Starting phenix.real_space_refine on Wed Feb 21 06:21:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6e_23693/02_2024/7m6e_23693_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6e_23693/02_2024/7m6e_23693.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6e_23693/02_2024/7m6e_23693.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6e_23693/02_2024/7m6e_23693.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6e_23693/02_2024/7m6e_23693_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6e_23693/02_2024/7m6e_23693_neut.pdb" } resolution = 3.3 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= 0.028 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 138 5.16 5 C 18992 2.51 5 N 4915 2.21 5 O 5751 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 287": "OD1" <-> "OD2" Residue "A PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 428": "OD1" <-> "OD2" Residue "A PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 467": "OD1" <-> "OD2" Residue "A PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 554": "OE1" <-> "OE2" Residue "A TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 614": "OD1" <-> "OD2" Residue "A ASP 775": "OD1" <-> "OD2" Residue "A PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 287": "OD1" <-> "OD2" Residue "B PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 428": "OD1" <-> "OD2" Residue "B PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 467": "OD1" <-> "OD2" Residue "B PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 554": "OE1" <-> "OE2" Residue "B TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 614": "OD1" <-> "OD2" Residue "B ASP 775": "OD1" <-> "OD2" Residue "B PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 287": "OD1" <-> "OD2" Residue "E PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 428": "OD1" <-> "OD2" Residue "E PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 467": "OD1" <-> "OD2" Residue "E PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 554": "OE1" <-> "OE2" Residue "E TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 614": "OD1" <-> "OD2" Residue "E ASP 775": "OD1" <-> "OD2" Residue "E PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 101": "OD1" <-> "OD2" Residue "H TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 30": "OD1" <-> "OD2" Residue "C PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 59": "OD1" <-> "OD2" Residue "G PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 59": "OD1" <-> "OD2" Residue "L ASP 30": "OD1" <-> "OD2" Residue "L PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 59": "OD1" <-> "OD2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 29796 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 8021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 8021 Classifications: {'peptide': 1034} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 56, 'TRANS': 977} Chain breaks: 7 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ASN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "B" Number of atoms: 8021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 8021 Classifications: {'peptide': 1034} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 56, 'TRANS': 977} Chain breaks: 7 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ASN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "D" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 947 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 118} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "E" Number of atoms: 8021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 8021 Classifications: {'peptide': 1034} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 56, 'TRANS': 977} Chain breaks: 7 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ASN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "F" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 947 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 118} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "H" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 947 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 118} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "C" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 802 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "G" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 802 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "L" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 802 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "I" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" 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: 15.21, per 1000 atoms: 0.51 Number of scatterers: 29796 At special positions: 0 Unit cell: (145.123, 139.909, 184.228, 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 138 16.00 O 5751 8.00 N 4915 7.00 C 18992 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.07 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.02 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.05 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.05 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.07 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.02 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.05 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.05 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 15 " - pdb=" SG CYS E 136 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 166 " distance=2.03 Simple disulfide: pdb=" SG CYS E 291 " - pdb=" SG CYS E 301 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.07 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.04 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.02 Simple disulfide: pdb=" SG CYS E 538 " - pdb=" SG CYS E 590 " distance=2.03 Simple disulfide: pdb=" SG CYS E 617 " - pdb=" SG CYS E 649 " distance=2.04 Simple disulfide: pdb=" SG CYS E 662 " - pdb=" SG CYS E 671 " distance=2.03 Simple disulfide: pdb=" SG CYS E 738 " - pdb=" SG CYS E 760 " distance=2.05 Simple disulfide: pdb=" SG CYS E 743 " - pdb=" SG CYS E 749 " distance=2.03 Simple disulfide: pdb=" SG CYS E1032 " - pdb=" SG CYS E1043 " distance=2.02 Simple disulfide: pdb=" SG CYS E1082 " - pdb=" SG CYS E1126 " distance=2.05 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 87 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 87 " distance=2.02 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 87 " distance=2.02 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=1, symmetry=0 Links applied BETA1-4 " NAG I 1 " - " NAG I 2 " BETA1-6 " NAG I 1 " - " FUC I 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A1301 " - " ASN A 165 " " NAG A1302 " - " ASN A 234 " " NAG A1303 " - " ASN A 61 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1074 " " NAG A1311 " - " ASN A 343 " " NAG B1301 " - " ASN B 165 " " NAG B1302 " - " ASN B 234 " " NAG B1303 " - " ASN B 61 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B1074 " " NAG D 301 " - " ASN E 343 " " NAG E1301 " - " ASN E 165 " " NAG E1302 " - " ASN E 234 " " NAG E1303 " - " ASN E 61 " " NAG E1304 " - " ASN E 282 " " NAG E1305 " - " ASN E 331 " " NAG E1306 " - " ASN E 603 " " NAG E1307 " - " ASN E 616 " " NAG E1308 " - " ASN E 657 " " NAG E1309 " - " ASN E 709 " " NAG E1310 " - " ASN E1074 " " NAG I 1 " - " ASN B 343 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.04 Conformation dependent library (CDL) restraints added in 5.2 seconds 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7050 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 65 sheets defined 21.3% alpha, 28.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.06 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 344 removed outlier: 3.753A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 383 through 390 removed outlier: 4.105A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 409 removed outlier: 4.019A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 850 through 855 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.544A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.327A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASN A 919 " --> pdb=" O VAL A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 966 removed outlier: 3.941A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.535A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 5.137A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.753A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 383 through 390 removed outlier: 4.105A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 409 removed outlier: 4.018A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 850 through 855 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.544A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.326A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN B 919 " --> pdb=" O VAL B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 966 removed outlier: 3.942A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.535A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 5.137A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.870A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 303 Processing helix chain 'E' and resid 337 through 344 