Starting phenix.real_space_refine on Wed Feb 21 15:41:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zr9_14887/02_2024/7zr9_14887.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zr9_14887/02_2024/7zr9_14887.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zr9_14887/02_2024/7zr9_14887.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zr9_14887/02_2024/7zr9_14887.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zr9_14887/02_2024/7zr9_14887.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zr9_14887/02_2024/7zr9_14887.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.080 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 141 5.16 5 C 19719 2.51 5 N 5108 2.21 5 O 6046 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1118": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 31014 Number of models: 1 Model: "" Number of chains: 24 Chain: "B" Number of atoms: 8281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1060, 8281 Classifications: {'peptide': 1060} Link IDs: {'PTRANS': 54, 'TRANS': 1005} Chain breaks: 6 Chain: "A" Number of atoms: 8287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1061, 8287 Classifications: {'peptide': 1061} Link IDs: {'PTRANS': 54, 'TRANS': 1006} Chain breaks: 6 Chain: "C" Number of atoms: 8287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1061, 8287 Classifications: {'peptide': 1061} Link IDs: {'PTRANS': 54, 'TRANS': 1006} Chain breaks: 6 Chain: "H" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 973 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 124} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "L" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 828 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Chain: "D" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 973 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 124} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "E" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 828 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Chain: "F" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 973 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 124} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "G" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 828 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" 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: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 16.19, per 1000 atoms: 0.52 Number of scatterers: 31014 At special positions: 0 Unit cell: (153.6, 163.2, 232.8, 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 141 16.00 O 6046 8.00 N 5108 7.00 C 19719 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 298 " distance=2.02 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 376 " - pdb=" SG CYS B 429 " distance=2.03 Simple disulfide: pdb=" SG CYS B 388 " - pdb=" SG CYS B 522 " distance=2.04 Simple disulfide: pdb=" SG CYS B 477 " - pdb=" SG CYS B 485 " distance=2.03 Simple disulfide: pdb=" SG CYS B 535 " - pdb=" SG CYS B 587 " distance=2.03 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 646 " distance=2.03 Simple disulfide: pdb=" SG CYS B 659 " - pdb=" SG CYS B 668 " distance=2.03 Simple disulfide: pdb=" SG CYS B 735 " - pdb=" SG CYS B 757 " distance=2.03 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 746 " distance=2.03 Simple disulfide: pdb=" SG CYS B1029 " - pdb=" SG CYS B1040 " distance=2.03 Simple disulfide: pdb=" SG CYS B1079 " - pdb=" SG CYS B1123 " distance=2.03 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 298 " distance=2.03 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 429 " distance=2.03 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 477 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 535 " - pdb=" SG CYS A 587 " distance=2.02 Simple disulfide: pdb=" SG CYS A 614 " - pdb=" SG CYS A 646 " distance=2.03 Simple disulfide: pdb=" SG CYS A 659 " - pdb=" SG CYS A 668 " distance=2.03 Simple disulfide: pdb=" SG CYS A 735 " - pdb=" SG CYS A 757 " distance=2.03 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 746 " distance=2.03 Simple disulfide: pdb=" SG CYS A1029 " - pdb=" SG CYS A1040 " distance=2.03 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1123 " distance=2.02 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 288 " - pdb=" SG CYS C 298 " distance=2.03 Simple disulfide: pdb=" SG CYS C 333 " - pdb=" SG CYS C 358 " distance=2.03 Simple disulfide: pdb=" SG CYS C 376 " - pdb=" SG CYS C 429 " distance=2.03 Simple disulfide: pdb=" SG CYS C 388 " - pdb=" SG CYS C 522 " distance=2.03 Simple disulfide: pdb=" SG CYS C 477 " - pdb=" SG CYS C 485 " distance=2.03 Simple disulfide: pdb=" SG CYS C 535 " - pdb=" SG CYS C 587 " distance=2.03 Simple disulfide: pdb=" SG CYS C 614 " - pdb=" SG CYS C 646 " distance=2.03 Simple disulfide: pdb=" SG CYS C 659 " - pdb=" SG CYS C 668 " distance=2.03 Simple disulfide: pdb=" SG CYS C 735 " - pdb=" SG CYS C 757 " distance=2.03 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 746 " distance=2.03 Simple disulfide: pdb=" SG CYS C1029 " - pdb=" SG CYS C1040 " distance=2.03 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1123 " distance=1.67 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 101 " - pdb=" SG CYS H 105 " distance=2.21 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 101 " - pdb=" SG CYS D 105 " distance=2.21 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 89 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 101 " - pdb=" SG CYS F 105 " distance=2.21 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 89 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 279 " " NAG A1303 " - " ASN A 328 " " NAG A1304 " - " ASN A 600 " " NAG A1305 " - " ASN A 613 " " NAG A1306 " - " ASN A 654 " " NAG A1307 " - " ASN A 706 " " NAG A1308 " - " ASN A1071 " " NAG A1309 " - " ASN A 165 " " NAG A1310 " - " ASN A 340 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 279 " " NAG B1303 " - " ASN B 328 " " NAG B1304 " - " ASN B 600 " " NAG B1305 " - " ASN B 613 " " NAG B1306 " - " ASN B 654 " " NAG B1307 " - " ASN B 706 " " NAG B1308 " - " ASN B1071 " " NAG B1309 " - " ASN B 165 " " NAG B1310 " - " ASN B 340 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 279 " " NAG C1303 " - " ASN C 328 " " NAG C1304 " - " ASN C 600 " " NAG C1305 " - " ASN C 613 " " NAG C1306 " - " ASN C 654 " " NAG C1307 " - " ASN C 706 " " NAG C1308 " - " ASN C1071 " " NAG C1309 " - " ASN C 165 " " NAG C1310 " - " ASN C 340 " " NAG I 1 " - " ASN B 714 " " NAG J 1 " - " ASN B 798 " " NAG K 1 " - " ASN B1095 " " NAG M 1 " - " ASN B1131 " " NAG N 1 " - " ASN A 714 " " NAG O 1 " - " ASN A 798 " " NAG P 1 " - " ASN A1095 " " NAG Q 1 " - " ASN A1131 " " NAG R 1 " - " ASN C 714 " " NAG S 1 " - " ASN C 798 " " NAG T 1 " - " ASN C1095 " " NAG U 1 " - " ASN C1131 " Time building additional restraints: 12.19 Conformation dependent library (CDL) restraints added in 5.5 seconds 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7234 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 69 sheets defined 22.2% alpha, 32.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.09 Creating SS restraints... Processing helix chain 'B' and resid 291 through 300 Processing helix chain 'B' and resid 334 through 340 removed outlier: 3.636A pdb=" N VAL B 338 " --> pdb=" O PRO B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 367 Processing helix chain 'B' and resid 382 through 386 removed outlier: 3.693A pdb=" N ASN B 385 " --> pdb=" O THR B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 405 removed outlier: 4.217A pdb=" N ARG B 405 " --> pdb=" O GLY B 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 401 through 405' Processing helix chain 'B' and resid 413 through 419 Processing helix chain 'B' and resid 435 through 440 removed outlier: 3.575A pdb=" N SER B 440 " --> pdb=" O ASN B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 734 through 741 Processing helix chain 'B' and resid 743 through 752 removed outlier: 3.745A pdb=" N GLN B 752 " --> pdb=" O ASN B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 780 Processing helix chain 'B' and resid 813 through 823 Processing helix chain 'B' and resid 863 through 882 Processing helix chain 'B' and resid 883 through 888 removed outlier: 3.544A pdb=" N ALA B 887 " --> pdb=" O TRP B 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 906 Processing helix chain 'B' and resid 909 through 916 removed outlier: 4.161A pdb=" N LEU B 913 " --> pdb=" O THR B 909 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR B 914 " --> pdb=" O GLN B 910 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 938 Processing helix chain 'B' and resid 942 through 963 removed outlier: 3.616A pdb=" N VAL B 948 " --> pdb=" O LYS B 944 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 973 through 981 Processing helix chain 'B' and resid 982 through 1029 removed outlier: 4.427A pdb=" N VAL B 988 " --> pdb=" O PRO B 984 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLN B 989 " --> pdb=" O GLU B 985 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG B 992 " --> pdb=" O VAL B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1137 through 1144 removed outlier: 4.132A pdb=" N GLU B1141 " --> pdb=" O PRO B1137 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 301 Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 361 through 367 Processing helix chain 'A' and resid 382 through 386 Processing helix chain 'A' and resid 403 through 407 Processing helix chain 'A' and resid 413 through 419 Processing helix chain 'A' and resid 435 through 440 removed outlier: 3.525A pdb=" N SER A 440 " --> pdb=" O ASN A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 740 Processing helix chain 'A' and resid 743 through 752 removed outlier: 3.768A pdb=" N GLN A 752 " --> pdb=" O ASN A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 