Starting phenix.real_space_refine on Wed Mar 20 11:48:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q9k_13872/03_2024/7q9k_13872.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q9k_13872/03_2024/7q9k_13872.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q9k_13872/03_2024/7q9k_13872.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q9k_13872/03_2024/7q9k_13872.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q9k_13872/03_2024/7q9k_13872.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q9k_13872/03_2024/7q9k_13872.pdb" } resolution = 4.5 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= -0.000 sd= 0.026 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 119 5.16 5 C 17312 2.51 5 N 4453 2.21 5 O 5341 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 27225 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 7336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 943, 7336 Classifications: {'peptide': 943} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 45, 'TRANS': 897} Chain breaks: 8 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 7819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7819 Classifications: {'peptide': 1002} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 49, 'TRANS': 952} Chain breaks: 7 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 7646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 979, 7646 Classifications: {'peptide': 979} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 47, 'TRANS': 931} Chain breaks: 8 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 980 Classifications: {'peptide': 125} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 120} Chain: "L" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 812 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "D" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 980 Classifications: {'peptide': 125} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 120} Chain: "E" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 812 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 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: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 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: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 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: 13.56, per 1000 atoms: 0.50 Number of scatterers: 27225 At special positions: 0 Unit cell: (140.22, 141.04, 205, 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 119 16.00 O 5341 8.00 N 4453 7.00 C 17312 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 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 535 " - pdb=" SG CYS A 587 " distance=2.03 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 B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 298 " distance=2.03 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=2.03 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=2.02 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 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=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.05 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.06 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.05 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.06 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 F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 279 " " NAG A1304 " - " ASN A 328 " " NAG A1305 " - " ASN A 600 " " NAG A1306 " - " ASN A 613 " " NAG A1307 " - " ASN A 654 " " NAG A1308 " - " ASN A 706 " " NAG A1309 " - " ASN A1071 " " NAG A1310 " - " ASN A 165 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 279 " " NAG B1304 " - " ASN B 328 " " NAG B1305 " - " ASN B 600 " " NAG B1306 " - " ASN B 613 " " NAG B1307 " - " ASN B 654 " " NAG B1308 " - " ASN B 706 " " NAG B1309 " - " ASN B1071 " " NAG B1310 " - " ASN B 165 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 279 " " NAG C1304 " - " ASN C 328 " " NAG C1305 " - " ASN C 600 " " NAG C1306 " - " ASN C 613 " " NAG C1307 " - " ASN C 654 " " NAG C1308 " - " ASN C 706 " " NAG C1309 " - " ASN C1071 " " NAG C1310 " - " ASN C 165 " " NAG F 1 " - " ASN A 234 " " NAG G 1 " - " ASN A 714 " " NAG I 1 " - " ASN A 798 " " NAG J 1 " - " ASN A1095 " " NAG K 1 " - " ASN A1131 " " NAG M 1 " - " ASN B 234 " " NAG N 1 " - " ASN B 714 " " NAG O 1 " - " ASN B 798 " " NAG P 1 " - " ASN B1095 " " NAG Q 1 " - " ASN B1131 " " NAG R 1 " - " ASN C 234 " " NAG S 1 " - " ASN C 714 " " NAG T 1 " - " ASN C 798 " " NAG U 1 " - " ASN C1095 " " NAG V 1 " - " ASN C1131 " Time building additional restraints: 10.10 Conformation dependent library (CDL) restraints added in 4.8 seconds 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6312 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 49 sheets defined 24.2% alpha, 31.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.73 Creating SS restraints... Processing helix chain 'A' and resid 291 through 301 Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 362 through 368 removed outlier: 3.563A pdb=" N TYR A 366 " --> pdb=" O TYR A 362 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER A 368 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 385 removed outlier: 4.247A pdb=" N ASN A 385 " --> pdb=" O THR A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 405 removed outlier: 4.363A pdb=" N ARG A 405 " --> pdb=" O GLY A 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 401 through 405' Processing helix chain 'A' and resid 413 through 419 Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 734 through 740 Processing helix chain 'A' and resid 743 through 751 Processing helix chain 'A' and resid 752 through 756 removed outlier: 7.054A pdb=" N SER A 755 " --> pdb=" O GLN A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 780 removed outlier: 3.594A pdb=" N ASN A 761 " --> pdb=" O CYS A 757 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP A 772 " --> pdb=" O ALA A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 821 Processing helix chain 'A' and resid 863 through 882 Processing helix chain 'A' and resid 883 through 888 removed outlier: 3.771A pdb=" N ALA A 887 " --> pdb=" O TRP A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 905 Processing helix chain 'A' and resid 909 through 916 removed outlier: 4.071A pdb=" N LEU A 913 " --> pdb=" O THR A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 938 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 962 removed outlier: 3.898A pdb=" N VAL A 948 " --> pdb=" O LYS A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 965 No H-bonds generated for 'chain 'A' and resid 963 through 965' Processing helix chain 'A' and resid 973 through 979 Processing helix chain 'A' and resid 982 through 1030 removed outlier: 4.603A pdb=" N VAL A 988 " --> pdb=" O PRO A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 1138 through 1144 Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 335 through 340 Processing helix chain 'B' and resid 362 through 368 removed outlier: 3.563A pdb=" N TYR B 366 " --> pdb=" O TYR B 362 