6.40e-01 2.26e+02 angle pdb=" C LYS C 901 " pdb=" N PRO C 902 " pdb=" CA PRO C 902 " ideal model delta sigma weight residual 120.79 140.01 -19.22 1.30e+00 5.92e-01 2.19e+02 angle pdb=" CA PRO C 902 " pdb=" N PRO C 902 " pdb=" CD PRO C 902 " ideal model delta sigma weight residual 112.00 98.49 13.51 1.40e+00 5.10e-01 9.32e+01 angle pdb=" CA PRO B 29 " pdb=" N PRO B 29 " pdb=" CD PRO B 29 " ideal model delta sigma weight residual 112.00 100.84 11.16 1.40e+00 5.10e-01 6.36e+01 ... (remaining 56265 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.17: 22850 21.17 - 42.34: 2267 42.34 - 63.51: 336 63.51 - 84.68: 88 84.68 - 105.85: 21 Dihedral angle restraints: 25562 sinusoidal: 10648 harmonic: 14914 Sorted by residual: dihedral pdb=" C ASN B 991 " pdb=" N ASN B 991 " pdb=" CA ASN B 991 " pdb=" CB ASN B 991 " ideal model delta harmonic sigma weight residual -122.60 -144.63 22.03 0 2.50e+00 1.60e-01 7.76e+01 dihedral pdb=" CB CYS B 470 " pdb=" SG CYS B 470 " pdb=" SG CYS B 563 " pdb=" CB CYS B 563 " ideal model delta sinusoidal sigma weight residual 93.00 19.32 73.68 1 1.00e+01 1.00e-02 6.90e+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 93.00 161.36 -68.36 1 1.00e+01 1.00e-02 6.06e+01 ... (remaining 25559 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.228: 6458 0.228 - 0.457: 48 0.457 - 0.685: 5 0.685 - 0.913: 1 0.913 - 1.142: 2 Chirality restraints: 6514 Sorted by residual: chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-02 2.50e+03 4.89e+01 chirality pdb=" C1 BMA L 3 " pdb=" O4 NAG L 2 " pdb=" C2 BMA L 3 " pdb=" O5 BMA L 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 4.17e+01 chirality pdb=" C1 BMA H 3 " pdb=" O4 NAG H 2 " pdb=" C2 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.28 -0.12 2.00e-02 2.50e+03 3.71e+01 ... (remaining 6511 not shown) Planarity restraints: 7230 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 2 " -0.351 2.00e-02 2.50e+03 3.01e-01 1.13e+03 pdb=" C7 NAG E 2 " 0.086 2.00e-02 2.50e+03 pdb=" C8 NAG E 2 " -0.152 2.00e-02 2.50e+03 pdb=" N2 NAG E 2 " 0.534 2.00e-02 2.50e+03 pdb=" O7 NAG E 2 " -0.117 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 1 " 0.314 2.00e-02 2.50e+03 2.70e-01 9.11e+02 pdb=" C7 NAG F 1 " -0.069 2.00e-02 2.50e+03 pdb=" C8 NAG F 1 " 0.010 2.00e-02 2.50e+03 pdb=" N2 NAG F 1 " -0.465 2.00e-02 2.50e+03 pdb=" O7 NAG F 1 " 0.211 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG L 1 " -0.307 2.00e-02 2.50e+03 2.64e-01 8.72e+02 pdb=" C7 NAG L 1 " 0.067 2.00e-02 2.50e+03 pdb=" C8 NAG L 1 " -0.004 2.00e-02 2.50e+03 pdb=" N2 NAG L 1 " 0.454 2.00e-02 2.50e+03 pdb=" O7 NAG L 1 " -0.211 2.00e-02 2.50e+03 ... (remaining 7227 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 832 2.51 - 3.11: 36462 3.11 - 3.70: 66679 3.70 - 4.30: 88971 4.30 - 4.90: 137942 Nonbonded interactions: 330886 Sorted by model distance: nonbonded pdb=" O PRO B 657 " pdb=" OG1 THR C 656 " model vdw 1.912 2.440 nonbonded pdb=" OG1 THR A 656 " pdb=" O PRO D 657 " model vdw 1.956 2.440 nonbonded pdb=" OG1 THR B 656 " pdb=" O PRO C 657 " model vdw 1.995 2.440 nonbonded pdb=" O GLN C1281 " pdb=" OG SER C1313 " model vdw 1.995 2.440 nonbonded pdb=" OG1 THR D1224 " pdb=" OD1 ASP D1227 " model vdw 2.021 2.440 ... (remaining 330881 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 26 through 1337 or resid 2001 through 2005)) selection = chain 'B' selection = (chain 'C' and (resid 26 through 1337 or resid 2001 through 2005)) selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'J' 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: 0.000 Normalize map: mean=0, sd=1: 1.820 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: 8.990 Check model and map are aligned: 0.540 Set scattering table: 0.320 Process input model: 93.140 Find NCS groups from input model: 5.410 Set up NCS constraints: 1.460 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 114.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 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 : 0.013 0.241 41420 Z= 0.872 Angle : 1.333 19.221 56270 Z= 0.768 Chirality : 0.074 1.142 6514 Planarity : 0.013 0.301 7202 Dihedral : 16.898 105.849 15830 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 20.97 Ramachandran Plot: Outliers : 0.33 % Allowed : 18.28 % Favored : 81.39 % Rotamer: Outliers : 1.07 % Allowed : 10.51 % Favored : 88.41 % Cbeta Deviations : 0.17 % 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: -5.78 (0.09), residues: 5110 helix: -3.17 (0.12), residues: 808 sheet: -3.84 (0.11), residues: 1268 loop : -4.22 (0.09), residues: 3034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.004 TRP B1237 HIS 0.024 0.003 HIS C 321 PHE 0.039 0.004 PHE C 365 TYR 0.041 0.004 TYR D 166 ARG 0.018 0.002 ARG D 270 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10220 Ramachandran restraints generated. 5110 Oldfield, 0 Emsley, 5110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10220 Ramachandran restraints generated. 5110 Oldfield, 0 Emsley, 5110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 955 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 907 time to evaluate : 4.431 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: A 167 ILE cc_start: 0.8475 (mt) cc_final: 0.8273 (tt) REVERT: A 216 GLU cc_start: 0.8327 (pm20) cc_final: 0.8066 (pm20) REVERT: A 256 TYR cc_start: 0.8364 (t80) cc_final: 0.7296 (t80) REVERT: A 290 PHE cc_start: 0.7461 (m-80) cc_final: 0.7240 (m-80) REVERT: A 393 TYR cc_start: 0.9212 (t80) cc_final: 0.8933 (t80) REVERT: A 436 TRP cc_start: 0.7475 (t-100) cc_final: 0.7247 (t-100) REVERT: A 496 TYR cc_start: 0.6104 (m-80) cc_final: 0.5881 (m-10) REVERT: A 514 LEU cc_start: 0.9051 (pt) cc_final: 0.8806 (mt) REVERT: A 543 TYR cc_start: 0.7987 (p90) cc_final: 0.7782 (p90) REVERT: A 612 GLU cc_start: 0.8087 (tt0) cc_final: 0.7736 (tt0) REVERT: A 669 PHE cc_start: 0.8863 (m-80) cc_final: 0.8554 (m-80) REVERT: A 787 ARG cc_start: 0.8321 (ptp90) cc_final: 0.8029 (ptp90) REVERT: A 829 GLU cc_start: 0.8581 (tp30) cc_final: 0.7750 (mp0) REVERT: A 975 GLN cc_start: 0.8503 (mm-40) cc_final: 0.7936 (mt0) REVERT: A 976 ASN cc_start: 0.9164 (t0) cc_final: 0.8756 (t0) REVERT: A 990 LEU cc_start: 0.9012 (mt) cc_final: 0.8639 (mm) REVERT: A 1015 GLN cc_start: 0.8445 (tp40) cc_final: 0.8173 (tp40) REVERT: A 1017 ASN cc_start: 0.8884 (m110) cc_final: 0.8508 (m-40) REVERT: A 1076 ASP cc_start: 0.7796 (p0) cc_final: 0.7573 (p0) REVERT: A 1087 LEU cc_start: 0.9553 (tt) cc_final: 0.9150 (mt) REVERT: A 1146 THR cc_start: 0.8870 (p) cc_final: 0.8665 (p) REVERT: A 1208 MET cc_start: 0.9205 (ppp) cc_final: 0.8787 (ppp) REVERT: A 1217 LEU cc_start: 0.9356 (mm) cc_final: 0.9097 (mm) REVERT: B 98 GLU cc_start: 0.8631 (tt0) cc_final: 0.8264 (tm-30) REVERT: B 113 GLU cc_start: 0.6589 (pt0) cc_final: 0.6369 (pm20) REVERT: B 121 MET cc_start: 0.8297 (tpp) cc_final: 0.7696 (tpp) REVERT: B 169 ASP cc_start: 0.6657 (t0) cc_final: 0.6457 (t0) REVERT: B 256 TYR cc_start: 0.8020 (t80) cc_final: 0.7509 (t80) REVERT: B 289 LYS cc_start: 0.9089 (mttm) cc_final: 0.8775 (mmtp) REVERT: B 318 MET cc_start: 0.8216 (mtt) cc_final: 0.7801 (tpt) REVERT: B 393 TYR cc_start: 0.9038 (t80) cc_final: 0.8475 (t80) REVERT: B 533 ASP cc_start: 0.8006 (t0) cc_final: 0.7635 (t0) REVERT: B 567 LYS cc_start: 0.9196 (tppt) cc_final: 0.8924 (mmtm) REVERT: B 635 ASN cc_start: 0.8299 (p0) cc_final: 0.8004 (p0) REVERT: B 637 GLN cc_start: 0.7364 (pp30) cc_final: 0.7086 (pp30) REVERT: B 669 PHE cc_start: 0.8552 (m-80) cc_final: 0.8020 (m-80) REVERT: B 673 MET cc_start: 0.8226 (tpp) cc_final: 0.7739 (tpp) REVERT: B 741 TRP cc_start: 0.8285 (t-100) cc_final: 0.7684 (t-100) REVERT: B 766 LYS cc_start: 0.8370 (tppt) cc_final: 0.8124 (tptp) REVERT: B 792 PHE cc_start: 0.7679 (t80) cc_final: 0.7471 (t80) REVERT: B 863 LYS cc_start: 0.8780 (ttpt) cc_final: 0.8507 (ttpt) REVERT: B 951 LEU cc_start: 0.6727 (OUTLIER) cc_final: 0.6438 (pp) REVERT: B 965 LEU cc_start: 0.9163 (tt) cc_final: 0.8770 (mm) REVERT: B 975 GLN cc_start: 0.9133 (mm110) cc_final: 0.8857 (mt0) REVERT: B 976 ASN cc_start: 0.9303 (t0) cc_final: 0.9028 (t0) REVERT: B 977 MET cc_start: 0.9403 (mmm) cc_final: 0.9173 (mmm) REVERT: B 1076 ASP cc_start: 0.7806 (p0) cc_final: 0.7432 (p0) REVERT: B 1123 ASN cc_start: 0.9196 (m110) cc_final: 0.8740 (m110) REVERT: B 1125 LEU cc_start: 0.9247 (mt) cc_final: 0.8861 (mm) REVERT: B 1133 LYS cc_start: 0.9122 (ttmt) cc_final: 0.8913 (mmtm) REVERT: B 1161 ASP cc_start: 0.9028 (p0) cc_final: 0.8730 (p0) REVERT: B 1237 TRP cc_start: 0.7443 (t60) cc_final: 0.7238 (t60) REVERT: B 1245 GLN cc_start: 0.9027 (tm-30) cc_final: 0.8680 (tm-30) REVERT: B 1323 TYR cc_start: 0.6543 (t80) cc_final: 0.5953 (t80) REVERT: B 1325 GLN cc_start: 0.7955 (tt0) cc_final: 0.6851 (tp40) REVERT: C 76 ASP cc_start: 0.8482 (p0) cc_final: 0.8036 (m-30) REVERT: C 101 MET cc_start: 0.8322 (mtp) cc_final: 0.7883 (mmm) REVERT: C 121 MET cc_start: 0.8165 (ttt) cc_final: 0.7396 (tpt) REVERT: C 368 GLN cc_start: 0.8870 (tt0) cc_final: 0.8565 (tm-30) REVERT: C 387 ARG cc_start: 0.8268 (mmt180) cc_final: 0.7846 (mmm160) REVERT: C 635 ASN cc_start: 0.8205 (p0) cc_final: 0.7651 (p0) REVERT: C 671 GLU cc_start: 0.9055 (tt0) cc_final: 0.8510 (tt0) REVERT: C 672 ASP cc_start: 0.8884 (t0) cc_final: 0.8614 (t0) REVERT: C 688 MET cc_start: 0.7528 (ppp) cc_final: 0.6947 (ppp) REVERT: C 737 GLU cc_start: 0.8116 (mp0) cc_final: 0.7814 (mp0) REVERT: C 787 ARG cc_start: 0.8445 (ptp90) cc_final: 0.8180 (mtp180) REVERT: C 800 TYR cc_start: 0.7696 (p90) cc_final: 0.7325 (p90) REVERT: C 916 PHE cc_start: 0.8655 (m-80) cc_final: 0.8368 (m-80) REVERT: C 967 GLN cc_start: 0.9051 (mt0) cc_final: 0.8803 (mp10) REVERT: C 977 MET cc_start: 0.9159 (mmm) cc_final: 0.8933 (mmm) REVERT: C 983 ASN cc_start: 0.9141 (m-40) cc_final: 0.8938 (m-40) REVERT: C 988 ASP cc_start: 0.8304 (t0) cc_final: 0.7823 (t70) REVERT: C 1015 GLN cc_start: 0.7744 (tp40) cc_final: 0.6655 (tp40) REVERT: C 1057 PHE cc_start: 0.8012 (t80) cc_final: 0.7607 (t80) REVERT: C 1072 GLN cc_start: 0.9096 (mt0) cc_final: 0.8838 (mt0) REVERT: C 1073 ARG cc_start: 0.9111 (mmt-90) cc_final: 0.8701 (mmp80) REVERT: C 1163 ARG cc_start: 0.8646 (tmm-80) cc_final: 0.8287 (ttt180) REVERT: C 1234 ILE cc_start: 0.8225 (pt) cc_final: 0.7967 (pt) REVERT: C 1254 THR cc_start: 0.9176 (m) cc_final: 0.8861 (m) REVERT: C 1312 TYR cc_start: 0.8946 (m-80) cc_final: 0.8580 (m-80) REVERT: C 1323 TYR cc_start: 0.6384 (t80) cc_final: 0.5971 (t80) REVERT: D 98 GLU cc_start: 0.8798 (tt0) cc_final: 0.8285 (tp30) REVERT: D 121 MET cc_start: 0.7942 (mmm) cc_final: 0.7687 (mmm) REVERT: D 175 ILE cc_start: 0.8719 (tp) cc_final: 0.8440 (tp) REVERT: D 203 TYR cc_start: 0.7078 (m-80) cc_final: 0.6177 (m-80) REVERT: D 256 TYR cc_start: 0.7275 (t80) cc_final: 0.6346 (t80) REVERT: D 381 ASN cc_start: 0.9115 (m-40) cc_final: 0.8717 (p0) REVERT: D 399 THR cc_start: 0.8561 (p) cc_final: 0.8262 (p) REVERT: D 669 PHE cc_start: 0.8667 (m-80) cc_final: 0.8184 (m-80) REVERT: D 671 GLU cc_start: 0.8752 (tt0) cc_final: 0.8463 (tt0) REVERT: D 682 LYS cc_start: 0.8717 (mttt) cc_final: 0.8376 (mmtp) REVERT: D 737 GLU cc_start: 0.8108 (mp0) cc_final: 0.7793 (mp0) REVERT: D 766 LYS cc_start: 0.8130 (mmtt) cc_final: 0.7563 (mmmt) REVERT: D 783 THR cc_start: 0.9490 (p) cc_final: 0.8727 (p) REVERT: D 976 ASN cc_start: 0.9274 (t0) cc_final: 0.8895 (t0) REVERT: D 992 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7914 (tt0) REVERT: D 1003 LYS cc_start: 0.9495 (tptt) cc_final: 0.9241 (tptp) REVERT: D 1089 ASN cc_start: 0.8828 (p0) cc_final: 0.8511 (p0) REVERT: D 1133 LYS cc_start: 0.9151 (ttmt) cc_final: 0.8660 (mmtm) REVERT: D 1144 VAL cc_start: 0.8648 (m) cc_final: 0.7788 (m) REVERT: D 1147 LYS cc_start: 0.9306 (mttp) cc_final: 0.8874 (mttp) REVERT: D 1150 LEU cc_start: 0.9590 (mm) cc_final: 0.9385 (mm) REVERT: D 1154 PHE cc_start: 0.8721 (m-80) cc_final: 0.8456 (m-80) REVERT: D 1208 MET cc_start: 0.9467 (ppp) cc_final: 0.8995 (ppp) REVERT: D 1243 ASN cc_start: 0.9266 (t0) cc_final: 0.8980 (t0) REVERT: D 1245 GLN cc_start: 0.8936 (tm-30) cc_final: 0.8656 (tm-30) REVERT: D 1269 PHE cc_start: 0.8709 (t80) cc_final: 0.8258 (t80) REVERT: D 1312 TYR cc_start: 0.9088 (m-80) cc_final: 0.8718 (m-80) outliers start: 48 outliers final: 26 residues processed: 946 average time/residue: 0.4841 time to fit residues: 755.3314 Evaluate side-chains 687 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 659 time to evaluate : 4.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ASN Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1308 LEU Chi-restraints excluded: chain A residue 1316 VAL Chi-restraints excluded: chain B residue 89 PHE Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 746 VAL Chi-restraints excluded: chain B residue 951 LEU Chi-restraints excluded: chain B residue 1056 ILE Chi-restraints excluded: chain C residue 55 ASN Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 627 LEU Chi-restraints excluded: chain C residue 1218 THR Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 486 THR Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 621 LEU Chi-restraints excluded: chain D residue 992 GLU Chi-restraints excluded: chain D residue 1056 ILE Chi-restraints excluded: chain D residue 1214 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 430 optimal weight: 7.9990 chunk 386 optimal weight: 10.0000 chunk 214 optimal weight: 10.0000 chunk 132 optimal weight: 2.9990 chunk 260 optimal weight: 20.0000 chunk 206 optimal weight: 20.0000 chunk 399 optimal weight: 6.9990 chunk 154 optimal weight: 8.9990 chunk 243 optimal weight: 4.9990 chunk 297 optimal weight: 6.9990 chunk 463 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 HIS A 106 GLN ** A 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 177 GLN A 217 HIS ** A 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 GLN A 413 ASN ** A 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN A 479 HIS A 511 HIS A 517 GLN A 523 HIS ** A 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 917 ASN A 963 GLN ** A 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 995 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1017 ASN ** A1038 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1065 GLN A1072 GLN ** A1187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 GLN B 132 GLN ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 GLN ** B 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 GLN B 381 ASN ** B 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN B 483 ASN B 511 HIS B 592 GLN B 637 GLN B 790 GLN B 827 GLN ** B 938 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 983 ASN B1035 ASN B1179 ASN ** B1187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 ASN C 200 GLN ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 361 GLN C 413 ASN ** C 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 511 HIS ** C 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 662 ASN C 680 ASN C 694 GLN C 790 GLN ** C 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1259 HIS D 132 GLN ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 302 GLN D 310 GLN ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 389 ASN ** D 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 474 GLN ** D 511 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 592 GLN D 637 GLN D 662 ASN D 827 GLN ** D 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 938 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1035 ASN ** D1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1072 GLN ** D1182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1187 GLN ** D1233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1241 GLN Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 41420 Z= 0.476 Angle : 1.014 12.651 56270 Z= 0.518 Chirality : 0.056 0.426 6514 Planarity : 0.007 0.071 7202 Dihedral : 10.634 62.845 6348 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 30.72 Ramachandran Plot: Outliers : 0.20 % Allowed : 13.62 % Favored : 86.18 % Rotamer: Outliers : 5.03 % Allowed : 17.92 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.75 % 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: -4.98 (0.10), residues: 5110 helix: -1.96 (0.15), residues: 802 sheet: -3.34 (0.11), residues: 1496 loop : -3.80 (0.10), residues: 2812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP B 739 HIS 0.014 0.002 HIS D 460 PHE 0.033 0.003 PHE B 286 TYR 0.034 0.003 TYR A1007 ARG 0.006 0.001 ARG B 360 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10220 Ramachandran restraints generated. 5110 Oldfield, 0 Emsley, 5110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10220 Ramachandran restraints generated. 5110 Oldfield, 0 Emsley, 5110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 980 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 225 poor density : 755 time to evaluate : 4.859 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: A 183 LEU cc_start: 0.7810 (pp) cc_final: 0.6951 (mt) REVERT: A 208 GLN cc_start: 0.6522 (tt0) cc_final: 0.6295 (tt0) REVERT: A 216 GLU cc_start: 0.8966 (pm20) cc_final: 0.8733 (pm20) REVERT: A 256 TYR cc_start: 0.8441 (t80) cc_final: 0.7522 (t80) REVERT: A 290 PHE cc_start: 0.7713 (m-80) cc_final: 0.7342 (m-80) REVERT: A 384 ILE cc_start: 0.8767 (pt) cc_final: 0.8453 (pt) REVERT: A 393 TYR cc_start: 0.9185 (t80) cc_final: 0.8874 (t80) REVERT: A 514 LEU cc_start: 0.8981 (pt) cc_final: 0.8753 (mt) REVERT: A 539 ARG cc_start: 0.8171 (mtt-85) cc_final: 0.7848 (mtp85) REVERT: A 572 PHE cc_start: 0.8328 (p90) cc_final: 0.7946 (p90) REVERT: A 602 GLN cc_start: 0.7031 (tm-30) cc_final: 0.6734 (tm-30) REVERT: A 612 GLU cc_start: 0.8163 (tt0) cc_final: 0.7848 (tt0) REVERT: A 619 TYR cc_start: 0.7784 (OUTLIER) cc_final: 0.6223 (m-80) REVERT: A 669 PHE cc_start: 0.8787 (m-80) cc_final: 0.8367 (m-80) REVERT: A 673 MET cc_start: 0.9362 (OUTLIER) cc_final: 0.8931 (tpp) REVERT: A 829 GLU cc_start: 0.8744 (tp30) cc_final: 0.7659 (mp0) REVERT: A 934 LYS cc_start: 0.8089 (OUTLIER) cc_final: 0.7199 (tppt) REVERT: A 975 GLN cc_start: 0.8528 (mm-40) cc_final: 0.8055 (mt0) REVERT: A 976 ASN cc_start: 0.9293 (t0) cc_final: 0.8471 (t0) REVERT: A 977 MET cc_start: 0.9359 (mmm) cc_final: 0.8844 (mmm) REVERT: A 1015 GLN cc_start: 0.8721 (tp40) cc_final: 0.7577 (tp40) REVERT: A 1017 ASN cc_start: 0.8974 (m-40) cc_final: 0.8601 (m-40) REVERT: A 1064 THR cc_start: 0.9304 (OUTLIER) cc_final: 0.9076 (p) REVERT: A 1065 GLN cc_start: 0.8982 (OUTLIER) cc_final: 0.8683 (mm110) REVERT: A 1087 LEU cc_start: 0.9546 (tt) cc_final: 0.9210 (mt) REVERT: A 1129 GLU cc_start: 0.9317 (OUTLIER) cc_final: 0.9090 (mp0) REVERT: A 1205 GLU cc_start: 0.8779 (pm20) cc_final: 0.8522 (pm20) REVERT: A 1208 MET cc_start: 0.9380 (ppp) cc_final: 0.8933 (ppp) REVERT: A 1217 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.9024 (mt) REVERT: B 98 GLU cc_start: 0.8615 (tt0) cc_final: 0.8369 (tm-30) REVERT: B 121 MET cc_start: 0.8294 (tpp) cc_final: 0.7696 (tpp) REVERT: B 318 MET cc_start: 0.8391 (mtt) cc_final: 0.7982 (tpt) REVERT: B 320 LEU cc_start: 0.9287 (mp) cc_final: 0.9016 (mp) REVERT: B 327 GLN cc_start: 0.8313 (OUTLIER) cc_final: 0.8074 (pp30) REVERT: B 342 GLU cc_start: 0.8934 (tp30) cc_final: 0.8679 (tp30) REVERT: B 373 ASP cc_start: 0.7577 (t0) cc_final: 0.7301 (t0) REVERT: B 393 TYR cc_start: 0.8840 (t80) cc_final: 0.8440 (t80) REVERT: B 408 SER cc_start: 0.8807 (OUTLIER) cc_final: 0.8589 (t) REVERT: B 637 GLN cc_start: 0.7429 (OUTLIER) cc_final: 0.7069 (pp30) REVERT: B 741 TRP cc_start: 0.8602 (t-100) cc_final: 0.8335 (t-100) REVERT: B 766 LYS cc_start: 0.8454 (tppt) cc_final: 0.8213 (tppt) REVERT: B 792 PHE cc_start: 0.7304 (t80) cc_final: 0.7103 (t80) REVERT: B 863 LYS cc_start: 0.8797 (ttpt) cc_final: 0.8553 (ttpt) REVERT: B 964 ASN cc_start: 0.9297 (t0) cc_final: 0.8899 (t0) REVERT: B 965 LEU cc_start: 0.9189 (tt) cc_final: 0.8724 (mp) REVERT: B 976 ASN cc_start: 0.9188 (t0) cc_final: 0.8904 (t0) REVERT: B 977 MET cc_start: 0.9263 (mmm) cc_final: 0.8964 (mmm) REVERT: B 1059 ASP cc_start: 0.7612 (OUTLIER) cc_final: 0.7011 (p0) REVERT: B 1076 ASP cc_start: 0.8145 (p0) cc_final: 0.7698 (p0) REVERT: B 1123 ASN cc_start: 0.9366 (m110) cc_final: 0.9030 (m110) REVERT: B 1170 LEU cc_start: 0.9495 (mm) cc_final: 0.9288 (pp) REVERT: B 1217 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.9021 (mm) REVERT: B 1325 GLN cc_start: 0.8352 (tt0) cc_final: 0.7652 (tp40) REVERT: B 1330 TYR cc_start: 0.8678 (p90) cc_final: 0.8411 (p90) REVERT: C 65 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7094 (mm-30) REVERT: C 154 ASN cc_start: 0.9068 (OUTLIER) cc_final: 0.8488 (p0) REVERT: C 458 PHE cc_start: 0.8419 (p90) cc_final: 0.8185 (p90) REVERT: C 481 ILE cc_start: 0.8806 (mp) cc_final: 0.8601 (mp) REVERT: C 539 ARG cc_start: 0.7770 (mtt-85) cc_final: 0.7173 (ttm-80) REVERT: C 576 GLN cc_start: 0.6588 (OUTLIER) cc_final: 0.6283 (pp30) REVERT: C 635 ASN cc_start: 0.8393 (p0) cc_final: 0.7863 (p0) REVERT: C 671 GLU cc_start: 0.9207 (tt0) cc_final: 0.8791 (tt0) REVERT: C 688 MET cc_start: 0.8075 (ppp) cc_final: 0.7802 (ppp) REVERT: C 737 GLU cc_start: 0.8077 (mp0) cc_final: 0.6938 (mp0) REVERT: C 787 ARG cc_start: 0.8623 (ptp90) cc_final: 0.8197 (mtp180) REVERT: C 916 PHE cc_start: 0.8702 (m-80) cc_final: 0.8405 (m-80) REVERT: C 977 MET cc_start: 0.9099 (mmm) cc_final: 0.8862 (mmm) REVERT: C 988 ASP cc_start: 0.8427 (t0) cc_final: 0.7788 (t70) REVERT: C 1015 GLN cc_start: 0.7836 (tp40) cc_final: 0.6802 (tp40) REVERT: C 1104 TYR cc_start: 0.8491 (t80) cc_final: 0.8048 (t80) REVERT: C 1147 LYS cc_start: 0.9174 (mttp) cc_final: 0.8214 (mmtp) REVERT: C 1207 GLU cc_start: 0.9016 (tt0) cc_final: 0.8799 (tt0) REVERT: C 1254 THR cc_start: 0.9234 (m) cc_final: 0.9020 (p) REVERT: C 1314 MET cc_start: 0.8690 (mpp) cc_final: 0.8433 (mmt) REVERT: C 1323 TYR cc_start: 0.6664 (t80) cc_final: 0.6169 (t80) REVERT: D 98 GLU cc_start: 0.8820 (tt0) cc_final: 0.8479 (tp30) REVERT: D 121 MET cc_start: 0.7930 (mmm) cc_final: 0.7647 (mmm) REVERT: D 126 ASP cc_start: 0.9235 (p0) cc_final: 0.8869 (p0) REVERT: D 203 TYR cc_start: 0.7498 (m-80) cc_final: 0.6296 (m-80) REVERT: D 290 PHE cc_start: 0.8376 (m-80) cc_final: 0.8047 (m-80) REVERT: D 313 ARG cc_start: 0.8266 (tpt90) cc_final: 0.8017 (tpt170) REVERT: D 325 GLN cc_start: 0.8522 (mp10) cc_final: 0.8297 (mp10) REVERT: D 557 LYS cc_start: 0.8909 (mttp) cc_final: 0.8696 (mmtp) REVERT: D 578 LEU cc_start: 0.8343 (tp) cc_final: 0.8033 (tp) REVERT: D 579 PRO cc_start: 0.6856 (Cg_endo) cc_final: 0.6593 (Cg_exo) REVERT: D 637 GLN cc_start: 0.8007 (OUTLIER) cc_final: 0.7778 (pp30) REVERT: D 669 PHE cc_start: 0.8737 (m-80) cc_final: 0.8087 (m-80) REVERT: D 671 GLU cc_start: 0.8867 (tt0) cc_final: 0.8201 (mm-30) REVERT: D 673 MET cc_start: 0.9069 (tpp) cc_final: 0.8818 (tpp) REVERT: D 682 LYS cc_start: 0.8700 (mttt) cc_final: 0.8427 (mmtp) REVERT: D 688 MET cc_start: 0.8359 (ppp) cc_final: 0.7945 (ppp) REVERT: D 737 GLU cc_start: 0.8295 (mp0) cc_final: 0.7766 (mp0) REVERT: D 758 VAL cc_start: 0.8036 (OUTLIER) cc_final: 0.7823 (p) REVERT: D 764 GLU cc_start: 0.8664 (mt-10) cc_final: 0.8131 (mp0) REVERT: D 766 LYS cc_start: 0.8091 (mmtt) cc_final: 0.7691 (mmtm) REVERT: D 827 GLN cc_start: 0.9270 (OUTLIER) cc_final: 0.9068 (pp30) REVERT: D 965 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8477 (mp) REVERT: D 976 ASN cc_start: 0.9337 (t0) cc_final: 0.9044 (t0) REVERT: D 977 MET cc_start: 0.9567 (mmm) cc_final: 0.9332 (mmm) REVERT: D 992 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8121 (tt0) REVERT: D 1003 LYS cc_start: 0.9453 (tptt) cc_final: 0.9173 (tppt) REVERT: D 1076 ASP cc_start: 0.7753 (p0) cc_final: 0.7486 (p0) REVERT: D 1089 ASN cc_start: 0.8873 (p0) cc_final: 0.8429 (p0) REVERT: D 1123 ASN cc_start: 0.9333 (m110) cc_final: 0.9132 (m110) REVERT: D 1133 LYS cc_start: 0.9244 (ttmt) cc_final: 0.8903 (tppt) REVERT: D 1154 PHE cc_start: 0.8938 (m-80) cc_final: 0.8684 (m-80) REVERT: D 1208 MET cc_start: 0.9411 (ppp) cc_final: 0.9128 (ppp) REVERT: D 1209 THR cc_start: 0.9757 (p) cc_final: 0.9556 (p) REVERT: D 1243 ASN cc_start: 0.9414 (t0) cc_final: 0.9149 (t0) REVERT: D 1245 GLN cc_start: 0.9084 (tm-30) cc_final: 0.8750 (tm-30) REVERT: D 1269 PHE cc_start: 0.8644 (t80) cc_final: 0.8144 (t80) REVERT: D 1312 TYR cc_start: 0.9049 (m-80) cc_final: 0.8737 (m-80) outliers start: 225 outliers final: 137 residues processed: 903 average time/residue: 0.4758 time to fit residues: 721.1588 Evaluate side-chains 791 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 635 time to evaluate : 3.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 97 ASN Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 345 ARG Chi-restraints excluded: chain A residue 381 ASN Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 619 TYR Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 656 THR Chi-restraints excluded: chain A residue 673 MET Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 856 VAL Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 934 LYS Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 1024 SER Chi-restraints excluded: chain A residue 1041 LEU Chi-restraints excluded: chain A residue 1064 THR Chi-restraints excluded: chain A residue 1065 GLN Chi-restraints excluded: chain A residue 1089 ASN Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1129 GLU Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1218 THR Chi-restraints excluded: chain A residue 1249 SER Chi-restraints excluded: chain A residue 1251 THR Chi-restraints excluded: chain A residue 1316 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 89 PHE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 286 PHE Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 327 GLN Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 381 ASN Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 407 PHE Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain B residue 637 GLN Chi-restraints excluded: chain B residue 758 VAL Chi-restraints excluded: chain B residue 787 ARG Chi-restraints excluded: chain B residue 831 SER Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 1041 LEU Chi-restraints excluded: chain B residue 1046 LEU Chi-restraints excluded: chain B residue 1059 ASP Chi-restraints excluded: chain B residue 1091 ILE Chi-restraints excluded: chain B residue 1115 THR Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1213 LEU Chi-restraints excluded: chain B residue 1217 LEU Chi-restraints excluded: chain B residue 1218 THR Chi-restraints excluded: chain B residue 1234 ILE Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 89 PHE Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 381 ASN Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 576 GLN Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain C residue 656 THR Chi-restraints excluded: chain C residue 662 ASN Chi-restraints excluded: chain C residue 680 ASN Chi-restraints excluded: chain C residue 742 ASP Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 934 LYS Chi-restraints excluded: chain C residue 948 VAL Chi-restraints excluded: chain C residue 1016 LEU Chi-restraints excluded: chain C residue 1110 LEU Chi-restraints excluded: chain C residue 1144 VAL Chi-restraints excluded: chain C residue 1156 LEU Chi-restraints excluded: chain C residue 1218 THR Chi-restraints excluded: chain C residue 1224 THR Chi-restraints excluded: chain C residue 1227 ASP Chi-restraints excluded: chain C residue 1239 THR Chi-restraints excluded: chain C residue 1251 THR Chi-restraints excluded: chain C residue 1252 GLN Chi-restraints excluded: chain C residue 1270 THR Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 286 PHE Chi-restraints excluded: chain D residue 373 ASP Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 405 VAL Chi-restraints excluded: chain D residue 458 PHE Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 486 THR Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 519 ASP Chi-restraints excluded: chain D residue 541 LEU Chi-restraints excluded: chain D residue 563 CYS Chi-restraints excluded: chain D residue 621 LEU Chi-restraints excluded: chain D residue 637 GLN Chi-restraints excluded: chain D residue 646 HIS Chi-restraints excluded: chain D residue 658 VAL Chi-restraints excluded: chain D residue 758 VAL Chi-restraints excluded: chain D residue 821 CYS Chi-restraints excluded: chain D residue 827 GLN Chi-restraints excluded: chain D residue 831 SER Chi-restraints excluded: chain D residue 887 VAL Chi-restraints excluded: chain D residue 965 LEU Chi-restraints excluded: chain D residue 992 GLU Chi-restraints excluded: chain D residue 1041 LEU Chi-restraints excluded: chain D residue 1056 ILE Chi-restraints excluded: chain D residue 1101 LEU Chi-restraints excluded: chain D residue 1109 LEU Chi-restraints excluded: chain D residue 1121 VAL Chi-restraints excluded: chain D residue 1224 THR Chi-restraints excluded: chain D residue 1305 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 257 optimal weight: 7.9990 chunk 143 optimal weight: 0.7980 chunk 385 optimal weight: 8.9990 chunk 315 optimal weight: 5.9990 chunk 127 optimal weight: 20.0000 chunk 463 optimal weight: 3.9990 chunk 501 optimal weight: 10.0000 chunk 413 optimal weight: 5.9990 chunk 460 optimal weight: 9.9990 chunk 158 optimal weight: 8.9990 chunk 372 optimal weight: 2.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 466 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 995 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1038 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 325 GLN ** B 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 827 GLN B 938 ASN ** B 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 479 HIS C 523 HIS ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 680 ASN ** C 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 HIS ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 GLN D 424 ASN ** D 460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 511 HIS ** D 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 938 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 963 GLN ** D 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 41420 Z= 0.351 Angle : 0.887 10.775 56270 Z= 0.447 Chirality : 0.052 0.398 6514 Planarity : 0.006 0.068 7202 Dihedral : 9.437 61.228 6326 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 27.67 Ramachandran Plot: Outliers : 0.12 % Allowed : 12.95 % Favored : 86.93 % Rotamer: Outliers : 5.75 % Allowed : 21.03 % Favored : 73.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.75 % 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: -4.49 (0.10), residues: 5110 helix: -1.37 (0.16), residues: 824 sheet: -3.04 (0.11), residues: 1532 loop : -3.55 (0.10), residues: 2754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B1237 HIS 0.010 0.001 HIS B 217 PHE 0.029 0.002 PHE B 286 TYR 0.027 0.002 TYR B1007 ARG 0.022 0.001 ARG A 360 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10220 Ramachandran restraints generated. 5110 Oldfield, 0 Emsley, 5110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10220 Ramachandran restraints generated. 5110 Oldfield, 0 Emsley, 5110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 981 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 257 poor density : 724 time to evaluate : 4.616 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: A 183 LEU cc_start: 0.7649 (OUTLIER) cc_final: 0.6925 (mt) REVERT: A 290 PHE cc_start: 0.7729 (m-80) cc_final: 0.7360 (m-80) REVERT: A 393 TYR cc_start: 0.9078 (t80) cc_final: 0.8770 (t80) REVERT: A 514 LEU cc_start: 0.8966 (pt) cc_final: 0.8666 (mt) REVERT: A 572 PHE cc_start: 0.8308 (p90) cc_final: 0.7985 (p90) REVERT: A 602 GLN cc_start: 0.6939 (tm-30) cc_final: 0.6522 (tm-30) REVERT: A 612 GLU cc_start: 0.8134 (tt0) cc_final: 0.7789 (tt0) REVERT: A 627 LEU cc_start: 0.8824 (tp) cc_final: 0.8591 (tp) REVERT: A 666 MET cc_start: 0.8320 (tpt) cc_final: 0.7765 (tpt) REVERT: A 668 SER cc_start: 0.8774 (t) cc_final: 0.8492 (p) REVERT: A 669 PHE cc_start: 0.8885 (m-80) cc_final: 0.8557 (m-80) REVERT: A 671 GLU cc_start: 0.8837 (tt0) cc_final: 0.8610 (tt0) REVERT: A 787 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.7956 (ttp-170) REVERT: A 798 MET cc_start: 0.6563 (mpp) cc_final: 0.6249 (mpp) REVERT: A 829 GLU cc_start: 0.8626 (tp30) cc_final: 0.7503 (mp0) REVERT: A 934 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7278 (tppt) REVERT: A 964 ASN cc_start: 0.8567 (t0) cc_final: 0.8318 (t0) REVERT: A 975 GLN cc_start: 0.8539 (mm-40) cc_final: 0.8039 (mt0) REVERT: A 977 MET cc_start: 0.9332 (mmm) cc_final: 0.8879 (mmm) REVERT: A 1017 ASN cc_start: 0.8933 (m-40) cc_final: 0.8613 (m-40) REVERT: A 1080 PHE cc_start: 0.8224 (m-80) cc_final: 0.7988 (m-10) REVERT: A 1087 LEU cc_start: 0.9569 (tt) cc_final: 0.9257 (mt) REVERT: A 1110 LEU cc_start: 0.9243 (mt) cc_final: 0.8861 (tp) REVERT: A 1165 GLU cc_start: 0.9019 (tm-30) cc_final: 0.8682 (pp20) REVERT: A 1178 ASP cc_start: 0.9459 (p0) cc_final: 0.9214 (p0) REVERT: A 1208 MET cc_start: 0.9397 (ppp) cc_final: 0.8975 (ppp) REVERT: A 1216 TYR cc_start: 0.8771 (m-80) cc_final: 0.8521 (m-80) REVERT: A 1217 LEU cc_start: 0.9250 (mm) cc_final: 0.8979 (mm) REVERT: B 78 GLU cc_start: 0.8487 (pt0) cc_final: 0.7827 (pm20) REVERT: B 98 GLU cc_start: 0.8642 (tt0) cc_final: 0.8268 (tm-30) REVERT: B 121 MET cc_start: 0.8268 (tpp) cc_final: 0.7854 (tpp) REVERT: B 318 MET cc_start: 0.8322 (mtt) cc_final: 0.7972 (tpt) REVERT: B 320 LEU cc_start: 0.9257 (mp) cc_final: 0.8957 (mp) REVERT: B 342 GLU cc_start: 0.8863 (tp30) cc_final: 0.8616 (tp30) REVERT: B 393 TYR cc_start: 0.8818 (t80) cc_final: 0.8543 (t80) REVERT: B 460 HIS cc_start: 0.8539 (t-90) cc_final: 0.8149 (t-90) REVERT: B 688 MET cc_start: 0.8560 (ppp) cc_final: 0.8130 (ppp) REVERT: B 741 TRP cc_start: 0.8614 (t-100) cc_final: 0.8405 (t-100) REVERT: B 798 MET cc_start: 0.8495 (ptm) cc_final: 0.7322 (ppp) REVERT: B 858 TRP cc_start: 0.6992 (m-90) cc_final: 0.6439 (m-90) REVERT: B 863 LYS cc_start: 0.8779 (ttpt) cc_final: 0.8564 (ttpt) REVERT: B 964 ASN cc_start: 0.9304 (t0) cc_final: 0.8909 (t0) REVERT: B 965 LEU cc_start: 0.9192 (tt) cc_final: 0.8849 (mp) REVERT: B 976 ASN cc_start: 0.9195 (t0) cc_final: 0.8908 (t0) REVERT: B 977 MET cc_start: 0.9275 (mmm) cc_final: 0.9019 (mmm) REVERT: B 1076 ASP cc_start: 0.8168 (p0) cc_final: 0.7721 (p0) REVERT: B 1098 GLU cc_start: 0.8098 (mm-30) cc_final: 0.7604 (mm-30) REVERT: B 1123 ASN cc_start: 0.9345 (m110) cc_final: 0.9043 (m110) REVERT: B 1183 TRP cc_start: 0.9149 (m-90) cc_final: 0.8576 (m-90) REVERT: B 1217 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8854 (mm) REVERT: B 1325 GLN cc_start: 0.8305 (tt0) cc_final: 0.7692 (tp-100) REVERT: B 1330 TYR cc_start: 0.8811 (p90) cc_final: 0.8484 (p90) REVERT: C 65 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7101 (mm-30) REVERT: C 154 ASN cc_start: 0.9071 (OUTLIER) cc_final: 0.8503 (p0) REVERT: C 189 GLN cc_start: 0.8685 (pm20) cc_final: 0.8112 (pp30) REVERT: C 360 ARG cc_start: 0.7645 (mmt90) cc_final: 0.6908 (mmt90) REVERT: C 393 TYR cc_start: 0.8706 (t80) cc_final: 0.8474 (t80) REVERT: C 436 TRP cc_start: 0.7755 (t-100) cc_final: 0.7482 (t-100) REVERT: C 458 PHE cc_start: 0.8493 (p90) cc_final: 0.8131 (p90) REVERT: C 460 HIS cc_start: 0.8113 (t-170) cc_final: 0.7409 (t-170) REVERT: C 481 ILE cc_start: 0.8921 (mp) cc_final: 0.8664 (mp) REVERT: C 500 MET cc_start: 0.8137 (ptm) cc_final: 0.7913 (ptm) REVERT: C 576 GLN cc_start: 0.6132 (OUTLIER) cc_final: 0.4528 (pp30) REVERT: C 612 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8431 (pm20) REVERT: C 635 ASN cc_start: 0.8458 (p0) cc_final: 0.8021 (p0) REVERT: C 671 GLU cc_start: 0.9231 (tt0) cc_final: 0.8736 (tt0) REVERT: C 688 MET cc_start: 0.8187 (ppp) cc_final: 0.7853 (ppp) REVERT: C 737 GLU cc_start: 0.8185 (mp0) cc_final: 0.7159 (mp0) REVERT: C 916 PHE cc_start: 0.8729 (m-80) cc_final: 0.8469 (m-80) REVERT: C 977 MET cc_start: 0.9113 (mmm) cc_final: 0.8895 (mmm) REVERT: C 988 ASP cc_start: 0.8454 (t0) cc_final: 0.7932 (t70) REVERT: C 1015 GLN cc_start: 0.7859 (tp40) cc_final: 0.6785 (mp10) REVERT: C 1079 CYS cc_start: 0.5123 (OUTLIER) cc_final: 0.4373 (p) REVERT: C 1104 TYR cc_start: 0.8579 (t80) cc_final: 0.8151 (t80) REVERT: C 1123 ASN cc_start: 0.8977 (OUTLIER) cc_final: 0.8520 (p0) REVERT: C 1205 GLU cc_start: 0.8709 (pm20) cc_final: 0.8082 (pm20) REVERT: C 1207 GLU cc_start: 0.9007 (tt0) cc_final: 0.8673 (tt0) REVERT: C 1254 THR cc_start: 0.9259 (m) cc_final: 0.8910 (p) REVERT: C 1258 LEU cc_start: 0.9257 (mp) cc_final: 0.9027 (mp) REVERT: C 1323 TYR cc_start: 0.6575 (t80) cc_final: 0.6221 (t80) REVERT: D 98 GLU cc_start: 0.8844 (tt0) cc_final: 0.8472 (tp30) REVERT: D 126 ASP cc_start: 0.9206 (p0) cc_final: 0.8872 (p0) REVERT: D 368 GLN cc_start: 0.8782 (OUTLIER) cc_final: 0.8372 (mp10) REVERT: D 542 ILE cc_start: 0.8579 (tt) cc_final: 0.8082 (mp) REVERT: D 557 LYS cc_start: 0.8896 (mttp) cc_final: 0.8566 (mmtp) REVERT: D 561 GLU cc_start: 0.8266 (tp30) cc_final: 0.7891 (tp30) REVERT: D 578 LEU cc_start: 0.8334 (tp) cc_final: 0.8075 (tp) REVERT: D 669 PHE cc_start: 0.8671 (m-80) cc_final: 0.8014 (m-80) REVERT: D 671 GLU cc_start: 0.8845 (tt0) cc_final: 0.8237 (mm-30) REVERT: D 673 MET cc_start: 0.9087 (tpp) cc_final: 0.8733 (tpp) REVERT: D 682 LYS cc_start: 0.8620 (mttt) cc_final: 0.8362 (mmtp) REVERT: D 688 MET cc_start: 0.8414 (ppp) cc_final: 0.7989 (ppp) REVERT: D 737 GLU cc_start: 0.8303 (mp0) cc_final: 0.7866 (mp0) REVERT: D 764 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8117 (mp0) REVERT: D 766 LYS cc_start: 0.8083 (mmtt) cc_final: 0.7667 (mmtm) REVERT: D 912 LYS cc_start: 0.8490 (ptpp) cc_final: 0.7957 (ptpp) REVERT: D 913 GLU cc_start: 0.8743 (pp20) cc_final: 0.8268 (pp20) REVERT: D 914 THR cc_start: 0.9218 (OUTLIER) cc_final: 0.8857 (p) REVERT: D 957 SER cc_start: 0.8603 (t) cc_final: 0.8379 (m) REVERT: D 965 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8509 (mp) REVERT: D 976 ASN cc_start: 0.9377 (t0) cc_final: 0.9036 (t0) REVERT: D 977 MET cc_start: 0.9436 (mmm) cc_final: 0.9197 (mmm) REVERT: D 1003 LYS cc_start: 0.9422 (tptt) cc_final: 0.8963 (tppt) REVERT: D 1007 TYR cc_start: 0.8175 (m-10) cc_final: 0.7369 (m-80) REVERT: D 1076 ASP cc_start: 0.7791 (p0) cc_final: 0.7451 (p0) REVERT: D 1089 ASN cc_start: 0.8794 (p0) cc_final: 0.8320 (p0) REVERT: D 1123 ASN cc_start: 0.9345 (m110) cc_final: 0.9121 (m110) REVERT: D 1133 LYS cc_start: 0.9236 (ttmt) cc_final: 0.8813 (mmtm) REVERT: D 1147 LYS cc_start: 0.9330 (mttp) cc_final: 0.8797 (mttp) REVERT: D 1154 PHE cc_start: 0.8816 (m-80) cc_final: 0.8476 (m-80) REVERT: D 1208 MET cc_start: 0.9373 (OUTLIER) cc_final: 0.9057 (ppp) REVERT: D 1233 ASN cc_start: 0.8554 (OUTLIER) cc_final: 0.8228 (t0) REVERT: D 1243 ASN cc_start: 0.9422 (t0) cc_final: 0.9154 (t0) REVERT: D 1245 GLN cc_start: 0.9172 (tm-30) cc_final: 0.8816 (tm-30) REVERT: D 1269 PHE cc_start: 0.8574 (t80) cc_final: 0.8068 (t80) outliers start: 257 outliers final: 159 residues processed: 915 average time/residue: 0.4652 time to fit residues: 720.0345 Evaluate side-chains 828 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 654 time to evaluate : 4.