780 Processing helix chain 'A' and resid 813 through 823 Processing helix chain 'A' and resid 863 through 882 Processing helix chain 'A' and resid 883 through 888 Processing helix chain 'A' and resid 894 through 907 Processing helix chain 'A' and resid 910 through 916 removed outlier: 3.951A pdb=" N TYR A 914 " --> pdb=" O GLN A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 937 Processing helix chain 'A' and resid 939 through 941 No H-bonds generated for 'chain 'A' and resid 939 through 941' Processing helix chain 'A' and resid 942 through 963 removed outlier: 4.066A pdb=" N VAL A 948 " --> pdb=" O LYS A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 981 removed outlier: 3.594A pdb=" N ILE A 977 " --> pdb=" O VAL A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 1029 removed outlier: 5.051A pdb=" N VAL A 988 " --> pdb=" O PRO A 984 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLN A 989 " --> pdb=" O GLU A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1144 removed outlier: 3.885A pdb=" N GLU A1141 " --> pdb=" O PRO A1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 301 Processing helix chain 'C' and resid 335 through 340 Processing helix chain 'C' and resid 346 through 350 Processing helix chain 'C' and resid 361 through 367 Processing helix chain 'C' and resid 382 through 387 removed outlier: 3.735A pdb=" N ASN C 385 " --> pdb=" O THR C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 407 Processing helix chain 'C' and resid 413 through 419 Processing helix chain 'C' and resid 435 through 440 Processing helix chain 'C' and resid 734 through 740 Processing helix chain 'C' and resid 743 through 752 removed outlier: 3.572A pdb=" N GLN C 752 " --> pdb=" O ASN C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 780 Processing helix chain 'C' and resid 813 through 823 Processing helix chain 'C' and resid 863 through 882 Processing helix chain 'C' and resid 883 through 888 removed outlier: 3.809A pdb=" N ALA C 887 " --> pdb=" O TRP C 883 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 907 Processing helix chain 'C' and resid 910 through 938 removed outlier: 5.599A pdb=" N LYS C 918 " --> pdb=" O TYR C 914 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LEU C 919 " --> pdb=" O GLU C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 939 through 941 No H-bonds generated for 'chain 'C' and resid 939 through 941' Processing helix chain 'C' and resid 942 through 963 removed outlier: 3.958A pdb=" N VAL C 948 " --> pdb=" O LYS C 944 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU C 963 " --> pdb=" O LEU C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 973 through 981 Processing helix chain 'C' and resid 982 through 1029 removed outlier: 4.927A pdb=" N VAL C 988 " --> pdb=" O PRO C 984 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLN C 989 " --> pdb=" O GLU C 985 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1144 removed outlier: 3.992A pdb=" N GLU C1141 " --> pdb=" O PRO C1137 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 52 through 56 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 30 through 32 No H-bonds generated for 'chain 'L' and resid 30 through 32' Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.740A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 52 through 56 Processing helix chain 'D' and resid 62 through 65 Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'E' and resid 30 through 32 No H-bonds generated for 'chain 'E' and resid 30 through 32' Processing helix chain 'E' and resid 80 through 84 removed outlier: 3.740A pdb=" N PHE E 84 " --> pdb=" O PRO E 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 32 Processing helix chain 'F' and resid 52 through 56 Processing helix chain 'F' and resid 62 through 65 Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'G' and resid 30 through 32 No H-bonds generated for 'chain 'G' and resid 30 through 32' Processing helix chain 'G' and resid 80 through 84 removed outlier: 3.740A pdb=" N PHE G 84 " --> pdb=" O PRO G 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 21 through 22 Processing sheet with id=AA2, first strand: chain 'B' and resid 27 through 30 removed outlier: 7.639A pdb=" N ASN B 61 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N TYR B 266 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 42 through 43 Processing sheet with id=AA4, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.533A pdb=" N THR B 271 " --> pdb=" O ASP B 287 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N ASP B 287 " --> pdb=" O THR B 271 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU B 273 " --> pdb=" O ALA B 285 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ALA B 285 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N LYS B 275 " --> pdb=" O THR B 283 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 84 through 85 removed outlier: 5.835A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 11.099A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 9.679A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.307A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.655A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 11.748A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 9.621A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 10.859A pdb=" N PHE B 140 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 8.817A pdb=" N SER B 155 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N GLY B 142 " --> pdb=" O MET B 153 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N MET B 153 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N TYR B 144 " --> pdb=" O SER B 151 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N SER B 151 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 84 through 85 removed outlier: 5.835A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N SER B 244 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LEU B 141 " --> pdb=" O SER B 244 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL B 143 " --> pdb=" O LEU B 246 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 308 through 316 removed outlier: 5.133A pdb=" N ILE B 309 " --> pdb=" O THR B 596 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N THR B 596 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N GLN B 311 " --> pdb=" O VAL B 594 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL B 594 " --> pdb=" O GLN B 311 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N GLY B 591 " --> pdb=" O GLN B 610 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 321 through 325 removed outlier: 4.475A pdb=" N GLU B 321 " --> pdb=" O CYS B 535 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N PHE B 562 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 351 through 355 Processing sheet with id=AB1, first strand: chain 'B' and resid 358 through 359 removed outlier: 6.807A pdb=" N CYS B 358 " --> pdb=" O CYS B 522 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AB3, first strand: chain 'B' and resid 470 through 471 Processing sheet with id=AB4, first strand: chain 'B' and resid 651 through 652 removed outlier: 3.509A pdb=" N ALA B 691 " --> pdb=" O GLU B 651 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ALA B 669 " --> pdb=" O PRO B 662 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 699 through 701 Processing sheet with id=AB6, first strand: chain 'B' and resid 708 through 712 Processing sheet with id=AB7, first strand: chain 'B' and resid 715 through 725 removed outlier: 6.931A pdb=" N GLY B1056 " --> pdb=" O SER B1052 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N SER B1052 " --> pdb=" O GLY B1056 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL B1058 " --> pdb=" O PRO B1050 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU B1060 " --> pdb=" O SER B1048 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N SER B1048 " --> pdb=" O LEU B1060 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N VAL B1062 " --> pdb=" O LEU B1046 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 731 through 733 Processing sheet with id=AB9, first strand: chain 'B' and resid 785 through 787 removed outlier: 5.659A pdb=" N ILE B 785 " --> pdb=" O ASN A 700 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'B' and resid 1117 through 1122 removed outlier: 4.448A pdb=" N ALA B1084 " --> pdb=" O SER B1120 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 1091 through 1094 Processing sheet with id=AC3, first strand: chain 'A' and resid 21 through 22 Processing sheet with id=AC4, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.974A pdb=" N ASN A 61 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N TYR A 266 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA A 260 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.388A pdb=" N THR A 271 " --> pdb=" O ASP A 287 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N ASP A 287 " --> pdb=" O THR A 271 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LEU A 273 " --> pdb=" O ALA A 285 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ALA A 285 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LYS A 275 " --> pdb=" O THR A 283 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 84 through 85 removed outlier: 5.885A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 151 through 160 removed outlier: 6.834A pdb=" N SER A 151 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N TYR A 144 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N MET A 153 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N GLY A 142 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 8.906A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 10.961A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.506A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.455A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N