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER B 368 " --> pdb=" O VAL B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 385 removed outlier: 4.247A pdb=" N ASN B 385 " --> pdb=" O THR B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 405 removed outlier: 4.362A 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 499 through 502 Processing helix chain 'B' and resid 734 through 740 Processing helix chain 'B' and resid 743 through 751 Processing helix chain 'B' and resid 752 through 756 removed outlier: 7.054A pdb=" N SER B 755 " --> pdb=" O GLN B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 780 removed outlier: 3.595A pdb=" N ASN B 761 " --> pdb=" O CYS B 757 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP B 772 " --> pdb=" O ALA B 768 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 821 Processing helix chain 'B' and resid 863 through 882 Processing helix chain 'B' and resid 883 through 888 removed outlier: 3.772A pdb=" N ALA B 887 " --> pdb=" O TRP B 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 905 Processing helix chain 'B' and resid 909 through 916 removed outlier: 4.068A pdb=" N LEU B 913 " --> pdb=" O THR B 909 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 938 Processing helix chain 'B' and resid 939 through 941 No H-bonds generated for 'chain 'B' and resid 939 through 941' Processing helix chain 'B' and resid 942 through 962 removed outlier: 3.896A pdb=" N VAL B 948 " --> pdb=" O LYS B 944 " (cutoff:3.500A) Processing helix chain 'B' and resid 963 through 965 No H-bonds generated for 'chain 'B' and resid 963 through 965' Processing helix chain 'B' and resid 973 through 979 Processing helix chain 'B' and resid 982 through 1030 removed outlier: 4.603A pdb=" N VAL B 988 " --> pdb=" O PRO B 984 " (cutoff:3.500A) Processing helix chain 'B' and resid 1138 through 1144 Processing helix chain 'C' and resid 291 through 301 Processing helix chain 'C' and resid 335 through 340 Processing helix chain 'C' and resid 362 through 368 removed outlier: 3.563A pdb=" N TYR C 366 " --> pdb=" O TYR C 362 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER C 368 " --> pdb=" O VAL C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 385 removed outlier: 4.247A pdb=" N ASN C 385 " --> pdb=" O THR C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 405 removed outlier: 4.363A pdb=" N ARG C 405 " --> pdb=" O GLY C 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 401 through 405' Processing helix chain 'C' and resid 413 through 419 Processing helix chain 'C' and resid 499 through 502 Processing helix chain 'C' and resid 734 through 740 Processing helix chain 'C' and resid 743 through 751 Processing helix chain 'C' and resid 752 through 756 removed outlier: 7.054A pdb=" N SER C 755 " --> pdb=" O GLN C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 780 removed outlier: 3.597A pdb=" N ASN C 761 " --> pdb=" O CYS C 757 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP C 772 " --> pdb=" O ALA C 768 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 821 Processing helix chain 'C' and resid 863 through 882 Processing helix chain 'C' and resid 883 through 888 removed outlier: 3.772A pdb=" N ALA C 887 " --> pdb=" O TRP C 883 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 905 Processing helix chain 'C' and resid 909 through 916 removed outlier: 4.069A pdb=" N LEU C 913 " --> pdb=" O THR C 909 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 938 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 962 removed outlier: 3.898A pdb=" N VAL C 948 " --> pdb=" O LYS C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 963 through 965 No H-bonds generated for 'chain 'C' and resid 963 through 965' Processing helix chain 'C' and resid 973 through 979 Processing helix chain 'C' and resid 982 through 1030 removed outlier: 4.602A pdb=" N VAL C 988 " --> pdb=" O PRO C 984 " (cutoff:3.500A) Processing helix chain 'C' and resid 1138 through 1144 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.744A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 107 through 111 removed outlier: 3.846A pdb=" N TRP H 111 " --> pdb=" O SER H 108 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.742A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 76 No H-bonds generated for 'chain 'D' and resid 74 through 76' Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'D' and resid 107 through 111 removed outlier: 3.846A pdb=" N TRP D 111 " --> pdb=" O SER D 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 3.504A pdb=" N THR A 29 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL A 62 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N ASN A 61 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N TYR A 266 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.747A pdb=" N ALA C 572 " --> pdb=" O GLY C 563 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ASP C 571 " --> pdb=" O ILE C 584 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLU C 321 " --> pdb=" O CYS C 535 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 52 removed outlier: 3.590A pdb=" N VAL A 47 " --> pdb=" O TYR A 276 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASP A 284 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.331A pdb=" N LEU A 141 " --> pdb=" O SER A 244 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.902A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ILE A 101 " --> pdb=" O ILE A 243 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 308 through 313 removed outlier: 6.892A pdb=" N VAL A 592 " --> pdb=" O THR A 312 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLY A 591 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 321 through 325 removed outlier: 4.387A pdb=" N GLU A 321 " --> pdb=" O CYS A 535 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N ASP A 571 " --> pdb=" O ILE A 584 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA A 572 " --> pdb=" O GLY A 563 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N PHE A 562 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 351 through 355 removed outlier: 3.646A pdb=" N ASN A 391 " --> pdb=" O GLU A 513 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 651 through 652 removed outlier: 5.954A pdb=" N GLU A 651 " --> pdb=" O ALA A 691 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N THR A 693 " --> pdb=" O GLU A 651 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE A 667 " --> pdb=" O ILE A 663 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 708 through 725 removed outlier: 6.381A pdb=" N SER A 708 " --> pdb=" O THR A1073 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N THR A1073 " --> pdb=" O SER A 708 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ALA A 710 " --> pdb=" O ASN A1071 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ASN A1071 " --> pdb=" O ALA A 710 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLU A1069 " --> pdb=" O PRO A 712 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ASN A 714 " --> pdb=" O ALA A1067 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N