removed outlier: 3.723A pdb=" N VAL E 341 " --> pdb=" O PRO E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 371 Processing helix chain 'E' and resid 383 through 390 removed outlier: 4.105A pdb=" N ASN E 388 " --> pdb=" O THR E 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 409 removed outlier: 4.019A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 422 Processing helix chain 'E' and resid 737 through 744 Processing helix chain 'E' and resid 746 through 754 Processing helix chain 'E' and resid 755 through 757 No H-bonds generated for 'chain 'E' and resid 755 through 757' Processing helix chain 'E' and resid 758 through 783 Processing helix chain 'E' and resid 816 through 826 Processing helix chain 'E' and resid 850 through 855 Processing helix chain 'E' and resid 866 through 885 Processing helix chain 'E' and resid 886 through 890 Processing helix chain 'E' and resid 897 through 909 removed outlier: 3.544A pdb=" N ILE E 909 " --> pdb=" O ARG E 905 " (cutoff:3.500A) Processing helix chain 'E' and resid 912 through 919 removed outlier: 4.326A pdb=" N LEU E 916 " --> pdb=" O THR E 912 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR E 917 " --> pdb=" O GLN E 913 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN E 919 " --> pdb=" O VAL E 915 " (cutoff:3.500A) Processing helix chain 'E' and resid 919 through 941 Processing helix chain 'E' and resid 942 through 944 No H-bonds generated for 'chain 'E' and resid 942 through 944' Processing helix chain 'E' and resid 945 through 966 removed outlier: 3.942A pdb=" N VAL E 951 " --> pdb=" O LYS E 947 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU E 966 " --> pdb=" O LEU E 962 " (cutoff:3.500A) Processing helix chain 'E' and resid 976 through 984 removed outlier: 3.535A pdb=" N ILE E 980 " --> pdb=" O VAL E 976 " (cutoff:3.500A) Processing helix chain 'E' and resid 985 through 1033 removed outlier: 5.137A pdb=" N VAL E 991 " --> pdb=" O PRO E 987 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN E 992 " --> pdb=" O GLU E 988 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.871A pdb=" N TYR F 32 " --> pdb=" O PHE F 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.871A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 82 removed outlier: 3.527A pdb=" N ASP C 81 " --> pdb=" O ARG C 78 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU C 82 " --> pdb=" O SER C 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 78 through 82' Processing helix chain 'G' and resid 78 through 82 removed outlier: 3.527A pdb=" N ASP G 81 " --> pdb=" O ARG G 78 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLU G 82 " --> pdb=" O SER G 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 78 through 82' Processing helix chain 'L' and resid 78 through 82 removed outlier: 3.527A pdb=" N ASP L 81 " --> pdb=" O ARG L 78 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU L 82 " --> pdb=" O SER L 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 78 through 82' Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.883A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG A 190 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU A 96 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU A 189 " --> pdb=" O THR A 208 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N THR A 208 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.207A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 7.457A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.560A pdb=" N ILE A 105 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 132 through 141 removed outlier: 3.520A pdb=" N GLU A 132 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N CYS A 136 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N TYR A 160 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ASP A 138 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ARG A 158 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.901A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.344A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.501A pdb=" N LYS A 356 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.501A pdb=" N LYS A 356 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 removed outlier: 3.816A pdb=" N TYR A 453 " --> pdb=" O GLN A 493 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.704A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 702 through 704 removed outlier: 3.801A pdb=" N LYS B 790 " --> pdb=" O ASN A 703 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 713 Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.928A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.027A pdb=" N ILE A 788 " --> pdb=" O ASN E 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.714A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.883A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG B 190 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU B 189 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N THR B 208 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR B 204 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.206A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55 removed outlier: 7.458A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.560A pdb=" N ILE B 105 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 132 through 141 removed outlier: 3.518A pdb=" N GLU B 132 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N CYS B 136 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N TYR B 160 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ASP B 138 " --> pdb=" O ARG B 158 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ARG B 158 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.901A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.343A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.500A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TRP B 436 " --> pdb=" O ARG B 509 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.500A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 removed outlier: 3.815A pdb=" N TYR B 453 " --> pdb=" O GLN B 493 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.704A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 702 through 704 removed outlier: 3.771A pdb=" N LYS E 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 713 Processing sheet with id=AD2, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.928A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.714A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.496A pdb=" N GLU D 10 " --> pdb=" O THR D 110 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 19 through 23 Processing sheet with id=AD7, first strand: chain 'D' and resid 56 through 59 removed outlier: 3.682A pdb=" N ASP D 56 " --> pdb=" O TYR D 52 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE D 51 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N VAL D 102 " --> pdb=" O ARG D 94 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 27 through 30 removed outlier: 3.883A pdb=" N ALA E 27 " --> pdb=" O TRP E 64 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ASN E 61 " --> pdb=" O TYR E 269 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N TYR E 269 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL E 90 " --> pdb=" O PHE E 194 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG E 190 " --> pdb=" O SER E 94 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU E 96 " --> pdb=" O ASN E 188 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN E 188 " --> pdb=" O GLU E 96 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU E 189 " --> pdb=" O THR E 208 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N THR E 208 " --> pdb=" O LEU E 189 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU E 191 " --> pdb=" O LYS E 206 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS E 206 " --> pdb=" O GLU E 191 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL E 193 " --> pdb=" O TYR E 204 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR E 204 " --> pdb=" O VAL E 193 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N PHE E 201 " --> pdb=" O ASP E 228 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N ASP E 228 " --> pdb=" O PHE E 201 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N ILE E 203 " --> pdb=" O LEU E 226 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N HIS E 207 " --> pdb=" O ALA E 222 " (cutoff:3.500A) removed outlier: 9.207A pdb=" N ALA E 222 " --> pdb=" O HIS E 207 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N VAL E 36 " --> pdb=" O LEU E 223 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 48 through 55 removed outlier: 7.458A pdb=" N THR E 274 " --> pdb=" O ASP E 290 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N ASP E 290 " --> pdb=" O THR E 274 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU E 276 " --> pdb=" O ALA E 288 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ALA E 288 " --> pdb=" O LEU E 276 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N LYS E 278 " --> pdb=" O THR E 286 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 84 through 85 removed outlier: 3.559A pdb=" N ILE E 105 " --> pdb=" O GLN E 239 