SER A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LEU A 141 " --> pdb=" O SER A 244 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL A 143 " --> pdb=" O LEU A 246 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 308 through 316 removed outlier: 5.195A pdb=" N ILE A 309 " --> pdb=" O THR A 596 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N THR A 596 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N GLN A 311 " --> pdb=" O VAL A 594 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL A 594 " --> pdb=" O GLN A 311 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLY A 591 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 322 through 325 Processing sheet with id=AD1, first strand: chain 'A' and resid 351 through 355 Processing sheet with id=AD2, first strand: chain 'A' and resid 358 through 359 removed outlier: 6.915A pdb=" N CYS A 358 " --> pdb=" O CYS A 522 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AD4, first strand: chain 'A' and resid 470 through 471 removed outlier: 3.511A pdb=" N TYR A 486 " --> pdb=" O TYR A 470 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 651 through 652 removed outlier: 6.503A pdb=" N ALA A 669 " --> pdb=" O PRO A 662 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 708 through 725 removed outlier: 6.700A pdb=" N SER A 708 " --> pdb=" O THR A1073 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N THR A1073 " --> pdb=" O SER A 708 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ALA A 710 " --> pdb=" O ASN A1071 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ASN A1071 " --> pdb=" O ALA A 710 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLU A1069 " --> pdb=" O PRO A 712 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ASN A 714 " --> pdb=" O ALA A1067 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N GLY A1056 " --> pdb=" O SER A1052 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N SER A1052 " --> pdb=" O GLY A1056 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL A1058 " --> pdb=" O PRO A1050 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU A1060 " --> pdb=" O SER A1048 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N SER A1048 " --> pdb=" O LEU A1060 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N VAL A1062 " --> pdb=" O LEU A1046 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 708 through 725 removed outlier: 6.700A pdb=" N SER A 708 " --> pdb=" O THR A1073 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N THR A1073 " --> pdb=" O SER A 708 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ALA A 710 " --> pdb=" O ASN A1071 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ASN A1071 " --> pdb=" O ALA A 710 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLU A1069 " --> pdb=" O PRO A 712 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ASN A 714 " --> pdb=" O ALA A1067 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 731 through 733 Processing sheet with id=AD9, first strand: chain 'A' and resid 785 through 787 removed outlier: 5.874A pdb=" N ILE A 785 " --> pdb=" O ASN C 700 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'A' and resid 1117 through 1122 removed outlier: 3.567A pdb=" N SER A1120 " --> pdb=" O ALA A1084 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ALA A1084 " --> pdb=" O SER A1120 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 21 through 22 Processing sheet with id=AE3, first strand: chain 'C' and resid 27 through 30 removed outlier: 7.859A pdb=" N ASN C 61 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N TYR C 266 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA C 260 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.009A pdb=" N ASP C 284 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 84 through 85 removed outlier: 13.398A pdb=" N PHE C 238 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 13.230A pdb=" N ASN C 137 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 10.156A pdb=" N THR C 240 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N HIS C 242 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LEU C 141 " --> pdb=" O HIS C 242 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N TYR C 145 " --> pdb=" O LEU C 246 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 11.189A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 9.340A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 10.663A pdb=" N PHE C 140 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N SER C 155 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N GLY C 142 " --> pdb=" O MET C 153 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N MET C 153 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N TYR C 144 " --> pdb=" O SER C 151 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N SER C 151 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.608A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ILE C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE C 101 " --> pdb=" O ILE C 243 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 308 through 316 removed outlier: 5.313A pdb=" N ILE C 309 " --> pdb=" O THR C 596 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N THR C 596 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N GLN C 311 " --> pdb=" O VAL C 594 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL C 594 " --> pdb=" O GLN C 311 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY C 591 " --> pdb=" O GLN C 610 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 321 through 325 removed outlier: 4.244A pdb=" N GLU C 321 " --> pdb=" O CYS C 535 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 351 through 355 Processing sheet with id=AF1, first strand: chain 'C' and resid 358 through 359 removed outlier: 6.863A pdb=" N CYS C 358 " --> pdb=" O CYS C 522 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'C' and resid 449 through 451 Processing sheet with id=AF3, first strand: chain 'C' and resid 470 through 471 Processing sheet with id=AF4, first strand: chain 'C' and resid 651 through 652 removed outlier: 6.557A pdb=" N ALA C 669 " --> pdb=" O PRO C 662 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 708 through 712 Processing sheet with id=AF6, first strand: chain 'C' and resid 715 through 725 removed outlier: 5.841A pdb=" N TYR C1064 " --> pdb=" O HIS C1045 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N HIS C1045 " --> pdb=" O TYR C1064 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 730 through 733 removed outlier: 4.366A pdb=" N LYS C 730 " --> pdb=" O LEU C 858 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 1117 through 1122 removed outlier: 3.747A pdb=" N SER C1120 " --> pdb=" O ALA C1084 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ALA C1084 " --> pdb=" O SER C1120 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 1091 through 1094 Processing sheet with id=AG1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AG2, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.683A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'L' and resid 4 through 7 removed outlier: 5.635A pdb=" N THR L 70 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 9.750A pdb=" N GLN L 27 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 9.691A pdb=" N SER L 68 " --> pdb=" O GLN L 27 " (cutoff:3.500A) removed outlier: 11.583A pdb=" N VAL L 29 " --> pdb=" O SER L 66 " (cutoff:3.500A) removed outlier: 12.122A pdb=" N SER L 66 " --> pdb=" O VAL L 29 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.630A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AG6, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AG7, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.683A pdb=" N GLY D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'E' and resid 4 through 7 removed outlier: 5.635A pdb=" N THR E 70 " --> pdb=" O ALA E 25 " (cutoff:3.500A) removed outlier: 9.749A pdb=" N GLN E 27 " --> pdb=" O SER E 68 " (cutoff:3.500A) removed outlier: 9.690A pdb=" N SER E 68 " --> pdb=" O GLN E 27 " (cutoff:3.500A) removed outlier: 11.582A pdb=" N VAL E 29 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 12.123A pdb=" N SER E 66 " --> pdb=" O VAL E 29 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.631A pdb=" N LEU E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N TYR E 50 " --> pdb=" O LEU E 34 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'E' and resid 10 through 13 Processing sheet with id=AH2, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AH3, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.683A pdb=" N GLY F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'G' and resid 4 through 7 removed outlier: 5.635A pdb=" N THR G 70 " --> pdb=" O ALA G 25 " (cutoff:3.500A) removed outlier: 9.750A pdb=" N GLN G 27 " --> pdb=" O SER G 68 " (cutoff:3.500A) removed outlier: 9.690A pdb=" N SER G 68 " --> pdb=" O GLN G 27 " (cutoff:3.500A) removed outlier: 11.581A pdb=" N VAL G 29 " --> pdb=" O SER G 66 " (cutoff:3.500A) removed outlier: 12.123A pdb=" N SER G 66 " --> pdb=" O VAL G 29 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'G' and resid 10 through 13 removed outlier: 6.630A pdb=" N LEU G 34 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N TYR G 50 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'G' and resid 10 through 13 1319 hydrogen bonds defined for protein. 3480 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: 17.31 Time building geometry restraints manager: 13.