TYR A1064 " --> pdb=" O HIS A1045 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N HIS A1045 " --> pdb=" O TYR A1064 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 708 through 725 removed outlier: 6.381A pdb=" N SER A 708 " --> pdb=" O THR A1073 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N THR A1073 " --> pdb=" O SER A 708 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ALA A 710 " --> pdb=" O ASN A1071 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ASN A1071 " --> pdb=" O ALA A 710 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLU A1069 " --> pdb=" O PRO A 712 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ASN A 714 " --> pdb=" O ALA A1067 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA A1075 " --> pdb=" O PHE A1092 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N PHE A1092 " --> pdb=" O ALA A1075 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 730 through 733 removed outlier: 4.560A pdb=" N LYS A 730 " --> pdb=" O LEU A 858 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1117 through 1122 removed outlier: 4.491A pdb=" N ALA A1084 " --> pdb=" O SER A1120 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 28 through 30 removed outlier: 3.504A pdb=" N THR B 29 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL B 62 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N ASN B 61 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N TYR B 266 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 47 through 52 removed outlier: 3.589A pdb=" N VAL B 47 " --> pdb=" O TYR B 276 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASP B 284 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.329A pdb=" N LEU B 141 " --> pdb=" O SER B 244 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.902A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ILE B 101 " --> pdb=" O ILE B 243 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 308 through 313 removed outlier: 6.892A pdb=" N VAL B 592 " --> pdb=" O THR B 312 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLY B 591 " --> pdb=" O GLN B 610 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 321 through 325 removed outlier: 4.385A pdb=" N GLU B 321 " --> pdb=" O CYS B 535 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ASP B 571 " --> pdb=" O ILE B 584 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA B 572 " --> pdb=" O GLY B 563 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N PHE B 562 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 351 through 355 removed outlier: 3.646A pdb=" N ASN B 391 " --> pdb=" O GLU B 513 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AC4, first strand: chain 'B' and resid 470 through 471 Processing sheet with id=AC5, first strand: chain 'B' and resid 651 through 652 removed outlier: 5.954A pdb=" N GLU B 651 " --> pdb=" O ALA B 691 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N THR B 693 " --> pdb=" O GLU B 651 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE B 667 " --> pdb=" O ILE B 663 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 708 through 725 removed outlier: 6.380A pdb=" N SER B 708 " --> pdb=" O THR B1073 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR B1073 " --> pdb=" O SER B 708 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ALA B 710 " --> pdb=" O ASN B1071 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N ASN B1071 " --> pdb=" O ALA B 710 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N GLU B1069 " --> pdb=" O PRO B 712 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ASN B 714 " --> pdb=" O ALA B1067 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N TYR B1064 " --> pdb=" O HIS B1045 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N HIS B1045 " --> pdb=" O TYR B1064 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 708 through 725 removed outlier: 6.380A pdb=" N SER B 708 " --> pdb=" O THR B1073 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR B1073 " --> pdb=" O SER B 708 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ALA B 710 " --> pdb=" O ASN B1071 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N ASN B1071 " --> pdb=" O ALA B 710 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N GLU B1069 " --> pdb=" O PRO B 712 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ASN B 714 " --> pdb=" O ALA B1067 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ALA B1075 " --> pdb=" O PHE B1092 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE B1092 " --> pdb=" O ALA B1075 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 730 through 733 removed outlier: 4.559A pdb=" N LYS B 730 " --> pdb=" O LEU B 858 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 1117 through 1122 removed outlier: 4.491A pdb=" N ALA B1084 " --> pdb=" O SER B1120 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 28 through 30 removed outlier: 3.504A pdb=" N THR C 29 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL C 62 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N ASN C 61 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N TYR C 266 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 47 through 52 removed outlier: 3.589A pdb=" N VAL C 47 " --> pdb=" O TYR C 276 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ASP C 284 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.331A pdb=" N LEU C 141 " --> pdb=" O SER C 244 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.902A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ILE C 101 " --> pdb=" O ILE C 243 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 308 through 313 removed outlier: 6.893A pdb=" N VAL C 592 " --> pdb=" O THR C 312 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLY C 591 " --> pdb=" O GLN C 610 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 351 through 355 removed outlier: 3.645A pdb=" N ASN C 391 " --> pdb=" O GLU C 513 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 449 through 450 Processing sheet with id=AD8, first strand: chain 'C' and resid 651 through 652 removed outlier: 5.955A pdb=" N GLU C 651 " --> pdb=" O ALA C 691 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N THR C 693 " --> pdb=" O GLU C 651 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE C 667 " --> pdb=" O ILE C 663 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 708 through 725 removed outlier: 6.380A pdb=" N SER C 708 " --> pdb=" O THR C1073 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N THR C1073 " --> pdb=" O SER C 708 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ALA C 710 " --> pdb=" O ASN C1071 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N ASN C1071 " --> pdb=" O ALA C 710 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N GLU C1069 " --> pdb=" O PRO C 712 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ASN C 714 " --> pdb=" O ALA C1067 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N TYR C1064 " --> pdb=" O HIS C1045 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N HIS C1045 " --> pdb=" O TYR C1064 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 