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY E 103 " --> pdb=" O LEU E 241 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N ARG E 102 " --> pdb=" O ASN E 121 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 132 through 141 removed outlier: 3.519A pdb=" N GLU E 132 " --> pdb=" O ASN E 164 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N SER E 162 " --> pdb=" O GLN E 134 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N CYS E 136 " --> pdb=" O TYR E 160 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N TYR E 160 " --> pdb=" O CYS E 136 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ASP E 138 " --> pdb=" O ARG E 158 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ARG E 158 " --> pdb=" O ASP E 138 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 311 through 319 removed outlier: 5.900A pdb=" N ILE E 312 " --> pdb=" O THR E 599 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N THR E 599 " --> pdb=" O ILE E 312 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N GLN E 314 " --> pdb=" O VAL E 597 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL E 597 " --> pdb=" O GLN E 314 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER E 316 " --> pdb=" O VAL E 595 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLY E 594 " --> pdb=" O GLN E 613 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 325 through 328 removed outlier: 5.344A pdb=" N ASP E 574 " --> pdb=" O ILE E 587 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA E 575 " --> pdb=" O GLY E 566 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 354 through 358 removed outlier: 3.763A pdb=" N VAL E 395 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TRP E 436 " --> pdb=" O ARG E 509 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 354 through 358 removed outlier: 3.763A pdb=" N VAL E 395 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 452 through 454 removed outlier: 3.815A pdb=" N TYR E 453 " --> pdb=" O GLN E 493 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 654 through 655 removed outlier: 5.704A pdb=" N GLU E 654 " --> pdb=" O ALA E 694 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N THR E 696 " --> pdb=" O GLU E 654 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ILE E 670 " --> pdb=" O ILE E 666 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 711 through 713 Processing sheet with id=AF1, first strand: chain 'E' and resid 718 through 728 removed outlier: 5.928A pdb=" N TYR E1067 " --> pdb=" O HIS E1048 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N HIS E1048 " --> pdb=" O TYR E1067 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 734 through 736 Processing sheet with id=AF3, first strand: chain 'E' and resid 1120 through 1125 removed outlier: 4.715A pdb=" N ALA E1087 " --> pdb=" O SER E1123 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.495A pdb=" N GLU F 10 " --> pdb=" O THR F 110 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 19 through 23 Processing sheet with id=AF6, first strand: chain 'F' and resid 56 through 59 removed outlier: 3.682A pdb=" N ASP F 56 " --> pdb=" O TYR F 52 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE F 51 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N VAL F 102 " --> pdb=" O ARG F 94 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N GLN F 96 " --> pdb=" O MET F 100H" (cutoff:3.500A) removed outlier: 6.288A pdb=" N MET F 100H" --> pdb=" O GLN F 96 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 99 through 100 removed outlier: 3.538A pdb=" N SER F 100C" --> pdb=" O ASN F 100 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.494A pdb=" N GLU H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 19 through 23 Processing sheet with id=AG1, first strand: chain 'H' and resid 56 through 59 removed outlier: 3.682A pdb=" N ASP H 56 " --> pdb=" O TYR H 52 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE H 51 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N VAL H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N GLN H 96 " --> pdb=" O MET H 100H" (cutoff:3.500A) removed outlier: 6.275A pdb=" N MET H 100H" --> pdb=" O GLN H 96 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'H' and resid 99 through 100 Processing sheet with id=AG3, first strand: chain 'C' and resid 9 through 12 removed outlier: 6.514A pdb=" N ALA C 10 " --> pdb=" O THR C 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'C' and resid 17 through 23 Processing sheet with id=AG5, first strand: chain 'C' and resid 33 through 37 Processing sheet with id=AG6, first strand: chain 'G' and resid 9 through 12 removed outlier: 6.515A pdb=" N ALA G 10 " --> pdb=" O THR G 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG6 Processing sheet with id=AG7, first strand: chain 'G' and resid 17 through 23 Processing sheet with id=AG8, first strand: chain 'G' and resid 33 through 37 Processing sheet with id=AG9, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.515A pdb=" N ALA L 10 " --> pdb=" O THR L 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG9 Processing sheet with id=AH1, first strand: chain 'L' and resid 17 through 23 Processing sheet with id=AH2, first strand: chain 'L' and resid 33 through 37 1129 hydrogen bonds defined for protein. 3060 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: 14.98 Time building geometry restraints manager: 12.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.30: 4834 1.30 - 1.45: 9326 1.45 - 1.60: 16170 1.60 - 1.75: 6 1.75 - 1.90: 171 Bond restraints: 30507 Sorted by residual: bond pdb=" C PRO A 295 " pdb=" O PRO A 295 " ideal model delta sigma weight residual 1.238 1.154 0.083 1.24e-02 6.50e+03 4.49e+01 bond pdb=" C PRO E 295 " pdb=" O PRO E 295 " ideal model delta sigma weight residual 1.238 1.156 0.081 1.24e-02 6.50e+03 4.28e+01 bond pdb=" C PRO B 295 " pdb=" O PRO B 295 " ideal model delta sigma weight residual 1.237 1.157 0.080 1.32e-02 5.74e+03 3.66e+01 bond pdb=" C GLN A 935 " pdb=" O GLN A 935 " ideal model delta sigma weight residual 1.236 1.191 0.045 1.15e-02 7.56e+03 1.56e+01 bond pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " ideal model delta sigma weight residual 1.808 1.679 0.129 3.30e-02 9.18e+02 1.54e+01 ... (remaining 30502 not shown) Histogram of bond angle deviations from ideal: 83.56 - 93.77: 1 93.77 - 103.98: 508 103.98 - 114.18: 17163 114.18 - 124.39: 22985 124.39 - 134.59: 899 Bond angle restraints: 41556 Sorted by residual: angle pdb=" C ASN E 343 " pdb=" CA ASN E 343 " pdb=" CB ASN E 343 " ideal model delta sigma weight residual 110.17 83.56 26.61 2.04e+00 2.40e-01 1.70e+02 angle pdb=" C ASN A 343 " pdb=" CA ASN A 343 " pdb=" CB ASN A 343 " ideal model delta sigma weight residual 110.88 98.42 12.46 1.57e+00 4.06e-01 6.30e+01 angle pdb=" CA CYS A 488 " pdb=" CB CYS A 488 " pdb=" SG CYS A 488 " ideal model delta sigma weight residual 114.40 129.42 -15.02 2.30e+00 1.89e-01 4.26e+01 angle pdb=" CA CYS E 488 " pdb=" CB CYS E 488 " pdb=" SG CYS E 488 " ideal model delta sigma weight residual 114.40 129.41 -15.01 2.30e+00 1.89e-01 4.26e+01 angle pdb=" CA TRP D 97 " pdb=" CB TRP D 97 " pdb=" CG TRP D 97 " ideal model delta sigma weight residual 113.60 125.99 -12.39 1.90e+00 2.77e-01 4.25e+01 ... (remaining 41551 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 17246 17.95 - 35.90: 889 35.90 - 53.84: 256 53.84 - 71.79: 91 71.79 - 89.74: 33 Dihedral angle restraints: 18515 sinusoidal: 7520 harmonic: 10995 Sorted by residual: dihedral pdb=" C ASN E 343 " pdb=" N ASN E 343 " pdb=" CA ASN E 343 " pdb=" CB ASN E 343 " ideal model delta harmonic sigma weight residual -122.60 -90.59 -32.01 0 2.50e+00 1.60e-01 1.64e+02 dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual -86.00 -13.46 -72.54 1 1.00e+01 1.00e-02 6.72e+01 dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual -86.00 -13.49 -72.51 1 1.00e+01 1.00e-02 6.72e+01 ... (remaining 18512 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.235: 4700 0.235 - 0.469: 61 0.469 - 0.704: 1 0.704 - 0.939: 0 0.939 - 1.173: 6 Chirality restraints: 4768 Sorted by residual: chirality pdb=" C1 FUC I 3 " pdb=" O6 NAG I 1 " pdb=" C2 FUC I 3 " pdb=" O5 FUC I 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-02 2.50e+03 1.18e+02 chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 7.54e+01 chirality pdb=" C1 NAG A1303 " pdb=" ND2 ASN A 61 " pdb=" C2 NAG A1303 " pdb=" O5 NAG A1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.23 -1.17 2.00e-01 2.50e+01 3.44e+01 ... (remaining 4765 not shown) Planarity restraints: 5362 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1311 " -0.182 2.00e-02 2.50e+03 1.53e-01 2.92e+02 pdb=" C7 NAG A1311 " 0.047 2.00e-02 2.50e+03 pdb=" C8 NAG A1311 " -0.132 2.00e-02 2.50e+03 pdb=" N2 NAG A1311 " 0.252 2.00e-02 2.50e+03 pdb=" O7 NAG A1311 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 61 " 0.009 2.00e-02 2.50e+03 6.31e-02 4.98e+01 pdb=" CG ASN B 61 " -0.060 2.00e-02 2.50e+03 pdb=" OD1 ASN B 61 " 0.070 2.00e-02 2.50e+03 pdb=" ND2 ASN B 61 " -0.084 2.00e-02 2.50e+03 pdb=" C1 NAG B1303 " 0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 61 " -0.009 2.00e-02 2.50e+03 6.28e-02 4.93e+01 pdb=" CG ASN A 61 " 0.060 2.00e-02 2.50e+03 pdb=" OD1 ASN A 61 " -0.070 2.00e-02 2.50e+03 pdb=" ND2 ASN A 61 " 0.083 2.00e-02 2.50e+03 pdb=" C1 NAG A1303 " -0.065 2.00e-02 2.50e+03 ... (remaining 5359 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 288 2.60 - 3.17: 25300 3.17 - 3.75: 45372 3.75 - 4.32: 64312 4.32 - 4.90: 107345 Nonbonded interactions: 242617 Sorted by model distance: nonbonded pdb=" OD2 ASP B 420 " pdb=" OH TYR E 369 " model vdw 2.022 2.440 nonbonded pdb=" OD2 ASP A 420 " pdb=" OH TYR B 369 " model vdw 2.026 2.440 nonbonded pdb=" OD1 ASP D 86 " pdb=" OH TYR D 90 " model vdw 2.034 2.440 nonbonded pdb=" OD1 ASP H 86 " pdb=" OH TYR H 90 " model vdw 2.034 2.440 nonbonded pdb=" OD1 ASP F 86 " pdb=" OH TYR F 90 " model vdw 2.034 2.440 ... (remaining 242612 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 15 through 1140 or resid 1301 through 1310)) selection = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'L' } ncs_group { reference = (chain 'D' and resid 2 through 112) selection = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 5.