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 TYR Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 89 PHE Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 345 ARG Chi-restraints excluded: chain A residue 352 PHE Chi-restraints excluded: chain A residue 392 ASN Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 505 ILE Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 619 TYR Chi-restraints excluded: chain A residue 626 ASP Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 787 ARG Chi-restraints excluded: chain A residue 934 LYS Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 959 MET Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1024 SER Chi-restraints excluded: chain A residue 1055 TYR Chi-restraints excluded: chain A residue 1065 GLN Chi-restraints excluded: chain A residue 1089 ASN Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1115 THR Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1129 GLU Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1214 LEU Chi-restraints excluded: chain A residue 1249 SER Chi-restraints excluded: chain A residue 1251 THR Chi-restraints excluded: chain A residue 1253 ASP Chi-restraints excluded: chain A residue 1255 VAL Chi-restraints excluded: chain A residue 1316 VAL Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 89 PHE Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 173 ASN Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 286 PHE Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 381 ASN Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 407 PHE Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 498 LEU Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 643 ILE Chi-restraints excluded: chain B residue 787 ARG Chi-restraints excluded: chain B residue 821 CYS Chi-restraints excluded: chain B residue 831 SER Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 938 ASN Chi-restraints excluded: chain B residue 1046 LEU Chi-restraints excluded: chain B residue 1091 ILE Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1144 VAL Chi-restraints excluded: chain B residue 1217 LEU Chi-restraints excluded: chain B residue 1224 THR Chi-restraints excluded: chain B residue 1227 ASP Chi-restraints excluded: chain B residue 1234 ILE Chi-restraints excluded: chain B residue 1251 THR Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 89 PHE Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 576 GLN Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 612 GLU Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 662 ASN Chi-restraints excluded: chain C residue 680 ASN Chi-restraints excluded: chain C residue 742 ASP Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 914 THR Chi-restraints excluded: chain C residue 1016 LEU Chi-restraints excluded: chain C residue 1041 LEU Chi-restraints excluded: chain C residue 1079 CYS Chi-restraints excluded: chain C residue 1109 LEU Chi-restraints excluded: chain C residue 1123 ASN Chi-restraints excluded: chain C residue 1127 CYS Chi-restraints excluded: chain C residue 1144 VAL Chi-restraints excluded: chain C residue 1156 LEU Chi-restraints excluded: chain C residue 1218 THR Chi-restraints excluded: chain C residue 1227 ASP Chi-restraints excluded: chain C residue 1251 THR Chi-restraints excluded: chain C residue 1252 GLN Chi-restraints excluded: chain C residue 1253 ASP Chi-restraints excluded: chain C residue 1311 GLU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 286 PHE Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 368 GLN Chi-restraints excluded: chain D residue 373 ASP Chi-restraints excluded: chain D residue 405 VAL Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain D residue 458 PHE Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 486 THR Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 519 ASP Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain D residue 560 VAL Chi-restraints excluded: chain D residue 563 CYS Chi-restraints excluded: chain D residue 600 VAL Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 621 LEU Chi-restraints excluded: chain D residue 643 ILE Chi-restraints excluded: chain D residue 658 VAL Chi-restraints excluded: chain D residue 764 GLU Chi-restraints excluded: chain D residue 783 THR Chi-restraints excluded: chain D residue 821 CYS Chi-restraints excluded: chain D residue 861 THR Chi-restraints excluded: chain D residue 887 VAL Chi-restraints excluded: chain D residue 914 THR Chi-restraints excluded: chain D residue 965 LEU Chi-restraints excluded: chain D residue 992 GLU Chi-restraints excluded: chain D residue 1041 LEU Chi-restraints excluded: chain D residue 1056 ILE Chi-restraints excluded: chain D residue 1080 PHE Chi-restraints excluded: chain D residue 1095 VAL Chi-restraints excluded: chain D residue 1101 LEU Chi-restraints excluded: chain D residue 1208 MET Chi-restraints excluded: chain D residue 1233 ASN Chi-restraints excluded: chain D residue 1270 THR Chi-restraints excluded: chain D residue 1305 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 458 optimal weight: 8.9990 chunk 348 optimal weight: 0.7980 chunk 240 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 221 optimal weight: 0.7980 chunk 311 optimal weight: 0.9980 chunk 465 optimal weight: 0.3980 chunk 492 optimal weight: 6.9990 chunk 243 optimal weight: 7.9990 chunk 441 optimal weight: 3.9990 chunk 132 optimal weight: 7.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 159 ASN ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 208 GLN A 466 HIS A 566 ASN A 964 ASN A 983 ASN ** A 995 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1038 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1065 GLN ** A1187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 GLN ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 GLN B 389 ASN B 424 ASN ** B 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 310 GLN ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 413 ASN C 466 HIS ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 680 ASN ** C 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 177 GLN D 182 GLN D 310 GLN D 368 GLN ** D 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 637 GLN ** D 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 938 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1123 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 41420 Z= 0.212 Angle : 0.811 12.958 56270 Z= 0.395 Chirality : 0.051 0.419 6514 Planarity : 0.005 0.065 7202 Dihedral : 8.431 63.120 6324 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 19.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.23 % Favored : 89.71 % Rotamer: Outliers : 4.43 % Allowed : 24.16 % Favored : 71.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.38 % 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: -3.87 (0.11), residues: 5110 helix: -0.55 (0.17), residues: 814 sheet: -2.60 (0.12), residues: 1572 loop : -3.26 (0.11), residues: 2724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 765 HIS 0.007 0.001 HIS C 358 PHE 0.026 0.002 PHE D 290 TYR 0.028 0.002 TYR B1007 ARG 0.009 0.001 ARG A 387 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10220 Ramachandran restraints generated. 5110 Oldfield, 0 Emsley, 5110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10220 Ramachandran restraints generated. 5110 Oldfield, 0 Emsley, 5110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 957 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 759 time to evaluate : 4.731 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: A 42 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7492 (tt0) REVERT: A 183 LEU cc_start: 0.7509 (OUTLIER) cc_final: 0.6791 (mt) REVERT: A 246 MET cc_start: 0.7177 (tpp) cc_final: 0.6876 (mmm) REVERT: A 290 PHE cc_start: 0.7598 (m-80) cc_final: 0.7261 (m-80) REVERT: A 318 MET cc_start: 0.8828 (tpp) cc_final: 0.8614 (tpp) REVERT: A 543 TYR cc_start: 0.7202 (p90) cc_final: 0.6430 (p90) REVERT: A 561 GLU cc_start: 0.7979 (tp30) cc_final: 0.7402 (tp30) REVERT: A 572 PHE cc_start: 0.8021 (p90) cc_final: 0.7800 (p90) REVERT: A 602 GLN cc_start: 0.6828 (tm-30) cc_final: 0.6378 (tm-30) REVERT: A 612 GLU cc_start: 0.8055 (tt0) cc_final: 0.7661 (tt0) REVERT: A 627 LEU cc_start: 0.8798 (tp) cc_final: 0.8394 (tt) REVERT: A 635 ASN cc_start: 0.8709 (OUTLIER) cc_final: 0.8366 (p0) REVERT: A 666 MET cc_start: 0.8022 (tpt) cc_final: 0.7528 (tpt) REVERT: A 669 PHE cc_start: 0.8689 (m-80) cc_final: 0.8381 (m-80) REVERT: A 671 GLU cc_start: 0.8601 (tt0) cc_final: 0.8367 (tt0) REVERT: A 682 LYS cc_start: 0.8675 (mttt) cc_final: 0.8268 (mmmt) REVERT: A 684 ARG cc_start: 0.8865 (mtp180) cc_final: 0.8635 (mtm180) REVERT: A 793 PHE cc_start: 0.8872 (p90) cc_final: 0.8590 (p90) REVERT: A 829 GLU cc_start: 0.8603 (tp30) cc_final: 0.7427 (mp0) REVERT: A 934 LYS cc_start: 0.7867 (OUTLIER) cc_final: 0.7009 (tppt) REVERT: A 964 ASN cc_start: 0.8522 (OUTLIER) cc_final: 0.8280 (t0) REVERT: A 975 GLN cc_start: 0.8451 (mm-40) cc_final: 0.8031 (mt0) REVERT: A 976 ASN cc_start: 0.9140 (t0) cc_final: 0.8569 (t0) REVERT: A 977 MET cc_start: 0.9250 (mmm) cc_final: 0.8730 (mmm) REVERT: A 1007 TYR cc_start: 0.8199 (m-10) cc_final: 0.7995 (m-80) REVERT: A 1015 GLN cc_start: 0.8757 (tp40) cc_final: 0.7857 (tp40) REVERT: A 1017 ASN cc_start: 0.8977 (m-40) cc_final: 0.8527 (m110) REVERT: A 1065 GLN cc_start: 0.8970 (OUTLIER) cc_final: 0.8755 (mm110) REVERT: A 1087 LEU cc_start: 0.9525 (tt) cc_final: 0.9255 (mt) REVERT: A 1110 LEU cc_start: 0.9141 (mt) cc_final: 0.8755 (tp) REVERT: A 1178 ASP cc_start: 0.9400 (p0) cc_final: 0.9100 (p0) REVERT: A 1216 TYR cc_start: 0.8693 (m-80) cc_final: 0.8373 (m-80) REVERT: A 1217 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.9014 (mm) REVERT: B 78 GLU cc_start: 0.8481 (pt0) cc_final: 0.7795 (pm20) REVERT: B 98 GLU cc_start: 0.8594 (tt0) cc_final: 0.8163 (tm-30) REVERT: B 121 MET cc_start: 0.8070 (tpp) cc_final: 0.7727 (tpp) REVERT: B 138 TYR cc_start: 0.6348 (m-80) cc_final: 0.6013 (m-10) REVERT: B 208 GLN cc_start: 0.8164 (tt0) cc_final: 0.7628 (tp40) REVERT: B 318 MET cc_start: 0.8231 (mtt) cc_final: 0.7275 (mmm) REVERT: B 342 GLU cc_start: 0.8739 (tp30) cc_final: 0.8493 (tp30) REVERT: B 393 TYR cc_start: 0.8702 (t80) cc_final: 0.8364 (t80) REVERT: B 542 ILE cc_start: 0.8394 (tp) cc_final: 0.7822 (mp) REVERT: B 649 TYR cc_start: 0.7767 (m-80) cc_final: 0.7478 (m-80) REVERT: B 669 PHE cc_start: 0.8480 (m-80) cc_final: 0.8203 (m-80) REVERT: B 688 MET cc_start: 0.8432 (ppp) cc_final: 0.8042 (ppp) REVERT: B 858 TRP cc_start: 0.7099 (m-90) cc_final: 0.6539 (m-90) REVERT: B 965 LEU cc_start: 0.9083 (tt) cc_final: 0.8858 (mp) REVERT: B 976 ASN cc_start: 0.9123 (t0) cc_final: 0.8886 (t0) REVERT: B 977 MET cc_start: 0.9167 (mmm) cc_final: 0.8927 (mmm) REVERT: B 1010 THR cc_start: 0.8569 (m) cc_final: 0.8310 (p) REVERT: B 1076 ASP cc_start: 0.8025 (p0) cc_final: 0.7592 (p0) REVERT: B 1098 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7784 (tp30) REVERT: B 1123 ASN cc_start: 0.9328 (m110) cc_final: 0.9041 (m110) REVERT: B 1168 LYS cc_start: 0.8936 (mttp) cc_final: 0.8678 (mttm) REVERT: B 1183 TRP cc_start: 0.8955 (m-90) cc_final: 0.8563 (m-90) REVERT: B 1217 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8742 (mm) REVERT: B 1325 GLN cc_start: 0.8142 (tt0) cc_final: 0.7624 (tp40) REVERT: B 1330 TYR cc_start: 0.8739 (p90) cc_final: 0.8401 (p90) REVERT: C 65 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7289 (mm-30) REVERT: C 98 GLU cc_start: 0.8570 (tm-30) cc_final: 0.8363 (tm-30) REVERT: C 121 MET cc_start: 0.6890 (tpp) cc_final: 0.6486 (tpp) REVERT: C 154 ASN cc_start: 0.8967 (OUTLIER) cc_final: 0.8409 (p0) REVERT: C 189 GLN cc_start: 0.8644 (pm20) cc_final: 0.8130 (pp30) REVERT: C 272 TYR cc_start: 0.4063 (OUTLIER) cc_final: 0.3450 (t80) REVERT: C 310 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.8154 (pm20) REVERT: C 421 VAL cc_start: 0.8877 (t) cc_final: 0.8488 (p) REVERT: C 436 TRP cc_start: 0.7640 (t-100) cc_final: 0.7374 (t-100) REVERT: C 458 PHE cc_start: 0.8217 (p90) cc_final: 0.7687 (p90) REVERT: C 481 ILE cc_start: 0.8826 (mp) cc_final: 0.8432 (mp) REVERT: C 499 ILE cc_start: 0.7664 (mp) cc_final: 0.7418 (tp) REVERT: C 601 ASP cc_start: 0.7909 (OUTLIER) cc_final: 0.7065 (t70) REVERT: C 625 LYS cc_start: 0.8711 (mtpt) cc_final: 0.8420 (mppt) REVERT: C 635 ASN cc_start: 0.8454 (p0) cc_final: 0.8014 (p0) REVERT: C 671 GLU cc_start: 0.9091 (tt0) cc_final: 0.8614 (mt-10) REVERT: C 673 MET cc_start: 0.8975 (tpp) cc_final: 0.8751 (tpp) REVERT: C 688 MET cc_start: 0.8191 (ppp) cc_final: 0.7654 (ptp) REVERT: C 737 GLU cc_start: 0.8116 (mp0) cc_final: 0.7272 (mp0) REVERT: C 916 PHE cc_start: 0.8761 (m-80) cc_final: 0.8410 (m-80) REVERT: C 976 ASN cc_start: 0.9052 (t0) cc_final: 0.8739 (t0) REVERT: C 977 MET cc_start: 0.9066 (mmm) cc_final: 0.8699 (mmm) REVERT: C 988 ASP cc_start: 0.8384 (t0) cc_final: 0.7914 (t70) REVERT: C 1015 GLN cc_start: 0.7863 (tp40) cc_final: 0.6603 (tp40) REVERT: C 1104 TYR cc_start: 0.8621 (t80) cc_final: 0.8250 (t80) REVERT: C 1129 GLU cc_start: 0.9406 (pt0) cc_final: 0.8975 (pp20) REVERT: C 1205 GLU cc_start: 0.8575 (pm20) cc_final: 0.7998 (pm20) REVERT: C 1254 THR cc_start: 0.9178 (m) cc_final: 0.8736 (p) REVERT: C 1258 LEU cc_start: 0.9162 (mp) cc_final: 0.8931 (mp) REVERT: D 98 GLU cc_start: 0.8818 (tt0) cc_final: 0.8428 (tp30) REVERT: D 108 LYS cc_start: 0.9285 (mmtt) cc_final: 0.8779 (mmmt) REVERT: D 126 ASP cc_start: 0.9070 (p0) cc_final: 0.8755 (p0) REVERT: D 177 GLN cc_start: 0.8919 (tt0) cc_final: 0.8597 (tm-30) REVERT: D 203 TYR cc_start: 0.7175 (m-80) cc_final: 0.5977 (m-80) REVERT: D 368 GLN cc_start: 0.8758 (pt0) cc_final: 0.8228 (mp10) REVERT: D 386 ILE cc_start: 0.8684 (mp) cc_final: 0.8451 (pt) REVERT: D 408 SER cc_start: 0.8902 (OUTLIER) cc_final: 0.8582 (m) REVERT: D 542 ILE cc_start: 0.8545 (tt) cc_final: 0.8134 (mp) REVERT: D 557 LYS cc_start: 0.8816 (mttp) cc_final: 0.8537 (mmtp) REVERT: D 561 GLU cc_start: 0.8075 (tp30) cc_final: 0.7665 (tp30) REVERT: D 637 GLN cc_start: 0.7764 (OUTLIER) cc_final: 0.7483 (pp30) REVERT: D 669 PHE cc_start: 0.8560 (m-80) cc_final: 0.7938 (m-80) REVERT: D 671 GLU cc_start: 0.8832 (tt0) cc_final: 0.8511 (tt0) REVERT: D 673 MET cc_start: 0.8852 (tpp) cc_final: 0.8414 (tpp) REVERT: D 682 LYS cc_start: 0.8558 (mttt) cc_final: 0.8287 (mmtp) REVERT: D 688 MET cc_start: 0.8344 (ppp) cc_final: 0.7931 (ppp) REVERT: D 737 GLU cc_start: 0.8037 (mp0) cc_final: 0.7729 (mp0) REVERT: D 741 TRP cc_start: 0.8107 (t-100) cc_final: 0.7902 (t60) REVERT: D 751 VAL cc_start: 0.7281 (OUTLIER) cc_final: 0.7029 (p) REVERT: D 764 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.7808 (mp0) REVERT: D 766 LYS cc_start: 0.7949 (mmtt) cc_final: 0.7664 (mmtm) REVERT: D 798 MET cc_start: 0.6785 (ptp) cc_final: 0.6409 (ptp) REVERT: D 861 THR cc_start: 0.8393 (OUTLIER) cc_final: 0.8155 (m) REVERT: D 912 LYS cc_start: 0.8238 (ptpp) cc_final: 0.7680 (ptpp) REVERT: D 913 GLU cc_start: 0.8564 (pp20) cc_final: 0.8059 (pp20) REVERT: D 914 THR cc_start: 0.9104 (OUTLIER) cc_final: 0.8876 (p) REVERT: D 957 SER cc_start: 0.8554 (t) cc_final: 0.8347 (m) REVERT: D 965 LEU cc_start: 0.8798 (tp) cc_final: 0.8589 (mt) REVERT: D 976 ASN cc_start: 0.9335 (t0) cc_final: 0.9090 (t0) REVERT: D 999 GLU cc_start: 0.9212 (mp0) cc_final: 0.8977 (mp0) REVERT: D 1003 LYS cc_start: 0.9345 (tptt) cc_final: 0.9028 (tppt) REVERT: D 1007 TYR cc_start: 0.7916 (m-10) cc_final: 0.7246 (m-80) REVERT: D 1076 ASP cc_start: 0.7760 (p0) cc_final: 0.7447 (p0) REVERT: D 1089 ASN cc_start: 0.8793 (p0) cc_final: 0.8261 (p0) REVERT: D 1123 ASN cc_start: 0.9284 (m-40) cc_final: 0.9048 (m110) REVERT: D 1133 LYS cc_start: 0.9208 (ttmt) cc_final: 0.8779 (tppt) REVERT: D 1147 LYS cc_start: 0.9272 (mttp) cc_final: 0.8872 (mttp) REVERT: D 1154 PHE cc_start: 0.8836 (m-80) cc_final: 0.8568 (m-80) REVERT: D 1183 TRP cc_start: 0.9034 (OUTLIER) cc_final: 0.8334 (m100) REVERT: D 1208 MET cc_start: 0.9297 (OUTLIER) cc_final: 0.9047 (ppp) REVERT: D 1243 ASN cc_start: 0.9379 (t0) cc_final: 0.9084 (t0) REVERT: D 1245 GLN cc_start: 0.9139 (tm-30) cc_final: 0.8719 (tm-30) REVERT: D 1269 PHE cc_start: 0.8479 (t80) cc_final: 0.7939 (t80) outliers start: 198 outliers final: 116 residues processed: 902 average time/residue: 0.4746 time to fit residues: 718.7234 Evaluate side-chains 810 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 674 time to evaluate : 4.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 TYR Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 345 ARG Chi-restraints excluded: chain A residue 365 PHE Chi-restraints excluded: chain A residue 392 ASN Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 566 ASN Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 619 TYR Chi-restraints excluded: chain A residue 635 ASN Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 656 THR Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 856 VAL Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 934 LYS Chi-restraints excluded: chain A residue 964 ASN Chi-restraints excluded: chain A residue 1024 SER Chi-restraints excluded: chain A residue 1055 TYR Chi-restraints excluded: chain A residue 1065 GLN Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1129 GLU Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1214 LEU Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1249 SER Chi-restraints excluded: chain A residue 1251 THR Chi-restraints excluded: chain A residue 1253 ASP Chi-restraints excluded: chain A residue 1255 VAL Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 89 PHE Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 173 ASN Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 286 PHE Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 407 PHE Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 643 ILE Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 732 ARG Chi-restraints excluded: chain B residue 821 CYS Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 872 VAL Chi-restraints excluded: chain B residue 1144 VAL Chi-restraints excluded: chain B residue 1217 LEU Chi-restraints excluded: chain B residue 1243 ASN Chi-restraints excluded: chain B residue 1251 THR Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 272 TYR Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 310 GLN Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 607 MET Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 758 VAL Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 793 PHE Chi-restraints excluded: chain C residue 1112 ILE Chi-restraints excluded: chain C residue 1127 CYS Chi-restraints excluded: chain C residue 1144 VAL Chi-restraints excluded: chain C residue 1218 THR Chi-restraints excluded: chain C residue 1251 THR Chi-restraints excluded: chain C residue 1270 THR Chi-restraints excluded: chain C residue 1311 GLU Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 173 ASN Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 286 PHE Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain D residue 458 PHE Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 486 THR Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 519 ASP Chi-restraints excluded: chain D residue 548 THR Chi-restraints excluded: chain D residue 563 CYS Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 637 GLN Chi-restraints excluded: chain D residue 643 ILE Chi-restraints excluded: chain D residue 658 VAL Chi-restraints excluded: chain D residue 751 VAL Chi-restraints excluded: chain D residue 761 THR Chi-restraints excluded: chain D residue 764 GLU Chi-restraints excluded: chain D residue 771 CYS Chi-restraints excluded: chain D residue 821 CYS Chi-restraints excluded: chain D residue 861 THR Chi-restraints excluded: chain D residue 887 VAL Chi-restraints excluded: chain D residue 914 THR Chi-restraints excluded: chain D residue 1080 PHE Chi-restraints excluded: chain D residue 1183 TRP Chi-restraints excluded: chain D residue 1208 MET Chi-restraints excluded: chain D residue 1224 THR Chi-restraints excluded: chain D residue 1251 THR Chi-restraints excluded: chain D residue 1270 THR Chi-restraints excluded: chain D residue 1305 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 410 optimal weight: 4.9990 chunk 279 optimal weight: 7.9990 chunk 7 optimal weight: 7.9990 chunk 367 optimal weight: 3.9990 chunk 203 optimal weight: 7.9990 chunk 420 optimal weight: 2.9990 chunk 340 optimal weight: 20.0000 chunk 0 optimal weight: 9.9990 chunk 251 optimal weight: 5.9990 chunk 442 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 938 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 964 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 995 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1038 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1241 GLN B 85 HIS B 132 GLN ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 381 ASN ** B 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 637 GLN ** B 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 960 GLN ** B1187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 GLN ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 310 GLN ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 381 ASN ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 602 GLN C 680 ASN ** C 967 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN D 177 GLN ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 938 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.4159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 41420 Z= 0.339 Angle : 0.852 13.405 56270 Z= 0.423 Chirality : 0.051 0.411 6514 Planarity : 0.006 0.095 7202 Dihedral : 8.272 59.662 6312 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 28.41 Ramachandran Plot: Outliers : 0.10 % Allowed : 12.11 % Favored : 87.79 % Rotamer: Outliers : 6.22 % Allowed : 24.47 % Favored : 69.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.38 % 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: -3.93 (0.11), residues: 5110 helix: -0.72 (0.17), residues: 816 sheet: -2.58 (0.12), residues: 1548 loop : -3.31 (0.11), residues: 2746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 858 HIS 0.010 0.001 HIS B 460 PHE 0.029 0.002 PHE A 155 TYR 0.023 0.002 TYR B1007 ARG 0.014 0.001 ARG A 360 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10220 Ramachandran restraints generated. 5110 Oldfield, 0 Emsley, 5110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10220 Ramachandran restraints generated. 