708 through 725 removed outlier: 6.380A pdb=" N SER C 708 " --> pdb=" O THR C1073 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N THR C1073 " --> pdb=" O SER C 708 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ALA C 710 " --> pdb=" O ASN C1071 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N ASN C1071 " --> pdb=" O ALA C 710 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N GLU C1069 " --> pdb=" O PRO C 712 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ASN C 714 " --> pdb=" O ALA C1067 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA C1075 " --> pdb=" O PHE C1092 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N PHE C1092 " --> pdb=" O ALA C1075 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 730 through 733 removed outlier: 4.558A pdb=" N LYS C 730 " --> pdb=" O LEU C 858 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 1117 through 1122 removed outlier: 4.492A pdb=" N ALA C1084 " --> pdb=" O SER C1120 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AE5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.749A pdb=" N MET H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N TRP H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'L' and resid 4 through 7 removed outlier: 4.228A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER L 67 " --> pdb=" O ASP L 70 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 10 through 14 removed outlier: 6.345A pdb=" N VAL L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N LYS L 107 " --> pdb=" O VAL L 11 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ALA L 13 " --> pdb=" O LYS L 107 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA L 84 " --> pdb=" O VAL L 104 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'L' and resid 10 through 14 removed outlier: 6.345A pdb=" N VAL L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N LYS L 107 " --> pdb=" O VAL L 11 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ALA L 13 " --> pdb=" O LYS L 107 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA L 84 " --> pdb=" O VAL L 104 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AF1, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.749A pdb=" N MET D 34 " --> pdb=" O TRP D 50 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N TRP D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N TRP D 36 " --> pdb=" O MET D 48 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 4 through 7 removed outlier: 4.228A pdb=" N ASP E 70 " --> pdb=" O SER E 67 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER E 67 " --> pdb=" O ASP E 70 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 10 through 14 removed outlier: 6.346A pdb=" N VAL E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N LYS E 107 " --> pdb=" O VAL E 11 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ALA E 13 " --> pdb=" O LYS E 107 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA E 84 " --> pdb=" O VAL E 104 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 10 through 14 removed outlier: 6.346A pdb=" N VAL E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N LYS E 107 " --> pdb=" O VAL E 11 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ALA E 13 " --> pdb=" O LYS E 107 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA E 84 " --> pdb=" O VAL E 104 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR E 97 " --> pdb=" O GLN E 90 " (cutoff:3.500A) 1164 hydrogen bonds defined for protein. 3162 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.37 Time building geometry restraints manager: 11.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.02 - 1.18: 1 1.18 - 1.35: 8616 1.35 - 1.51: 8406 1.51 - 1.67: 10655 1.67 - 1.83: 153 Bond restraints: 27831 Sorted by residual: bond pdb=" C ASN A 328 " pdb=" N ILE A 329 " ideal model delta sigma weight residual 1.331 1.020 0.311 1.05e-02 9.07e+03 8.78e+02 bond pdb=" C TYR D 104 " pdb=" O TYR D 104 " ideal model delta sigma weight residual 1.233 1.346 -0.113 1.21e-02 6.83e+03 8.76e+01 bond pdb=" C TYR H 104 " pdb=" O TYR H 104 " ideal model delta sigma weight residual 1.233 1.345 -0.112 1.21e-02 6.83e+03 8.56e+01 bond pdb=" N PRO B 524 " pdb=" CD PRO B 524 " ideal model delta sigma weight residual 1.473 1.524 -0.051 1.40e-02 5.10e+03 1.35e+01 bond pdb=" CA TYR H 104 " pdb=" C TYR H 104 " ideal model delta sigma weight residual 1.523 1.557 -0.033 1.30e-02 5.92e+03 6.63e+00 ... (remaining 27826 not shown) Histogram of bond angle deviations from ideal: 46.89 - 67.91: 2 67.91 - 88.93: 0 88.93 - 109.95: 4598 109.95 - 130.98: 33181 130.98 - 152.00: 80 Bond angle restraints: 37861 Sorted by residual: angle pdb=" C ASN A 328 " pdb=" N ILE A 329 " pdb=" CA ILE A 329 " ideal model delta sigma weight residual 122.48 49.07 73.41 1.25e+00 6.40e-01 3.45e+03 angle pdb=" CA ASN A 328 " pdb=" C ASN A 328 " pdb=" N ILE A 329 " ideal model delta sigma weight residual 116.84 46.89 69.95 1.71e+00 3.42e-01 1.67e+03 angle pdb=" O ASN A 328 " pdb=" C ASN A 328 " pdb=" N ILE A 329 " ideal model delta sigma weight residual 122.59 152.00 -29.41 1.33e+00 5.65e-01 4.89e+02 angle pdb=" CA LYS A 525 " pdb=" C LYS A 525 " pdb=" N LYS A 526 " ideal model delta sigma weight residual 115.78 98.22 17.56 1.35e+00 5.49e-01 1.69e+02 angle pdb=" C LYS A 525 " pdb=" N LYS A 526 " pdb=" CA LYS A 526 " ideal model delta sigma weight residual 121.54 99.60 21.94 1.91e+00 2.74e-01 1.32e+02 ... (remaining 37856 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 16429 17.85 - 35.71: 604 35.71 - 53.56: 152 53.56 - 71.41: 75 71.41 - 89.27: 20 Dihedral angle restraints: 17280 sinusoidal: 7458 harmonic: 9822 Sorted by residual: dihedral pdb=" CB CYS B1029 " pdb=" SG CYS B1029 " pdb=" SG CYS B1040 " pdb=" CB CYS B1040 " ideal model delta sinusoidal sigma weight residual -86.00 -163.36 77.36 1 1.00e+01 1.00e-02 7.50e+01 dihedral pdb=" CB CYS A1029 " pdb=" SG CYS A1029 " pdb=" SG CYS A1040 " pdb=" CB CYS A1040 " ideal model delta sinusoidal sigma weight residual -86.00 -163.35 77.35 1 1.00e+01 1.00e-02 7.50e+01 dihedral pdb=" CB CYS C1029 " pdb=" SG CYS C1029 " pdb=" SG CYS C1040 " pdb=" CB CYS C1040 " ideal model delta sinusoidal sigma weight residual -86.00 -163.34 77.34 1 1.00e+01 1.00e-02 7.50e+01 ... (remaining 17277 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 4022 0.088 - 0.176: 423 0.176 - 0.264: 6 0.264 - 0.352: 7 0.352 - 0.439: 2 Chirality restraints: 4460 Sorted by residual: chirality pdb=" CA ASN A 328 " pdb=" N ASN A 328 " pdb=" C ASN A 328 " pdb=" CB ASN A 328 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.83e+00 chirality pdb=" C1 NAG C1304 " pdb=" ND2 ASN C 328 " pdb=" C2 NAG C1304 " pdb=" O5 NAG C1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.79 0.39 2.00e-01 2.50e+01 3.80e+00 chirality pdb=" C1 NAG B1301 " pdb=" ND2 ASN B 61 " pdb=" C2 NAG B1301 " pdb=" O5 NAG B1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.90e+00 ... (remaining 4457 not shown) Planarity restraints: 4849 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 525 " -0.075 2.00e-02 2.50e+03 1.62e-01 2.61e+02 pdb=" C LYS A 525 " 