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9769 1.34 - 1.46: 7184 1.46 - 1.58: 14598 1.58 - 1.70: 0 1.70 - 1.82: 180 Bond restraints: 31731 Sorted by residual: bond pdb=" CA TRP D 121 " pdb=" C TRP D 121 " ideal model delta sigma weight residual 1.520 1.398 0.121 1.16e-02 7.43e+03 1.10e+02 bond pdb=" CA TRP H 121 " pdb=" C TRP H 121 " ideal model delta sigma weight residual 1.520 1.399 0.121 1.16e-02 7.43e+03 1.09e+02 bond pdb=" CA TRP F 121 " pdb=" C TRP F 121 " ideal model delta sigma weight residual 1.520 1.399 0.121 1.16e-02 7.43e+03 1.08e+02 bond pdb=" CA CYS H 101 " pdb=" CB CYS H 101 " ideal model delta sigma weight residual 1.531 1.464 0.067 1.51e-02 4.39e+03 1.96e+01 bond pdb=" CA CYS D 101 " pdb=" CB CYS D 101 " ideal model delta sigma weight residual 1.531 1.464 0.067 1.51e-02 4.39e+03 1.94e+01 ... (remaining 31726 not shown) Histogram of bond angle deviations from ideal: 98.88 - 106.63: 1016 106.63 - 114.38: 18572 114.38 - 122.13: 17272 122.13 - 129.88: 6191 129.88 - 137.63: 129 Bond angle restraints: 43180 Sorted by residual: angle pdb=" C CYS H 105 " pdb=" N PRO H 106 " pdb=" CA PRO H 106 " ideal model delta sigma weight residual 119.84 109.93 9.91 1.25e+00 6.40e-01 6.29e+01 angle pdb=" C CYS D 105 " pdb=" N PRO D 106 " pdb=" CA PRO D 106 " ideal model delta sigma weight residual 119.84 109.95 9.89 1.25e+00 6.40e-01 6.26e+01 angle pdb=" C CYS F 105 " pdb=" N PRO F 106 " pdb=" CA PRO F 106 " ideal model delta sigma weight residual 119.84 109.96 9.88 1.25e+00 6.40e-01 6.25e+01 angle pdb=" CA CYS D 101 " pdb=" CB CYS D 101 " pdb=" SG CYS D 101 " ideal model delta sigma weight residual 114.40 98.88 15.52 2.30e+00 1.89e-01 4.55e+01 angle pdb=" CA CYS H 101 " pdb=" CB CYS H 101 " pdb=" SG CYS H 101 " ideal model delta sigma weight residual 114.40 98.90 15.50 2.30e+00 1.89e-01 4.54e+01 ... (remaining 43175 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 18518 17.85 - 35.71: 810 35.71 - 53.56: 162 53.56 - 71.41: 42 71.41 - 89.26: 18 Dihedral angle restraints: 19550 sinusoidal: 8264 harmonic: 11286 Sorted by residual: dihedral pdb=" C CYS D 101 " pdb=" N CYS D 101 " pdb=" CA CYS D 101 " pdb=" CB CYS D 101 " ideal model delta harmonic sigma weight residual -122.60 -109.26 -13.34 0 2.50e+00 1.60e-01 2.85e+01 dihedral pdb=" C CYS H 101 " pdb=" N CYS H 101 " pdb=" CA CYS H 101 " pdb=" CB CYS H 101 " ideal model delta harmonic sigma weight residual -122.60 -109.26 -13.34 0 2.50e+00 1.60e-01 2.85e+01 dihedral pdb=" C CYS F 101 " pdb=" N CYS F 101 " pdb=" CA CYS F 101 " pdb=" CB CYS F 101 " ideal model delta harmonic sigma weight residual -122.60 -109.33 -13.27 0 2.50e+00 1.60e-01 2.82e+01 ... (remaining 19547 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 3586 0.046 - 0.091: 909 0.091 - 0.137: 414 0.137 - 0.183: 81 0.183 - 0.229: 25 Chirality restraints: 5015 Sorted by residual: chirality pdb=" CA PRO H 53 " pdb=" N PRO H 53 " pdb=" C PRO H 53 " pdb=" CB PRO H 53 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA PRO F 53 " pdb=" N PRO F 53 " pdb=" C PRO F 53 " pdb=" CB PRO F 53 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA PRO D 53 " pdb=" N PRO D 53 " pdb=" C PRO D 53 " pdb=" CB PRO D 53 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 5012 not shown) Planarity restraints: 5555 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1308 " -0.240 2.00e-02 2.50e+03 2.01e-01 5.03e+02 pdb=" C7 NAG B1308 " 0.063 2.00e-02 2.50e+03 pdb=" C8 NAG B1308 " -0.166 2.00e-02 2.50e+03 pdb=" N2 NAG B1308 " 0.335 2.00e-02 2.50e+03 pdb=" O7 NAG B1308 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP L 36 " 0.058 2.00e-02 2.50e+03 3.51e-02 3.08e+01 pdb=" CG TRP L 36 " -0.007 2.00e-02 2.50e+03 pdb=" CD1 TRP L 36 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TRP L 36 " -0.049 2.00e-02 2.50e+03 pdb=" NE1 TRP L 36 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP L 36 " -0.028 2.00e-02 2.50e+03 pdb=" CE3 TRP L 36 " -0.049 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 36 " 0.018 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 36 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP L 36 " 0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 36 " -0.058 2.00e-02 2.50e+03 3.50e-02 3.07e+01 pdb=" CG TRP E 36 " 0.007 2.00e-02 2.50e+03 pdb=" CD1 TRP E 36 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TRP E 36 " 0.049 2.00e-02 2.50e+03 pdb=" NE1 TRP E 36 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP E 36 " 0.029 2.00e-02 2.50e+03 pdb=" CE3 TRP E 36 " 0.048 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 36 " -0.018 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 36 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP E 36 " -0.054 2.00e-02 2.50e+03 ... (remaining 5552 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 958 2.71 - 3.25: 30537 3.25 - 3.80: 50386 3.80 - 4.35: 63216 4.35 - 4.90: 106475 Nonbonded interactions: 251572 Sorted by model distance: nonbonded pdb=" O GLY C 877 " pdb=" OG SER C 881 " model vdw 2.158 2.440 nonbonded pdb=" O GLU A 658 " pdb=" OH TYR A 692 " model vdw 2.172 2.440 nonbonded pdb=" O GLU B 306 " pdb=" OH TYR B 310 " model vdw 2.174 2.440 nonbonded pdb=" O ASN B 436 " pdb=" OG SER B 440 " model vdw 2.177 2.440 nonbonded pdb=" OD1 ASN C 99 " pdb=" NH2 ARG C 190 " model vdw 2.178 2.520 ... (remaining 251567 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 13 through 619 or resid 638 through 1144 or resid 1301 thr \ ough 1310)) selection = chain 'B' selection = (chain 'C' and (resid 13 through 619 or resid 638 through 1144 or resid 1301 thr \ ough 1310)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } 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: 2.500 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: 11.760 Check model and map are aligned: 0.460 Set scattering table: 0.300 Process input model: 87.780 Find NCS groups from input model: 2.450 Set up NCS constraints: 0.460 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: 0.020 Load rotamer database and sin/cos tables:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 108.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 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 : 0.006 0.121 31731 Z= 0.420 Angle : 0.864 15.518 43180 Z= 0.510 Chirality : 0.052 0.229 5015 Planarity : 0.006 0.201 5513 Dihedral : 10.861 89.264 12163 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.69 % Favored : 96.20 % Rotamer: Outliers : 1.22 % Allowed : 4.90 % Favored : 93.88 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.13), residues: 3845 helix: 1.21 (0.20), residues: 706 sheet: 0.16 (0.15), residues: 1043 loop : -0.59 (0.13), residues: 2096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.006 TRP L 36 HIS 0.006 0.001 HIS B1045 PHE 0.032 0.002 PHE D 64 TYR 0.041 0.003 TYR F 94 ARG 0.014 0.001 ARG G 55 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 3374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 378 time to evaluate : 3.478 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: B 135 PHE cc_start: 0.5455 (m-80) cc_final: 0.5008 (m-10) REVERT: B 177 MET cc_start: 0.0753 (ttm) cc_final: 0.0388 (ttp) REVERT: B 239 GLN cc_start: 0.7634 (tt0) cc_final: 0.7408 (tt0) REVERT: B 267 LEU cc_start: 0.8901 (mt) cc_final: 0.8598 (mp) REVERT: B 284 ASP cc_start: 0.7423 (t0) cc_final: 0.6945 (t0) REVERT: B 612 VAL cc_start: 0.8468 (OUTLIER) cc_final: 0.8225 (p) REVERT: B 760 LEU cc_start: 0.9542 (mt) cc_final: 0.9300 (mt) REVERT: A 54 LEU cc_start: 0.8996 (mt) cc_final: 0.8622 (mm) REVERT: A 65 PHE cc_start: 0.8646 (OUTLIER) cc_final: 0.8368 (m-80) REVERT: A 104 TRP cc_start: 0.7425 (m-90) cc_final: 0.7199 (m-90) REVERT: A 118 LEU cc_start: 0.8355 (tp) cc_final: 0.7741 (mp) REVERT: A 133 PHE cc_start: 0.6574 (m-80) cc_final: 0.4814 (m-80) REVERT: A 177 MET cc_start: 0.3712 (ttm) cc_final: 0.2445 (mtp) REVERT: A 221 SER cc_start: 0.7487 (t) cc_final: 0.7143 (m) REVERT: A 1139 GLN cc_start: 0.8813 (tp40) cc_final: 0.8469 (tm-30) REVERT: C 87 ASN cc_start: 0.8432 (m-40) cc_final: 0.7585 (m110) REVERT: C 143 VAL cc_start: 0.4888 (OUTLIER) cc_final: 0.4677 (p) REVERT: C 177 MET cc_start: 0.0661 (ttm) cc_final: -0.2168 (mmt) REVERT: C 263 TYR cc_start: 0.6344 (OUTLIER) cc_final: 0.5732 (m-80) REVERT: C 266 TYR cc_start: 0.7389 (m-80) cc_final: 0.7176 (m-10) REVERT: C 717 ILE cc_start: 0.9016 (mm) cc_final: 0.8811 (tt) REVERT: C 893 ILE cc_start: 0.9563 (OUTLIER) cc_final: 0.9215 (mt) REVERT: C 1020 ASN cc_start: 0.8699 (m-40) cc_final: 0.7381 (m-40) REVERT: H 81 MET cc_start: 0.4206 (tmm) cc_final: 0.3753 (ptt) REVERT: L 49 ILE cc_start: 0.7689 (mm) cc_final: 0.6809 (mm) REVERT: L 88 TYR cc_start: 0.1343 (m-80) cc_final: 0.1081 (m-80) REVERT: E 98 THR cc_start: 0.5772 (p) cc_final: 0.5217 (t) REVERT: G 4 MET cc_start: 0.4329 (mmm) cc_final: 0.3699 (mtt) outliers start: 41 outliers final: 12 residues processed: 416 average time/residue: 0.4308 time to fit residues: 286.7609 Evaluate side-chains 190 residues out of total 3374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 173 time to evaluate : 3.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1116 ASN Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 263 TYR Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 778 VAL Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain G residue 14 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 326 optimal weight: 5.9990 chunk 293 optimal weight: 0.9990 chunk 162 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 chunk 197 optimal weight: 4.9990 chunk 156 optimal weight: 5.9990 chunk 303 optimal weight: 0.9990 chunk 117 optimal weight: 5.9990 chunk 184 optimal weight: 5.9990 chunk 225 optimal weight: 6.9990 chunk 351 optimal weight: 0.0870 overall best weight: 2.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 ASN ** B 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 687 GLN ** A 946 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 975 ASN ** A 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 391 ASN C 638 ASN C 752 GLN ** C 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 801 GLN C 950 ASN C 962 GLN ** C1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 GLN E 91 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 31731 Z= 0.276 Angle : 0.585 9.023 43180 Z= 0.306 Chirality : 0.044 0.197 5015 Planarity : 0.004 0.051 5513 Dihedral : 6.773 58.766 5360 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.18 % Allowed : 9.34 % Favored : 88.