5110 Oldfield, 0 Emsley, 5110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 959 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 278 poor density : 681 time to evaluate : 4.542 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: A 183 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.6798 (mt) REVERT: A 290 PHE cc_start: 0.7791 (m-80) cc_final: 0.7320 (m-80) REVERT: A 304 VAL cc_start: 0.7282 (OUTLIER) cc_final: 0.7025 (m) REVERT: A 460 HIS cc_start: 0.8546 (t-90) cc_final: 0.8259 (t-90) REVERT: A 539 ARG cc_start: 0.8205 (mtt-85) cc_final: 0.7509 (mtt90) REVERT: A 541 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7488 (pt) REVERT: A 543 TYR cc_start: 0.7783 (p90) cc_final: 0.6945 (p90) REVERT: A 561 GLU cc_start: 0.8112 (tp30) cc_final: 0.7513 (tp30) REVERT: A 566 ASN cc_start: 0.8381 (t0) cc_final: 0.7653 (t0) REVERT: A 572 PHE cc_start: 0.8315 (p90) cc_final: 0.8012 (p90) REVERT: A 602 GLN cc_start: 0.6978 (tm-30) cc_final: 0.6496 (tm-30) REVERT: A 612 GLU cc_start: 0.8102 (tt0) cc_final: 0.7703 (tt0) REVERT: A 627 LEU cc_start: 0.8800 (tp) cc_final: 0.7768 (tp) REVERT: A 635 ASN cc_start: 0.8648 (OUTLIER) cc_final: 0.8239 (p0) REVERT: A 666 MET cc_start: 0.8186 (tpt) cc_final: 0.7872 (tpt) REVERT: A 669 PHE cc_start: 0.8766 (m-80) cc_final: 0.8390 (m-80) REVERT: A 671 GLU cc_start: 0.8838 (tt0) cc_final: 0.8552 (tt0) REVERT: A 682 LYS cc_start: 0.8721 (mttt) cc_final: 0.8309 (mmmt) REVERT: A 783 THR cc_start: 0.8939 (OUTLIER) cc_final: 0.8728 (t) REVERT: A 829 GLU cc_start: 0.8708 (tp30) cc_final: 0.8392 (tm-30) REVERT: A 858 TRP cc_start: 0.5159 (m100) cc_final: 0.4947 (m100) REVERT: A 870 PHE cc_start: 0.5802 (m-80) cc_final: 0.4932 (m-80) REVERT: A 934 LYS cc_start: 0.7982 (OUTLIER) cc_final: 0.7684 (tptp) REVERT: A 964 ASN cc_start: 0.8611 (t0) cc_final: 0.8395 (t0) REVERT: A 968 MET cc_start: 0.8761 (tpt) cc_final: 0.8560 (tpp) REVERT: A 975 GLN cc_start: 0.8485 (mm-40) cc_final: 0.8038 (mt0) REVERT: A 977 MET cc_start: 0.9280 (mmm) cc_final: 0.8715 (mmm) REVERT: A 1017 ASN cc_start: 0.8999 (m-40) cc_final: 0.8549 (m110) REVERT: A 1080 PHE cc_start: 0.8012 (m-80) cc_final: 0.7604 (m-10) REVERT: A 1087 LEU cc_start: 0.9539 (tt) cc_final: 0.9203 (mt) REVERT: A 1098 GLU cc_start: 0.8570 (pm20) cc_final: 0.8238 (mm-30) REVERT: A 1110 LEU cc_start: 0.9355 (mt) cc_final: 0.9025 (tp) REVERT: A 1178 ASP cc_start: 0.9452 (p0) cc_final: 0.9157 (p0) REVERT: A 1208 MET cc_start: 0.9433 (ppp) cc_final: 0.8911 (ppp) REVERT: A 1217 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.9012 (mm) REVERT: B 78 GLU cc_start: 0.8536 (pt0) cc_final: 0.7875 (pm20) REVERT: B 98 GLU cc_start: 0.8638 (tt0) cc_final: 0.8283 (tm-30) REVERT: B 121 MET cc_start: 0.8058 (tpp) cc_final: 0.7846 (tpp) REVERT: B 208 GLN cc_start: 0.8352 (tt0) cc_final: 0.7774 (tp40) REVERT: B 318 MET cc_start: 0.8464 (mtt) cc_final: 0.7454 (mmm) REVERT: B 342 GLU cc_start: 0.8795 (tp30) cc_final: 0.8533 (tp30) REVERT: B 393 TYR cc_start: 0.8751 (t80) cc_final: 0.8430 (t80) REVERT: B 460 HIS cc_start: 0.8562 (t-90) cc_final: 0.7985 (m-70) REVERT: B 461 LEU cc_start: 0.9211 (mp) cc_final: 0.8895 (mp) REVERT: B 500 MET cc_start: 0.5726 (mmm) cc_final: 0.5282 (mmm) REVERT: B 649 TYR cc_start: 0.7857 (m-80) cc_final: 0.7565 (m-80) REVERT: B 688 MET cc_start: 0.8504 (ppp) cc_final: 0.8065 (ppp) REVERT: B 798 MET cc_start: 0.8619 (ptt) cc_final: 0.8184 (ptm) REVERT: B 808 PHE cc_start: 0.9240 (t80) cc_final: 0.8583 (t80) REVERT: B 976 ASN cc_start: 0.9236 (t0) cc_final: 0.8934 (t0) REVERT: B 977 MET cc_start: 0.9202 (mmm) cc_final: 0.8930 (mmm) REVERT: B 1010 THR cc_start: 0.8618 (m) cc_final: 0.8341 (p) REVERT: B 1059 ASP cc_start: 0.7628 (OUTLIER) cc_final: 0.7105 (p0) REVERT: B 1076 ASP cc_start: 0.8335 (p0) cc_final: 0.7942 (p0) REVERT: B 1098 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7854 (tp30) REVERT: B 1123 ASN cc_start: 0.9444 (m110) cc_final: 0.9156 (m110) REVERT: B 1183 TRP cc_start: 0.9008 (m-90) cc_final: 0.8618 (m-90) REVERT: B 1208 MET cc_start: 0.9527 (ppp) cc_final: 0.9128 (ppp) REVERT: B 1217 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8803 (mm) REVERT: B 1325 GLN cc_start: 0.8321 (tt0) cc_final: 0.7874 (tp40) REVERT: B 1329 LYS cc_start: 0.8078 (ptmt) cc_final: 0.7863 (pttm) REVERT: B 1330 TYR cc_start: 0.8844 (p90) cc_final: 0.8506 (p90) REVERT: C 65 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7147 (mm-30) REVERT: C 139 LYS cc_start: 0.7903 (OUTLIER) cc_final: 0.7414 (mttm) REVERT: C 154 ASN cc_start: 0.9013 (OUTLIER) cc_final: 0.8507 (p0) REVERT: C 189 GLN cc_start: 0.8700 (pm20) cc_final: 0.8256 (pp30) REVERT: C 272 TYR cc_start: 0.4475 (OUTLIER) cc_final: 0.3751 (t80) REVERT: C 310 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.8153 (pm20) REVERT: C 360 ARG cc_start: 0.7471 (mmt90) cc_final: 0.6780 (mmt90) REVERT: C 370 ARG cc_start: 0.8682 (OUTLIER) cc_final: 0.8481 (ttp-170) REVERT: C 436 TRP cc_start: 0.7809 (t-100) cc_final: 0.7480 (t-100) REVERT: C 458 PHE cc_start: 0.8398 (p90) cc_final: 0.7739 (p90) REVERT: C 481 ILE cc_start: 0.8860 (mp) cc_final: 0.8578 (mp) REVERT: C 499 ILE cc_start: 0.7518 (mp) cc_final: 0.7291 (tp) REVERT: C 625 LYS cc_start: 0.8760 (mtpt) cc_final: 0.8458 (mppt) REVERT: C 635 ASN cc_start: 0.8506 (p0) cc_final: 0.7993 (p0) REVERT: C 669 PHE cc_start: 0.8695 (m-10) cc_final: 0.8158 (m-80) REVERT: C 671 GLU cc_start: 0.9205 (tt0) cc_final: 0.8870 (mt-10) REVERT: C 688 MET cc_start: 0.8177 (ppp) cc_final: 0.7748 (ppp) REVERT: C 737 GLU cc_start: 0.8331 (mp0) cc_final: 0.7530 (mp0) REVERT: C 751 VAL cc_start: 0.7771 (OUTLIER) cc_final: 0.7526 (p) REVERT: C 787 ARG cc_start: 0.8629 (ptp90) cc_final: 0.8037 (mtp180) REVERT: C 916 PHE cc_start: 0.8750 (m-80) cc_final: 0.8408 (m-80) REVERT: C 968 MET cc_start: 0.8928 (tpt) cc_final: 0.8653 (tpp) REVERT: C 988 ASP cc_start: 0.8543 (t0) cc_final: 0.8044 (t70) REVERT: C 1015 GLN cc_start: 0.7966 (tp40) cc_final: 0.6910 (mp10) REVERT: C 1079 CYS cc_start: 0.5526 (OUTLIER) cc_final: 0.4817 (p) REVERT: C 1104 TYR cc_start: 0.8742 (t80) cc_final: 0.8397 (t80) REVERT: C 1123 ASN cc_start: 0.9032 (OUTLIER) cc_final: 0.8617 (p0) REVERT: C 1168 LYS cc_start: 0.9437 (mttt) cc_final: 0.9219 (mttt) REVERT: C 1205 GLU cc_start: 0.8615 (pm20) cc_final: 0.8123 (pm20) REVERT: C 1207 GLU cc_start: 0.9087 (tt0) cc_final: 0.8747 (tp30) REVERT: C 1254 THR cc_start: 0.9156 (m) cc_final: 0.8860 (p) REVERT: D 32 MET cc_start: 0.8679 (ttm) cc_final: 0.8468 (tpp) REVERT: D 98 GLU cc_start: 0.8761 (tt0) cc_final: 0.8375 (tp30) REVERT: D 151 MET cc_start: 0.7771 (mtm) cc_final: 0.7444 (mpp) REVERT: D 203 TYR cc_start: 0.7511 (m-80) cc_final: 0.6184 (m-80) REVERT: D 368 GLN cc_start: 0.8827 (pt0) cc_final: 0.8369 (mp10) REVERT: D 370 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.8346 (ptt180) REVERT: D 386 ILE cc_start: 0.8690 (mp) cc_final: 0.8263 (pt) REVERT: D 500 MET cc_start: 0.5395 (mtt) cc_final: 0.5044 (mtt) REVERT: D 542 ILE cc_start: 0.8612 (tt) cc_final: 0.8130 (mp) REVERT: D 557 LYS cc_start: 0.8837 (mttp) cc_final: 0.8524 (mmtp) REVERT: D 561 GLU cc_start: 0.8221 (tp30) cc_final: 0.7834 (tp30) REVERT: D 669 PHE cc_start: 0.8711 (m-80) cc_final: 0.8022 (m-80) REVERT: D 671 GLU cc_start: 0.8842 (tt0) cc_final: 0.8298 (mm-30) REVERT: D 673 MET cc_start: 0.9047 (tpp) cc_final: 0.8535 (tpp) REVERT: D 682 LYS cc_start: 0.8598 (mttt) cc_final: 0.8341 (mmtp) REVERT: D 764 GLU cc_start: 0.8727 (mt-10) cc_final: 0.8181 (mp0) REVERT: D 766 LYS cc_start: 0.8079 (mmtt) cc_final: 0.7697 (mmtm) REVERT: D 861 THR cc_start: 0.8650 (OUTLIER) cc_final: 0.8432 (m) REVERT: D 913 GLU cc_start: 0.8674 (pp20) cc_final: 0.8295 (pp20) REVERT: D 965 LEU cc_start: 0.8900 (tp) cc_final: 0.8630 (mt) REVERT: D 976 ASN cc_start: 0.9395 (t0) cc_final: 0.9149 (t0) REVERT: D 977 MET cc_start: 0.9609 (mmm) cc_final: 0.9348 (mmm) REVERT: D 1003 LYS cc_start: 0.9420 (tptt) cc_final: 0.9077 (tppt) REVERT: D 1007 TYR cc_start: 0.8023 (m-10) cc_final: 0.7330 (m-80) REVERT: D 1076 ASP cc_start: 0.7851 (p0) cc_final: 0.7523 (p0) REVERT: D 1089 ASN cc_start: 0.8832 (p0) cc_final: 0.8608 (p0) REVERT: D 1123 ASN cc_start: 0.9434 (m-40) cc_final: 0.9180 (m110) REVERT: D 1133 LYS cc_start: 0.9289 (ttmt) cc_final: 0.8851 (tppt) REVERT: D 1154 PHE cc_start: 0.8955 (m-80) cc_final: 0.8711 (m-80) REVERT: D 1183 TRP cc_start: 0.8978 (OUTLIER) cc_final: 0.8105 (m100) REVERT: D 1208 MET cc_start: 0.9277 (OUTLIER) cc_final: 0.8737 (ppp) REVERT: D 1243 ASN cc_start: 0.9433 (t0) cc_final: 0.9154 (t0) REVERT: D 1245 GLN cc_start: 0.9178 (tm-30) cc_final: 0.8771 (tm-30) REVERT: D 1269 PHE cc_start: 0.8589 (t80) cc_final: 0.8027 (t80) REVERT: D 1331 ASN cc_start: 0.6851 (OUTLIER) cc_final: 0.6052 (m-40) outliers start: 278 outliers final: 192 residues processed: 879 average time/residue: 0.4602 time to fit residues: 684.9875 Evaluate side-chains 847 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 633 time to evaluate : 4.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 TYR Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 89 PHE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 286 PHE Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 345 ARG Chi-restraints excluded: chain A residue 352 PHE Chi-restraints excluded: chain A residue 392 ASN Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 619 TYR Chi-restraints excluded: chain A residue 626 ASP Chi-restraints excluded: chain A residue 635 ASN Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 656 THR Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 787 ARG Chi-restraints excluded: chain A residue 856 VAL Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 878 GLU Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 934 LYS Chi-restraints excluded: chain A residue 959 MET Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1024 SER Chi-restraints excluded: chain A residue 1041 LEU Chi-restraints excluded: chain A residue 1055 TYR Chi-restraints excluded: chain A residue 1076 ASP Chi-restraints excluded: chain A residue 1101 LEU Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1115 THR Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1214 LEU Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1218 THR Chi-restraints excluded: chain A residue 1224 THR Chi-restraints excluded: chain A residue 1249 SER Chi-restraints excluded: chain A residue 1251 THR Chi-restraints excluded: chain A residue 1255 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 89 PHE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 173 ASN Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 246 MET Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 286 PHE Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 407 PHE Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 637 GLN Chi-restraints excluded: chain B residue 643 ILE Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 732 ARG Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 787 ARG Chi-restraints excluded: chain B residue 793 PHE Chi-restraints excluded: chain B residue 831 SER Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 872 VAL Chi-restraints excluded: chain B residue 964 ASN Chi-restraints excluded: chain B residue 965 LEU Chi-restraints excluded: chain B residue 1046 LEU Chi-restraints excluded: chain B residue 1059 ASP Chi-restraints excluded: chain B residue 1080 PHE Chi-restraints excluded: chain B residue 1091 ILE Chi-restraints excluded: chain B residue 1115 THR Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1127 CYS Chi-restraints excluded: chain B residue 1144 VAL Chi-restraints excluded: chain B residue 1217 LEU Chi-restraints excluded: chain B residue 1218 THR Chi-restraints excluded: chain B residue 1224 THR Chi-restraints excluded: chain B residue 1227 ASP Chi-restraints excluded: chain B residue 1234 ILE Chi-restraints excluded: chain B residue 1243 ASN Chi-restraints excluded: chain B residue 1251 THR Chi-restraints excluded: chain B residue 1299 LEU Chi-restraints excluded: chain C residue 31 TYR Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 89 PHE Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 272 TYR Chi-restraints excluded: chain C residue 286 PHE Chi-restraints excluded: chain C residue 310 GLN Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 370 ARG Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 423 VAL Chi-restraints excluded: chain C residue 460 HIS Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 607 MET Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain C residue 742 ASP Chi-restraints excluded: chain C residue 751 VAL Chi-restraints excluded: chain C residue 758 VAL Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 835 LEU Chi-restraints excluded: chain C residue 899 VAL Chi-restraints excluded: chain C residue 1003 LYS Chi-restraints excluded: chain C residue 1041 LEU Chi-restraints excluded: chain C residue 1055 TYR Chi-restraints excluded: chain C residue 1079 CYS Chi-restraints excluded: chain C residue 1101 LEU Chi-restraints excluded: chain C residue 1123 ASN Chi-restraints excluded: chain C residue 1127 CYS Chi-restraints excluded: chain C residue 1144 VAL Chi-restraints excluded: chain C residue 1218 THR Chi-restraints excluded: chain C residue 1224 THR Chi-restraints excluded: chain C residue 1227 ASP Chi-restraints excluded: chain C residue 1239 THR Chi-restraints excluded: chain C residue 1251 THR Chi-restraints excluded: chain C residue 1253 ASP Chi-restraints excluded: chain C residue 1270 THR Chi-restraints excluded: chain C residue 1311 GLU Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 173 ASN Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 286 PHE Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 353 VAL Chi-restraints excluded: chain D residue 370 ARG Chi-restraints excluded: chain D residue 372 VAL Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 405 VAL Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain D residue 458 PHE Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 486 THR Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 519 ASP Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 548 THR Chi-restraints excluded: chain D residue 560 VAL Chi-restraints excluded: chain D residue 563 CYS Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 621 LEU Chi-restraints excluded: chain D residue 643 ILE Chi-restraints excluded: chain D residue 658 VAL Chi-restraints excluded: chain D residue 751 VAL Chi-restraints excluded: chain D residue 771 CYS Chi-restraints excluded: chain D residue 783 THR Chi-restraints excluded: chain D residue 821 CYS Chi-restraints excluded: chain D residue 861 THR Chi-restraints excluded: chain D residue 887 VAL Chi-restraints excluded: chain D residue 983 ASN Chi-restraints excluded: chain D residue 1041 LEU Chi-restraints excluded: chain D residue 1080 PHE Chi-restraints excluded: chain D residue 1101 LEU Chi-restraints excluded: chain D residue 1183 TRP Chi-restraints excluded: chain D residue 1208 MET Chi-restraints excluded: chain D residue 1224 THR Chi-restraints excluded: chain D residue 1250 SER Chi-restraints excluded: chain D residue 1270 THR Chi-restraints excluded: chain D residue 1305 LEU Chi-restraints excluded: chain D residue 1331 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 165 optimal weight: 9.9990 chunk 443 optimal weight: 6.9990 chunk 97 optimal weight: 10.0000 chunk 289 optimal weight: 6.9990 chunk 121 optimal weight: 20.0000 chunk 493 optimal weight: 1.9990 chunk 409 optimal weight: 7.9990 chunk 228 optimal weight: 0.7980 chunk 41 optimal weight: 6.9990 chunk 163 optimal weight: 8.9990 chunk 259 optimal weight: 5.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 GLN ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 208 GLN A 361 GLN A 368 GLN ** A 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 938 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 964 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 995 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1015 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1038 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1065 GLN ** A1187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 GLN ** B 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1072 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 106 GLN ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 310 GLN ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 662 ASN C 680 ASN C 851 ASN ** C 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 637 GLN ** D 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 938 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1051 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.4551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 41420 Z= 0.378 Angle : 0.874 11.583 56270 Z= 0.436 Chirality : 0.052 0.414 6514 Planarity : 0.006 0.074 7202 Dihedral : 8.353 59.863 6312 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 32.48 Ramachandran Plot: Outliers : 0.10 % Allowed : 13.07 % Favored : 86.83 % Rotamer: Outliers : 6.60 % Allowed : 25.59 % Favored : 67.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.38 % 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: -4.00 (0.11), residues: 5110 helix: -0.88 (0.16), residues: 814 sheet: -2.65 (0.12), residues: 1548 loop : -3.30 (0.11), residues: 2748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 858 HIS 0.011 0.001 HIS B 321 PHE 0.030 0.002 PHE D 290 TYR 0.041 0.002 TYR C1007 ARG 0.010 0.001 ARG A 360 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10220 Ramachandran restraints generated. 5110 Oldfield, 0 Emsley, 5110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10220 Ramachandran restraints generated. 5110 Oldfield, 0 Emsley, 5110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 957 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 295 poor density : 662 time to evaluate : 4.283 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: A 290 PHE cc_start: 0.7985 (m-80) cc_final: 0.7436 (m-80) REVERT: A 304 VAL cc_start: 0.7345 (OUTLIER) cc_final: 0.7143 (m) REVERT: A 318 MET cc_start: 0.8853 (tpp) cc_final: 0.8625 (tpp) REVERT: A 368 GLN cc_start: 0.8345 (tt0) cc_final: 0.7798 (tm-30) REVERT: A 434 TYR cc_start: 0.6258 (OUTLIER) cc_final: 0.4756 (m-10) REVERT: A 436 TRP cc_start: 0.7000 (t-100) cc_final: 0.6777 (t-100) REVERT: A 458 PHE cc_start: 0.7855 (OUTLIER) cc_final: 0.7642 (p90) REVERT: A 460 HIS cc_start: 0.8540 (t-90) cc_final: 0.8200 (t-90) REVERT: A 539 ARG cc_start: 0.8181 (mtt-85) cc_final: 0.7773 (mtt-85) REVERT: A 543 TYR cc_start: 0.7935 (p90) cc_final: 0.7162 (p90) REVERT: A 572 PHE cc_start: 0.8427 (p90) cc_final: 0.8097 (p90) REVERT: A 602 GLN cc_start: 0.7093 (tm-30) cc_final: 0.6479 (pt0) REVERT: A 612 GLU cc_start: 0.8174 (tt0) cc_final: 0.7786 (tt0) REVERT: A 627 LEU cc_start: 0.8750 (tp) cc_final: 0.8283 (tt) REVERT: A 635 ASN cc_start: 0.8506 (OUTLIER) cc_final: 0.8197 (p0) REVERT: A 669 PHE cc_start: 0.8767 (m-80) cc_final: 0.8374 (m-80) REVERT: A 671 GLU cc_start: 0.8886 (tt0) cc_final: 0.8455 (mt-10) REVERT: A 682 LYS cc_start: 0.8744 (mttt) cc_final: 0.8340 (mmmt) REVERT: A 783 THR cc_start: 0.9039 (OUTLIER) cc_final: 0.8811 (t) REVERT: A 793 PHE cc_start: 0.8897 (p90) cc_final: 0.8595 (p90) REVERT: A 829 GLU cc_start: 0.8719 (tp30) cc_final: 0.8439 (tm-30) REVERT: A 870 PHE cc_start: 0.5953 (m-80) cc_final: 0.5182 (m-80) REVERT: A 964 ASN cc_start: 0.8714 (t0) cc_final: 0.8491 (t0) REVERT: A 975 GLN cc_start: 0.8537 (mm-40) cc_final: 0.8001 (mt0) REVERT: A 977 MET cc_start: 0.9309 (mmm) cc_final: 0.8840 (mmm) REVERT: A 985 TYR cc_start: 0.7276 (m-10) cc_final: 0.7046 (m-10) REVERT: A 1017 ASN cc_start: 0.9015 (m-40) cc_final: 0.8561 (m110) REVERT: A 1047 LYS cc_start: 0.9364 (ptmt) cc_final: 0.9041 (ptpp) REVERT: A 1064 THR cc_start: 0.9409 (OUTLIER) cc_final: 0.9130 (p) REVERT: A 1065 GLN cc_start: 0.9151 (OUTLIER) cc_final: 0.8803 (mm110) REVERT: A 1080 PHE cc_start: 0.8080 (m-80) cc_final: 0.7653 (m-10) REVERT: A 1087 LEU cc_start: 0.9554 (tt) cc_final: 0.9214 (mt) REVERT: A 1098 GLU cc_start: 0.8582 (pm20) cc_final: 0.8268 (mm-30) REVERT: A 1110 LEU cc_start: 0.9350 (mt) cc_final: 0.9032 (tp) REVERT: A 1111 GLU cc_start: 0.8717 (mm-30) cc_final: 0.8477 (mm-30) REVERT: A 1123 ASN cc_start: 0.9161 (OUTLIER) cc_final: 0.8506 (p0) REVERT: A 1129 GLU cc_start: 0.9362 (OUTLIER) cc_final: 0.9141 (pm20) REVERT: A 1208 MET cc_start: 0.9482 (ppp) cc_final: 0.9078 (ppp) REVERT: A 1217 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.9007 (mm) REVERT: B 78 GLU cc_start: 0.8567 (pt0) cc_final: 0.7986 (pm20) REVERT: B 98 GLU cc_start: 0.8616 (tt0) cc_final: 0.8278 (tm-30) REVERT: B 121 MET cc_start: 0.8065 (tpp) cc_final: 0.7795 (tpp) REVERT: B 208 GLN cc_start: 0.8503 (tt0) cc_final: 0.7849 (tp40) REVERT: B 318 MET cc_start: 0.8542 (mtt) cc_final: 0.7593 (mmm) REVERT: B 342 GLU cc_start: 0.8813 (tp30) cc_final: 0.8551 (tp30) REVERT: B 393 TYR cc_start: 0.8805 (t80) cc_final: 0.8456 (t80) REVERT: B 567 LYS cc_start: 0.9335 (tppt) cc_final: 0.9121 (mmtm) REVERT: B 637 GLN cc_start: 0.7305 (OUTLIER) cc_final: 0.7088 (pp30) REVERT: B 649 TYR cc_start: 0.7879 (m-80) cc_final: 0.7551 (m-80) REVERT: B 688 MET cc_start: 0.8544 (ppp) cc_final: 0.8085 (ppp) REVERT: B 798 MET cc_start: 0.8622 (ptt) cc_final: 0.8174 (ptm) REVERT: B 808 PHE cc_start: 0.9344 (t80) cc_final: 0.8751 (t80) REVERT: B 858 TRP cc_start: 0.7170 (m-90) cc_final: 0.6755 (m-90) REVERT: B 976 ASN cc_start: 0.9278 (t0) cc_final: 0.8984 (t0) REVERT: B 977 MET cc_start: 0.9221 (mmm) cc_final: 0.8935 (mmm) REVERT: B 1010 THR cc_start: 0.8625 (m) cc_final: 0.8348 (p) REVERT: B 1059 ASP cc_start: 0.7497 (OUTLIER) cc_final: 0.6992 (p0) REVERT: B 1076 ASP cc_start: 0.8389 (p0) cc_final: 0.7993 (p0) REVERT: B 1098 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7727 (tp30) REVERT: B 1123 ASN cc_start: 0.9457 (m110) cc_final: 0.9182 (m110) REVERT: B 1183 TRP cc_start: 0.9029 (m-90) cc_final: 0.8673 (m-90) REVERT: B 1217 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8852 (mm) REVERT: B 1325 GLN cc_start: 0.8394 (tt0) cc_final: 0.7988 (tp-100) REVERT: B 1329 LYS cc_start: 0.8157 (ptmt) cc_final: 0.7862 (pttm) REVERT: B 1330 TYR cc_start: 0.8916 (p90) cc_final: 0.8555 (p90) REVERT: C 65 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7148 (mm-30) REVERT: C 76 ASP cc_start: 0.8670 (p0) cc_final: 0.8339 (m-30) REVERT: C 121 MET cc_start: 0.6890 (tpp) cc_final: 0.6592 (tmm) REVERT: C 139 LYS cc_start: 0.7851 (OUTLIER) cc_final: 0.7329 (mttm) REVERT: C 154 ASN cc_start: 0.9063 (OUTLIER) cc_final: 0.8501 (p0) REVERT: C 189 GLN cc_start: 0.8791 (pm20) cc_final: 0.8345 (pp30) REVERT: C 272 TYR cc_start: 0.4480 (OUTLIER) cc_final: 0.3760 (t80) REVERT: C 310 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.8042 (pm20) REVERT: C 393 TYR cc_start: 0.8918 (t80) cc_final: 0.8483 (t80) REVERT: C 436 TRP cc_start: 0.7854 (t-100) cc_final: 0.7445 (t-100) REVERT: C 458 PHE cc_start: 0.8487 (p90) cc_final: 0.7621 (p90) REVERT: C 481 ILE cc_start: 0.9003 (mp) cc_final: 0.8672 (mp) REVERT: C 635 ASN cc_start: 0.8554 (p0) cc_final: 0.8084 (p0) REVERT: C 669 PHE cc_start: 0.8804 (m-10) cc_final: 0.8227 (m-80) REVERT: C 671 GLU cc_start: 0.9192 (tt0) cc_final: 0.8863 (mt-10) REVERT: C 737 GLU cc_start: 0.8384 (mp0) cc_final: 0.7671 (mp0) REVERT: C 751 VAL cc_start: 0.7888 (OUTLIER) cc_final: 0.7664 (p) REVERT: C 787 ARG cc_start: 0.8697 (ptp90) cc_final: 0.8050 (mtp180) REVERT: C 798 MET cc_start: 0.5191 (ptt) cc_final: 0.4942 (ptt) REVERT: C 800 TYR cc_start: 0.7922 (p90) cc_final: 0.7660 (p90) REVERT: C 916 PHE cc_start: 0.8728 (m-80) cc_final: 0.8422 (m-80) REVERT: C 968 MET cc_start: 0.8911 (tpt) cc_final: 0.8666 (tpp) REVERT: C 977 MET cc_start: 0.9171 (mmm) cc_final: 0.8966 (mmm) REVERT: C 988 ASP cc_start: 0.8510 (t0) cc_final: 0.8085 (t0) REVERT: C 1015 GLN cc_start: 0.8050 (tp40) cc_final: 0.7458 (tp40) REVERT: C 1079 CYS cc_start: 0.5500 (OUTLIER) cc_final: 0.4774 (p) REVERT: C 1104 TYR cc_start: 0.8769 (t80) cc_final: 0.8412 (t80) REVERT: C 1123 ASN cc_start: 0.9082 (OUTLIER) cc_final: 0.8676 (p0) REVERT: C 1165 GLU cc_start: 0.9240 (tp30) cc_final: 0.9014 (tp30) REVERT: C 1205 GLU cc_start: 0.8660 (pm20) cc_final: 0.8227 (pm20) REVERT: C 1207 GLU cc_start: 0.9108 (tt0) cc_final: 0.8756 (tp30) REVERT: C 1254 THR cc_start: 0.9222 (m) cc_final: 0.8915 (p) REVERT: C 1258 LEU cc_start: 0.9289 (mp) cc_final: 0.9075 (mp) REVERT: D 98 GLU cc_start: 0.8822 (tt0) cc_final: 0.8431 (tp30) REVERT: D 151 MET cc_start: 0.7809 (mtm) cc_final: 0.7479 (mpp) REVERT: D 203 TYR cc_start: 0.7623 (m-80) cc_final: 0.6320 (m-80) REVERT: D 368 GLN cc_start: 0.8875 (pt0) cc_final: 0.8381 (mp10) REVERT: D 462 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.7727 (pp20) REVERT: D 500 MET cc_start: 0.5495 (mtt) cc_final: 0.5177 (mtt) REVERT: D 561 GLU cc_start: 0.8361 (tp30) cc_final: 0.7968 (tp30) REVERT: D 637 GLN cc_start: 0.7731 (OUTLIER) cc_final: 0.7470 (pp30) REVERT: D 669 PHE cc_start: 0.8726 (m-80) cc_final: 0.8037 (m-80) REVERT: D 671 GLU cc_start: 0.8791 (tt0) cc_final: 0.8314 (mm-30) REVERT: D 673 MET cc_start: 0.9098 (tpp) cc_final: 0.8572 (tpp) REVERT: D 682 LYS cc_start: 0.8543 (mttt) cc_final: 0.8336 (mmtp) REVERT: D 739 TRP cc_start: 0.8100 (t60) cc_final: 0.7508 (t60) REVERT: D 766 LYS cc_start: 0.8158 (mmtt) cc_final: 0.7815 (mmtm) REVERT: D 913 GLU cc_start: 0.8607 (pp20) cc_final: 0.8243 (pp20) REVERT: D 965 LEU cc_start: 0.8966 (tp) cc_final: 0.8712 (mt) REVERT: D 976 ASN cc_start: 0.9415 (t0) cc_final: 0.9033 (t0) REVERT: D 977 MET cc_start: 0.9569 (mmm) cc_final: 0.9261 (mmm) REVERT: D 1089 ASN cc_start: 0.9095 (p0) cc_final: 0.8634 (p0) REVERT: D 1133 LYS cc_start: 0.9301 (ttmt) cc_final: 0.8858 (tppt) REVERT: D 1183 TRP cc_start: 0.8990 (OUTLIER) cc_final: 0.8006 (m100) REVERT: D 1208 MET cc_start: 0.9291 (OUTLIER) cc_final: 0.8789 (ppp) REVERT: D 1243 ASN cc_start: 0.9425 (t0) cc_final: 0.9147 (t0) REVERT: D 1245 GLN cc_start: 0.9194 (tm-30) cc_final: 0.8816 (tm-30) REVERT: D 1269 PHE cc_start: 0.8673 (t80) cc_final: 0.7829 (t80) REVERT: D 1331 ASN cc_start: 0.6886 (OUTLIER) cc_final: 0.6100 (m-40) outliers start: 295 outliers final: 216 residues processed: 880 average time/residue: 0.4650 time to fit residues: 695.3541 Evaluate side-chains 870 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 241 poor density : 629 time to evaluate : 4.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 TYR Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 89 PHE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 345 ARG Chi-restraints excluded: chain A residue 392 ASN Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 434 TYR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 619 TYR Chi-restraints excluded: chain A residue 626 ASP Chi-restraints excluded: chain A residue 635 ASN Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 656 THR Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 787 ARG Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 856 VAL Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 878 GLU Chi-restraints excluded: chain A residue 933 LEU Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1024 SER Chi-restraints excluded: chain A residue 1055 TYR Chi-restraints excluded: chain A residue 1064 THR Chi-restraints excluded: chain A residue 1065 GLN Chi-restraints excluded: chain A residue 1076 ASP Chi-restraints excluded: chain A residue 1082 SER Chi-restraints excluded: chain A residue 1101 LEU Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1115 THR Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1123 ASN Chi-restraints excluded: chain A residue 1129 GLU Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1214 LEU Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1218 THR Chi-restraints excluded: chain A residue 1224 THR Chi-restraints excluded: chain A residue 1249 SER Chi-restraints excluded: chain A residue 1251 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 89 PHE Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 173 ASN Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 246 MET Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 286 PHE Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 407 PHE Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 458 PHE Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 637 GLN Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 732 ARG Chi-restraints excluded: chain B residue 758 VAL Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 787 ARG Chi-restraints excluded: chain B residue 793 PHE Chi-restraints excluded: chain B residue 797 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 831 SER Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 872 VAL Chi-restraints excluded: chain B residue 964 ASN Chi-restraints excluded: chain B residue 1041 LEU Chi-restraints excluded: chain B residue 1046 LEU Chi-restraints excluded: chain B residue 1059 ASP Chi-restraints excluded: chain B residue 1080 PHE Chi-restraints excluded: chain B residue 1087 LEU Chi-restraints excluded: chain B residue 1091 ILE Chi-restraints excluded: chain B residue 1115 THR Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1127 CYS Chi-restraints excluded: chain B residue 1144 VAL Chi-restraints excluded: chain B residue 1217 LEU Chi-restraints excluded: chain B residue 1218 THR Chi-restraints excluded: chain B residue 1224 THR Chi-restraints excluded: chain B residue 1227 ASP Chi-restraints excluded: chain B residue 1234 ILE Chi-restraints excluded: chain B residue 1243 ASN Chi-restraints excluded: chain B residue 1251 THR Chi-restraints excluded: chain C residue 31 TYR Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 89 PHE Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 272 TYR Chi-restraints excluded: chain C residue 286 PHE Chi-restraints excluded: chain C residue 310 GLN Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 366 PHE Chi-restraints excluded: chain C residue 371 LEU Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 534 ILE Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain C residue 680 ASN Chi-restraints excluded: chain C residue 742 ASP Chi-restraints excluded: chain C residue 751 VAL Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 899 VAL Chi-restraints excluded: chain C residue 930 GLU Chi-restraints excluded: chain C residue 1041 LEU Chi-restraints excluded: chain C residue 1055 TYR Chi-restraints excluded: chain C residue 1079 CYS Chi-restraints excluded: chain C residue 1101 LEU Chi-restraints excluded: chain C residue 1112 ILE Chi-restraints excluded: chain C residue 1123 ASN Chi-restraints excluded: chain C residue 1127 CYS Chi-restraints excluded: chain C residue 1144 VAL Chi-restraints excluded: chain C residue 1206 VAL Chi-restraints excluded: chain C residue 1218 THR Chi-restraints excluded: chain C residue 1224 THR Chi-restraints excluded: chain C residue 1227 ASP Chi-restraints excluded: chain C residue 1239 THR Chi-restraints excluded: chain C residue 1251 THR Chi-restraints excluded: chain C residue 1253 ASP Chi-restraints excluded: chain C residue 1270 THR Chi-restraints excluded: chain C residue 1311 GLU Chi-restraints excluded: chain C residue 1316 VAL Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 173 ASN Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 286 PHE Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 372 VAL Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain D residue 409 ILE Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain D residue 458 PHE Chi-restraints excluded: chain D residue 462 GLU Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 486 THR Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 519 ASP Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 548 THR Chi-restraints excluded: chain D residue 563 CYS Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 637 GLN Chi-restraints excluded: chain D residue 643 ILE Chi-restraints excluded: chain D residue 648 VAL Chi-restraints excluded: chain D residue 658 VAL Chi-restraints excluded: chain D residue 751 VAL Chi-restraints excluded: chain D residue 771 CYS Chi-restraints excluded: chain D residue 783 THR Chi-restraints excluded: chain D residue 792 PHE Chi-restraints excluded: chain D residue 821 CYS Chi-restraints excluded: chain D residue 868 VAL Chi-restraints excluded: chain D residue 887 VAL Chi-restraints excluded: chain D residue 957 SER Chi-restraints excluded: chain D residue 1021 TYR Chi-restraints excluded: chain D residue 1026 SER Chi-restraints excluded: chain D residue 1041 LEU Chi-restraints excluded: chain D residue 1080 PHE Chi-restraints excluded: chain D residue 1101 LEU Chi-restraints excluded: chain D residue 1115 THR Chi-restraints excluded: chain D residue 1183 TRP Chi-restraints excluded: chain D residue 1208 MET Chi-restraints excluded: chain D residue 1224 THR Chi-restraints excluded: chain D residue 1234 ILE Chi-restraints excluded: chain D residue 1250 SER Chi-restraints excluded: chain D residue 1270 THR Chi-restraints excluded: chain D residue 1305 LEU Chi-restraints excluded: chain D residue 1331 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 475 optimal weight: 0.7980 chunk 55 optimal weight: 0.0040 chunk 281 optimal weight: 9.9990 chunk 360 optimal weight: 1.9990 chunk 279 optimal weight: 6.9990 chunk 415 optimal weight: 3.9990 chunk 275 optimal weight: 5.9990 chunk 491 optimal weight: 8.9990 chunk 307 optimal weight: 10.0000 chunk 299 optimal weight: 8.9990 chunk 226 optimal weight: 4.9990 overall best weight: 2.3598 ------------------------------------------------------------------------------- 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 208 GLN ** A 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 938 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 964 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 995 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1015 GLN ** A1038 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1065 GLN A1179 ASN ** A1187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 827 GLN ** B 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1072 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 106 GLN ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 310 GLN ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 680 ASN ** C 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 637 GLN ** D 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 938 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.4802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 41420 Z= 0.259 Angle : 0.817 13.572 56270 Z= 0.398 Chirality : 0.051 0.420 6514 Planarity : 0.005 0.074 7202 Dihedral : 8.081 59.979 6312 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 26.38 Ramachandran Plot: Outliers : 0.10 % Allowed : 11.74 % Favored : 88.16 % Rotamer: Outliers : 5.86 % Allowed : 26.53 % Favored : 67.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.38 % Twisted General : 0.02 % 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: -3.73 (0.11), residues: 5110 helix: -0.53 (0.17), residues: 800 sheet: -2.44 (0.12), residues: 1476 loop : -3.19 (0.11), residues: 2834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP B 739 HIS 0.008 0.001 HIS B 460 PHE 0.036 0.002 PHE D 290 TYR 0.031 0.002 TYR D 256 ARG 0.014 0.001 ARG A 360 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10220 Ramachandran restraints generated. 5110 Oldfield, 0 Emsley, 5110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10220 Ramachandran restraints generated. 5110 Oldfield, 0 Emsley, 5110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 934 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 262 poor density : 672 time to evaluate : 4.064 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: A 151 MET cc_start: 0.5804 (tpp) cc_final: 0.5527 (tpp) REVERT: A 183 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.6669 (mt) REVERT: A 272 TYR cc_start: 0.3803 (OUTLIER) cc_final: 0.2820 (t80) REVERT: A 290 PHE cc_start: 0.7983 (m-80) cc_final: 0.7429 (m-80) REVERT: A 318 MET cc_start: 0.8922 (tpp) cc_final: 0.8440 (tpp) REVERT: A 360 ARG cc_start: 0.8207 (tpt170) cc_final: 0.7991 (tpt170) REVERT: A 458 PHE cc_start: 0.7743 (OUTLIER) cc_final: 0.7403 (p90) REVERT: A 460 HIS cc_start: 0.8546 (t-90) cc_final: 0.8140 (t-90) REVERT: A 543 TYR cc_start: 0.7722 (p90) cc_final: 0.6997 (p90) REVERT: A 572 PHE cc_start: 0.8333 (p90) cc_final: 0.8021 (p90) REVERT: A 602 GLN cc_start: 0.7044 (tm-30) cc_final: 0.6519 (pt0) REVERT: A 612 GLU cc_start: 0.8158 (tt0) cc_final: 0.7770 (tt0) REVERT: A 627 LEU cc_start: 0.8770 (tp) cc_final: 0.8356 (tt) REVERT: A 635 ASN cc_start: 0.8622 (OUTLIER) cc_final: 0.8256 (p0) REVERT: A 669 PHE cc_start: 0.8690 (m-80) cc_final: 0.8338 (m-80) REVERT: A 671 GLU cc_start: 0.8814 (tt0) cc_final: 0.8503 (tt0) REVERT: A 682 LYS cc_start: 0.8739 (mttt) cc_final: 0.8313 (mmmt) REVERT: A 783 THR cc_start: 0.9008 (OUTLIER) cc_final: 0.8799 (t) REVERT: A 793 PHE cc_start: 0.8866 (p90) cc_final: 0.8570 (p90) REVERT: A 829 GLU cc_start: 0.8576 (tp30) cc_final: 0.7797 (mp0) REVERT: A 964 ASN cc_start: 0.8647 (t0) cc_final: 0.8405 (t0) REVERT: A 968 MET cc_start: 0.8864 (tpp) cc_final: 0.8600 (tpp) REVERT: A 975 GLN cc_start: 0.8507 (mm-40) cc_final: 0.7859 (tm-30) REVERT: A 977 MET cc_start: 0.9299 (mmm) cc_final: 0.8855 (mmm) REVERT: A 985 TYR cc_start: 0.7087 (m-10) cc_final: 0.6878 (m-10) REVERT: A 1007 TYR cc_start: 0.8445 (m-10) cc_final: 0.8241 (m-80) REVERT: A 1017 ASN cc_start: 0.9008 (m-40) cc_final: 0.8549 (m110) REVERT: A 1065 GLN cc_start: 0.9128 (OUTLIER) cc_final: 0.8840 (mm-40) REVERT: A 1080 PHE cc_start: 0.7993 (m-80) cc_final: 0.7590 (m-10) REVERT: A 1087 LEU cc_start: 0.9545 (tt) cc_final: 0.9237 (mt) REVERT: A 1098 GLU cc_start: 0.8486 (pm20) cc_final: 0.8180 (mm-30) REVERT: A 1110 LEU cc_start: 0.9342 (mt) cc_final: 0.9031 (tp) REVERT: A 1111 GLU cc_start: 0.8664 (mm-30) cc_final: 0.8399 (mm-30) REVERT: A 1208 MET cc_start: 0.9433 (ppp) cc_final: 0.8987 (ppp) REVERT: A 1217 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.9050 (mm) REVERT: B 78 GLU cc_start: 0.8551 (pt0) cc_final: 0.7972 (pm20) REVERT: B 98 GLU cc_start: 0.8576 (tt0) cc_final: 0.8177 (tm-30) REVERT: B 121 MET cc_start: 0.7978 (tpp) cc_final: 0.7706 (tpp) REVERT: B 208 GLN cc_start: 0.8426 (tt0) cc_final: 0.7881 (tp40) REVERT: B 318 MET cc_start: 0.8553 (mtt) cc_final: 0.7838 (mmm) REVERT: B 342 GLU cc_start: 0.8739 (tp30) cc_final: 0.8459 (tp30) REVERT: B 393 TYR cc_start: 0.8752 (t80) cc_final: 0.8426 (t80) REVERT: B 460 HIS cc_start: 0.8706 (t-90) cc_final: 0.8038 (m-70) REVERT: B 461 LEU cc_start: 0.9181 (mp) cc_final: 0.8823 (mp) REVERT: B 500 MET cc_start: 0.5482 (mmm) cc_final: 0.5257 (mmm) REVERT: B 649 TYR cc_start: 0.7757 (m-80) cc_final: 0.7349 (m-80) REVERT: B 688 MET cc_start: 0.8550 (ppp) cc_final: 0.8129 (ppp) REVERT: B 798 MET cc_start: 0.8678 (ptt) cc_final: 0.8194 (ptm) REVERT: B 858 TRP cc_start: 0.7183 (m-90) cc_final: 0.6719 (m-90) REVERT: B 863 LYS cc_start: 0.8781 (ttpt) cc_final: 0.8533 (ttpt) REVERT: B 880 GLN cc_start: 0.8051 (OUTLIER) cc_final: 0.7621 (pm20) REVERT: B 976 ASN cc_start: 0.9214 (t0) cc_final: 0.8971 (t0) REVERT: B 977 MET cc_start: 0.9179 (mmm) cc_final: 0.8891 (mmm) REVERT: B 1010 THR cc_start: 0.8586 (m) cc_final: 0.8318 (p) REVERT: B 1013 GLN cc_start: 0.9053 (mm-40) cc_final: 0.8320 (mm-40) REVERT: B 1059 ASP cc_start: 0.7382 (OUTLIER) cc_final: 0.6931 (p0) REVERT: B 1076 ASP cc_start: 0.8282 (p0) cc_final: 0.7895 (p0) REVERT: B 1098 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7792 (tp30) REVERT: B 1123 ASN cc_start: 0.9437 (m110) cc_final: 0.9126 (m110) REVERT: B 1129 GLU cc_start: 0.9230 (mt-10) cc_final: 0.8933 (mp0) REVERT: B 1183 TRP cc_start: 0.8960 (m-90) cc_final: 0.8632 (m-90) REVERT: B 1217 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8810 (mm) REVERT: B 1325 GLN cc_start: 0.8307 (tt0) cc_final: 0.7945 (tp40) REVERT: B 1330 TYR cc_start: 0.8905 (p90) cc_final: 0.8557 (p90) REVERT: C 65 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7381 (mm-30) REVERT: C 121 MET cc_start: 0.6850 (tpp) cc_final: 0.6521 (tmm) REVERT: C 151 MET cc_start: 0.7515 (tpp) cc_final: 0.7226 (tpp) REVERT: C 154 ASN cc_start: 0.9063 (OUTLIER) cc_final: 0.8502 (p0) REVERT: C 189 GLN cc_start: 0.8790 (pm20) cc_final: 0.8360 (pp30) REVERT: C 272 TYR cc_start: 0.4502 (OUTLIER) cc_final: 0.3690 (t80) REVERT: C 310 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.8138 (pm20) REVERT: C 436 TRP cc_start: 0.7881 (t-100) cc_final: 0.7517 (t-100) REVERT: C 458 PHE cc_start: 0.8425 (p90) cc_final: 0.7471 (p90) REVERT: C 481 ILE cc_start: 0.8940 (mp) cc_final: 0.8592 (mp) REVERT: C 499 ILE cc_start: 0.7555 (mp) cc_final: 0.7312 (tp) REVERT: C 598 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7645 (ttt90) REVERT: C 625 LYS cc_start: 0.8731 (mtpt) cc_final: 0.8421 (mttt) REVERT: C 635 ASN cc_start: 0.8573 (p0) cc_final: 0.8108 (p0) REVERT: C 666 MET cc_start: 0.8528 (tpt) cc_final: 0.8201 (mmm) REVERT: C 669 PHE cc_start: 0.8771 (m-10) cc_final: 0.8197 (m-80) REVERT: C 671 GLU cc_start: 0.9129 (tt0) cc_final: 0.8780 (mt-10) REVERT: C 737 GLU cc_start: 0.8296 (mp0) cc_final: 0.7710 (mp0) REVERT: C 751 VAL cc_start: 0.8119 (OUTLIER) cc_final: 0.7913 (p) REVERT: C 798 MET cc_start: 0.4959 (ptt) cc_final: 0.4671 (ptt) REVERT: C 916 PHE cc_start: 0.8737 (m-80) cc_final: 0.8428 (m-80) REVERT: C 977 MET cc_start: 0.9117 (mmm) cc_final: 0.8905 (mmm) REVERT: C 988 ASP cc_start: 0.8394 (t0) cc_final: 0.8081 (t70) REVERT: C 1015 GLN cc_start: 0.8055 (tp40) cc_final: 0.7471 (tp40) REVERT: C 1079 CYS cc_start: 0.5373 (OUTLIER) cc_final: 0.4504 (p) REVERT: C 1104 TYR cc_start: 0.8796 (t80) cc_final: 0.8432 (t80) REVERT: C 1123 ASN cc_start: 0.9009 (OUTLIER) cc_final: 0.8590 (p0) REVERT: C 1129 GLU cc_start: 0.9458 (pt0) cc_final: 0.9161 (pp20) REVERT: C 1203 SER cc_start: 0.9224 (OUTLIER) cc_final: 0.8961 (p) REVERT: C 1207 GLU cc_start: 0.9009 (tt0) cc_final: 0.8755 (tp30) REVERT: C 1254 THR cc_start: 0.9200 (m) cc_final: 0.8871 (p) REVERT: C 1258 LEU cc_start: 0.9237 (mp) cc_final: 0.8985 (mp) REVERT: D 98 GLU cc_start: 0.8802 (tt0) cc_final: 0.8386 (tp30) REVERT: D 151 MET cc_start: 0.7833 (mtm) cc_final: 0.7508 (mpp) REVERT: D 203 TYR cc_start: 0.7484 (m-80) cc_final: 0.6248 (m-80) REVERT: D 368 GLN cc_start: 0.8892 (pt0) cc_final: 0.8453 (mp10) REVERT: D 462 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.7764 (pp20) REVERT: D 500 MET cc_start: 0.5341 (mtt) cc_final: 0.5027 (mtt) REVERT: D 542 ILE cc_start: 0.8531 (tt) cc_final: 0.8123 (mp) REVERT: D 561 GLU cc_start: 0.8244 (tp30) cc_final: 0.7884 (tp30) REVERT: D 637 GLN cc_start: 0.7854 (OUTLIER) cc_final: 0.7532 (pp30) REVERT: D 669 PHE cc_start: 0.8629 (m-80) cc_final: 0.7963 (m-80) REVERT: D 671 GLU cc_start: 0.8733 (tt0) cc_final: 0.8313 (mm-30) REVERT: D 673 MET cc_start: 0.9014 (tpp) cc_final: 0.8493 (tpp) REVERT: D 682 LYS cc_start: 0.8488 (mttt) cc_final: 0.8269 (mmtp) REVERT: D 766 LYS cc_start: 0.8140 (mmtt) cc_final: 0.7772 (mmtm) REVERT: D 912 LYS cc_start: 0.8175 (ptpp) cc_final: 0.7621 (ptpp) REVERT: D 913 GLU cc_start: 0.8531 (pp20) cc_final: 0.8150 (pp20) REVERT: D 965 LEU cc_start: 0.8953 (tp) cc_final: 0.8638 (mp) REVERT: D 976 ASN cc_start: 0.9399 (t0) cc_final: 0.9080 (t0) REVERT: D 977 MET cc_start: 0.9501 (mmm) cc_final: 0.9221 (mmm) REVERT: D 1089 ASN cc_start: 0.9056 (p0) cc_final: 0.8558 (p0) REVERT: D 1133 LYS cc_start: 0.9296 (ttmt) cc_final: 0.8859 (tppt) REVERT: D 1154 PHE cc_start: 0.8928 (m-80) cc_final: 0.8352 (m-80) REVERT: D 1183 TRP cc_start: 0.8969 (OUTLIER) cc_final: 0.8624 (m100) REVERT: D 1208 MET cc_start: 0.9233 (OUTLIER) cc_final: 0.8713 (ppp) REVERT: D 1243 ASN cc_start: 0.9414 (t0) cc_final: 0.9099 (t0) REVERT: D 1245 GLN cc_start: 0.9205 (tm-30) cc_final: 0.8714 (tm-30) REVERT: D 1269 PHE cc_start: 0.8645 (t80) cc_final: 0.7862 (t80) REVERT: D 1331 ASN cc_start: 0.6851 (OUTLIER) cc_final: 0.6016 (m-40) outliers start: 262 outliers final: 197 residues processed: 861 average time/residue: 0.4630 time to fit residues: 677.5065 Evaluate side-chains 863 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 643 time to evaluate : 4.