0.279 2.00e-02 2.50e+03 pdb=" O LYS A 525 " -0.119 2.00e-02 2.50e+03 pdb=" N LYS A 526 " -0.084 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 328 " 0.125 2.00e-02 2.50e+03 1.33e-01 2.23e+02 pdb=" CG ASN C 328 " -0.048 2.00e-02 2.50e+03 pdb=" OD1 ASN C 328 " -0.043 2.00e-02 2.50e+03 pdb=" ND2 ASN C 328 " -0.202 2.00e-02 2.50e+03 pdb=" C1 NAG C1304 " 0.168 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 328 " -0.016 2.00e-02 2.50e+03 1.00e-01 1.01e+02 pdb=" C ASN A 328 " -0.157 2.00e-02 2.50e+03 pdb=" O ASN A 328 " 0.071 2.00e-02 2.50e+03 pdb=" N ILE A 329 " 0.102 2.00e-02 2.50e+03 ... (remaining 4846 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.14: 12 2.14 - 2.83: 8211 2.83 - 3.52: 34867 3.52 - 4.21: 65473 4.21 - 4.90: 112251 Nonbonded interactions: 220814 Sorted by model distance: nonbonded pdb=" CB PRO B 518 " pdb=" OH TYR C 200 " model vdw 1.447 3.440 nonbonded pdb=" CB ASN A 328 " pdb=" N ILE A 329 " model vdw 1.680 2.816 nonbonded pdb=" O ASN A 328 " pdb=" CA ILE A 329 " model vdw 1.849 2.776 nonbonded pdb=" CG PRO B 518 " pdb=" CZ TYR C 200 " model vdw 1.927 3.660 nonbonded pdb=" CG PRO B 518 " pdb=" CE1 TYR C 200 " model vdw 1.952 3.740 ... (remaining 220809 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' selection = (chain 'B' and (resid 27 through 439 or resid 499 through 1144 or resid 1301 thr \ ough 1310)) selection = (chain 'C' and (resid 27 through 439 or resid 499 through 1144 or resid 1301 thr \ ough 1310)) } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'L' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' } 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: 3.070 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: 0.020 Extract box with map and model: 14.750 Check model and map are aligned: 0.410 Set scattering table: 0.240 Process input model: 73.600 Find NCS groups from input model: 2.010 Set up NCS constraints: 0.340 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6703 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 : 0.005 0.311 27831 Z= 0.316 Angle : 0.879 73.409 37861 Z= 0.541 Chirality : 0.050 0.439 4460 Planarity : 0.005 0.162 4804 Dihedral : 11.189 89.267 10845 Min Nonbonded Distance : 1.447 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.36 % Allowed : 3.73 % Favored : 95.91 % Rotamer: Outliers : 0.44 % Allowed : 2.15 % Favored : 97.41 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.73 % 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 (0.14), residues: 3328 helix: 0.67 (0.19), residues: 660 sheet: 0.45 (0.16), residues: 913 loop : -0.25 (0.14), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 50 HIS 0.005 0.001 HIS C1045 PHE 0.016 0.001 PHE B 55 TYR 0.018 0.002 TYR D 33 ARG 0.005 0.001 ARG D 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 378 time to evaluate : 3.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1092 PHE cc_start: 0.4942 (m-80) cc_final: 0.4157 (m-80) REVERT: B 37 TYR cc_start: 0.6585 (p90) cc_final: 0.6201 (p90) REVERT: B 49 HIS cc_start: 0.8914 (t70) cc_final: 0.8507 (t70) REVERT: B 711 ILE cc_start: 0.7722 (mt) cc_final: 0.7521 (tt) REVERT: B 745 GLU cc_start: 0.8714 (mp0) cc_final: 0.8150 (tm-30) REVERT: B 767 ILE cc_start: 0.9390 (mt) cc_final: 0.8819 (pt) REVERT: B 770 GLU cc_start: 0.8964 (pt0) cc_final: 0.8696 (pp20) REVERT: C 55 PHE cc_start: 0.9124 (m-80) cc_final: 0.8220 (m-80) REVERT: C 744 THR cc_start: 0.9401 (m) cc_final: 0.9101 (p) REVERT: C 1106 PHE cc_start: 0.9221 (t80) cc_final: 0.8992 (t80) REVERT: L 4 MET cc_start: 0.8379 (mmm) cc_final: 0.7985 (mmm) REVERT: D 81 MET cc_start: 0.4418 (tmm) cc_final: 0.3288 (ppp) outliers start: 13 outliers final: 4 residues processed: 389 average time/residue: 0.4357 time to fit residues: 256.3305 Evaluate side-chains 203 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 199 time to evaluate : 3.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 282 optimal weight: 6.9990 chunk 253 optimal weight: 8.9990 chunk 140 optimal weight: 7.9990 chunk 86 optimal weight: 10.0000 chunk 171 optimal weight: 7.9990 chunk 135 optimal weight: 20.0000 chunk 262 optimal weight: 0.9990 chunk 101 optimal weight: 30.0000 chunk 159 optimal weight: 10.0000 chunk 195 optimal weight: 0.9990 chunk 304 optimal weight: 30.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 801 GLN A 869 GLN A 898 GLN ** A 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1007 GLN ** A1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 869 GLN ** B 898 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 904 ASN B 954 GLN B 999 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1007 GLN ** B1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 748 ASN ** C 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 869 GLN C 898 GLN C 916 ASN C 989 GLN C1002 GLN C1051 GLN ** C1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 117 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 27831 Z= 0.287 Angle : 0.693 14.530 37861 Z= 0.364 Chirality : 0.047 0.254 4460 Planarity : 0.005 0.057 4804 Dihedral : 6.421 56.354 4879 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.25 % Favored : 97.66 % Rotamer: Outliers : 0.07 % Allowed : 1.40 % Favored : 98.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.14), residues: 3328 helix: 1.21 (0.20), residues: 656 sheet: 0.43 (0.16), residues: 910 loop : -0.22 (0.14), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 36 HIS 0.011 0.002 HIS C 49 PHE 0.027 0.002 PHE B1100 TYR 0.040 0.002 TYR A 200 ARG 0.015 0.001 ARG A 992 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 247 time to evaluate : 2.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 737 MET cc_start: 0.9317 (tpt) cc_final: 0.9075 (tpp) REVERT: A 993 LEU cc_start: 0.9411 (pp) cc_final: 0.9160 (mm) REVERT: B 37 TYR cc_start: 0.7386 (p90) cc_final: 0.7186 (p90) REVERT: B 745 GLU cc_start: 0.8758 (mp0) cc_final: 0.8413 (tt0) REVERT: B 866 MET cc_start: 0.9130 (mtm) cc_final: 0.8901 (ptp) REVERT: B 976 ASP cc_start: 0.9319 (m-30) cc_final: 0.9103 (m-30) REVERT: C 331 ASN cc_start: 0.9063 (t0) cc_final: 0.8791 (p0) REVERT: C 753 TYR cc_start: 0.7630 (m-80) cc_final: 0.7181 (m-80) REVERT: C 915 GLU cc_start: 0.9017 (OUTLIER) cc_final: 0.8810 (pm20) REVERT: C 982 ASP cc_start: 0.8845 (p0) cc_final: 0.8403 (p0) REVERT: C 985 GLU cc_start: 0.9030 (pt0) cc_final: 0.8605 (pm20) REVERT: H 70 MET cc_start: 0.8548 (ttm) cc_final: 0.8344 (ttt) REVERT: H 81 MET cc_start: 0.3695 (mmm) cc_final: 0.2495 (mmm) REVERT: D 81 MET cc_start: 0.4644 (tmm) cc_final: 0.3888 (ttt) outliers start: 2 outliers final: 0 residues processed: 249 average time/residue: 0.4319 time to fit residues: 167.8585 Evaluate side-chains 163 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 162 time to evaluate : 2.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 169 optimal weight: 0.9980 chunk 94 optimal weight: 20.0000 chunk 253 optimal weight: 6.9990 chunk 207 optimal weight: 20.0000 chunk 83 optimal weight: 7.9990 chunk 304 optimal weight: 1.9990 chunk 329 optimal weight: 50.0000 chunk 271 optimal weight: 1.9990 chunk 302 optimal weight: 50.0000 chunk 103 optimal weight: 9.9990 chunk 244 optimal weight: 4.