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.13), residues: 3845 helix: 1.57 (0.19), residues: 703 sheet: 0.21 (0.15), residues: 1051 loop : -0.45 (0.14), residues: 2091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 883 HIS 0.006 0.001 HIS B1045 PHE 0.021 0.002 PHE A 135 TYR 0.033 0.001 TYR A 266 ARG 0.006 0.000 ARG C 574 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 3374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 177 time to evaluate : 3.768 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: B 135 PHE cc_start: 0.5260 (m-80) cc_final: 0.4977 (m-10) REVERT: B 177 MET cc_start: 0.1333 (ttm) cc_final: 0.1096 (ttp) REVERT: B 267 LEU cc_start: 0.9007 (mt) cc_final: 0.8690 (mp) REVERT: B 384 LEU cc_start: 0.8255 (mt) cc_final: 0.7728 (mt) REVERT: B 420 TYR cc_start: 0.5222 (t80) cc_final: 0.4850 (t80) REVERT: B 612 VAL cc_start: 0.8580 (OUTLIER) cc_final: 0.8346 (p) REVERT: B 696 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7634 (mt) REVERT: B 855 LEU cc_start: 0.8542 (mp) cc_final: 0.8232 (pp) REVERT: A 65 PHE cc_start: 0.8631 (OUTLIER) cc_final: 0.8355 (m-80) REVERT: A 177 MET cc_start: 0.4152 (ttm) cc_final: 0.2997 (mtp) REVERT: A 1139 GLN cc_start: 0.8875 (tp40) cc_final: 0.8557 (tm-30) REVERT: C 87 ASN cc_start: 0.8623 (m-40) cc_final: 0.7639 (m110) REVERT: C 118 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.8017 (mt) REVERT: C 177 MET cc_start: 0.1431 (ttm) cc_final: -0.1370 (mmt) REVERT: C 203 ILE cc_start: 0.9032 (OUTLIER) cc_final: 0.8812 (pt) REVERT: C 263 TYR cc_start: 0.6479 (OUTLIER) cc_final: 0.5883 (m-80) REVERT: C 717 ILE cc_start: 0.9025 (mm) cc_final: 0.8765 (tt) REVERT: C 777 GLU cc_start: 0.8357 (tt0) cc_final: 0.8156 (tt0) REVERT: C 893 ILE cc_start: 0.9578 (OUTLIER) cc_final: 0.9219 (mt) REVERT: C 959 LEU cc_start: 0.9433 (tp) cc_final: 0.9219 (tp) REVERT: H 81 MET cc_start: 0.4559 (tmm) cc_final: 0.3437 (ptt) REVERT: D 47 TRP cc_start: 0.2128 (t60) cc_final: 0.0605 (t60) REVERT: D 48 MET cc_start: 0.2294 (mtm) cc_final: 0.1246 (ptp) REVERT: E 4 MET cc_start: 0.4542 (mmt) cc_final: 0.4280 (mmt) REVERT: G 4 MET cc_start: 0.3697 (mmm) cc_final: 0.3331 (mtt) outliers start: 73 outliers final: 43 residues processed: 241 average time/residue: 0.4142 time to fit residues: 166.0612 Evaluate side-chains 181 residues out of total 3374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 131 time to evaluate : 3.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 263 TYR Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 769 VAL Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 881 SER Chi-restraints excluded: chain B residue 1063 THR Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1116 ASN Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1103 GLN Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 263 TYR Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 388 CYS Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 778 VAL Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 1027 SER Chi-restraints excluded: chain C residue 1112 ILE Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain E residue 14 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 195 optimal weight: 7.9990 chunk 109 optimal weight: 6.9990 chunk 292 optimal weight: 0.2980 chunk 239 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 352 optimal weight: 3.9990 chunk 380 optimal weight: 5.9990 chunk 313 optimal weight: 4.9990 chunk 349 optimal weight: 5.9990 chunk 120 optimal weight: 8.9990 chunk 282 optimal weight: 0.8980 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 781 GLN A 946 GLN A 975 ASN ** A 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 391 ASN ** C 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 801 GLN C 932 GLN C 954 GLN ** C1080 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 31731 Z= 0.273 Angle : 0.570 9.554 43180 Z= 0.295 Chirality : 0.043 0.284 5015 Planarity : 0.004 0.061 5513 Dihedral : 6.245 56.300 5354 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.01 % Allowed : 10.00 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.13), residues: 3845 helix: 1.79 (0.20), residues: 711 sheet: 0.18 (0.15), residues: 1071 loop : -0.45 (0.14), residues: 2063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 104 HIS 0.007 0.001 HIS B1045 PHE 0.025 0.002 PHE A 140 TYR 0.019 0.001 TYR B1064 ARG 0.006 0.000 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 3374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 148 time to evaluate : 3.233 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: B 177 MET cc_start: 0.1496 (ttm) cc_final: 0.0991 (ttt) REVERT: B 267 LEU cc_start: 0.9008 (mt) cc_final: 0.8696 (mp) REVERT: B 284 ASP cc_start: 0.7566 (t0) cc_final: 0.7139 (t0) REVERT: B 420 TYR cc_start: 0.4959 (t80) cc_final: 0.4560 (t80) REVERT: B 612 VAL cc_start: 0.8685 (OUTLIER) cc_final: 0.8412 (p) REVERT: B 696 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7622 (mt) REVERT: A 65 PHE cc_start: 0.8667 (OUTLIER) cc_final: 0.8381 (m-80) REVERT: A 153 MET cc_start: 0.4963 (mmt) cc_final: 0.4696 (mmt) REVERT: A 177 MET cc_start: 0.4259 (ttm) cc_final: 0.3227 (mtp) REVERT: A 799 PHE cc_start: 0.8238 (m-80) cc_final: 0.7991 (m-10) REVERT: C 24 LEU cc_start: 0.1203 (OUTLIER) cc_final: 0.0787 (tp) REVERT: C 118 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8023 (mt) REVERT: C 177 MET cc_start: 0.1073 (ttm) cc_final: -0.2148 (tpp) REVERT: C 203 ILE cc_start: 0.9015 (OUTLIER) cc_final: 0.8781 (pt) REVERT: C 263 TYR cc_start: 0.6491 (OUTLIER) cc_final: 0.5950 (m-80) REVERT: C 717 ILE cc_start: 0.9011 (mm) cc_final: 0.8772 (tt) REVERT: C 899 MET cc_start: 0.9088 (tpp) cc_final: 0.8762 (tpp) REVERT: C 976 ASP cc_start: 0.8634 (OUTLIER) cc_final: 0.8107 (t70) REVERT: H 81 MET cc_start: 0.3744 (tmm) cc_final: 0.3452 (tmm) REVERT: D 48 MET cc_start: 0.1862 (mtm) cc_final: 0.1261 (ptm) REVERT: G 4 MET cc_start: 0.3690 (mmm) cc_final: 0.3407 (mtt) outliers start: 101 outliers final: 68 residues processed: 241 average time/residue: 0.3851 time to fit residues: 157.6484 Evaluate side-chains 197 residues out of total 3374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 121 time to evaluate : 3.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 263 TYR Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 731 THR Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 767 ILE Chi-restraints excluded: chain B residue 802 ILE Chi-restraints excluded: chain B residue 881 SER Chi-restraints excluded: chain B residue 965 SER Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1057 VAL Chi-restraints excluded: chain B residue 1063 THR Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1116 ASN Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain A residue 976 ASP Chi-restraints excluded: chain A residue 1038 ASP Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1103 GLN Chi-restraints excluded: chain A residue 1116 ASN Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 263 TYR Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 388 CYS Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 568 ASP Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 696 LEU Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 778 VAL Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 1027 SER Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1112 ILE Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain E residue 14 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 347 optimal weight: 20.0000 chunk 264 optimal weight: 4.9990 chunk 182 optimal weight: 7.9990 chunk 38 optimal weight: 0.9980 chunk 168 optimal weight: 2.9990 chunk 236 optimal weight: 1.9990 chunk 353 optimal weight: 0.9980 chunk 374 optimal weight: 40.0000 chunk 184 optimal weight: 0.8980 chunk 334 optimal weight: 0.8980 chunk 100 optimal weight: 0.8980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 391 ASN ** C 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 950 ASN C 952 ASN C1080 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 31731 Z= 0.155 Angle : 0.505 9.313 43180 Z= 0.259 Chirality : 0.042 0.218 5015 Planarity : 0.003 0.057 5513 Dihedral : 5.626 54.556 5354 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.51 % Allowed : 11.01 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.14), residues: 3845 helix: 2.05 (0.20), residues: 709 sheet: 0.29 (0.15), residues: 1052 loop : -0.33 (0.14), residues: 2084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 104 HIS 0.004 0.001 HIS B1045 PHE 0.013 0.001 PHE B 140 TYR 0.017 0.001 TYR C 486 ARG 0.004 0.000 ARG B1011 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 3374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 148 time to evaluate : 3.588 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: B 135 PHE cc_start: 0.5120 (m-80) cc_final: 0.4797 (m-10) REVERT: B 177 MET cc_start: 0.1075 (ttm) cc_final: 0.0741 (ttt) REVERT: B 267 LEU cc_start: 0.8952 (mt) cc_final: 0.8667 (mp) REVERT: B 612 VAL cc_start: 0.8665 (OUTLIER) cc_final: 0.8399 (p) REVERT: B 696 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7648 (mt) REVERT: B 759 GLN cc_start: 0.8514 (pp30) cc_final: 0.8282 (pp30) REVERT: B 855 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8165 (pp) REVERT: A 65 PHE cc_start: 0.8617 (OUTLIER) cc_final: 0.8313 (m-80) REVERT: A 153 MET cc_start: 0.4880 (mmt) cc_final: 0.4601 (mmt) REVERT: A 177 MET cc_start: 0.3938 (ttm) cc_final: 0.2884 (mtp) REVERT: A 975 ASN cc_start: 0.9011 (t160) cc_final: 0.8784 (t0) REVERT: A 999 GLN cc_start: 0.8482 (tm-30) cc_final: 0.7964 (tm-30) REVERT: C 118 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7897 (mt) REVERT: C 120 VAL cc_start: 0.8054 (m) cc_final: 0.7762 (p) REVERT: C 177 MET cc_start: 0.0953 (ttm) cc_final: -0.2204 (tpp) REVERT: C 263 TYR cc_start: 0.6319 (OUTLIER) cc_final: 0.5873 (m-80) REVERT: C 893 ILE cc_start: 0.9542 (OUTLIER) cc_final: 0.9202 (mt) REVERT: C 959 LEU cc_start: 0.9463 (tp) cc_final: 0.9243 (tp) REVERT: C 976 ASP cc_start: 0.8667 (OUTLIER) cc_final: 0.8117 (t0) REVERT: H 63 LYS cc_start: 0.1714 (ptmt) cc_final: 0.1471 (mmtt) REVERT: D 32 TYR cc_start: 0.2256 (t80) cc_final: 0.2040 (t80) REVERT: D 48 MET cc_start: 0.2061 (mtm) cc_final: 0.1513 (ptm) REVERT: D 64 PHE cc_start: 0.3659 (m-80) cc_final: 0.2827 (m-80) REVERT: G 4 MET cc_start: 0.3601 (mmm) cc_final: 0.3305 (mtt) outliers start: 84 outliers final: 49 residues processed: 221 average time/residue: 0.3911 time to fit residues: 147.8975 Evaluate side-chains 188 residues out of total 3374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 131 time to evaluate : 3.