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 19.660 Check model and map are aligned: 0.480 Set scattering table: 0.240 Process input model: 81.860 Find NCS groups from input model: 2.410 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 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 : 0.010 0.158 30507 Z= 0.628 Angle : 1.367 26.607 41556 Z= 0.803 Chirality : 0.087 1.173 4768 Planarity : 0.010 0.153 5329 Dihedral : 13.076 89.741 11321 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.74 % Favored : 95.18 % Rotamer: Outliers : 1.03 % Allowed : 1.21 % Favored : 97.76 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.12), residues: 3735 helix: 0.43 (0.18), residues: 618 sheet: -0.17 (0.16), residues: 900 loop : -0.55 (0.12), residues: 2217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.006 TRP F 97 HIS 0.017 0.003 HIS D 100D PHE 0.079 0.006 PHE B 497 TYR 0.084 0.005 TYR H 52 ARG 0.034 0.003 ARG L 78 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 3294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 582 time to evaluate : 3.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 LYS cc_start: 0.6448 (mmtt) cc_final: 0.6231 (tppt) REVERT: A 274 THR cc_start: 0.7463 (p) cc_final: 0.6402 (p) REVERT: A 360 ASN cc_start: 0.7481 (t0) cc_final: 0.7209 (t0) REVERT: A 373 SER cc_start: 0.8279 (p) cc_final: 0.8072 (p) REVERT: A 396 TYR cc_start: 0.7940 (m-80) cc_final: 0.7519 (m-80) REVERT: A 449 TYR cc_start: 0.6375 (m-10) cc_final: 0.6068 (m-10) REVERT: B 274 THR cc_start: 0.7574 (p) cc_final: 0.6618 (p) REVERT: B 437 ASN cc_start: 0.8586 (t0) cc_final: 0.8370 (t0) REVERT: B 858 LEU cc_start: 0.8822 (mp) cc_final: 0.8608 (mp) REVERT: B 900 MET cc_start: 0.5846 (mtp) cc_final: 0.5428 (mtp) REVERT: B 933 LYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7766 (mtpt) REVERT: B 994 ASP cc_start: 0.7878 (t0) cc_final: 0.7670 (t0) REVERT: B 1108 ASN cc_start: 0.7647 (m-40) cc_final: 0.7349 (m-40) REVERT: D 100 HIS cc_start: 0.6989 (OUTLIER) cc_final: 0.6709 (t-90) REVERT: E 105 ILE cc_start: 0.6185 (mp) cc_final: 0.5977 (pt) REVERT: E 177 MET cc_start: 0.0802 (mpp) cc_final: 0.0590 (mpp) REVERT: E 274 THR cc_start: 0.7532 (p) cc_final: 0.6521 (p) REVERT: E 347 PHE cc_start: 0.6936 (m-10) cc_final: 0.6237 (m-80) REVERT: E 923 ILE cc_start: 0.6895 (tt) cc_final: 0.6659 (tt) REVERT: E 933 LYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7629 (mtpt) REVERT: E 960 ASN cc_start: 0.8488 (t0) cc_final: 0.8210 (t0) REVERT: F 94 ARG cc_start: 0.8159 (ttp80) cc_final: 0.7841 (ptt-90) REVERT: F 101 ASP cc_start: 0.7615 (OUTLIER) cc_final: 0.7259 (p0) REVERT: H 46 GLU cc_start: 0.6329 (mp0) cc_final: 0.5683 (mp0) REVERT: C 29 SER cc_start: 0.5469 (p) cc_final: 0.4858 (t) REVERT: G 82 GLU cc_start: 0.4153 (OUTLIER) cc_final: 0.3160 (pp20) REVERT: L 29 SER cc_start: 0.4845 (p) cc_final: 0.4302 (t) outliers start: 33 outliers final: 9 residues processed: 604 average time/residue: 0.3775 time to fit residues: 374.6779 Evaluate side-chains 426 residues out of total 3294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 412 time to evaluate : 3.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 933 LYS Chi-restraints excluded: chain D residue 100 HIS Chi-restraints excluded: chain E residue 933 LYS Chi-restraints excluded: chain F residue 96 GLN Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain H residue 97 TRP Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain G residue 82 GLU Chi-restraints excluded: chain L residue 82 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 316 optimal weight: 0.9980 chunk 284 optimal weight: 3.9990 chunk 157 optimal weight: 2.9990 chunk 97 optimal weight: 0.5980 chunk 191 optimal weight: 1.9990 chunk 151 optimal weight: 6.9990 chunk 293 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 chunk 178 optimal weight: 0.9990 chunk 218 optimal weight: 20.0000 chunk 340 optimal weight: 6.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 196 ASN A 394 ASN A 498 GLN A 606 ASN A 856 ASN ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 GLN B 52 GLN B 196 ASN B 370 ASN B 394 ASN B 498 GLN B 606 ASN B 777 ASN ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN B1011 GLN E 196 ASN E 394 ASN E 498 GLN E 641 ASN E 856 ASN E 901 GLN ** E 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1011 GLN C 36 GLN G 36 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 30507 Z= 0.302 Angle : 0.728 10.156 41556 Z= 0.382 Chirality : 0.054 0.807 4768 Planarity : 0.005 0.055 5329 Dihedral : 7.664 74.814 4838 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.46 % Allowed : 8.19 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.12), residues: 3735 helix: 1.00 (0.19), residues: 621 sheet: 0.06 (0.15), residues: 951 loop : -0.56 (0.12), residues: 2163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.003 TRP D 97 HIS 0.009 0.002 HIS E 66 PHE 0.026 0.002 PHE B 168 TYR 0.018 0.002 TYR C 95B ARG 0.007 0.001 ARG B 509 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 3294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 471 time to evaluate : 3.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.8348 (ptp90) cc_final: 0.8050 (mtt180) REVERT: A 326 ILE cc_start: 0.8370 (mm) cc_final: 0.8031 (pt) REVERT: A 347 PHE cc_start: 0.7665 (m-10) cc_final: 0.7405 (m-80) REVERT: A 353 TRP cc_start: 0.8335 (p-90) cc_final: 0.7893 (p-90) REVERT: A 373 SER cc_start: 0.8477 (p) cc_final: 0.8253 (p) REVERT: A 394 ASN cc_start: 0.7865 (OUTLIER) cc_final: 0.7655 (m-40) REVERT: A 396 TYR cc_start: 0.8004 (m-80) cc_final: 0.7246 (m-80) REVERT: B 32 PHE cc_start: 0.7423 (m-10) cc_final: 0.7219 (m-10) REVERT: B 394 ASN cc_start: 0.7874 (OUTLIER) cc_final: 0.7652 (m-40) REVERT: B 900 MET cc_start: 0.5780 (mtp) cc_final: 0.5191 (mtp) REVERT: B 902 MET cc_start: 0.8017 (tpt) cc_final: 0.7427 (tpt) REVERT: B 933 LYS cc_start: 0.8156 (OUTLIER) cc_final: 0.7922 (mmtm) REVERT: B 994 ASP cc_start: 0.7937 (t0) cc_final: 0.7653 (t0) REVERT: B 1108 ASN cc_start: 0.7701 (m-40) cc_final: 0.7323 (t0) REVERT: D 107 THR cc_start: 0.7203 (m) cc_final: 0.6963 (m) REVERT: E 353 TRP cc_start: 0.8389 (p-90) cc_final: 0.7884 (p-90) REVERT: E 394 ASN cc_start: 0.7853 (OUTLIER) cc_final: 0.7619 (m-40) REVERT: C 82 GLU cc_start: 0.3646 (mm-30) cc_final: 0.3031 (pp20) REVERT: L 82 GLU cc_start: 0.3649 (mm-30) cc_final: 0.3042 (pp20) outliers start: 79 outliers final: 51 residues processed: 509 average time/residue: 0.3727 time to fit residues: 319.3341 Evaluate side-chains 446 residues out of total 3294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 391 time to evaluate : 3.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 489 TYR Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 663 ASP Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 933 LYS Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 94 ARG Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 196 ASN Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain E residue 394 ASN Chi-restraints excluded: chain E residue 489 TYR Chi-restraints excluded: chain E residue 490 PHE Chi-restraints excluded: chain E residue 495 TYR Chi-restraints excluded: chain E residue 551 VAL Chi-restraints excluded: chain E residue 560 LEU Chi-restraints excluded: chain E residue 605 SER Chi-restraints excluded: chain E residue 618 THR Chi-restraints excluded: chain E residue 641 ASN Chi-restraints excluded: chain E residue 642 VAL Chi-restraints excluded: chain E residue 705 VAL Chi-restraints excluded: chain E residue 730 SER Chi-restraints excluded: chain E residue 737 ASP Chi-restraints excluded: chain E residue 739 THR Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain L residue 13 THR Chi-restraints excluded: chain L residue 27 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 189 optimal weight: 1.9990 chunk 105 optimal weight: 7.9990 chunk 283 optimal weight: 0.6980 chunk 231 optimal weight: 8.9990 chunk 93 optimal weight: 2.9990 chunk 341 optimal weight: 10.0000 chunk 368 optimal weight: 2.9990 chunk 303 optimal weight: 3.9990 chunk 338 optimal weight: 0.9990 chunk 116 optimal weight: 9.9990 chunk 273 optimal weight: 6.