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN B 196 ASN ** B 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 916 ASN C 999 GLN C1002 GLN ** C1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 117 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 27831 Z= 0.207 Angle : 0.571 9.346 37861 Z= 0.297 Chirality : 0.045 0.772 4460 Planarity : 0.004 0.061 4804 Dihedral : 5.753 54.720 4879 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.09 % Favored : 96.88 % Rotamer: Outliers : 0.03 % Allowed : 1.43 % Favored : 98.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.73 % 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: 0.41 (0.14), residues: 3328 helix: 1.33 (0.21), residues: 661 sheet: 0.53 (0.16), residues: 911 loop : -0.22 (0.15), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 47 HIS 0.008 0.001 HIS A 49 PHE 0.026 0.001 PHE B1100 TYR 0.018 0.001 TYR C 870 ARG 0.008 0.001 ARG A1011 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 228 time to evaluate : 3.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 745 GLU cc_start: 0.8861 (mp0) cc_final: 0.8539 (tt0) REVERT: B 961 LYS cc_start: 0.9512 (ptpp) cc_final: 0.9223 (pttp) REVERT: B 982 ASP cc_start: 0.8494 (p0) cc_final: 0.8070 (p0) REVERT: B 984 PRO cc_start: 0.8676 (Cg_exo) cc_final: 0.8161 (Cg_endo) REVERT: B 1107 TYR cc_start: 0.8307 (t80) cc_final: 0.7807 (t80) REVERT: C 331 ASN cc_start: 0.9108 (t0) cc_final: 0.8837 (p0) REVERT: C 753 TYR cc_start: 0.7858 (m-80) cc_final: 0.7293 (m-80) REVERT: C 982 ASP cc_start: 0.8873 (p0) cc_final: 0.8534 (p0) REVERT: C 985 GLU cc_start: 0.9051 (pt0) cc_final: 0.8451 (pm20) outliers start: 1 outliers final: 1 residues processed: 228 average time/residue: 0.3992 time to fit residues: 144.4137 Evaluate side-chains 151 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 150 time to evaluate : 3.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 301 optimal weight: 50.0000 chunk 229 optimal weight: 6.9990 chunk 158 optimal weight: 9.9990 chunk 33 optimal weight: 50.0000 chunk 145 optimal weight: 0.6980 chunk 204 optimal weight: 5.9990 chunk 305 optimal weight: 20.0000 chunk 323 optimal weight: 50.0000 chunk 159 optimal weight: 10.0000 chunk 289 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 898 GLN ** A 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN B 484 ASN ** B 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1007 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 117 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.4455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 27831 Z= 0.238 Angle : 0.609 13.558 37861 Z= 0.316 Chirality : 0.045 0.618 4460 Planarity : 0.004 0.062 4804 Dihedral : 5.420 53.419 4879 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.31 % Favored : 96.66 % Rotamer: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.73 % 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: 0.24 (0.14), residues: 3328 helix: 1.10 (0.21), residues: 661 sheet: 0.40 (0.16), residues: 928 loop : -0.26 (0.15), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 36 HIS 0.005 0.001 HIS A1061 PHE 0.021 0.002 PHE B1049 TYR 0.041 0.002 TYR A1064 ARG 0.012 0.001 ARG B 992 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 208 time to evaluate : 3.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 737 MET cc_start: 0.9418 (tpp) cc_final: 0.8924 (tpp) REVERT: A 1064 TYR cc_start: 0.7807 (t80) cc_final: 0.7306 (t80) REVERT: B 607 VAL cc_start: 0.8938 (m) cc_final: 0.8720 (m) REVERT: B 961 LYS cc_start: 0.9572 (ptpp) cc_final: 0.9318 (ptpp) REVERT: B 982 ASP cc_start: 0.8554 (p0) cc_final: 0.8311 (p0) REVERT: C 331 ASN cc_start: 0.9198 (t0) cc_final: 0.8938 (p0) REVERT: C 753 TYR cc_start: 0.7819 (m-80) cc_final: 0.7517 (m-80) REVERT: C 760 LEU cc_start: 0.9500 (mt) cc_final: 0.8994 (mt) REVERT: H 81 MET cc_start: 0.2944 (mmm) cc_final: 0.2170 (mmm) REVERT: D 81 MET cc_start: -0.0021 (ttm) cc_final: -0.0234 (mtp) outliers start: 0 outliers final: 0 residues processed: 208 average time/residue: 0.4046 time to fit residues: 133.4391 Evaluate side-chains 139 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 3.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 269 optimal weight: 8.9990 chunk 183 optimal weight: 8.9990 chunk 4 optimal weight: 7.9990 chunk 241 optimal weight: 4.9990 chunk 133 optimal weight: 0.6980 chunk 276 optimal weight: 0.9990 chunk 223 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 165 optimal weight: 9.9990 chunk 290 optimal weight: 20.0000 chunk 81 optimal weight: 0.9980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1132 ASN ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN ** B 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1103 GLN ** C1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.4637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 27831 Z= 0.153 Angle : 0.525 9.170 37861 Z= 0.271 Chirality : 0.044 0.513 4460 Planarity : 0.004 0.056 4804 Dihedral : 5.206 58.370 4879 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.15), residues: 3328 helix: 1.35 (0.21), residues: 665 sheet: 0.40 (0.16), residues: 933 loop : -0.19 (0.15), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 883 HIS 0.004 0.001 HIS C1045 PHE 0.023 0.001 PHE C 779 TYR 0.022 0.001 TYR A1064 ARG 0.010 0.000 ARG B 902 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 3.378 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: A 737 MET cc_start: 0.9409 (tpp) cc_final: 0.8889 (tpp) REVERT: A 1064 TYR cc_start: 0.8130 (t80) cc_final: 0.7654 (t80) REVERT: B 961 LYS cc_start: 0.9531 (ptpp) cc_final: 0.9314 (ptpp) REVERT: B 976 ASP cc_start: 0.9358 (m-30) cc_final: 0.9156 (m-30) REVERT: B 982 ASP cc_start: 0.8540 (p0) cc_final: 0.8294 (p0) REVERT: B 1099 TRP cc_start: 0.8869 (m100) cc_final: 0.8620 (m100) REVERT: C 331 ASN cc_start: 0.9156 (t0) cc_final: 0.8892 (p0) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.3931 time to fit residues: 126.8519 Evaluate side-chains 134 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 3.