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 TYR Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 272 TYR Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 345 ARG Chi-restraints excluded: chain A residue 352 PHE Chi-restraints excluded: chain A residue 365 PHE Chi-restraints excluded: chain A residue 392 ASN Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 619 TYR Chi-restraints excluded: chain A residue 626 ASP Chi-restraints excluded: chain A residue 635 ASN Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 656 THR Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 878 GLU Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1024 SER Chi-restraints excluded: chain A residue 1055 TYR Chi-restraints excluded: chain A residue 1065 GLN Chi-restraints excluded: chain A residue 1076 ASP Chi-restraints excluded: chain A residue 1082 SER Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1115 THR Chi-restraints excluded: chain A residue 1129 GLU Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1214 LEU Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1224 THR Chi-restraints excluded: chain A residue 1249 SER Chi-restraints excluded: chain A residue 1251 THR Chi-restraints excluded: chain A residue 1253 ASP Chi-restraints excluded: chain A residue 1333 LEU Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 89 PHE Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 173 ASN Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 286 PHE Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 407 PHE Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 458 PHE Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 643 ILE Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 732 ARG Chi-restraints excluded: chain B residue 758 VAL Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 787 ARG Chi-restraints excluded: chain B residue 793 PHE Chi-restraints excluded: chain B residue 797 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 831 SER Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 872 VAL Chi-restraints excluded: chain B residue 880 GLN Chi-restraints excluded: chain B residue 1046 LEU Chi-restraints excluded: chain B residue 1059 ASP Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain B residue 1080 PHE Chi-restraints excluded: chain B residue 1091 ILE Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1127 CYS Chi-restraints excluded: chain B residue 1144 VAL Chi-restraints excluded: chain B residue 1217 LEU Chi-restraints excluded: chain B residue 1218 THR Chi-restraints excluded: chain B residue 1234 ILE Chi-restraints excluded: chain B residue 1243 ASN Chi-restraints excluded: chain B residue 1251 THR Chi-restraints excluded: chain C residue 31 TYR Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 272 TYR Chi-restraints excluded: chain C residue 286 PHE Chi-restraints excluded: chain C residue 310 GLN Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 366 PHE Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 421 VAL Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 534 ILE Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain C residue 598 ARG Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 607 MET Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain C residue 742 ASP Chi-restraints excluded: chain C residue 751 VAL Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 899 VAL Chi-restraints excluded: chain C residue 914 THR Chi-restraints excluded: chain C residue 930 GLU Chi-restraints excluded: chain C residue 1003 LYS Chi-restraints excluded: chain C residue 1055 TYR Chi-restraints excluded: chain C residue 1079 CYS Chi-restraints excluded: chain C residue 1112 ILE Chi-restraints excluded: chain C residue 1123 ASN Chi-restraints excluded: chain C residue 1127 CYS Chi-restraints excluded: chain C residue 1144 VAL Chi-restraints excluded: chain C residue 1203 SER Chi-restraints excluded: chain C residue 1206 VAL Chi-restraints excluded: chain C residue 1218 THR Chi-restraints excluded: chain C residue 1227 ASP Chi-restraints excluded: chain C residue 1239 THR Chi-restraints excluded: chain C residue 1251 THR Chi-restraints excluded: chain C residue 1253 ASP Chi-restraints excluded: chain C residue 1270 THR Chi-restraints excluded: chain C residue 1311 GLU Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 173 ASN Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 286 PHE Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 372 VAL Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 405 VAL Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain D residue 458 PHE Chi-restraints excluded: chain D residue 462 GLU Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 486 THR Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 519 ASP Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 548 THR Chi-restraints excluded: chain D residue 560 VAL Chi-restraints excluded: chain D residue 563 CYS Chi-restraints excluded: chain D residue 637 GLN Chi-restraints excluded: chain D residue 643 ILE Chi-restraints excluded: chain D residue 658 VAL Chi-restraints excluded: chain D residue 751 VAL Chi-restraints excluded: chain D residue 761 THR Chi-restraints excluded: chain D residue 771 CYS Chi-restraints excluded: chain D residue 783 THR Chi-restraints excluded: chain D residue 792 PHE Chi-restraints excluded: chain D residue 821 CYS Chi-restraints excluded: chain D residue 849 CYS Chi-restraints excluded: chain D residue 861 THR Chi-restraints excluded: chain D residue 868 VAL Chi-restraints excluded: chain D residue 887 VAL Chi-restraints excluded: chain D residue 1080 PHE Chi-restraints excluded: chain D residue 1115 THR Chi-restraints excluded: chain D residue 1183 TRP Chi-restraints excluded: chain D residue 1208 MET Chi-restraints excluded: chain D residue 1224 THR Chi-restraints excluded: chain D residue 1234 ILE Chi-restraints excluded: chain D residue 1250 SER Chi-restraints excluded: chain D residue 1251 THR Chi-restraints excluded: chain D residue 1270 THR Chi-restraints excluded: chain D residue 1305 LEU Chi-restraints excluded: chain D residue 1331 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 304 optimal weight: 8.9990 chunk 196 optimal weight: 0.9980 chunk 293 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 312 optimal weight: 4.9990 chunk 334 optimal weight: 7.9990 chunk 243 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 386 optimal weight: 6.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 208 GLN ** A 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 938 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 964 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 995 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1038 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1065 GLN ** A1187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 310 GLN ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 637 GLN ** D 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 938 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 983 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.5021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 41420 Z= 0.231 Angle : 0.798 14.039 56270 Z= 0.385 Chirality : 0.050 0.542 6514 Planarity : 0.005 0.068 7202 Dihedral : 7.850 59.854 6312 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 24.01 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.27 % Favored : 88.67 % Rotamer: Outliers : 5.28 % Allowed : 27.63 % Favored : 67.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.38 % 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: -3.58 (0.11), residues: 5110 helix: -0.33 (0.17), residues: 792 sheet: -2.31 (0.12), residues: 1510 loop : -3.12 (0.11), residues: 2808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 739 HIS 0.007 0.001 HIS B 460 PHE 0.026 0.002 PHE D 290 TYR 0.025 0.002 TYR D 256 ARG 0.007 0.000 ARG A 360 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10220 Ramachandran restraints generated. 5110 Oldfield, 0 Emsley, 5110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10220 Ramachandran restraints generated. 5110 Oldfield, 0 Emsley, 5110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 932 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 696 time to evaluate : 4.608 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: A 151 MET cc_start: 0.5982 (tpp) cc_final: 0.5270 (tpp) REVERT: A 183 LEU cc_start: 0.7337 (OUTLIER) cc_final: 0.6400 (mt) REVERT: A 272 TYR cc_start: 0.3915 (OUTLIER) cc_final: 0.2906 (t80) REVERT: A 290 PHE cc_start: 0.7894 (m-80) cc_final: 0.7584 (m-80) REVERT: A 318 MET cc_start: 0.8907 (tpp) cc_final: 0.8444 (tpp) REVERT: A 356 ASP cc_start: 0.8517 (t0) cc_final: 0.8199 (t0) REVERT: A 368 GLN cc_start: 0.8176 (tt0) cc_final: 0.7713 (tm-30) REVERT: A 436 TRP cc_start: 0.6922 (t-100) cc_final: 0.6627 (t-100) REVERT: A 543 TYR cc_start: 0.7542 (p90) cc_final: 0.6840 (p90) REVERT: A 572 PHE cc_start: 0.8310 (p90) cc_final: 0.8025 (p90) REVERT: A 602 GLN cc_start: 0.6947 (tm-30) cc_final: 0.6570 (pt0) REVERT: A 627 LEU cc_start: 0.8785 (tp) cc_final: 0.8378 (tt) REVERT: A 635 ASN cc_start: 0.8657 (OUTLIER) cc_final: 0.8294 (p0) REVERT: A 666 MET cc_start: 0.8017 (tpt) cc_final: 0.7501 (tpt) REVERT: A 669 PHE cc_start: 0.8658 (m-80) cc_final: 0.8275 (m-80) REVERT: A 671 GLU cc_start: 0.8713 (tt0) cc_final: 0.8274 (mt-10) REVERT: A 682 LYS cc_start: 0.8725 (mttt) cc_final: 0.8265 (mmmt) REVERT: A 793 PHE cc_start: 0.8862 (p90) cc_final: 0.8659 (p90) REVERT: A 829 GLU cc_start: 0.8621 (tp30) cc_final: 0.7781 (mp0) REVERT: A 964 ASN cc_start: 0.8644 (t0) cc_final: 0.8419 (t0) REVERT: A 975 GLN cc_start: 0.8510 (mm-40) cc_final: 0.7997 (mt0) REVERT: A 977 MET cc_start: 0.9234 (mmm) cc_final: 0.8795 (mmm) REVERT: A 985 TYR cc_start: 0.7037 (m-10) cc_final: 0.6833 (m-10) REVERT: A 1017 ASN cc_start: 0.9015 (m-40) cc_final: 0.8553 (m110) REVERT: A 1080 PHE cc_start: 0.8038 (m-80) cc_final: 0.7618 (m-10) REVERT: A 1087 LEU cc_start: 0.9534 (tt) cc_final: 0.9231 (mt) REVERT: A 1098 GLU cc_start: 0.8386 (pm20) cc_final: 0.8169 (mm-30) REVERT: A 1110 LEU cc_start: 0.9320 (mt) cc_final: 0.9016 (tp) REVERT: A 1111 GLU cc_start: 0.8659 (mm-30) cc_final: 0.8379 (mm-30) REVERT: A 1147 LYS cc_start: 0.9168 (mttp) cc_final: 0.8468 (mttp) REVERT: A 1208 MET cc_start: 0.9402 (ppp) cc_final: 0.8913 (ppp) REVERT: A 1217 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.9054 (mm) REVERT: B 78 GLU cc_start: 0.8545 (pt0) cc_final: 0.7968 (pm20) REVERT: B 98 GLU cc_start: 0.8546 (tt0) cc_final: 0.8031 (tm-30) REVERT: B 121 MET cc_start: 0.7970 (tpp) cc_final: 0.7751 (tpp) REVERT: B 208 GLN cc_start: 0.8391 (tt0) cc_final: 0.7876 (tp-100) REVERT: B 246 MET cc_start: 0.6712 (OUTLIER) cc_final: 0.6510 (ppp) REVERT: B 318 MET cc_start: 0.8518 (mtt) cc_final: 0.7813 (mmm) REVERT: B 342 GLU cc_start: 0.8652 (tp30) cc_final: 0.8365 (tp30) REVERT: B 393 TYR cc_start: 0.8762 (t80) cc_final: 0.8408 (t80) REVERT: B 460 HIS cc_start: 0.8757 (t-90) cc_final: 0.8106 (m-70) REVERT: B 461 LEU cc_start: 0.9159 (mp) cc_final: 0.8495 (mp) REVERT: B 542 ILE cc_start: 0.8359 (tp) cc_final: 0.7791 (mp) REVERT: B 562 ASN cc_start: 0.7948 (m-40) cc_final: 0.7484 (m-40) REVERT: B 567 LYS cc_start: 0.9260 (tppt) cc_final: 0.9048 (mmpt) REVERT: B 649 TYR cc_start: 0.7855 (m-80) cc_final: 0.7387 (m-80) REVERT: B 688 MET cc_start: 0.8540 (ppp) cc_final: 0.8122 (ppp) REVERT: B 739 TRP cc_start: 0.6383 (t60) cc_final: 0.6126 (t60) REVERT: B 798 MET cc_start: 0.8737 (ptt) cc_final: 0.8317 (ptm) REVERT: B 858 TRP cc_start: 0.7199 (m-90) cc_final: 0.6740 (m-90) REVERT: B 863 LYS cc_start: 0.8770 (ttpt) cc_final: 0.8528 (ttpt) REVERT: B 880 GLN cc_start: 0.8006 (OUTLIER) cc_final: 0.7565 (pm20) REVERT: B 976 ASN cc_start: 0.9168 (t0) cc_final: 0.8965 (t0) REVERT: B 977 MET cc_start: 0.9166 (mmm) cc_final: 0.8876 (mmm) REVERT: B 1010 THR cc_start: 0.8571 (m) cc_final: 0.8303 (p) REVERT: B 1013 GLN cc_start: 0.9087 (mm-40) cc_final: 0.8403 (mm-40) REVERT: B 1076 ASP cc_start: 0.8262 (p0) cc_final: 0.7866 (p0) REVERT: B 1098 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7880 (tp30) REVERT: B 1123 ASN cc_start: 0.9433 (m110) cc_final: 0.9167 (m110) REVERT: B 1183 TRP cc_start: 0.8914 (m-90) cc_final: 0.8646 (m-90) REVERT: B 1217 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8774 (mm) REVERT: B 1237 TRP cc_start: 0.7344 (t60) cc_final: 0.6981 (t60) REVERT: B 1325 GLN cc_start: 0.8271 (tt0) cc_final: 0.7964 (tp40) REVERT: B 1330 TYR cc_start: 0.8864 (p90) cc_final: 0.8486 (p90) REVERT: C 65 GLU cc_start: 0.7673 (mt-10) cc_final: 0.7335 (mm-30) REVERT: C 76 ASP cc_start: 0.8639 (p0) cc_final: 0.8409 (m-30) REVERT: C 154 ASN cc_start: 0.9014 (OUTLIER) cc_final: 0.8446 (p0) REVERT: C 187 LEU cc_start: 0.8860 (tt) cc_final: 0.8649 (tp) REVERT: C 189 GLN cc_start: 0.8786 (pm20) cc_final: 0.8354 (pp30) REVERT: C 272 TYR cc_start: 0.4510 (OUTLIER) cc_final: 0.3618 (t80) REVERT: C 310 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.7989 (pm20) REVERT: C 436 TRP cc_start: 0.7873 (t-100) cc_final: 0.7496 (t-100) REVERT: C 458 PHE cc_start: 0.8361 (p90) cc_final: 0.7373 (p90) REVERT: C 481 ILE cc_start: 0.8923 (mp) cc_final: 0.8556 (mp) REVERT: C 539 ARG cc_start: 0.8040 (ttm-80) cc_final: 0.7780 (ttm-80) REVERT: C 540 LEU cc_start: 0.8706 (tp) cc_final: 0.8480 (tp) REVERT: C 635 ASN cc_start: 0.8581 (p0) cc_final: 0.8130 (p0) REVERT: C 666 MET cc_start: 0.8394 (tpt) cc_final: 0.7988 (mmm) REVERT: C 669 PHE cc_start: 0.8732 (m-10) cc_final: 0.8100 (m-80) REVERT: C 671 GLU cc_start: 0.9080 (tt0) cc_final: 0.8697 (mt-10) REVERT: C 737 GLU cc_start: 0.8336 (mp0) cc_final: 0.7821 (mp0) REVERT: C 787 ARG cc_start: 0.8686 (ptp90) cc_final: 0.7947 (mtp180) REVERT: C 916 PHE cc_start: 0.8754 (m-80) cc_final: 0.8428 (m-80) REVERT: C 988 ASP cc_start: 0.8377 (t0) cc_final: 0.8094 (t70) REVERT: C 1015 GLN cc_start: 0.8057 (tp40) cc_final: 0.7535 (tp40) REVERT: C 1079 CYS cc_start: 0.5380 (OUTLIER) cc_final: 0.4496 (p) REVERT: C 1089 ASN cc_start: 0.9113 (m-40) cc_final: 0.8524 (p0) REVERT: C 1104 TYR cc_start: 0.8773 (t80) cc_final: 0.8437 (t80) REVERT: C 1123 ASN cc_start: 0.8994 (OUTLIER) cc_final: 0.8581 (p0) REVERT: C 1129 GLU cc_start: 0.9436 (pt0) cc_final: 0.9141 (pp20) REVERT: C 1163 ARG cc_start: 0.8717 (ttt180) cc_final: 0.8486 (tmm-80) REVERT: C 1207 GLU cc_start: 0.9021 (tt0) cc_final: 0.8816 (tp30) REVERT: C 1254 THR cc_start: 0.9192 (m) cc_final: 0.8858 (p) REVERT: C 1258 LEU cc_start: 0.9224 (mp) cc_final: 0.8959 (mp) REVERT: D 151 MET cc_start: 0.7853 (mtm) cc_final: 0.7421 (mpp) REVERT: D 203 TYR cc_start: 0.7421 (m-80) cc_final: 0.6199 (m-80) REVERT: D 368 GLN cc_start: 0.8861 (pt0) cc_final: 0.8421 (mp10) REVERT: D 432 TYR cc_start: 0.7624 (p90) cc_final: 0.6737 (p90) REVERT: D 462 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8088 (pp20) REVERT: D 542 ILE cc_start: 0.8550 (tt) cc_final: 0.8170 (mp) REVERT: D 557 LYS cc_start: 0.8783 (mttp) cc_final: 0.8567 (mmtp) REVERT: D 561 GLU cc_start: 0.8148 (tp30) cc_final: 0.7777 (tp30) REVERT: D 621 LEU cc_start: 0.9312 (mm) cc_final: 0.9062 (mm) REVERT: D 637 GLN cc_start: 0.7862 (OUTLIER) cc_final: 0.7601 (pp30) REVERT: D 669 PHE cc_start: 0.8609 (m-80) cc_final: 0.8002 (m-80) REVERT: D 671 GLU cc_start: 0.8754 (tt0) cc_final: 0.8302 (mm-30) REVERT: D 673 MET cc_start: 0.8964 (tpp) cc_final: 0.8229 (tpp) REVERT: D 766 LYS cc_start: 0.8138 (mmtt) cc_final: 0.7767 (mmtm) REVERT: D 798 MET cc_start: 0.7154 (pmm) cc_final: 0.6791 (pmm) REVERT: D 912 LYS cc_start: 0.8160 (ptpp) cc_final: 0.7707 (ptpp) REVERT: D 913 GLU cc_start: 0.8508 (pp20) cc_final: 0.8142 (pp20) REVERT: D 965 LEU cc_start: 0.8971 (tp) cc_final: 0.8664 (mp) REVERT: D 976 ASN cc_start: 0.9388 (t0) cc_final: 0.9085 (t0) REVERT: D 977 MET cc_start: 0.9488 (mmm) cc_final: 0.9261 (mmm) REVERT: D 996 LEU cc_start: 0.8335 (pt) cc_final: 0.7495 (tp) REVERT: D 1089 ASN cc_start: 0.9101 (p0) cc_final: 0.8580 (p0) REVERT: D 1133 LYS cc_start: 0.9295 (ttmt) cc_final: 0.8907 (tppt) REVERT: D 1154 PHE cc_start: 0.8911 (m-80) cc_final: 0.8291 (m-80) REVERT: D 1183 TRP cc_start: 0.8949 (OUTLIER) cc_final: 0.8692 (m100) REVERT: D 1208 MET cc_start: 0.9176 (OUTLIER) cc_final: 0.8686 (ppp) REVERT: D 1243 ASN cc_start: 0.9416 (t0) cc_final: 0.9104 (t0) REVERT: D 1245 GLN cc_start: 0.9209 (tm-30) cc_final: 0.8718 (tm-30) REVERT: D 1269 PHE cc_start: 0.8653 (t80) cc_final: 0.7833 (t80) outliers start: 236 outliers final: 188 residues processed: 863 average time/residue: 0.4580 time to fit residues: 670.1368 Evaluate side-chains 857 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 653 time to evaluate : 4.