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 394 ASN A 498 GLN A 901 GLN A 907 ASN A 913 GLN ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN B 196 ASN B 394 ASN B 493 GLN B 498 GLN B 777 ASN B 901 GLN B 907 ASN B 913 GLN ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 66 HIS E 196 ASN E 394 ASN E 498 GLN E 907 ASN E 913 GLN ** E1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 GLN L 36 GLN L 52 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 30507 Z= 0.323 Angle : 0.684 9.754 41556 Z= 0.356 Chirality : 0.051 0.662 4768 Planarity : 0.005 0.040 5329 Dihedral : 7.077 58.149 4811 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.30 % Allowed : 10.62 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.13), residues: 3735 helix: 1.04 (0.19), residues: 615 sheet: -0.02 (0.15), residues: 987 loop : -0.71 (0.12), residues: 2133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP H 97 HIS 0.004 0.001 HIS E1064 PHE 0.022 0.002 PHE A 168 TYR 0.018 0.002 TYR L 95B ARG 0.006 0.001 ARG B 509 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 3294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 412 time to evaluate : 3.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 ILE cc_start: 0.8422 (mm) cc_final: 0.8151 (pt) REVERT: A 373 SER cc_start: 0.8565 (p) cc_final: 0.8283 (p) REVERT: A 396 TYR cc_start: 0.8087 (m-80) cc_final: 0.7660 (m-80) REVERT: A 794 ILE cc_start: 0.8316 (mm) cc_final: 0.8091 (tt) REVERT: B 32 PHE cc_start: 0.7541 (m-10) cc_final: 0.7267 (m-10) REVERT: B 238 PHE cc_start: 0.3507 (OUTLIER) cc_final: 0.3058 (p90) REVERT: B 902 MET cc_start: 0.8041 (tpt) cc_final: 0.7486 (tpt) REVERT: B 933 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7946 (mmtm) REVERT: B 994 ASP cc_start: 0.8018 (t0) cc_final: 0.7642 (t0) REVERT: B 1108 ASN cc_start: 0.7735 (m-40) cc_final: 0.7402 (t0) REVERT: D 94 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.8010 (ptt-90) REVERT: E 796 ASP cc_start: 0.5695 (t0) cc_final: 0.5435 (p0) REVERT: H 46 GLU cc_start: 0.6402 (mp0) cc_final: 0.5898 (mp0) REVERT: C 82 GLU cc_start: 0.3624 (mm-30) cc_final: 0.3016 (pp20) REVERT: G 6 GLN cc_start: 0.7412 (mt0) cc_final: 0.7200 (mt0) REVERT: L 55 SER cc_start: 0.6108 (m) cc_final: 0.5756 (p) REVERT: L 82 GLU cc_start: 0.3625 (mm-30) cc_final: 0.3122 (pp20) outliers start: 106 outliers final: 73 residues processed: 469 average time/residue: 0.3734 time to fit residues: 293.1475 Evaluate side-chains 456 residues out of total 3294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 380 time to evaluate : 3.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 933 LYS Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 94 ARG Chi-restraints excluded: chain D residue 96 GLN Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain E residue 346 ARG Chi-restraints excluded: chain E residue 489 TYR Chi-restraints excluded: chain E residue 495 TYR Chi-restraints excluded: chain E residue 560 LEU Chi-restraints excluded: chain E residue 576 VAL Chi-restraints excluded: chain E residue 605 SER Chi-restraints excluded: chain E residue 618 THR Chi-restraints excluded: chain E residue 642 VAL Chi-restraints excluded: chain E residue 649 CYS Chi-restraints excluded: chain E residue 705 VAL Chi-restraints excluded: chain E residue 716 THR Chi-restraints excluded: chain E residue 730 SER Chi-restraints excluded: chain E residue 739 THR Chi-restraints excluded: chain E residue 912 THR Chi-restraints excluded: chain E residue 969 ASN Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 36 GLN Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain L residue 13 THR Chi-restraints excluded: chain L residue 27 ASN Chi-restraints excluded: chain L residue 29 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 337 optimal weight: 8.9990 chunk 256 optimal weight: 2.9990 chunk 177 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 162 optimal weight: 0.0470 chunk 229 optimal weight: 9.9990 chunk 342 optimal weight: 0.9990 chunk 362 optimal weight: 3.9990 chunk 178 optimal weight: 0.7980 chunk 324 optimal weight: 0.0870 chunk 97 optimal weight: 2.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A1036 GLN A1134 ASN B 394 ASN B 493 GLN B 498 GLN B1036 GLN B1134 ASN E 196 ASN ** E 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1036 GLN E1134 ASN H 6 GLN L 36 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 30507 Z= 0.184 Angle : 0.606 9.386 41556 Z= 0.311 Chirality : 0.048 0.562 4768 Planarity : 0.004 0.035 5329 Dihedral : 6.744 58.628 4811 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.08 % Allowed : 11.90 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.13), residues: 3735 helix: 1.45 (0.20), residues: 618 sheet: -0.10 (0.15), residues: 1014 loop : -0.66 (0.13), residues: 2103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP H 97 HIS 0.005 0.001 HIS E1048 PHE 0.018 0.001 PHE H 100F TYR 0.017 0.001 TYR C 33 ARG 0.005 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 3294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 430 time to evaluate : 3.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.8258 (ptp90) cc_final: 0.8015 (mtt180) REVERT: A 153 MET cc_start: 0.0286 (mmt) cc_final: -0.1374 (tmm) REVERT: A 326 ILE cc_start: 0.8398 (mm) cc_final: 0.8106 (pt) REVERT: A 373 SER cc_start: 0.8546 (p) cc_final: 0.8216 (p) REVERT: A 396 TYR cc_start: 0.8039 (m-80) cc_final: 0.7572 (m-80) REVERT: A 794 ILE cc_start: 0.8340 (mm) cc_final: 0.8122 (tt) REVERT: B 32 PHE cc_start: 0.7578 (m-10) cc_final: 0.7277 (m-10) REVERT: B 238 PHE cc_start: 0.3207 (OUTLIER) cc_final: 0.2993 (p90) REVERT: B 902 MET cc_start: 0.7953 (tpt) cc_final: 0.7389 (tpt) REVERT: B 985 ASP cc_start: 0.6616 (m-30) cc_final: 0.6369 (m-30) REVERT: B 994 ASP cc_start: 0.7948 (t0) cc_final: 0.7579 (t0) REVERT: B 1108 ASN cc_start: 0.7708 (m-40) cc_final: 0.7339 (t0) REVERT: D 94 ARG cc_start: 0.8330 (OUTLIER) cc_final: 0.8035 (ptt-90) REVERT: D 103 TRP cc_start: 0.8256 (m100) cc_final: 0.7399 (m100) REVERT: E 333 THR cc_start: 0.7964 (OUTLIER) cc_final: 0.7748 (m) REVERT: E 869 MET cc_start: 0.6269 (mtp) cc_final: 0.6002 (mtp) REVERT: E 933 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7909 (mmtm) REVERT: C 82 GLU cc_start: 0.3677 (mm-30) cc_final: 0.3055 (pp20) REVERT: G 6 GLN cc_start: 0.7246 (mt0) cc_final: 0.6785 (mt0) REVERT: G 68 THR cc_start: 0.7805 (p) cc_final: 0.7430 (t) REVERT: L 55 SER cc_start: 0.5957 (m) cc_final: 0.5588 (p) REVERT: L 82 GLU cc_start: 0.3526 (mm-30) cc_final: 0.3073 (pp20) outliers start: 99 outliers final: 71 residues processed: 486 average time/residue: 0.3807 time to fit residues: 307.3014 Evaluate side-chains 457 residues out of total 3294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 382 time to evaluate : 3.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 490 PHE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 737 ASP Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 737 ASP Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 94 ARG Chi-restraints excluded: chain D residue 97 TRP Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain E residue 196 ASN Chi-restraints excluded: chain E residue 238 PHE Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 346 ARG Chi-restraints excluded: chain E residue 490 PHE Chi-restraints excluded: chain E residue 495 TYR Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain E residue 605 SER Chi-restraints excluded: chain E residue 618 THR Chi-restraints excluded: chain E residue 642 VAL Chi-restraints excluded: chain E residue 649 CYS Chi-restraints excluded: chain E residue 705 VAL Chi-restraints excluded: chain E residue 730 SER Chi-restraints excluded: chain E residue 737 ASP Chi-restraints excluded: chain E residue 933 LYS Chi-restraints excluded: chain E residue 969 ASN Chi-restraints excluded: chain E residue 1032 CYS Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 73 LYS Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 50 ASN Chi-restraints excluded: chain L residue 13 THR Chi-restraints excluded: chain L residue 36 GLN Chi-restraints excluded: chain L residue 102 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 301 optimal weight: 8.9990 chunk 205 optimal weight: 4.9990 chunk 5 optimal weight: 10.0000 chunk 269 optimal weight: 6.9990 chunk 149 optimal weight: 1.9990 chunk 309 optimal weight: 3.9990 chunk 250 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 185 optimal weight: 4.9990 chunk 325 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN A 388 ASN A 655 HIS A 907 ASN B 137 ASN B 196 ASN B 388 ASN B 493 GLN B 655 HIS ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 ASN E 394 ASN E 606 ASN E 655 HIS H 6 GLN ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 30507 Z= 0.465 Angle : 0.763 10.580 41556 Z= 0.395 Chirality : 0.054 0.530 4768 Planarity : 0.005 0.044 5329 Dihedral : 7.059 59.824 4806 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 4.74 % Allowed : 11.34 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.13), residues: 3735 helix: 0.62 (0.19), residues: 633 sheet: -0.33 (0.16), residues: 888 loop : -0.96 (0.12), residues: 2214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP F 97 HIS 0.006 0.002 HIS E1064 PHE 0.029 0.003 PHE F 100F TYR 0.026 0.003 TYR A 279 ARG 0.008 0.001 ARG L 78 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 3294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 379 time to evaluate : 3.