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 263 TYR Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 447 ASN Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 855 LEU Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1116 ASN Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 976 ASP Chi-restraints excluded: chain A residue 1103 GLN Chi-restraints excluded: chain A residue 1116 ASN Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 263 TYR Chi-restraints excluded: chain C residue 311 GLN Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 366 TYR Chi-restraints excluded: chain C residue 388 CYS Chi-restraints excluded: chain C residue 537 ASN Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 696 LEU Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 1027 SER Chi-restraints excluded: chain C residue 1112 ILE Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain G residue 28 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 311 optimal weight: 0.4980 chunk 212 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 278 optimal weight: 2.9990 chunk 154 optimal weight: 20.0000 chunk 319 optimal weight: 2.9990 chunk 258 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 191 optimal weight: 2.9990 chunk 335 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 ASN ** A 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 748 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 801 GLN ** A 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 391 ASN C 771 GLN ** C 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 65 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 31731 Z= 0.240 Angle : 0.541 10.108 43180 Z= 0.277 Chirality : 0.042 0.309 5015 Planarity : 0.004 0.054 5513 Dihedral : 5.461 53.819 5351 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.22 % Allowed : 11.28 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.14), residues: 3845 helix: 2.04 (0.20), residues: 698 sheet: 0.28 (0.15), residues: 1054 loop : -0.36 (0.14), residues: 2093 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 104 HIS 0.006 0.001 HIS B1045 PHE 0.019 0.001 PHE C1086 TYR 0.023 0.001 TYR C 486 ARG 0.004 0.000 ARG D 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 3374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 140 time to evaluate : 3.404 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: B 177 MET cc_start: 0.1088 (ttm) cc_final: 0.0707 (ttt) REVERT: B 267 LEU cc_start: 0.8973 (mt) cc_final: 0.8673 (mp) REVERT: B 284 ASP cc_start: 0.7554 (t0) cc_final: 0.7117 (t0) REVERT: B 420 TYR cc_start: 0.4701 (t80) cc_final: 0.4308 (t80) REVERT: B 612 VAL cc_start: 0.8716 (OUTLIER) cc_final: 0.8466 (p) REVERT: B 696 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7602 (mt) REVERT: B 759 GLN cc_start: 0.8612 (pp30) cc_final: 0.8086 (pp30) REVERT: B 855 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8210 (pp) REVERT: A 65 PHE cc_start: 0.8637 (OUTLIER) cc_final: 0.8350 (m-80) REVERT: A 153 MET cc_start: 0.5010 (mmt) cc_final: 0.4708 (mmt) REVERT: A 177 MET cc_start: 0.4482 (ttm) cc_final: 0.3549 (mtp) REVERT: A 696 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8731 (mt) REVERT: A 799 PHE cc_start: 0.8247 (m-80) cc_final: 0.7991 (m-10) REVERT: A 975 ASN cc_start: 0.9117 (t160) cc_final: 0.8869 (t0) REVERT: A 999 GLN cc_start: 0.8567 (tm-30) cc_final: 0.8086 (tm-30) REVERT: C 24 LEU cc_start: 0.1520 (OUTLIER) cc_final: 0.1163 (tp) REVERT: C 118 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7929 (mt) REVERT: C 177 MET cc_start: 0.1180 (ttm) cc_final: -0.2095 (mmp) REVERT: C 263 TYR cc_start: 0.6306 (OUTLIER) cc_final: 0.5989 (m-80) REVERT: C 899 MET cc_start: 0.8997 (tpp) cc_final: 0.8710 (tpp) REVERT: C 959 LEU cc_start: 0.9511 (tp) cc_final: 0.9304 (tp) REVERT: C 976 ASP cc_start: 0.8687 (OUTLIER) cc_final: 0.8139 (t0) REVERT: H 39 GLN cc_start: 0.4569 (pp30) cc_final: 0.3732 (tt0) REVERT: H 63 LYS cc_start: 0.2219 (ptmt) cc_final: 0.1794 (mttm) REVERT: H 81 MET cc_start: 0.3841 (tmm) cc_final: 0.2770 (tmm) REVERT: D 48 MET cc_start: 0.1765 (mtm) cc_final: 0.1277 (ptm) REVERT: E 4 MET cc_start: 0.3740 (mmt) cc_final: 0.3517 (tpp) REVERT: G 4 MET cc_start: 0.3639 (mmm) cc_final: 0.3336 (mtt) outliers start: 108 outliers final: 73 residues processed: 229 average time/residue: 0.3730 time to fit residues: 146.7909 Evaluate side-chains 208 residues out of total 3374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 126 time to evaluate : 3.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 263 TYR Chi-restraints excluded: chain B residue 447 ASN Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 767 ILE Chi-restraints excluded: chain B residue 802 ILE Chi-restraints excluded: chain B residue 855 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1057 VAL Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1116 ASN Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain A residue 958 THR Chi-restraints excluded: chain A residue 976 ASP Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1103 GLN Chi-restraints excluded: chain A residue 1116 ASN Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 263 TYR Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 366 TYR Chi-restraints excluded: chain C residue 388 CYS Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 537 ASN Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 778 VAL Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 802 ILE Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 1005 VAL Chi-restraints excluded: chain C residue 1027 SER Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1112 ILE Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain F residue 57 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 125 optimal weight: 0.0040 chunk 336 optimal weight: 20.0000 chunk 73 optimal weight: 6.9990 chunk 219 optimal weight: 0.6980 chunk 92 optimal weight: 0.9980 chunk 374 optimal weight: 50.0000 chunk 310 optimal weight: 3.9990 chunk 173 optimal weight: 6.9990 chunk 31 optimal weight: 20.0000 chunk 123 optimal weight: 0.9990 chunk 196 optimal weight: 3.9990 overall best weight: 1.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 801 GLN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 367 ASN A 434 ASN ** A 748 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 801 GLN A 932 GLN A 975 ASN ** A 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 91 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 31731 Z= 0.173 Angle : 0.504 9.089 43180 Z= 0.258 Chirality : 0.042 0.199 5015 Planarity : 0.003 0.052 5513 Dihedral : 5.128 52.706 5351 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.66 % Allowed : 11.82 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.14), residues: 3845 helix: 2.08 (0.20), residues: 700 sheet: 0.34 (0.15), residues: 1042 loop : -0.31 (0.14), residues: 2103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 104 HIS 0.005 0.001 HIS B1045 PHE 0.012 0.001 PHE B1086 TYR 0.015 0.001 TYR A 366 ARG 0.003 0.000 ARG C1036 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 3374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 150 time to evaluate : 3.810 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: B 177 MET cc_start: 0.0784 (ttm) cc_final: 0.0237 (ttt) REVERT: B 267 LEU cc_start: 0.8935 (mt) cc_final: 0.8630 (mp) REVERT: B 284 ASP cc_start: 0.7381 (t0) cc_final: 0.6961 (t0) REVERT: B 420 TYR cc_start: 0.4621 (t80) cc_final: 0.4219 (t80) REVERT: B 612 VAL cc_start: 0.8707 (OUTLIER) cc_final: 0.8445 (p) REVERT: B 759 GLN cc_start: 0.8578 (pp30) cc_final: 0.8046 (pp30) REVERT: A 153 MET cc_start: 0.4763 (mmt) cc_final: 0.4446 (mmt) REVERT: A 177 MET cc_start: 0.3510 (ttm) cc_final: 0.2367 (mtp) REVERT: A 897 MET cc_start: 0.8813 (mmt) cc_final: 0.8580 (mmt) REVERT: A 975 ASN cc_start: 0.9143 (t0) cc_final: 0.8852 (t0) REVERT: A 999 GLN cc_start: 0.8577 (tm-30) cc_final: 0.8027 (tm-30) REVERT: C 24 LEU cc_start: 0.1744 (OUTLIER) cc_final: 0.1375 (tp) REVERT: C 118 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7853 (mt) REVERT: C 120 VAL cc_start: 0.8077 (m) cc_final: 0.7800 (p) REVERT: C 177 MET cc_start: 0.1077 (ttm) cc_final: -0.2146 (mmp) REVERT: C 893 ILE cc_start: 0.9519 (OUTLIER) cc_final: 0.9180 (mt) REVERT: C 899 MET cc_start: 0.8979 (tpp) cc_final: 0.8708 (tpp) REVERT: C 959 LEU cc_start: 0.9453 (tp) cc_final: 0.9244 (tp) REVERT: C 976 ASP cc_start: 0.8697 (OUTLIER) cc_final: 0.8134 (t0) REVERT: H 39 GLN cc_start: 0.4750 (pp30) cc_final: 0.3961 (tt0) REVERT: H 63 LYS cc_start: 0.2236 (ptmt) cc_final: 0.1861 (mttm) REVERT: H 81 MET cc_start: 0.3693 (tmm) cc_final: 0.2682 (tmm) REVERT: E 4 MET cc_start: 0.3656 (mmt) cc_final: 0.3223 (tpp) REVERT: G 4 MET cc_start: 0.3900 (mmm) cc_final: 0.3541 (mtt) outliers start: 89 outliers final: 64 residues processed: 224 average time/residue: 0.3843 time to fit residues: 147.2665 Evaluate side-chains 205 residues out of total 3374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 136 time to evaluate : 3.