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 TYR Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 89 PHE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 272 TYR Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 345 ARG Chi-restraints excluded: chain A residue 392 ASN Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 619 TYR Chi-restraints excluded: chain A residue 635 ASN Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 656 THR Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 787 ARG Chi-restraints excluded: chain A residue 856 VAL Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 878 GLU Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1024 SER Chi-restraints excluded: chain A residue 1055 TYR Chi-restraints excluded: chain A residue 1065 GLN Chi-restraints excluded: chain A residue 1076 ASP Chi-restraints excluded: chain A residue 1101 LEU Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1129 GLU Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1214 LEU Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1224 THR Chi-restraints excluded: chain A residue 1251 THR Chi-restraints excluded: chain A residue 1253 ASP Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 89 PHE Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 173 ASN Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 246 MET Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 286 PHE Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 407 PHE Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 458 PHE Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 643 ILE Chi-restraints excluded: chain B residue 732 ARG Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 793 PHE Chi-restraints excluded: chain B residue 797 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 872 VAL Chi-restraints excluded: chain B residue 880 GLN Chi-restraints excluded: chain B residue 1046 LEU Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain B residue 1080 PHE Chi-restraints excluded: chain B residue 1091 ILE Chi-restraints excluded: chain B residue 1115 THR Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1127 CYS Chi-restraints excluded: chain B residue 1144 VAL Chi-restraints excluded: chain B residue 1217 LEU Chi-restraints excluded: chain B residue 1218 THR Chi-restraints excluded: chain B residue 1227 ASP Chi-restraints excluded: chain B residue 1234 ILE Chi-restraints excluded: chain B residue 1243 ASN Chi-restraints excluded: chain B residue 1251 THR Chi-restraints excluded: chain C residue 31 TYR Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 272 TYR Chi-restraints excluded: chain C residue 286 PHE Chi-restraints excluded: chain C residue 310 GLN Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 366 PHE Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 460 HIS Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 534 ILE Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 607 MET Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 821 CYS Chi-restraints excluded: chain C residue 899 VAL Chi-restraints excluded: chain C residue 914 THR Chi-restraints excluded: chain C residue 1003 LYS Chi-restraints excluded: chain C residue 1055 TYR Chi-restraints excluded: chain C residue 1079 CYS Chi-restraints excluded: chain C residue 1112 ILE Chi-restraints excluded: chain C residue 1123 ASN Chi-restraints excluded: chain C residue 1127 CYS Chi-restraints excluded: chain C residue 1144 VAL Chi-restraints excluded: chain C residue 1218 THR Chi-restraints excluded: chain C residue 1224 THR Chi-restraints excluded: chain C residue 1227 ASP Chi-restraints excluded: chain C residue 1251 THR Chi-restraints excluded: chain C residue 1253 ASP Chi-restraints excluded: chain C residue 1270 THR Chi-restraints excluded: chain C residue 1311 GLU Chi-restraints excluded: chain C residue 1316 VAL Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 173 ASN Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 286 PHE Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 372 VAL Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain D residue 458 PHE Chi-restraints excluded: chain D residue 462 GLU Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 486 THR Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 519 ASP Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 548 THR Chi-restraints excluded: chain D residue 563 CYS Chi-restraints excluded: chain D residue 637 GLN Chi-restraints excluded: chain D residue 643 ILE Chi-restraints excluded: chain D residue 731 VAL Chi-restraints excluded: chain D residue 751 VAL Chi-restraints excluded: chain D residue 761 THR Chi-restraints excluded: chain D residue 771 CYS Chi-restraints excluded: chain D residue 783 THR Chi-restraints excluded: chain D residue 792 PHE Chi-restraints excluded: chain D residue 821 CYS Chi-restraints excluded: chain D residue 849 CYS Chi-restraints excluded: chain D residue 868 VAL Chi-restraints excluded: chain D residue 887 VAL Chi-restraints excluded: chain D residue 957 SER Chi-restraints excluded: chain D residue 1026 SER Chi-restraints excluded: chain D residue 1080 PHE Chi-restraints excluded: chain D residue 1115 THR Chi-restraints excluded: chain D residue 1183 TRP Chi-restraints excluded: chain D residue 1208 MET Chi-restraints excluded: chain D residue 1224 THR Chi-restraints excluded: chain D residue 1234 ILE Chi-restraints excluded: chain D residue 1250 SER Chi-restraints excluded: chain D residue 1251 THR Chi-restraints excluded: chain D residue 1270 THR Chi-restraints excluded: chain D residue 1305 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 447 optimal weight: 6.9990 chunk 470 optimal weight: 3.9990 chunk 429 optimal weight: 9.9990 chunk 458 optimal weight: 4.9990 chunk 275 optimal weight: 5.9990 chunk 199 optimal weight: 4.9990 chunk 359 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 413 optimal weight: 1.9990 chunk 433 optimal weight: 0.3980 chunk 456 optimal weight: 10.0000 overall best weight: 2.4788 ------------------------------------------------------------------------------- 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 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 938 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 964 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 995 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1038 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1065 GLN ** A1187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 310 GLN ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1182 HIS ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 637 GLN ** D 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 938 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.5212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 41420 Z= 0.261 Angle : 0.813 13.939 56270 Z= 0.394 Chirality : 0.050 0.460 6514 Planarity : 0.005 0.062 7202 Dihedral : 7.788 59.992 6312 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 25.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.76 % Favored : 88.18 % Rotamer: Outliers : 5.37 % Allowed : 28.19 % Favored : 66.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.38 % 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: -3.53 (0.11), residues: 5110 helix: -0.27 (0.17), residues: 804 sheet: -2.25 (0.13), residues: 1460 loop : -3.13 (0.11), residues: 2846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A1183 HIS 0.008 0.001 HIS B 460 PHE 0.018 0.002 PHE D 290 TYR 0.023 0.002 TYR A1007 ARG 0.005 0.000 ARG D 270 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10220 Ramachandran restraints generated. 5110 Oldfield, 0 Emsley, 5110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10220 Ramachandran restraints generated. 5110 Oldfield, 0 Emsley, 5110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 911 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 240 poor density : 671 time to evaluate : 4.140 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: A 151 MET cc_start: 0.6085 (tpp) cc_final: 0.5805 (tpp) REVERT: A 183 LEU cc_start: 0.7226 (OUTLIER) cc_final: 0.6348 (mt) REVERT: A 272 TYR cc_start: 0.3874 (OUTLIER) cc_final: 0.2906 (t80) REVERT: A 290 PHE cc_start: 0.7929 (m-80) cc_final: 0.7593 (m-80) REVERT: A 318 MET cc_start: 0.8909 (tpp) cc_final: 0.8475 (tpp) REVERT: A 368 GLN cc_start: 0.8150 (tt0) cc_final: 0.7703 (tm-30) REVERT: A 373 ASP cc_start: 0.8261 (t0) cc_final: 0.7621 (m-30) REVERT: A 436 TRP cc_start: 0.7004 (t-100) cc_final: 0.6653 (t-100) REVERT: A 543 TYR cc_start: 0.7638 (p90) cc_final: 0.6929 (p90) REVERT: A 572 PHE cc_start: 0.8377 (p90) cc_final: 0.8106 (p90) REVERT: A 602 GLN cc_start: 0.6937 (tm-30) cc_final: 0.6455 (pt0) REVERT: A 612 GLU cc_start: 0.8146 (tt0) cc_final: 0.7844 (tt0) REVERT: A 627 LEU cc_start: 0.8812 (tp) cc_final: 0.8387 (tt) REVERT: A 635 ASN cc_start: 0.8695 (OUTLIER) cc_final: 0.8342 (p0) REVERT: A 669 PHE cc_start: 0.8694 (m-80) cc_final: 0.8327 (m-80) REVERT: A 671 GLU cc_start: 0.8700 (tt0) cc_final: 0.8311 (mt-10) REVERT: A 682 LYS cc_start: 0.8725 (mttt) cc_final: 0.8260 (mmmt) REVERT: A 793 PHE cc_start: 0.8908 (p90) cc_final: 0.8645 (p90) REVERT: A 829 GLU cc_start: 0.8599 (tp30) cc_final: 0.7852 (mp0) REVERT: A 870 PHE cc_start: 0.6184 (m-80) cc_final: 0.5609 (m-80) REVERT: A 945 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.8042 (ptm160) REVERT: A 964 ASN cc_start: 0.8693 (t0) cc_final: 0.8467 (t0) REVERT: A 975 GLN cc_start: 0.8503 (mm-40) cc_final: 0.7956 (mt0) REVERT: A 977 MET cc_start: 0.9230 (mmm) cc_final: 0.8779 (mmm) REVERT: A 1017 ASN cc_start: 0.9033 (m-40) cc_final: 0.8582 (m110) REVERT: A 1065 GLN cc_start: 0.9139 (OUTLIER) cc_final: 0.8861 (mm-40) REVERT: A 1080 PHE cc_start: 0.8076 (m-80) cc_final: 0.7725 (m-10) REVERT: A 1087 LEU cc_start: 0.9542 (tt) cc_final: 0.9243 (mt) REVERT: A 1101 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8765 (pp) REVERT: A 1110 LEU cc_start: 0.9337 (mt) cc_final: 0.9050 (tp) REVERT: A 1111 GLU cc_start: 0.8656 (mm-30) cc_final: 0.8372 (mm-30) REVERT: A 1129 GLU cc_start: 0.9148 (OUTLIER) cc_final: 0.8875 (pm20) REVERT: A 1147 LYS cc_start: 0.9134 (mttp) cc_final: 0.8459 (mttp) REVERT: A 1217 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.9067 (mm) REVERT: B 78 GLU cc_start: 0.8543 (pt0) cc_final: 0.7991 (pm20) REVERT: B 98 GLU cc_start: 0.8476 (tt0) cc_final: 0.8051 (tm-30) REVERT: B 121 MET cc_start: 0.7955 (tpp) cc_final: 0.7697 (tpp) REVERT: B 208 GLN cc_start: 0.8410 (tt0) cc_final: 0.7883 (tp-100) REVERT: B 246 MET cc_start: 0.6847 (OUTLIER) cc_final: 0.6547 (ppp) REVERT: B 318 MET cc_start: 0.8486 (mtt) cc_final: 0.7791 (mmm) REVERT: B 342 GLU cc_start: 0.8632 (tp30) cc_final: 0.8330 (tp30) REVERT: B 393 TYR cc_start: 0.8756 (t80) cc_final: 0.8395 (t80) REVERT: B 460 HIS cc_start: 0.8815 (t-90) cc_final: 0.8136 (m-70) REVERT: B 461 LEU cc_start: 0.9131 (mp) cc_final: 0.8775 (mp) REVERT: B 567 LYS cc_start: 0.9265 (tppt) cc_final: 0.9061 (mmpt) REVERT: B 649 TYR cc_start: 0.7745 (m-80) cc_final: 0.7281 (m-80) REVERT: B 688 MET cc_start: 0.8528 (ppp) cc_final: 0.8092 (ppp) REVERT: B 798 MET cc_start: 0.8707 (ptt) cc_final: 0.8310 (ptm) REVERT: B 858 TRP cc_start: 0.7226 (m-90) cc_final: 0.6767 (m-90) REVERT: B 863 LYS cc_start: 0.8773 (ttpt) cc_final: 0.8545 (ttpt) REVERT: B 880 GLN cc_start: 0.8063 (OUTLIER) cc_final: 0.7425 (pm20) REVERT: B 959 MET cc_start: 0.7988 (pmm) cc_final: 0.7191 (pmm) REVERT: B 976 ASN cc_start: 0.9198 (t0) cc_final: 0.8965 (t0) REVERT: B 977 MET cc_start: 0.9177 (mmm) cc_final: 0.8862 (mmm) REVERT: B 1010 THR cc_start: 0.8587 (m) cc_final: 0.8315 (p) REVERT: B 1013 GLN cc_start: 0.9083 (mm-40) cc_final: 0.8364 (mm-40) REVERT: B 1076 ASP cc_start: 0.8301 (p0) cc_final: 0.7911 (p0) REVERT: B 1098 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7682 (tp30) REVERT: B 1123 ASN cc_start: 0.9461 (m110) cc_final: 0.9210 (m110) REVERT: B 1183 TRP cc_start: 0.8944 (m-90) cc_final: 0.8687 (m-90) REVERT: B 1217 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8786 (mm) REVERT: B 1325 GLN cc_start: 0.8293 (tt0) cc_final: 0.8030 (tp40) REVERT: B 1330 TYR cc_start: 0.8858 (p90) cc_final: 0.8484 (p90) REVERT: C 65 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7329 (mm-30) REVERT: C 81 ASN cc_start: 0.8063 (p0) cc_final: 0.7847 (p0) REVERT: C 151 MET cc_start: 0.7161 (tpp) cc_final: 0.5728 (tpp) REVERT: C 154 ASN cc_start: 0.9065 (OUTLIER) cc_final: 0.8577 (p0) REVERT: C 187 LEU cc_start: 0.8937 (tt) cc_final: 0.8693 (tp) REVERT: C 189 GLN cc_start: 0.8795 (pm20) cc_final: 0.8366 (pp30) REVERT: C 310 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.8158 (pm20) REVERT: C 436 TRP cc_start: 0.7906 (t-100) cc_final: 0.7557 (t-100) REVERT: C 458 PHE cc_start: 0.8387 (p90) cc_final: 0.7804 (p90) REVERT: C 481 ILE cc_start: 0.8968 (mp) cc_final: 0.8695 (mp) REVERT: C 499 ILE cc_start: 0.7194 (mp) cc_final: 0.6914 (tp) REVERT: C 539 ARG cc_start: 0.8019 (ttm-80) cc_final: 0.7787 (ttm170) REVERT: C 598 ARG cc_start: 0.8157 (OUTLIER) cc_final: 0.7601 (ttt90) REVERT: C 635 ASN cc_start: 0.8611 (p0) cc_final: 0.8158 (p0) REVERT: C 671 GLU cc_start: 0.9146 (tt0) cc_final: 0.8780 (mt-10) REVERT: C 737 GLU cc_start: 0.8410 (mp0) cc_final: 0.7763 (mp0) REVERT: C 787 ARG cc_start: 0.8677 (ptp90) cc_final: 0.8024 (mtp180) REVERT: C 798 MET cc_start: 0.4783 (ptt) cc_final: 0.4544 (ptt) REVERT: C 916 PHE cc_start: 0.8762 (m-80) cc_final: 0.8424 (m-80) REVERT: C 988 ASP cc_start: 0.8383 (t0) cc_final: 0.7993 (t0) REVERT: C 1063 ILE cc_start: 0.8910 (pp) cc_final: 0.8652 (pp) REVERT: C 1079 CYS cc_start: 0.5390 (OUTLIER) cc_final: 0.4504 (p) REVERT: C 1089 ASN cc_start: 0.9105 (m-40) cc_final: 0.8519 (p0) REVERT: C 1104 TYR cc_start: 0.8783 (t80) cc_final: 0.8444 (t80) REVERT: C 1123 ASN cc_start: 0.8999 (OUTLIER) cc_final: 0.8596 (p0) REVERT: C 1163 ARG cc_start: 0.8764 (ttt180) cc_final: 0.8530 (tmm-80) REVERT: C 1207 GLU cc_start: 0.9024 (tt0) cc_final: 0.8800 (tp30) REVERT: C 1254 THR cc_start: 0.9210 (m) cc_final: 0.8863 (p) REVERT: C 1258 LEU cc_start: 0.9239 (mp) cc_final: 0.8992 (mp) REVERT: D 31 TYR cc_start: 0.8317 (OUTLIER) cc_final: 0.7826 (p90) REVERT: D 98 GLU cc_start: 0.8740 (tt0) cc_final: 0.8417 (tp30) REVERT: D 151 MET cc_start: 0.7830 (mtm) cc_final: 0.7361 (mpp) REVERT: D 203 TYR cc_start: 0.7492 (m-80) cc_final: 0.6236 (m-80) REVERT: D 289 LYS cc_start: 0.9294 (mttm) cc_final: 0.8832 (mmtp) REVERT: D 368 GLN cc_start: 0.8882 (pt0) cc_final: 0.8430 (mp10) REVERT: D 432 TYR cc_start: 0.7686 (p90) cc_final: 0.6754 (p90) REVERT: D 462 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8162 (pp20) REVERT: D 542 ILE cc_start: 0.8563 (tt) cc_final: 0.8232 (mt) REVERT: D 561 GLU cc_start: 0.8239 (tp30) cc_final: 0.7859 (tp30) REVERT: D 621 LEU cc_start: 0.9334 (mm) cc_final: 0.9081 (mm) REVERT: D 637 GLN cc_start: 0.8029 (OUTLIER) cc_final: 0.7787 (pp30) REVERT: D 669 PHE cc_start: 0.8669 (m-80) cc_final: 0.8029 (m-80) REVERT: D 671 GLU cc_start: 0.8740 (tt0) cc_final: 0.8361 (tp30) REVERT: D 673 MET cc_start: 0.9019 (tpp) cc_final: 0.8521 (tpp) REVERT: D 766 LYS cc_start: 0.8157 (mmtt) cc_final: 0.7414 (mmtm) REVERT: D 913 GLU cc_start: 0.8495 (pp20) cc_final: 0.8164 (pp20) REVERT: D 965 LEU cc_start: 0.8957 (tp) cc_final: 0.8640 (mp) REVERT: D 976 ASN cc_start: 0.9386 (t0) cc_final: 0.9117 (t0) REVERT: D 996 LEU cc_start: 0.8390 (pt) cc_final: 0.7614 (tp) REVERT: D 1089 ASN cc_start: 0.9085 (p0) cc_final: 0.8599 (p0) REVERT: D 1133 LYS cc_start: 0.9299 (ttmt) cc_final: 0.8925 (tppt) REVERT: D 1183 TRP cc_start: 0.8912 (OUTLIER) cc_final: 0.8669 (m100) REVERT: D 1208 MET cc_start: 0.9137 (OUTLIER) cc_final: 0.8673 (ppp) REVERT: D 1243 ASN cc_start: 0.9414 (t0) cc_final: 0.9089 (t0) REVERT: D 1245 GLN cc_start: 0.9230 (tm-30) cc_final: 0.8735 (tm-30) REVERT: D 1269 PHE cc_start: 0.8669 (t80) cc_final: 0.7901 (t80) REVERT: D 1331 ASN cc_start: 0.6909 (OUTLIER) cc_final: 0.6010 (m110) outliers start: 240 outliers final: 198 residues processed: 849 average time/residue: 0.4694 time to fit residues: 681.2636 Evaluate side-chains 866 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 646 time to evaluate : 4.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 TYR Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 89 PHE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 272 TYR Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 392 ASN Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 619 TYR Chi-restraints excluded: chain A residue 635 ASN Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 656 THR Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 787 ARG Chi-restraints excluded: chain A residue 856 VAL Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 878 GLU Chi-restraints excluded: chain A residue 945 ARG Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1024 SER Chi-restraints excluded: chain A residue 1055 TYR Chi-restraints excluded: chain A residue 1065 GLN Chi-restraints excluded: chain A residue 1076 ASP Chi-restraints excluded: chain A residue 1101 LEU Chi-restraints excluded: chain A residue 1112 ILE Chi-restraints excluded: chain A residue 1115 THR Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1129 GLU Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1224 THR Chi-restraints excluded: chain A residue 1251 THR Chi-restraints excluded: chain A residue 1333 LEU Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 89 PHE Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 173 ASN Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 246 MET Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 286 PHE Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 407 PHE Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 458 PHE Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 643 ILE Chi-restraints excluded: chain B residue 732 ARG Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 793 PHE Chi-restraints excluded: chain B residue 797 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 831 SER Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 872 VAL Chi-restraints excluded: chain B residue 880 GLN Chi-restraints excluded: chain B residue 1046 LEU Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain B residue 1080 PHE Chi-restraints excluded: chain B residue 1091 ILE Chi-restraints excluded: chain B residue 1115 THR Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1127 CYS Chi-restraints excluded: chain B residue 1144 VAL Chi-restraints excluded: chain B residue 1217 LEU Chi-restraints excluded: chain B residue 1218 THR Chi-restraints excluded: chain B residue 1227 ASP Chi-restraints excluded: chain B residue 1234 ILE Chi-restraints excluded: chain B residue 1243 ASN Chi-restraints excluded: chain B residue 1251 THR Chi-restraints excluded: chain C residue 31 TYR Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 89 PHE Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 272 TYR Chi-restraints excluded: chain C residue 286 PHE Chi-restraints excluded: chain C residue 310 GLN Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 366 PHE Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 460 HIS Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain C residue 571 SER Chi-restraints excluded: chain C residue 598 ARG Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 607 MET Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain C residue 835 LEU Chi-restraints excluded: chain C residue 899 VAL Chi-restraints excluded: chain C residue 914 THR Chi-restraints excluded: chain C residue 930 GLU Chi-restraints excluded: chain C residue 1003 LYS Chi-restraints excluded: chain C residue 1055 TYR Chi-restraints excluded: chain C residue 1079 CYS Chi-restraints excluded: chain C residue 1112 ILE Chi-restraints excluded: chain C residue 1123 ASN Chi-restraints excluded: chain C residue 1127 CYS Chi-restraints excluded: chain C residue 1144 VAL Chi-restraints excluded: chain C residue 1218 THR Chi-restraints excluded: chain C residue 1224 THR Chi-restraints excluded: chain C residue 1227 ASP Chi-restraints excluded: chain C residue 1239 THR Chi-restraints excluded: chain C residue 1251 THR Chi-restraints excluded: chain C residue 1253 ASP Chi-restraints excluded: chain C residue 1270 THR Chi-restraints excluded: chain C residue 1311 GLU Chi-restraints excluded: chain C residue 1316 VAL Chi-restraints excluded: chain D residue 31 TYR Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 173 ASN Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 286 PHE Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 372 VAL Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain D residue 458 PHE Chi-restraints excluded: chain D residue 462 GLU Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 486 THR Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 519 ASP Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 548 THR Chi-restraints excluded: chain D residue 563 CYS Chi-restraints excluded: chain D residue 637 GLN Chi-restraints excluded: chain D residue 643 ILE Chi-restraints excluded: chain D residue 731 VAL Chi-restraints excluded: chain D residue 761 THR Chi-restraints excluded: chain D residue 771 CYS Chi-restraints excluded: chain D residue 783 THR Chi-restraints excluded: chain D residue 821 CYS Chi-restraints excluded: chain D residue 868 VAL Chi-restraints excluded: chain D residue 887 VAL Chi-restraints excluded: chain D residue 1026 SER Chi-restraints excluded: chain D residue 1080 PHE Chi-restraints excluded: chain D residue 1115 THR Chi-restraints excluded: chain D residue 1183 TRP Chi-restraints excluded: chain D residue 1208 MET Chi-restraints excluded: chain D residue 1224 THR Chi-restraints excluded: chain D residue 1234 ILE Chi-restraints excluded: chain D residue 1250 SER Chi-restraints excluded: chain D residue 1251 THR Chi-restraints excluded: chain D residue 1270 THR Chi-restraints excluded: chain D residue 1305 LEU Chi-restraints excluded: chain D residue 1331 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 300 optimal weight: 0.5980 chunk 484 optimal weight: 6.9990 chunk 295 optimal weight: 50.0000 chunk 229 optimal weight: 2.9990 chunk 336 optimal weight: 5.9990 chunk 508 optimal weight: 10.0000 chunk 467 optimal weight: 0.9990 chunk 404 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 chunk 312 optimal weight: 5.9990 chunk 248 optimal weight: 5.