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 TYR cc_start: 0.6897 (m-80) cc_final: 0.6685 (m-80) REVERT: A 317 ASN cc_start: 0.7583 (m-40) cc_final: 0.6838 (m110) REVERT: A 326 ILE cc_start: 0.8564 (mm) cc_final: 0.8255 (pt) REVERT: A 396 TYR cc_start: 0.8023 (m-80) cc_final: 0.7412 (m-80) REVERT: A 529 LYS cc_start: 0.8178 (ptmt) cc_final: 0.7881 (pttm) REVERT: B 153 MET cc_start: 0.0689 (mmt) cc_final: -0.1144 (tmm) REVERT: B 238 PHE cc_start: 0.4172 (OUTLIER) cc_final: 0.2942 (p90) REVERT: B 326 ILE cc_start: 0.8416 (mm) cc_final: 0.8172 (pt) REVERT: B 737 ASP cc_start: 0.7668 (m-30) cc_final: 0.7344 (t0) REVERT: B 994 ASP cc_start: 0.8161 (t0) cc_final: 0.7695 (t0) REVERT: D 94 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7901 (ptt-90) REVERT: D 97 TRP cc_start: 0.8470 (OUTLIER) cc_final: 0.7959 (t60) REVERT: E 333 THR cc_start: 0.8065 (OUTLIER) cc_final: 0.7846 (m) REVERT: E 346 ARG cc_start: 0.7646 (OUTLIER) cc_final: 0.6980 (mmp-170) REVERT: E 529 LYS cc_start: 0.8004 (ptmt) cc_final: 0.7714 (tptt) REVERT: E 933 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7760 (mmtm) REVERT: H 46 GLU cc_start: 0.6350 (mp0) cc_final: 0.5858 (mp0) REVERT: C 82 GLU cc_start: 0.4008 (mm-30) cc_final: 0.3199 (pp20) REVERT: L 55 SER cc_start: 0.6312 (m) cc_final: 0.5992 (p) REVERT: L 82 GLU cc_start: 0.3750 (mm-30) cc_final: 0.3324 (pp20) outliers start: 152 outliers final: 98 residues processed: 466 average time/residue: 0.3916 time to fit residues: 305.6290 Evaluate side-chains 459 residues out of total 3294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 355 time to evaluate : 3.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 94 ARG Chi-restraints excluded: chain D residue 96 GLN Chi-restraints excluded: chain D residue 97 TRP Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain E residue 238 PHE Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 346 ARG Chi-restraints excluded: chain E residue 393 THR Chi-restraints excluded: chain E residue 489 TYR Chi-restraints excluded: chain E residue 490 PHE Chi-restraints excluded: chain E residue 495 TYR Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain E residue 576 VAL Chi-restraints excluded: chain E residue 605 SER Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 618 THR Chi-restraints excluded: chain E residue 642 VAL Chi-restraints excluded: chain E residue 649 CYS Chi-restraints excluded: chain E residue 716 THR Chi-restraints excluded: chain E residue 719 THR Chi-restraints excluded: chain E residue 730 SER Chi-restraints excluded: chain E residue 739 THR Chi-restraints excluded: chain E residue 912 THR Chi-restraints excluded: chain E residue 933 LYS Chi-restraints excluded: chain E residue 969 ASN Chi-restraints excluded: chain E residue 1051 SER Chi-restraints excluded: chain E residue 1127 ASP Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 97 TRP Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 50 ASN Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 50 ASN Chi-restraints excluded: chain L residue 13 THR Chi-restraints excluded: chain L residue 27 ASN Chi-restraints excluded: chain L residue 50 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 121 optimal weight: 10.0000 chunk 326 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 212 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 362 optimal weight: 6.9990 chunk 301 optimal weight: 0.6980 chunk 167 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 120 optimal weight: 0.9990 chunk 190 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN A 907 ASN B 115 GLN B 196 ASN B 317 ASN B 493 GLN B 907 ASN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 GLN E 196 ASN E 317 ASN E 394 ASN E 907 ASN ** H 100DHIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 GLN ** G 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 30507 Z= 0.207 Angle : 0.612 8.789 41556 Z= 0.313 Chirality : 0.048 0.473 4768 Planarity : 0.004 0.037 5329 Dihedral : 6.728 59.557 4806 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.35 % Favored : 96.63 % Rotamer: Outliers : 3.27 % Allowed : 13.55 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.13), residues: 3735 helix: 1.30 (0.20), residues: 615 sheet: -0.35 (0.16), residues: 966 loop : -0.83 (0.13), residues: 2154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP F 97 HIS 0.005 0.001 HIS E1048 PHE 0.033 0.002 PHE G 46 TYR 0.017 0.002 TYR C 33 ARG 0.004 0.000 ARG F 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 3294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 394 time to evaluate : 2.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.0428 (mmt) cc_final: -0.1294 (tmm) REVERT: A 187 LYS cc_start: 0.6472 (mmtt) cc_final: 0.6213 (mmtp) REVERT: A 266 TYR cc_start: 0.6800 (m-80) cc_final: 0.6567 (m-80) REVERT: A 396 TYR cc_start: 0.7944 (m-80) cc_final: 0.7247 (m-80) REVERT: A 529 LYS cc_start: 0.8210 (ptmt) cc_final: 0.7847 (tptt) REVERT: B 153 MET cc_start: 0.0655 (mmt) cc_final: -0.1157 (tmm) REVERT: B 238 PHE cc_start: 0.3557 (OUTLIER) cc_final: 0.2774 (p90) REVERT: B 326 ILE cc_start: 0.8482 (mm) cc_final: 0.8273 (pt) REVERT: B 650 LEU cc_start: 0.6976 (tp) cc_final: 0.6541 (tp) REVERT: B 994 ASP cc_start: 0.8038 (t0) cc_final: 0.7565 (t0) REVERT: B 1021 SER cc_start: 0.8231 (t) cc_final: 0.7825 (p) REVERT: D 97 TRP cc_start: 0.7953 (OUTLIER) cc_final: 0.7323 (t60) REVERT: E 153 MET cc_start: 0.0401 (mmt) cc_final: -0.1101 (tmm) REVERT: E 529 LYS cc_start: 0.8045 (ptmt) cc_final: 0.7760 (tptt) REVERT: E 1021 SER cc_start: 0.8094 (t) cc_final: 0.7673 (p) REVERT: F 97 TRP cc_start: 0.6584 (p-90) cc_final: 0.6238 (p-90) REVERT: C 46 PHE cc_start: 0.7786 (OUTLIER) cc_final: 0.6560 (t80) REVERT: G 6 GLN cc_start: 0.7428 (mt0) cc_final: 0.6954 (mt0) REVERT: L 55 SER cc_start: 0.6094 (m) cc_final: 0.5847 (p) REVERT: L 82 GLU cc_start: 0.3425 (mm-30) cc_final: 0.2915 (pp20) outliers start: 105 outliers final: 77 residues processed: 453 average time/residue: 0.3796 time to fit residues: 284.7481 Evaluate side-chains 448 residues out of total 3294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 368 time to evaluate : 3.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 490 PHE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 94 ARG Chi-restraints excluded: chain D residue 97 TRP Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 196 ASN Chi-restraints excluded: chain E residue 238 PHE Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 346 ARG Chi-restraints excluded: chain E residue 393 THR Chi-restraints excluded: chain E residue 490 PHE Chi-restraints excluded: chain E residue 495 TYR Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain E residue 605 SER Chi-restraints excluded: chain E residue 617 CYS Chi-restraints excluded: chain E residue 618 THR Chi-restraints excluded: chain E residue 730 SER Chi-restraints excluded: chain E residue 1017 GLU Chi-restraints excluded: chain E residue 1032 CYS Chi-restraints excluded: chain E residue 1128 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 73 LYS Chi-restraints excluded: chain H residue 97 TRP Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 46 PHE Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 50 ASN Chi-restraints excluded: chain L residue 13 THR Chi-restraints excluded: chain L residue 27 ASN Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 50 ASN Chi-restraints excluded: chain L residue 102 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 349 optimal weight: 0.0970 chunk 40 optimal weight: 6.9990 chunk 206 optimal weight: 0.0870 chunk 264 optimal weight: 0.8980 chunk 205 optimal weight: 3.9990 chunk 305 optimal weight: 0.9990 chunk 202 optimal weight: 0.8980 chunk 361 optimal weight: 10.0000 chunk 226 optimal weight: 9.9990 chunk 220 optimal weight: 0.8980 chunk 166 optimal weight: 2.9990 overall best weight: 0.5756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 317 ASN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 ASN B 907 ASN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 196 ASN E 317 ASN E 907 ASN C 36 GLN ** G 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.3798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 30507 Z= 0.190 Angle : 0.585 10.799 41556 Z= 0.299 Chirality : 0.047 0.447 4768 Planarity : 0.004 0.038 5329 Dihedral : 6.415 59.175 4806 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.07 % Favored : 95.90 % Rotamer: Outliers : 3.05 % Allowed : 14.45 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.13), residues: 3735 helix: 1.65 (0.20), residues: 606 sheet: -0.32 (0.15), residues: 987 loop : -0.76 (0.13), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP F 97 HIS 0.005 0.001 HIS B1048 PHE 0.035 0.002 PHE G 46 TYR 0.017 0.001 TYR B 266 ARG 0.006 0.000 ARG F 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 3294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 396 time to evaluate : 3.