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 263 TYR Chi-restraints excluded: chain B residue 447 ASN Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 802 ILE Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 881 SER Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1116 ASN Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 767 ILE Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 976 ASP Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1103 GLN Chi-restraints excluded: chain A residue 1116 ASN Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 366 TYR Chi-restraints excluded: chain C residue 388 CYS Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 537 ASN Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 778 VAL Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 1027 SER Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1112 ILE Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain E residue 14 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 361 optimal weight: 10.0000 chunk 42 optimal weight: 8.9990 chunk 213 optimal weight: 3.9990 chunk 273 optimal weight: 0.5980 chunk 211 optimal weight: 0.8980 chunk 315 optimal weight: 0.9990 chunk 209 optimal weight: 0.9980 chunk 373 optimal weight: 3.9990 chunk 233 optimal weight: 5.9990 chunk 227 optimal weight: 4.9990 chunk 172 optimal weight: 5.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 GLN ** A 748 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 801 GLN ** C 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 932 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 31731 Z= 0.188 Angle : 0.513 9.284 43180 Z= 0.262 Chirality : 0.042 0.198 5015 Planarity : 0.003 0.051 5513 Dihedral : 4.956 52.588 5349 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.84 % Allowed : 12.09 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.14), residues: 3845 helix: 2.10 (0.20), residues: 699 sheet: 0.38 (0.15), residues: 1038 loop : -0.33 (0.14), residues: 2108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 104 HIS 0.005 0.001 HIS B1045 PHE 0.032 0.001 PHE A 799 TYR 0.024 0.001 TYR C 263 ARG 0.003 0.000 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 3374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 144 time to evaluate : 3.314 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: B 177 MET cc_start: 0.0856 (ttm) cc_final: 0.0300 (ttt) REVERT: B 267 LEU cc_start: 0.8882 (mt) cc_final: 0.8559 (mp) REVERT: B 284 ASP cc_start: 0.7561 (t0) cc_final: 0.7148 (t0) REVERT: B 420 TYR cc_start: 0.4618 (t80) cc_final: 0.4215 (t80) REVERT: B 612 VAL cc_start: 0.8731 (OUTLIER) cc_final: 0.8482 (p) REVERT: B 696 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7712 (mt) REVERT: B 759 GLN cc_start: 0.8531 (pp30) cc_final: 0.8032 (pp30) REVERT: A 65 PHE cc_start: 0.8605 (OUTLIER) cc_final: 0.8316 (m-80) REVERT: A 153 MET cc_start: 0.4682 (mmt) cc_final: 0.4355 (mmt) REVERT: A 177 MET cc_start: 0.3417 (ttm) cc_final: 0.2365 (mtp) REVERT: A 897 MET cc_start: 0.8804 (mmt) cc_final: 0.8522 (mmt) REVERT: A 999 GLN cc_start: 0.8590 (tm-30) cc_final: 0.8046 (tm-30) REVERT: C 118 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7859 (mt) REVERT: C 120 VAL cc_start: 0.8086 (m) cc_final: 0.7800 (p) REVERT: C 177 MET cc_start: 0.1097 (ttm) cc_final: -0.2087 (mmp) REVERT: C 893 ILE cc_start: 0.9516 (OUTLIER) cc_final: 0.9183 (mt) REVERT: C 899 MET cc_start: 0.9023 (tpp) cc_final: 0.8751 (tpp) REVERT: C 976 ASP cc_start: 0.8684 (OUTLIER) cc_final: 0.8113 (t0) REVERT: H 39 GLN cc_start: 0.4645 (pp30) cc_final: 0.3856 (tt0) REVERT: H 63 LYS cc_start: 0.2225 (ptmt) cc_final: 0.1923 (mttm) REVERT: H 81 MET cc_start: 0.3506 (tmm) cc_final: 0.2284 (tmm) REVERT: E 4 MET cc_start: 0.3422 (mmt) cc_final: 0.2902 (tpp) REVERT: G 4 MET cc_start: 0.3611 (mmm) cc_final: 0.3325 (mtt) outliers start: 95 outliers final: 74 residues processed: 222 average time/residue: 0.3742 time to fit residues: 142.7695 Evaluate side-chains 211 residues out of total 3374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 131 time to evaluate : 3.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 263 TYR Chi-restraints excluded: chain B residue 447 ASN Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 731 THR Chi-restraints excluded: chain B residue 767 ILE Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 802 ILE Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 881 SER Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1057 VAL Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1116 ASN Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 717 ILE Chi-restraints excluded: chain A residue 728 MET Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 976 ASP Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1103 GLN Chi-restraints excluded: chain A residue 1116 ASN Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 311 GLN Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 366 TYR Chi-restraints excluded: chain C residue 388 CYS Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 537 ASN Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 767 ILE Chi-restraints excluded: chain C residue 778 VAL Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 802 ILE Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 1027 SER Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1112 ILE Chi-restraints excluded: chain C residue 1129 ILE Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain E residue 14 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 230 optimal weight: 2.9990 chunk 148 optimal weight: 0.9990 chunk 222 optimal weight: 9.9990 chunk 112 optimal weight: 30.0000 chunk 73 optimal weight: 5.9990 chunk 72 optimal weight: 0.5980 chunk 237 optimal weight: 0.8980 chunk 254 optimal weight: 8.9990 chunk 184 optimal weight: 0.9990 chunk 34 optimal weight: 0.0000 chunk 293 optimal weight: 0.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 748 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 999 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 898 GLN ** C1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 31731 Z= 0.135 Angle : 0.499 12.874 43180 Z= 0.252 Chirality : 0.042 0.183 5015 Planarity : 0.003 0.051 5513 Dihedral : 4.664 51.815 5349 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.30 % Allowed : 12.54 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.14), residues: 3845 helix: 2.14 (0.20), residues: 698 sheet: 0.46 (0.15), residues: 1038 loop : -0.32 (0.14), residues: 2109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 104 HIS 0.005 0.001 HIS B1080 PHE 0.046 0.001 PHE A 799 TYR 0.020 0.001 TYR C 486 ARG 0.010 0.000 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 3374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 139 time to evaluate : 3.666 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: B 177 MET cc_start: 0.0439 (ttm) cc_final: 0.0021 (ttt) REVERT: B 267 LEU cc_start: 0.8851 (mt) cc_final: 0.8533 (mp) REVERT: B 420 TYR cc_start: 0.4516 (t80) cc_final: 0.4128 (t80) REVERT: B 612 VAL cc_start: 0.8685 (OUTLIER) cc_final: 0.8460 (p) REVERT: B 696 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7603 (mt) REVERT: B 759 GLN cc_start: 0.8527 (pp30) cc_final: 0.8056 (pp30) REVERT: A 177 MET cc_start: 0.3292 (ttm) cc_final: 0.2005 (mtp) REVERT: A 704 TYR cc_start: 0.8785 (t80) cc_final: 0.8421 (t80) REVERT: A 897 MET cc_start: 0.8799 (mmt) cc_final: 0.8555 (mmt) REVERT: A 999 GLN cc_start: 0.8596 (tm130) cc_final: 0.8050 (tm-30) REVERT: C 62 VAL cc_start: 0.8810 (OUTLIER) cc_final: 0.8519 (p) REVERT: C 118 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7835 (mt) REVERT: C 120 VAL cc_start: 0.8074 (m) cc_final: 0.7794 (p) REVERT: C 177 MET cc_start: 0.0508 (ttm) cc_final: -0.2559 (mmp) REVERT: C 899 MET cc_start: 0.8939 (tpp) cc_final: 0.8643 (tpp) REVERT: C 976 ASP cc_start: 0.8713 (OUTLIER) cc_final: 0.8139 (t0) REVERT: H 63 LYS cc_start: 0.2194 (ptmt) cc_final: 0.1866 (mttm) REVERT: H 81 MET cc_start: 0.3452 (tmm) cc_final: 0.2138 (tmm) REVERT: D 48 MET cc_start: -0.0231 (ptm) cc_final: -0.0915 (ptm) REVERT: E 4 MET cc_start: 0.3741 (mmt) cc_final: 0.3347 (tpp) REVERT: G 4 MET cc_start: 0.3854 (mmm) cc_final: 0.3524 (mtt) outliers start: 77 outliers final: 62 residues processed: 202 average time/residue: 0.4001 time to fit residues: 138.1367 Evaluate side-chains 191 residues out of total 3374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 124 time to evaluate : 3.