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- 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 389 ASN ** A 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 938 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 964 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 995 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1038 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1065 GLN ** A1187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1036 GLN ** B1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 413 ASN ** D 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 938 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.5394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 41420 Z= 0.303 Angle : 0.842 13.264 56270 Z= 0.410 Chirality : 0.051 0.500 6514 Planarity : 0.005 0.062 7202 Dihedral : 7.843 59.867 6312 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 28.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 12.05 % Favored : 87.89 % Rotamer: Outliers : 5.50 % Allowed : 28.50 % Favored : 66.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.38 % 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: -3.60 (0.11), residues: 5110 helix: -0.45 (0.17), residues: 808 sheet: -2.29 (0.13), residues: 1482 loop : -3.13 (0.11), residues: 2820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP B 739 HIS 0.009 0.001 HIS B 460 PHE 0.021 0.002 PHE A 155 TYR 0.021 0.002 TYR C1007 ARG 0.005 0.001 ARG D 270 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10220 Ramachandran restraints generated. 5110 Oldfield, 0 Emsley, 5110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10220 Ramachandran restraints generated. 5110 Oldfield, 0 Emsley, 5110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 901 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 246 poor density : 655 time to evaluate : 4.083 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: A 128 LEU cc_start: 0.7255 (OUTLIER) cc_final: 0.6909 (pt) REVERT: A 183 LEU cc_start: 0.7259 (OUTLIER) cc_final: 0.6350 (mt) REVERT: A 209 LYS cc_start: 0.9260 (ttmt) cc_final: 0.9001 (ttmt) REVERT: A 272 TYR cc_start: 0.3966 (OUTLIER) cc_final: 0.2952 (t80) REVERT: A 290 PHE cc_start: 0.7997 (m-80) cc_final: 0.7647 (m-80) REVERT: A 318 MET cc_start: 0.8872 (tpp) cc_final: 0.8455 (tpp) REVERT: A 368 GLN cc_start: 0.8219 (tt0) cc_final: 0.7807 (tm-30) REVERT: A 373 ASP cc_start: 0.8350 (t0) cc_final: 0.7841 (m-30) REVERT: A 436 TRP cc_start: 0.7066 (t-100) cc_final: 0.6689 (t-100) REVERT: A 543 TYR cc_start: 0.7761 (p90) cc_final: 0.7026 (p90) REVERT: A 550 ASP cc_start: 0.7499 (t0) cc_final: 0.6871 (t0) REVERT: A 572 PHE cc_start: 0.8414 (p90) cc_final: 0.8131 (p90) REVERT: A 602 GLN cc_start: 0.7063 (tm-30) cc_final: 0.6611 (tm-30) REVERT: A 627 LEU cc_start: 0.8787 (tp) cc_final: 0.8361 (tt) REVERT: A 635 ASN cc_start: 0.8613 (OUTLIER) cc_final: 0.8267 (p0) REVERT: A 666 MET cc_start: 0.8175 (tpt) cc_final: 0.7697 (tpt) REVERT: A 669 PHE cc_start: 0.8726 (m-80) cc_final: 0.8387 (m-80) REVERT: A 671 GLU cc_start: 0.8705 (tt0) cc_final: 0.8351 (mt-10) REVERT: A 682 LYS cc_start: 0.8707 (mttt) cc_final: 0.8184 (mmmt) REVERT: A 793 PHE cc_start: 0.8868 (p90) cc_final: 0.8611 (p90) REVERT: A 798 MET cc_start: 0.6253 (mpp) cc_final: 0.5818 (mpp) REVERT: A 829 GLU cc_start: 0.8633 (tp30) cc_final: 0.7867 (mp0) REVERT: A 870 PHE cc_start: 0.6244 (m-80) cc_final: 0.5565 (m-80) REVERT: A 945 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.7995 (ptm160) REVERT: A 964 ASN cc_start: 0.8736 (t0) cc_final: 0.8490 (t0) REVERT: A 975 GLN cc_start: 0.8508 (mm-40) cc_final: 0.7962 (mt0) REVERT: A 977 MET cc_start: 0.9239 (mmm) cc_final: 0.8805 (mmm) REVERT: A 1017 ASN cc_start: 0.9035 (m-40) cc_final: 0.8582 (m110) REVERT: A 1080 PHE cc_start: 0.8078 (m-80) cc_final: 0.7822 (m-10) REVERT: A 1087 LEU cc_start: 0.9564 (tt) cc_final: 0.9286 (mt) REVERT: A 1098 GLU cc_start: 0.8544 (pm20) cc_final: 0.8235 (mm-30) REVERT: A 1110 LEU cc_start: 0.9362 (mt) cc_final: 0.9069 (tp) REVERT: A 1111 GLU cc_start: 0.8681 (mm-30) cc_final: 0.8403 (mm-30) REVERT: A 1208 MET cc_start: 0.9291 (ppp) cc_final: 0.8993 (ppp) REVERT: A 1217 LEU cc_start: 0.9328 (OUTLIER) cc_final: 0.9118 (mm) REVERT: A 1330 TYR cc_start: 0.8320 (p90) cc_final: 0.7364 (p90) REVERT: B 78 GLU cc_start: 0.8644 (pt0) cc_final: 0.8107 (pm20) REVERT: B 98 GLU cc_start: 0.8386 (tt0) cc_final: 0.8055 (tm-30) REVERT: B 208 GLN cc_start: 0.8440 (tt0) cc_final: 0.7989 (tp-100) REVERT: B 246 MET cc_start: 0.7033 (OUTLIER) cc_final: 0.6644 (ppp) REVERT: B 318 MET cc_start: 0.8579 (mtt) cc_final: 0.7859 (mmm) REVERT: B 342 GLU cc_start: 0.8657 (tp30) cc_final: 0.8349 (tp30) REVERT: B 381 ASN cc_start: 0.9088 (m110) cc_final: 0.8812 (p0) REVERT: B 393 TYR cc_start: 0.8770 (t80) cc_final: 0.8412 (t80) REVERT: B 460 HIS cc_start: 0.8933 (t-90) cc_final: 0.8249 (m-70) REVERT: B 461 LEU cc_start: 0.9120 (mp) cc_final: 0.8751 (mp) REVERT: B 567 LYS cc_start: 0.9273 (tppt) cc_final: 0.9072 (mmpt) REVERT: B 649 TYR cc_start: 0.7779 (m-80) cc_final: 0.7276 (m-80) REVERT: B 688 MET cc_start: 0.8532 (ppp) cc_final: 0.8075 (ppp) REVERT: B 798 MET cc_start: 0.8719 (ptt) cc_final: 0.8367 (ptm) REVERT: B 858 TRP cc_start: 0.7248 (m-90) cc_final: 0.6787 (m-90) REVERT: B 863 LYS cc_start: 0.8788 (ttpt) cc_final: 0.8565 (ttpt) REVERT: B 880 GLN cc_start: 0.8163 (OUTLIER) cc_final: 0.7529 (pm20) REVERT: B 959 MET cc_start: 0.8040 (pmm) cc_final: 0.7260 (pmm) REVERT: B 976 ASN cc_start: 0.9214 (t0) cc_final: 0.8991 (t0) REVERT: B 977 MET cc_start: 0.9190 (mmm) cc_final: 0.8883 (mmm) REVERT: B 1010 THR cc_start: 0.8600 (m) cc_final: 0.8329 (p) REVERT: B 1013 GLN cc_start: 0.9054 (mm-40) cc_final: 0.8384 (mm-40) REVERT: B 1059 ASP cc_start: 0.7332 (OUTLIER) cc_final: 0.6834 (p0) REVERT: B 1076 ASP cc_start: 0.8419 (p0) cc_final: 0.8045 (p0) REVERT: B 1098 GLU cc_start: 0.8242 (mm-30) cc_final: 0.7697 (tp30) REVERT: B 1123 ASN cc_start: 0.9478 (m110) cc_final: 0.9199 (m-40) REVERT: B 1183 TRP cc_start: 0.8941 (m-90) cc_final: 0.8705 (m-90) REVERT: B 1217 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8795 (mm) REVERT: B 1325 GLN cc_start: 0.8356 (tt0) cc_final: 0.8098 (tp40) REVERT: B 1330 TYR cc_start: 0.8890 (p90) cc_final: 0.8508 (p90) REVERT: C 65 GLU cc_start: 0.7661 (mt-10) cc_final: 0.7337 (mm-30) REVERT: C 151 MET cc_start: 0.7076 (tpp) cc_final: 0.5657 (tpp) REVERT: C 154 ASN cc_start: 0.9015 (OUTLIER) cc_final: 0.8530 (p0) REVERT: C 187 LEU cc_start: 0.8977 (tt) cc_final: 0.8695 (tp) REVERT: C 189 GLN cc_start: 0.8812 (pm20) cc_final: 0.8387 (pp30) REVERT: C 310 GLN cc_start: 0.8538 (pt0) cc_final: 0.8123 (pm20) REVERT: C 436 TRP cc_start: 0.7932 (t-100) cc_final: 0.7562 (t-100) REVERT: C 458 PHE cc_start: 0.8394 (p90) cc_final: 0.7788 (p90) REVERT: C 481 ILE cc_start: 0.9026 (mp) cc_final: 0.8744 (mp) REVERT: C 539 ARG cc_start: 0.8009 (ttm-80) cc_final: 0.7732 (ttm170) REVERT: C 540 LEU cc_start: 0.8777 (tp) cc_final: 0.8559 (tp) REVERT: C 561 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7524 (mp0) REVERT: C 598 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7680 (ttt90) REVERT: C 635 ASN cc_start: 0.8629 (p0) cc_final: 0.8209 (p0) REVERT: C 671 GLU cc_start: 0.9143 (tt0) cc_final: 0.8806 (mt-10) REVERT: C 737 GLU cc_start: 0.8501 (mp0) cc_final: 0.7903 (mp0) REVERT: C 787 ARG cc_start: 0.8663 (ptp90) cc_final: 0.8045 (mtp180) REVERT: C 916 PHE cc_start: 0.8759 (m-80) cc_final: 0.8466 (m-80) REVERT: C 988 ASP cc_start: 0.8414 (t0) cc_final: 0.8139 (t70) REVERT: C 1063 ILE cc_start: 0.8895 (pp) cc_final: 0.8672 (pp) REVERT: C 1079 CYS cc_start: 0.5426 (OUTLIER) cc_final: 0.4468 (p) REVERT: C 1089 ASN cc_start: 0.9116 (m-40) cc_final: 0.8551 (p0) REVERT: C 1104 TYR cc_start: 0.8817 (t80) cc_final: 0.8506 (t80) REVERT: C 1123 ASN cc_start: 0.9004 (OUTLIER) cc_final: 0.8623 (p0) REVERT: C 1207 GLU cc_start: 0.9100 (tt0) cc_final: 0.8877 (tp30) REVERT: C 1254 THR cc_start: 0.9226 (m) cc_final: 0.8889 (p) REVERT: C 1258 LEU cc_start: 0.9274 (mp) cc_final: 0.9005 (mp) REVERT: D 31 TYR cc_start: 0.8416 (OUTLIER) cc_final: 0.7906 (p90) REVERT: D 98 GLU cc_start: 0.8751 (tt0) cc_final: 0.8424 (tp30) REVERT: D 151 MET cc_start: 0.7879 (mtm) cc_final: 0.7380 (mpp) REVERT: D 203 TYR cc_start: 0.7597 (m-80) cc_final: 0.6308 (m-80) REVERT: D 368 GLN cc_start: 0.8873 (pt0) cc_final: 0.8467 (mp10) REVERT: D 432 TYR cc_start: 0.7731 (p90) cc_final: 0.6777 (p90) REVERT: D 462 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8249 (pp20) REVERT: D 500 MET cc_start: 0.5594 (mtm) cc_final: 0.5283 (mtm) REVERT: D 542 ILE cc_start: 0.8572 (tt) cc_final: 0.8192 (mp) REVERT: D 561 GLU cc_start: 0.8290 (tp30) cc_final: 0.7978 (tp30) REVERT: D 621 LEU cc_start: 0.9369 (mm) cc_final: 0.9140 (mm) REVERT: D 669 PHE cc_start: 0.8696 (m-80) cc_final: 0.8049 (m-80) REVERT: D 671 GLU cc_start: 0.8715 (tt0) cc_final: 0.8277 (mm-30) REVERT: D 912 LYS cc_start: 0.8298 (ptpp) cc_final: 0.7783 (ptpp) REVERT: D 913 GLU cc_start: 0.8487 (pp20) cc_final: 0.8072 (pp20) REVERT: D 965 LEU cc_start: 0.8988 (tp) cc_final: 0.8658 (mp) REVERT: D 976 ASN cc_start: 0.9387 (t0) cc_final: 0.9083 (t0) REVERT: D 996 LEU cc_start: 0.8525 (pt) cc_final: 0.7721 (tp) REVERT: D 1089 ASN cc_start: 0.9063 (p0) cc_final: 0.8562 (p0) REVERT: D 1133 LYS cc_start: 0.9319 (ttmt) cc_final: 0.8939 (tppt) REVERT: D 1154 PHE cc_start: 0.8855 (m-80) cc_final: 0.8270 (m-80) REVERT: D 1183 TRP cc_start: 0.8922 (OUTLIER) cc_final: 0.8624 (m100) REVERT: D 1208 MET cc_start: 0.9135 (OUTLIER) cc_final: 0.8724 (ppp) REVERT: D 1243 ASN cc_start: 0.9421 (t0) cc_final: 0.9115 (t0) REVERT: D 1245 GLN cc_start: 0.9242 (tm-30) cc_final: 0.8848 (tm-30) REVERT: D 1269 PHE cc_start: 0.8678 (t80) cc_final: 0.7917 (t80) REVERT: D 1331 ASN cc_start: 0.6966 (OUTLIER) cc_final: 0.5591 (m-40) outliers start: 246 outliers final: 206 residues processed: 836 average time/residue: 0.4671 time to fit residues: 665.0613 Evaluate side-chains 860 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 225 poor density : 635 time to evaluate : 4.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 TYR Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 89 PHE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 272 TYR Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 277 ASP Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 352 PHE Chi-restraints excluded: chain A residue 392 ASN Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 534 ILE Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 593 SER Chi-restraints excluded: chain A residue 600 VAL Chi-restraints excluded: chain A residue 619 TYR Chi-restraints excluded: chain A residue 635 ASN Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain A residue 656 THR Chi-restraints excluded: chain A residue 681 SER Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 787 ARG Chi-restraints excluded: chain A residue 856 VAL Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 878 GLU Chi-restraints excluded: chain A residue 945 ARG Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1024 SER Chi-restraints excluded: chain A residue 1055 TYR Chi-restraints excluded: chain A residue 1076 ASP Chi-restraints excluded: chain A residue 1101 LEU Chi-restraints excluded: chain A residue 1115 THR Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1129 GLU Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1156 LEU Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1218 THR Chi-restraints excluded: chain A residue 1224 THR Chi-restraints excluded: chain A residue 1251 THR Chi-restraints excluded: chain A residue 1253 ASP Chi-restraints excluded: chain A residue 1333 LEU Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 89 PHE Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 173 ASN Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 246 MET Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 286 PHE Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain B residue 407 PHE Chi-restraints excluded: chain B residue 458 PHE Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 475 THR Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 545 VAL Chi-restraints excluded: chain B residue 548 THR Chi-restraints excluded: chain B residue 571 SER Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 643 ILE Chi-restraints excluded: chain B residue 732 ARG Chi-restraints excluded: chain B residue 758 VAL Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 787 ARG Chi-restraints excluded: chain B residue 793 PHE Chi-restraints excluded: chain B residue 797 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 831 SER Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 872 VAL Chi-restraints excluded: chain B residue 880 GLN Chi-restraints excluded: chain B residue 1046 LEU Chi-restraints excluded: chain B residue 1059 ASP Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain B residue 1080 PHE Chi-restraints excluded: chain B residue 1091 ILE Chi-restraints excluded: chain B residue 1115 THR Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain B residue 1127 CYS Chi-restraints excluded: chain B residue 1144 VAL Chi-restraints excluded: chain B residue 1217 LEU Chi-restraints excluded: chain B residue 1218 THR Chi-restraints excluded: chain B residue 1224 THR Chi-restraints excluded: chain B residue 1227 ASP Chi-restraints excluded: chain B residue 1234 ILE Chi-restraints excluded: chain B residue 1243 ASN Chi-restraints excluded: chain B residue 1251 THR Chi-restraints excluded: chain C residue 31 TYR Chi-restraints excluded: chain C residue 63 SER Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 89 PHE Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 131 VAL Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 272 TYR Chi-restraints excluded: chain C residue 286 PHE Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 366 PHE Chi-restraints excluded: chain C residue 370 ARG Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 385 PHE Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain C residue 571 SER Chi-restraints excluded: chain C residue 598 ARG Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 607 MET Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 643 ILE Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain C residue 742 ASP Chi-restraints excluded: chain C residue 835 LEU Chi-restraints excluded: chain C residue 899 VAL Chi-restraints excluded: chain C residue 914 THR Chi-restraints excluded: chain C residue 930 GLU Chi-restraints excluded: chain C residue 1003 LYS Chi-restraints excluded: chain C residue 1055 TYR Chi-restraints excluded: chain C residue 1079 CYS Chi-restraints excluded: chain C residue 1112 ILE Chi-restraints excluded: chain C residue 1123 ASN Chi-restraints excluded: chain C residue 1127 CYS Chi-restraints excluded: chain C residue 1144 VAL Chi-restraints excluded: chain C residue 1218 THR Chi-restraints excluded: chain C residue 1224 THR Chi-restraints excluded: chain C residue 1227 ASP Chi-restraints excluded: chain C residue 1239 THR Chi-restraints excluded: chain C residue 1251 THR Chi-restraints excluded: chain C residue 1253 ASP Chi-restraints excluded: chain C residue 1270 THR Chi-restraints excluded: chain C residue 1311 GLU Chi-restraints excluded: chain C residue 1316 VAL Chi-restraints excluded: chain D residue 31 TYR Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 54 LEU Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 173 ASN Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 286 PHE Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 336 THR Chi-restraints excluded: chain D residue 372 VAL Chi-restraints excluded: chain D residue 377 VAL Chi-restraints excluded: chain D residue 409 ILE Chi-restraints excluded: chain D residue 450 LEU Chi-restraints excluded: chain D residue 458 PHE Chi-restraints excluded: chain D residue 462 GLU Chi-restraints excluded: chain D residue 475 THR Chi-restraints excluded: chain D residue 481 ILE Chi-restraints excluded: chain D residue 486 THR Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 519 ASP Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain D residue 545 VAL Chi-restraints excluded: chain D residue 548 THR Chi-restraints excluded: chain D residue 550 ASP Chi-restraints excluded: chain D residue 643 ILE Chi-restraints excluded: chain D residue 731 VAL Chi-restraints excluded: chain D residue 761 THR Chi-restraints excluded: chain D residue 771 CYS Chi-restraints excluded: chain D residue 783 THR Chi-restraints excluded: chain D residue 821 CYS Chi-restraints excluded: chain D residue 849 CYS Chi-restraints excluded: chain D residue 868 VAL Chi-restraints excluded: chain D residue 887 VAL Chi-restraints excluded: chain D residue 1026 SER Chi-restraints excluded: chain D residue 1080 PHE Chi-restraints excluded: chain D residue 1115 THR Chi-restraints excluded: chain D residue 1183 TRP Chi-restraints excluded: chain D residue 1208 MET Chi-restraints excluded: chain D residue 1224 THR Chi-restraints excluded: chain D residue 1234 ILE Chi-restraints excluded: chain D residue 1250 SER Chi-restraints excluded: chain D residue 1251 THR Chi-restraints excluded: chain D residue 1270 THR Chi-restraints excluded: chain D residue 1305 LEU Chi-restraints excluded: chain D residue 1331 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 321 optimal weight: 7.9990 chunk 430 optimal weight: 1.9990 chunk 123 optimal weight: 6.9990 chunk 373 optimal weight: 0.4980 chunk 59 optimal weight: 3.9990 chunk 112 optimal weight: 0.0870 chunk 405 optimal weight: 5.9990 chunk 169 optimal weight: 0.0010 chunk 416 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 chunk 74 optimal weight: 7.9990 overall best weight: 0.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 917 ASN A 938 ASN ** A 964 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 983 ASN ** A 995 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1038 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1036 GLN ** B1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 466 HIS ** C 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1242 GLN ** D 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 827 GLN ** D 880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 938 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 976 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.103383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.079826 restraints weight = 140567.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.082967 restraints weight = 84791.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.085304 restraints weight = 58832.669| |-----------------------------------------------------------------------------| r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.5658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 41420 Z= 0.202 Angle : 0.823 14.606 56270 Z= 0.388 Chirality : 0.051 0.499 6514 Planarity : 0.005 0.063 7202 Dihedral : 7.481 59.496 6312 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 20.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.61 % Favored : 90.33 % Rotamer: Outliers : 3.87 % Allowed : 30.29 % Favored : 65.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.38 % 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: -3.27 (0.11), residues: 5110 helix: -0.10 (0.17), residues: 826 sheet: -2.02 (0.13), residues: 1522 loop : -3.01 (0.11), residues: 2762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.002 TRP B 739 HIS 0.008 0.001 HIS C 893 PHE 0.022 0.001 PHE B 102 TYR 0.023 0.001 TYR C1012 ARG 0.005 0.001 ARG B 787 =============================================================================== Job complete usr+sys time: 11233.89 seconds wall clock time: 205 minutes 45.28 seconds (12345.28 seconds total)