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.0389 (mmt) cc_final: -0.1320 (tmm) REVERT: A 187 LYS cc_start: 0.6342 (mmtt) cc_final: 0.6127 (mmtp) REVERT: A 266 TYR cc_start: 0.6785 (m-80) cc_final: 0.6527 (m-80) REVERT: A 396 TYR cc_start: 0.8031 (m-80) cc_final: 0.7202 (m-80) REVERT: A 529 LYS cc_start: 0.8221 (ptmt) cc_final: 0.7923 (pttm) REVERT: B 153 MET cc_start: 0.0624 (mmt) cc_final: -0.1206 (tmm) REVERT: B 326 ILE cc_start: 0.8578 (mm) cc_final: 0.8307 (pt) REVERT: B 650 LEU cc_start: 0.6737 (tp) cc_final: 0.6282 (tp) REVERT: B 994 ASP cc_start: 0.8105 (t0) cc_final: 0.7817 (t0) REVERT: B 1021 SER cc_start: 0.8191 (t) cc_final: 0.7782 (p) REVERT: D 94 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.7838 (ptt-90) REVERT: E 153 MET cc_start: 0.0363 (mmt) cc_final: -0.1192 (tmm) REVERT: E 420 ASP cc_start: 0.7696 (m-30) cc_final: 0.7394 (m-30) REVERT: E 529 LYS cc_start: 0.8049 (ptmt) cc_final: 0.7793 (tptt) REVERT: E 697 MET cc_start: 0.7214 (ptm) cc_final: 0.6401 (ttt) REVERT: H 46 GLU cc_start: 0.5873 (mp0) cc_final: 0.5546 (mp0) REVERT: C 46 PHE cc_start: 0.7847 (OUTLIER) cc_final: 0.6372 (t80) REVERT: G 6 GLN cc_start: 0.7376 (mt0) cc_final: 0.6465 (mt0) REVERT: L 46 PHE cc_start: 0.8045 (t80) cc_final: 0.7681 (t80) REVERT: L 82 GLU cc_start: 0.3524 (mm-30) cc_final: 0.3041 (pp20) outliers start: 98 outliers final: 82 residues processed: 447 average time/residue: 0.4100 time to fit residues: 300.3572 Evaluate side-chains 456 residues out of total 3294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 372 time to evaluate : 4.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 490 PHE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 94 ARG Chi-restraints excluded: chain D residue 97 TRP Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain E residue 238 PHE Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 346 ARG Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 393 THR Chi-restraints excluded: chain E residue 489 TYR Chi-restraints excluded: chain E residue 490 PHE Chi-restraints excluded: chain E residue 495 TYR Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain E residue 605 SER Chi-restraints excluded: chain E residue 617 CYS Chi-restraints excluded: chain E residue 618 THR Chi-restraints excluded: chain E residue 705 VAL Chi-restraints excluded: chain E residue 730 SER Chi-restraints excluded: chain E residue 873 TYR Chi-restraints excluded: chain E residue 969 ASN Chi-restraints excluded: chain E residue 1017 GLU Chi-restraints excluded: chain E residue 1032 CYS Chi-restraints excluded: chain E residue 1123 SER Chi-restraints excluded: chain E residue 1128 VAL Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 73 LYS Chi-restraints excluded: chain H residue 97 TRP Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 36 GLN Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 46 PHE Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 50 ASN Chi-restraints excluded: chain L residue 13 THR Chi-restraints excluded: chain L residue 27 ASN Chi-restraints excluded: chain L residue 102 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 223 optimal weight: 10.0000 chunk 144 optimal weight: 9.9990 chunk 215 optimal weight: 3.9990 chunk 108 optimal weight: 7.9990 chunk 71 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 229 optimal weight: 10.0000 chunk 246 optimal weight: 4.9990 chunk 178 optimal weight: 0.0000 chunk 33 optimal weight: 0.8980 chunk 284 optimal weight: 5.9990 overall best weight: 2.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN B 317 ASN D 6 GLN E 317 ASN E 907 ASN ** G 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 30507 Z= 0.358 Angle : 0.665 8.349 41556 Z= 0.342 Chirality : 0.050 0.441 4768 Planarity : 0.005 0.049 5329 Dihedral : 6.613 59.992 4805 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.25 % Favored : 94.73 % Rotamer: Outliers : 3.74 % Allowed : 14.27 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.13), residues: 3735 helix: 1.12 (0.20), residues: 618 sheet: -0.39 (0.16), residues: 909 loop : -0.91 (0.13), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP H 97 HIS 0.006 0.001 HIS E1048 PHE 0.027 0.002 PHE G 46 TYR 0.020 0.002 TYR B 495 ARG 0.006 0.001 ARG D 38 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 3294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 376 time to evaluate : 3.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.0345 (mmt) cc_final: -0.1450 (tmm) REVERT: A 266 TYR cc_start: 0.6711 (m-80) cc_final: 0.6317 (m-80) REVERT: A 396 TYR cc_start: 0.8072 (m-80) cc_final: 0.7339 (m-80) REVERT: A 529 LYS cc_start: 0.8278 (ptmt) cc_final: 0.7972 (tptt) REVERT: B 153 MET cc_start: 0.0602 (mmt) cc_final: -0.1288 (tmm) REVERT: B 238 PHE cc_start: 0.4070 (OUTLIER) cc_final: 0.2832 (p90) REVERT: B 326 ILE cc_start: 0.8568 (mm) cc_final: 0.8293 (pt) REVERT: B 650 LEU cc_start: 0.6902 (tp) cc_final: 0.6493 (tp) REVERT: B 994 ASP cc_start: 0.8155 (t0) cc_final: 0.7634 (t0) REVERT: D 94 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.7987 (ptt-90) REVERT: D 97 TRP cc_start: 0.8279 (OUTLIER) cc_final: 0.7627 (t60) REVERT: E 153 MET cc_start: 0.0148 (mmt) cc_final: -0.1443 (tmm) REVERT: E 360 ASN cc_start: 0.7496 (t0) cc_final: 0.7161 (t0) REVERT: E 420 ASP cc_start: 0.7765 (m-30) cc_final: 0.7440 (m-30) REVERT: E 529 LYS cc_start: 0.8082 (ptmt) cc_final: 0.7857 (tptt) REVERT: E 933 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7855 (mmtm) REVERT: H 46 GLU cc_start: 0.6008 (mp0) cc_final: 0.5634 (mp0) REVERT: C 46 PHE cc_start: 0.7896 (OUTLIER) cc_final: 0.6472 (t80) REVERT: G 55 SER cc_start: 0.5648 (m) cc_final: 0.5324 (p) REVERT: L 82 GLU cc_start: 0.3625 (mm-30) cc_final: 0.3098 (pp20) outliers start: 120 outliers final: 97 residues processed: 441 average time/residue: 0.4065 time to fit residues: 295.9315 Evaluate side-chains 466 residues out of total 3294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 364 time to evaluate : 3.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 490 PHE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1051 SER Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 94 ARG Chi-restraints excluded: chain D residue 97 TRP Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain E residue 238 PHE Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain E residue 318 PHE Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 346 ARG Chi-restraints excluded: chain E residue 393 THR Chi-restraints excluded: chain E residue 490 PHE Chi-restraints excluded: chain E residue 495 TYR Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain E residue 605 SER Chi-restraints excluded: chain E residue 617 CYS Chi-restraints excluded: chain E residue 618 THR Chi-restraints excluded: chain E residue 697 MET Chi-restraints excluded: chain E residue 730 SER Chi-restraints excluded: chain E residue 739 THR Chi-restraints excluded: chain E residue 873 TYR Chi-restraints excluded: chain E residue 933 LYS Chi-restraints excluded: chain E residue 969 ASN Chi-restraints excluded: chain E residue 1017 GLU Chi-restraints excluded: chain E residue 1032 CYS Chi-restraints excluded: chain E residue 1094 VAL Chi-restraints excluded: chain E residue 1123 SER Chi-restraints excluded: chain E residue 1128 VAL Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 97 TRP Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 46 PHE Chi-restraints excluded: chain C residue 50 ASN Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 50 ASN Chi-restraints excluded: chain L residue 13 THR Chi-restraints excluded: chain L residue 27 ASN Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 50 ASN Chi-restraints excluded: chain L residue 52 GLN Chi-restraints excluded: chain L residue 102 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 328 optimal weight: 5.9990 chunk 346 optimal weight: 2.9990 chunk 315 optimal weight: 0.3980 chunk 336 optimal weight: 4.9990 chunk 202 optimal weight: 1.9990 chunk 146 optimal weight: 20.0000 chunk 264 optimal weight: 0.9990 chunk 103 optimal weight: 10.0000 chunk 304 optimal weight: 0.1980 chunk 318 optimal weight: 0.6980 chunk 335 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN B 317 ASN D 6 GLN E 317 ASN E 907 ASN E1108 ASN ** H 100DHIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.4184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30507 Z= 0.207 Angle : 0.592 8.198 41556 Z= 0.303 Chirality : 0.047 0.417 4768 Planarity : 0.004 0.039 5329 Dihedral : 6.340 59.477 4805 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.99 % Favored : 95.98 % Rotamer: Outliers : 2.77 % Allowed : 15.45 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.13), residues: 3735 helix: 1.40 (0.20), residues: 618 sheet: -0.28 (0.17), residues: 846 loop : -0.84 (0.13), residues: 2271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D 103 HIS 0.005 0.001 HIS A1048 PHE 0.041 0.002 PHE G 46 TYR 0.017 0.001 TYR C 33 ARG 0.007 0.000 ARG A 646 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 3294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 384 time to evaluate : 3.