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 108 optimal weight: 20.0000 chunk 291 optimal weight: 10.0000 chunk 64 optimal weight: 0.2980 chunk 190 optimal weight: 0.0060 chunk 79 optimal weight: 10.0000 chunk 324 optimal weight: 50.0000 chunk 269 optimal weight: 6.9990 chunk 150 optimal weight: 20.0000 chunk 26 optimal weight: 50.0000 chunk 107 optimal weight: 5.9990 chunk 170 optimal weight: 6.9990 overall best weight: 4.0602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN B 445 ASN ** B 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 898 GLN ** B 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN E 37 GLN ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.5463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 27831 Z= 0.236 Angle : 0.594 8.984 37861 Z= 0.312 Chirality : 0.045 0.494 4460 Planarity : 0.004 0.055 4804 Dihedral : 5.285 54.356 4879 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.14), residues: 3328 helix: 0.92 (0.20), residues: 678 sheet: 0.34 (0.16), residues: 934 loop : -0.30 (0.15), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 883 HIS 0.006 0.001 HIS C1045 PHE 0.015 0.002 PHE B1106 TYR 0.018 0.001 TYR B1107 ARG 0.011 0.001 ARG B1011 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 2.962 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: A 737 MET cc_start: 0.9411 (tpp) cc_final: 0.8903 (tpp) REVERT: B 711 ILE cc_start: 0.9194 (mt) cc_final: 0.8990 (mp) REVERT: B 866 MET cc_start: 0.8626 (mtp) cc_final: 0.8420 (mtp) REVERT: B 961 LYS cc_start: 0.9567 (ptpp) cc_final: 0.9284 (pttm) REVERT: B 982 ASP cc_start: 0.8615 (p0) cc_final: 0.8347 (p0) REVERT: B 1092 PHE cc_start: 0.6067 (m-80) cc_final: 0.5469 (m-10) REVERT: B 1099 TRP cc_start: 0.9090 (m100) cc_final: 0.8765 (m100) REVERT: C 331 ASN cc_start: 0.9201 (t0) cc_final: 0.8939 (p0) REVERT: C 1047 MET cc_start: 0.8896 (tpt) cc_final: 0.8648 (tpt) REVERT: H 81 MET cc_start: 0.3862 (mmt) cc_final: 0.3312 (mmt) REVERT: D 81 MET cc_start: 0.1153 (mmm) cc_final: 0.0846 (mmm) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.4103 time to fit residues: 120.4705 Evaluate side-chains 121 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 3.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 312 optimal weight: 8.9990 chunk 36 optimal weight: 40.0000 chunk 184 optimal weight: 20.0000 chunk 236 optimal weight: 1.9990 chunk 183 optimal weight: 10.0000 chunk 272 optimal weight: 3.9990 chunk 180 optimal weight: 3.9990 chunk 322 optimal weight: 7.9990 chunk 202 optimal weight: 20.0000 chunk 196 optimal weight: 10.0000 chunk 149 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 GLN ** A 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 577 GLN ** A 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN ** B 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 951 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 952 ASN ** B1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 748 ASN C 869 GLN ** C1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.6472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 27831 Z= 0.275 Angle : 0.636 14.116 37861 Z= 0.336 Chirality : 0.046 0.469 4460 Planarity : 0.005 0.068 4804 Dihedral : 5.715 54.000 4879 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 21.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.73 % 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: -0.08 (0.14), residues: 3328 helix: 0.62 (0.20), residues: 661 sheet: 0.36 (0.17), residues: 863 loop : -0.46 (0.15), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 111 HIS 0.006 0.001 HIS C1045 PHE 0.025 0.002 PHE C 58 TYR 0.033 0.002 TYR B 498 ARG 0.019 0.001 ARG B 762 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 3.141 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: A 562 PHE cc_start: 0.9057 (m-10) cc_final: 0.8851 (m-80) REVERT: A 737 MET cc_start: 0.9355 (tpp) cc_final: 0.8891 (tpp) REVERT: A 1064 TYR cc_start: 0.8798 (t80) cc_final: 0.8331 (t80) REVERT: B 858 LEU cc_start: 0.9172 (tp) cc_final: 0.8970 (tp) REVERT: B 866 MET cc_start: 0.8588 (mtp) cc_final: 0.8350 (mtp) REVERT: B 961 LYS cc_start: 0.9565 (ptpp) cc_final: 0.9324 (ptpp) REVERT: B 982 ASP cc_start: 0.8654 (p0) cc_final: 0.8330 (p0) REVERT: B 1092 PHE cc_start: 0.6484 (m-80) cc_final: 0.5871 (m-10) REVERT: B 1099 TRP cc_start: 0.9296 (m100) cc_final: 0.8957 (m100) REVERT: C 331 ASN cc_start: 0.9248 (t0) cc_final: 0.8992 (p0) REVERT: C 568 ASP cc_start: 0.8924 (t0) cc_final: 0.8699 (t0) REVERT: C 753 TYR cc_start: 0.8214 (m-80) cc_final: 0.7978 (m-80) REVERT: C 914 TYR cc_start: 0.6845 (m-80) cc_final: 0.6190 (m-10) REVERT: C 919 LEU cc_start: 0.9162 (tp) cc_final: 0.8794 (pp) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.4073 time to fit residues: 112.9496 Evaluate side-chains 124 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 3.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 199 optimal weight: 30.0000 chunk 128 optimal weight: 50.0000 chunk 192 optimal weight: 8.9990 chunk 97 optimal weight: 8.9990 chunk 63 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 205 optimal weight: 9.9990 chunk 219 optimal weight: 5.9990 chunk 159 optimal weight: 1.9990 chunk 30 optimal weight: 50.0000 chunk 253 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN ** B 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 577 GLN B 761 ASN ** B 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 904 ASN B 952 ASN ** B1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.6961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 27831 Z= 0.245 Angle : 0.599 10.150 37861 Z= 0.313 Chirality : 0.045 0.439 4460 Planarity : 0.004 0.059 4804 Dihedral : 5.729 55.294 4879 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 19.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.73 % 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 (0.14), residues: 3328 helix: 0.73 (0.20), residues: 673 sheet: 0.28 (0.17), residues: 862 loop : -0.50 (0.15), residues: 1793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 883 HIS 0.006 0.001 HIS C1045 PHE 0.037 0.002 PHE A1086 TYR 0.027 0.002 TYR B 914 ARG 0.014 0.001 ARG B 762 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 3.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 562 PHE cc_start: 0.9081 (m-10) cc_final: 0.8866 (m-80) REVERT: A 737 MET cc_start: 0.9330 (tpp) cc_final: 0.8900 (tpp) REVERT: A 1092 PHE cc_start: 0.6337 (m-10) cc_final: 0.5184 (m-80) REVERT: B 767 ILE cc_start: 0.9559 (mm) cc_final: 0.9053 (mt) REVERT: B 858 LEU cc_start: 0.9179 (tp) cc_final: 0.8959 (tp) REVERT: B 961 LYS cc_start: 0.9562 (ptpp) cc_final: 0.9335 (ptpp) REVERT: B 982 ASP cc_start: 0.8711 (p0) cc_final: 0.8384 (p0) REVERT: B 1092 PHE cc_start: 0.6493 (m-80) cc_final: 0.5176 (m-80) REVERT: B 1099 TRP cc_start: 0.9332 (m100) cc_final: 0.9060 (m100) REVERT: C 331 ASN cc_start: 0.9212 (t0) cc_final: 0.8966 (p0) REVERT: C 568 ASP cc_start: 0.8948 (t0) cc_final: 0.8714 (t0) REVERT: C 753 TYR cc_start: 0.8141 (m-80) cc_final: 0.7918 (m-80) REVERT: C 914 TYR cc_start: 0.6710 (m-80) cc_final: 0.5913 (m-10) REVERT: C 919 LEU cc_start: 0.9122 (tp) cc_final: 0.8728 (pp) REVERT: D 81 MET cc_start: 0.1391 (mmm) cc_final: 0.0960 (mmm) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.4143 time to fit residues: 108.8157 Evaluate side-chains 112 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 2.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 293 optimal weight: 8.9990 chunk 309 optimal weight: 50.0000 chunk 282 optimal weight: 5.9990 chunk 300 optimal weight: 50.0000 chunk 181 optimal weight: 6.9990 chunk 131 optimal weight: 20.0000 chunk 236 optimal weight: 8.9990 chunk 92 optimal weight: 20.0000 chunk 271 optimal weight: 9.9990 chunk 284 optimal weight: 10.0000 chunk 299 optimal weight: 9.