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 263 TYR Chi-restraints excluded: chain B residue 447 ASN Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 731 THR Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 767 ILE Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 881 SER Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1113 THR Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 976 ASP Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1103 GLN Chi-restraints excluded: chain A residue 1116 ASN Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 311 GLN Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 366 TYR Chi-restraints excluded: chain C residue 388 CYS Chi-restraints excluded: chain C residue 537 ASN Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 778 VAL Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 1027 SER Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1112 ILE Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain E residue 14 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 339 optimal weight: 3.9990 chunk 357 optimal weight: 50.0000 chunk 326 optimal weight: 5.9990 chunk 347 optimal weight: 0.0060 chunk 209 optimal weight: 2.9990 chunk 151 optimal weight: 8.9990 chunk 272 optimal weight: 9.9990 chunk 106 optimal weight: 20.0000 chunk 314 optimal weight: 0.0050 chunk 328 optimal weight: 7.9990 chunk 346 optimal weight: 4.9990 overall best weight: 2.4016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 ASN ** A 748 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 771 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 391 ASN ** C 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1008 GLN D 35 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 31731 Z= 0.268 Angle : 0.568 12.169 43180 Z= 0.289 Chirality : 0.043 0.213 5015 Planarity : 0.004 0.049 5513 Dihedral : 4.889 54.264 5345 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.45 % Allowed : 12.75 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.14), residues: 3845 helix: 2.09 (0.20), residues: 689 sheet: 0.38 (0.15), residues: 1045 loop : -0.35 (0.14), residues: 2111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 64 HIS 0.006 0.001 HIS B1045 PHE 0.036 0.002 PHE C 453 TYR 0.037 0.001 TYR C 486 ARG 0.006 0.000 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 3374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 125 time to evaluate : 3.803 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: B 177 MET cc_start: 0.0950 (ttm) cc_final: 0.0450 (ttt) REVERT: B 267 LEU cc_start: 0.8892 (mt) cc_final: 0.8591 (mp) REVERT: B 284 ASP cc_start: 0.7573 (t0) cc_final: 0.7146 (t0) REVERT: B 420 TYR cc_start: 0.4639 (t80) cc_final: 0.4233 (t80) REVERT: B 612 VAL cc_start: 0.8789 (OUTLIER) cc_final: 0.8536 (p) REVERT: B 696 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.7767 (mt) REVERT: B 1026 MET cc_start: 0.8843 (tpp) cc_final: 0.8581 (tpp) REVERT: A 65 PHE cc_start: 0.8537 (OUTLIER) cc_final: 0.8255 (m-80) REVERT: A 177 MET cc_start: 0.3864 (ttm) cc_final: 0.1860 (mtp) REVERT: A 696 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8837 (mt) REVERT: A 897 MET cc_start: 0.8868 (mmt) cc_final: 0.8553 (mmt) REVERT: C 118 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7908 (mt) REVERT: C 177 MET cc_start: 0.0597 (ttm) cc_final: -0.2114 (mmp) REVERT: C 976 ASP cc_start: 0.8676 (OUTLIER) cc_final: 0.8074 (t0) REVERT: H 63 LYS cc_start: 0.2195 (ptmt) cc_final: 0.1883 (mtmt) REVERT: H 81 MET cc_start: 0.3513 (tmm) cc_final: 0.2121 (tmm) REVERT: D 48 MET cc_start: 0.0040 (ptm) cc_final: -0.0715 (ptm) REVERT: E 4 MET cc_start: 0.3873 (mmt) cc_final: 0.3440 (tpp) REVERT: G 4 MET cc_start: 0.3635 (mmm) cc_final: 0.3345 (mtt) outliers start: 82 outliers final: 70 residues processed: 194 average time/residue: 0.3920 time to fit residues: 131.2525 Evaluate side-chains 195 residues out of total 3374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 119 time to evaluate : 3.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 263 TYR Chi-restraints excluded: chain B residue 447 ASN Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 731 THR Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 767 ILE Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 881 SER Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1057 VAL Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1113 THR Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1103 GLN Chi-restraints excluded: chain A residue 1116 ASN Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 366 TYR Chi-restraints excluded: chain C residue 388 CYS Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 537 ASN Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 778 VAL Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 1005 VAL Chi-restraints excluded: chain C residue 1027 SER Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1112 ILE Chi-restraints excluded: chain C residue 1129 ILE Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain G residue 22 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 228 optimal weight: 7.9990 chunk 367 optimal weight: 50.0000 chunk 224 optimal weight: 8.9990 chunk 174 optimal weight: 0.9990 chunk 255 optimal weight: 20.0000 chunk 385 optimal weight: 0.8980 chunk 354 optimal weight: 20.0000 chunk 307 optimal weight: 2.9990 chunk 31 optimal weight: 9.9990 chunk 237 optimal weight: 0.5980 chunk 188 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 904 ASN ** A 748 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 391 ASN ** C 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 31731 Z= 0.187 Angle : 0.528 9.877 43180 Z= 0.267 Chirality : 0.042 0.206 5015 Planarity : 0.003 0.059 5513 Dihedral : 4.754 54.550 5345 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.21 % Allowed : 13.25 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.14), residues: 3845 helix: 2.16 (0.20), residues: 691 sheet: 0.45 (0.15), residues: 1028 loop : -0.36 (0.14), residues: 2126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 104 HIS 0.005 0.001 HIS B1045 PHE 0.022 0.001 PHE A 799 TYR 0.023 0.001 TYR C 486 ARG 0.005 0.000 ARG L 24 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 3374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 128 time to evaluate : 3.553 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: B 177 MET cc_start: 0.1005 (ttm) cc_final: 0.0543 (ttt) REVERT: B 267 LEU cc_start: 0.8851 (mt) cc_final: 0.8541 (mp) REVERT: B 284 ASP cc_start: 0.7411 (t0) cc_final: 0.6991 (t0) REVERT: B 420 TYR cc_start: 0.4547 (t80) cc_final: 0.4141 (t80) REVERT: B 579 LEU cc_start: 0.8654 (mm) cc_final: 0.8267 (pt) REVERT: B 612 VAL cc_start: 0.8767 (OUTLIER) cc_final: 0.8514 (p) REVERT: B 696 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7782 (mt) REVERT: B 1026 MET cc_start: 0.8819 (tpp) cc_final: 0.8534 (tpp) REVERT: A 177 MET cc_start: 0.3564 (ttm) cc_final: 0.2430 (mtp) REVERT: C 62 VAL cc_start: 0.8787 (OUTLIER) cc_final: 0.8488 (p) REVERT: C 118 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7898 (mt) REVERT: C 177 MET cc_start: 0.0421 (ttm) cc_final: -0.2360 (mmp) REVERT: C 893 ILE cc_start: 0.9523 (OUTLIER) cc_final: 0.9121 (mt) REVERT: C 976 ASP cc_start: 0.8690 (OUTLIER) cc_final: 0.8110 (t0) REVERT: H 63 LYS cc_start: 0.2230 (ptmt) cc_final: 0.1892 (mtmt) REVERT: H 81 MET cc_start: 0.3531 (tmm) cc_final: 0.2131 (tmm) REVERT: D 48 MET cc_start: 0.0139 (ptm) cc_final: -0.0593 (ptm) REVERT: E 4 MET cc_start: 0.3943 (mmt) cc_final: 0.3460 (tpp) REVERT: G 4 MET cc_start: 0.3640 (mmm) cc_final: 0.3363 (mtt) outliers start: 74 outliers final: 63 residues processed: 192 average time/residue: 0.3939 time to fit residues: 130.3971 Evaluate side-chains 190 residues out of total 3374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 121 time to evaluate : 3.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 263 TYR Chi-restraints excluded: chain B residue 447 ASN Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 731 THR Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 767 ILE Chi-restraints excluded: chain B residue 778 VAL Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 881 SER Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1057 VAL Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1113 THR Chi-restraints excluded: chain A residue 65 PHE Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1103 GLN Chi-restraints excluded: chain A residue 1116 ASN Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 65 PHE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 366 TYR Chi-restraints excluded: chain C residue 388 CYS Chi-restraints excluded: chain C residue 392 VAL Chi-restraints excluded: chain C residue 537 ASN Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 595 ILE Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 721 THR Chi-restraints excluded: chain C residue 778 VAL Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 893 ILE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 ASP Chi-restraints excluded: chain C residue 1027 SER Chi-restraints excluded: chain C residue 1063 THR Chi-restraints excluded: chain C residue 1101 VAL Chi-restraints excluded: chain C residue 1112 ILE Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 129 VAL Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain D residue 80 TYR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain F residue 57 THR Chi-restraints excluded: chain G residue 28 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 387 random chunks: chunk 243 optimal weight: 8.9990 chunk 327 optimal weight: 7.9990 chunk 94 optimal weight: 3.9990 chunk 283 optimal weight: 4.9990 chunk 45 optimal weight: 20.0000 chunk 85 optimal weight: 0.9980 chunk 307 optimal weight: 2.9990 chunk 128 optimal weight: 0.4980 chunk 315 optimal weight: 0.9980 chunk 38 optimal weight: 7.9990 chunk 56 optimal weight: 2.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 748 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 391 ASN ** C 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.120456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.087417 restraints weight = 166082.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.086100 restraints weight = 133275.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.086040 restraints weight = 114403.009| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 31731 Z= 0.209 Angle : 0.539 10.223 43180 Z= 0.273 Chirality : 0.042 0.207 5015 Planarity : 0.004 0.054 5513 Dihedral : 4.764 54.956 5345 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.45 % Allowed : 13.10 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.14), residues: 3845 helix: 2.08 (0.20), residues: 696 sheet: 0.37 (0.15), residues: 1046 loop : -0.37 (0.14), residues: 2103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 64 HIS 0.005 0.001 HIS B1045 PHE 0.018 0.001 PHE A 799 TYR 0.019 0.001 TYR C 486 ARG 0.002 0.000 ARG A 997 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5180.19 seconds wall clock time: 96 minutes 41.70 seconds (5801.70 seconds total)