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.0340 (mmt) cc_final: -0.1372 (tmm) REVERT: A 396 TYR cc_start: 0.8048 (m-80) cc_final: 0.7242 (m-80) REVERT: A 529 LYS cc_start: 0.8280 (ptmt) cc_final: 0.7973 (tptt) REVERT: A 697 MET cc_start: 0.7197 (ptm) cc_final: 0.6316 (ttt) REVERT: B 153 MET cc_start: 0.0536 (mmt) cc_final: -0.1326 (tmm) REVERT: B 202 LYS cc_start: 0.7121 (tttm) cc_final: 0.6835 (tptm) REVERT: B 326 ILE cc_start: 0.8557 (mm) cc_final: 0.8299 (pt) REVERT: B 994 ASP cc_start: 0.8091 (t0) cc_final: 0.7809 (t0) REVERT: B 1021 SER cc_start: 0.8196 (t) cc_final: 0.7827 (p) REVERT: D 94 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.7610 (ptt-90) REVERT: D 97 TRP cc_start: 0.7872 (OUTLIER) cc_final: 0.7416 (t60) REVERT: D 103 TRP cc_start: 0.8223 (m100) cc_final: 0.7471 (m100) REVERT: E 153 MET cc_start: 0.0241 (mmt) cc_final: -0.1316 (tmm) REVERT: E 529 LYS cc_start: 0.8108 (ptmt) cc_final: 0.7889 (tptt) REVERT: E 697 MET cc_start: 0.7220 (OUTLIER) cc_final: 0.6357 (ttt) REVERT: H 46 GLU cc_start: 0.5775 (mp0) cc_final: 0.5468 (mp0) REVERT: C 46 PHE cc_start: 0.7813 (OUTLIER) cc_final: 0.6449 (t80) REVERT: G 55 SER cc_start: 0.5594 (m) cc_final: 0.5359 (p) REVERT: L 82 GLU cc_start: 0.3523 (mm-30) cc_final: 0.3035 (pp20) outliers start: 89 outliers final: 80 residues processed: 430 average time/residue: 0.3816 time to fit residues: 269.4932 Evaluate side-chains 454 residues out of total 3294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 370 time to evaluate : 3.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 490 PHE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 94 ARG Chi-restraints excluded: chain D residue 97 TRP Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain E residue 238 PHE Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 346 ARG Chi-restraints excluded: chain E residue 393 THR Chi-restraints excluded: chain E residue 490 PHE Chi-restraints excluded: chain E residue 495 TYR Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain E residue 605 SER Chi-restraints excluded: chain E residue 617 CYS Chi-restraints excluded: chain E residue 618 THR Chi-restraints excluded: chain E residue 697 MET Chi-restraints excluded: chain E residue 873 TYR Chi-restraints excluded: chain E residue 900 MET Chi-restraints excluded: chain E residue 969 ASN Chi-restraints excluded: chain E residue 1017 GLU Chi-restraints excluded: chain E residue 1032 CYS Chi-restraints excluded: chain E residue 1094 VAL Chi-restraints excluded: chain E residue 1123 SER Chi-restraints excluded: chain E residue 1128 VAL Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 97 TRP Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 46 PHE Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 50 ASN Chi-restraints excluded: chain L residue 13 THR Chi-restraints excluded: chain L residue 27 ASN Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 50 ASN Chi-restraints excluded: chain L residue 102 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 221 optimal weight: 8.9990 chunk 356 optimal weight: 0.9980 chunk 217 optimal weight: 0.7980 chunk 168 optimal weight: 2.9990 chunk 247 optimal weight: 4.9990 chunk 373 optimal weight: 0.9990 chunk 343 optimal weight: 2.9990 chunk 297 optimal weight: 0.5980 chunk 30 optimal weight: 5.9990 chunk 229 optimal weight: 10.0000 chunk 182 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN B 317 ASN B1108 ASN E 196 ASN E 317 ASN E 907 ASN ** G 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.4315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 30507 Z= 0.203 Angle : 0.583 8.053 41556 Z= 0.299 Chirality : 0.047 0.406 4768 Planarity : 0.004 0.037 5329 Dihedral : 6.135 59.206 4805 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.58 % Favored : 95.39 % Rotamer: Outliers : 2.77 % Allowed : 15.61 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.13), residues: 3735 helix: 1.47 (0.20), residues: 630 sheet: -0.18 (0.17), residues: 840 loop : -0.81 (0.13), residues: 2265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP H 97 HIS 0.005 0.001 HIS E1048 PHE 0.026 0.001 PHE E 168 TYR 0.015 0.001 TYR B 495 ARG 0.007 0.000 ARG D 38 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7470 Ramachandran restraints generated. 3735 Oldfield, 0 Emsley, 3735 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 3294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 382 time to evaluate : 3.417 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: A 153 MET cc_start: 0.0334 (mmt) cc_final: -0.1388 (tmm) REVERT: A 396 TYR cc_start: 0.8040 (m-80) cc_final: 0.7181 (m-80) REVERT: A 529 LYS cc_start: 0.8265 (ptmt) cc_final: 0.7964 (tptt) REVERT: B 153 MET cc_start: 0.0579 (mmt) cc_final: -0.1311 (tmm) REVERT: B 326 ILE cc_start: 0.8587 (mm) cc_final: 0.8298 (pt) REVERT: B 697 MET cc_start: 0.7094 (OUTLIER) cc_final: 0.6200 (ttt) REVERT: B 1021 SER cc_start: 0.8166 (t) cc_final: 0.7808 (p) REVERT: D 94 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.7763 (ptt-90) REVERT: D 103 TRP cc_start: 0.8225 (m100) cc_final: 0.7455 (m100) REVERT: E 130 VAL cc_start: 0.7980 (t) cc_final: 0.7698 (p) REVERT: E 153 MET cc_start: 0.0220 (mmt) cc_final: -0.1327 (tmm) REVERT: E 420 ASP cc_start: 0.7629 (m-30) cc_final: 0.7356 (m-30) REVERT: E 495 TYR cc_start: 0.8054 (OUTLIER) cc_final: 0.7743 (p90) REVERT: E 697 MET cc_start: 0.7180 (OUTLIER) cc_final: 0.6468 (ttt) REVERT: H 46 GLU cc_start: 0.5729 (mp0) cc_final: 0.5393 (mp0) REVERT: H 100 MET cc_start: 0.8361 (mtt) cc_final: 0.8157 (mtm) REVERT: C 46 PHE cc_start: 0.7808 (OUTLIER) cc_final: 0.6475 (t80) REVERT: G 82 GLU cc_start: 0.3912 (mm-30) cc_final: 0.3237 (pp20) REVERT: L 82 GLU cc_start: 0.3464 (mm-30) cc_final: 0.3009 (pp20) outliers start: 89 outliers final: 75 residues processed: 432 average time/residue: 0.3982 time to fit residues: 282.0868 Evaluate side-chains 439 residues out of total 3294 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 359 time to evaluate : 3.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 490 PHE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 969 ASN Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1123 SER Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 94 ARG Chi-restraints excluded: chain D residue 97 TRP Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain E residue 238 PHE Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 346 ARG Chi-restraints excluded: chain E residue 393 THR Chi-restraints excluded: chain E residue 490 PHE Chi-restraints excluded: chain E residue 495 TYR Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain E residue 617 CYS Chi-restraints excluded: chain E residue 618 THR Chi-restraints excluded: chain E residue 697 MET Chi-restraints excluded: chain E residue 739 THR Chi-restraints excluded: chain E residue 900 MET Chi-restraints excluded: chain E residue 969 ASN Chi-restraints excluded: chain E residue 1017 GLU Chi-restraints excluded: chain E residue 1032 CYS Chi-restraints excluded: chain E residue 1094 VAL Chi-restraints excluded: chain E residue 1123 SER Chi-restraints excluded: chain E residue 1128 VAL Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 73 LYS Chi-restraints excluded: chain H residue 97 TRP Chi-restraints excluded: chain C residue 13 THR Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 46 PHE Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 50 ASN Chi-restraints excluded: chain L residue 13 THR Chi-restraints excluded: chain L residue 27 ASN Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 50 ASN Chi-restraints excluded: chain L residue 102 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 236 optimal weight: 6.9990 chunk 316 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 274 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 297 optimal weight: 0.7980 chunk 124 optimal weight: 9.9990 chunk 305 optimal weight: 0.9980 chunk 37 optimal weight: 0.0570 chunk 54 optimal weight: 4.9990 overall best weight: 0.7700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 ASN A 658 ASN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN B 317 ASN E 196 ASN E 317 ASN E 907 ASN E1108 ASN ** G 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.189455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.157543 restraints weight = 44721.978| |-----------------------------------------------------------------------------| r_work (start): 0.3917 rms_B_bonded: 2.59 r_work: 0.3794 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3661 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.4411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 30507 Z= 0.193 Angle : 0.586 10.117 41556 Z= 0.298 Chirality : 0.046 0.400 4768 Planarity : 0.004 0.037 5329 Dihedral : 6.038 59.226 4805 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.18 % Favored : 95.80 % Rotamer: Outliers : 2.71 % Allowed : 15.89 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.13), residues: 3735 helix: 1.56 (0.20), residues: 630 sheet: -0.12 (0.17), residues: 840 loop : -0.76 (0.13), residues: 2265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP H 97 HIS 0.005 0.001 HIS B1048 PHE 0.021 0.001 PHE B 32 TYR 0.026 0.001 TYR B 707 ARG 0.007 0.000 ARG F 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7323.97 seconds wall clock time: 133 minutes 46.39 seconds (8026.39 seconds total)