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 781 GLN ** A 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 821 ASN ** A 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1085 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN ** B 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 781 GLN ** B 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 821 ASN ** B 932 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 952 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1132 ASN ** C 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 748 ASN ** C 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 821 ASN ** C 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1008 GLN ** C1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1132 ASN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.8290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.155 27831 Z= 0.419 Angle : 0.818 10.659 37861 Z= 0.435 Chirality : 0.050 0.442 4460 Planarity : 0.006 0.119 4804 Dihedral : 6.861 58.399 4879 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 34.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.73 % 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: -0.98 (0.14), residues: 3328 helix: -0.73 (0.18), residues: 671 sheet: -0.03 (0.18), residues: 851 loop : -0.87 (0.15), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 64 HIS 0.011 0.002 HIS C1085 PHE 0.042 0.003 PHE A1086 TYR 0.036 0.003 TYR C 753 ARG 0.014 0.001 ARG A 762 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 2.877 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: A 561 GLN cc_start: 0.9413 (tp-100) cc_final: 0.9199 (tp-100) REVERT: A 737 MET cc_start: 0.9343 (tpp) cc_final: 0.9027 (tpp) REVERT: B 858 LEU cc_start: 0.9247 (tp) cc_final: 0.9034 (tp) REVERT: B 961 LYS cc_start: 0.9605 (ptpp) cc_final: 0.9347 (pttp) REVERT: B 982 ASP cc_start: 0.8740 (p0) cc_final: 0.8453 (p0) REVERT: B 1039 PHE cc_start: 0.5814 (t80) cc_final: 0.5309 (t80) REVERT: B 1092 PHE cc_start: 0.7540 (m-80) cc_final: 0.6948 (m-10) REVERT: B 1099 TRP cc_start: 0.9550 (m100) cc_final: 0.9224 (m100) REVERT: C 753 TYR cc_start: 0.8234 (m-80) cc_final: 0.7965 (m-80) REVERT: C 919 LEU cc_start: 0.9239 (tp) cc_final: 0.8810 (pp) REVERT: D 81 MET cc_start: 0.2342 (mmm) cc_final: 0.2050 (mmm) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.4225 time to fit residues: 97.7631 Evaluate side-chains 102 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 3.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 197 optimal weight: 0.8980 chunk 318 optimal weight: 40.0000 chunk 194 optimal weight: 5.9990 chunk 150 optimal weight: 5.9990 chunk 221 optimal weight: 4.9990 chunk 333 optimal weight: 9.9990 chunk 307 optimal weight: 40.0000 chunk 265 optimal weight: 8.9990 chunk 27 optimal weight: 8.9990 chunk 205 optimal weight: 5.9990 chunk 162 optimal weight: 7.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 652 HIS A 781 GLN ** A 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1085 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1103 GLN ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN ** B 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 652 HIS ** B 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 952 ASN ** B1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 318 GLN C 652 HIS C 748 ASN ** C 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 821 ASN C 904 ASN ** C1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 52 ASN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.8390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 27831 Z= 0.264 Angle : 0.633 9.006 37861 Z= 0.332 Chirality : 0.046 0.408 4460 Planarity : 0.004 0.073 4804 Dihedral : 6.459 58.937 4879 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 23.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.73 % 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: -0.74 (0.14), residues: 3328 helix: -0.02 (0.19), residues: 672 sheet: -0.00 (0.18), residues: 846 loop : -0.87 (0.15), residues: 1810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 36 HIS 0.007 0.002 HIS C1045 PHE 0.029 0.002 PHE A1086 TYR 0.028 0.002 TYR A1064 ARG 0.011 0.001 ARG B 762 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6656 Ramachandran restraints generated. 3328 Oldfield, 0 Emsley, 3328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 3.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 561 GLN cc_start: 0.9353 (tp-100) cc_final: 0.9128 (tp-100) REVERT: A 797 PHE cc_start: 0.7481 (m-10) cc_final: 0.7250 (m-10) REVERT: A 1092 PHE cc_start: 0.6589 (m-10) cc_final: 0.5509 (m-80) REVERT: B 767 ILE cc_start: 0.9544 (mm) cc_final: 0.9247 (mt) REVERT: B 858 LEU cc_start: 0.9277 (tp) cc_final: 0.9061 (tp) REVERT: B 961 LYS cc_start: 0.9564 (ptpp) cc_final: 0.9303 (pttp) REVERT: B 982 ASP cc_start: 0.8688 (p0) cc_final: 0.8373 (p0) REVERT: B 1092 PHE cc_start: 0.7080 (m-80) cc_final: 0.6078 (m-80) REVERT: B 1099 TRP cc_start: 0.9541 (m100) cc_final: 0.9263 (m100) REVERT: C 753 TYR cc_start: 0.8173 (m-80) cc_final: 0.7913 (m-80) REVERT: C 919 LEU cc_start: 0.9174 (tp) cc_final: 0.8717 (pp) REVERT: C 1059 PHE cc_start: 0.8725 (m-80) cc_final: 0.8500 (m-10) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.4203 time to fit residues: 98.1855 Evaluate side-chains 114 residues out of total 2940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 2.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 335 random chunks: chunk 211 optimal weight: 30.0000 chunk 283 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 245 optimal weight: 10.0000 chunk 39 optimal weight: 8.9990 chunk 73 optimal weight: 8.9990 chunk 266 optimal weight: 4.9990 chunk 111 optimal weight: 40.0000 chunk 273 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 49 optimal weight: 20.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 999 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1085 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN ** B 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 672 GLN B 781 GLN ** B 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1085 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 759 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.070024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.048141 restraints weight = 317761.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.048879 restraints weight = 215847.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.049551 restraints weight = 144631.197| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.8833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 27831 Z= 0.277 Angle : 0.635 8.104 37861 Z= 0.334 Chirality : 0.045 0.391 4460 Planarity : 0.005 0.073 4804 Dihedral : 6.414 58.562 4879 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 24.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.73 % 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: -0.72 (0.14), residues: 3328 helix: 0.13 (0.20), residues: 671 sheet: -0.02 (0.18), residues: 837 loop : -0.91 (0.14), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 36 HIS 0.011 0.002 HIS C 652 PHE 0.044 0.002 PHE B 640 TYR 0.025 0.002 TYR A1064 ARG 0.010 0.001 ARG B 762 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4820.70 seconds wall clock time: 89 minutes 35.25 seconds (5375.25 seconds total)