Starting phenix.real_space_refine on Mon Apr 15 01:22:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j1v_35934/04_2024/8j1v_35934.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j1v_35934/04_2024/8j1v_35934.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j1v_35934/04_2024/8j1v_35934.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j1v_35934/04_2024/8j1v_35934.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j1v_35934/04_2024/8j1v_35934.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j1v_35934/04_2024/8j1v_35934.pdb" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4143 atoms to isotropic. 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 18603 2.51 5 N 4833 2.21 5 O 5631 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 568": "OD1" <-> "OD2" Residue "A ASP 578": "OD1" <-> "OD2" Residue "A TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 568": "OD1" <-> "OD2" Residue "B ASP 578": "OD1" <-> "OD2" Residue "B TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 191": "OE1" <-> "OE2" Residue "E TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 568": "OD1" <-> "OD2" Residue "E ASP 578": "OD1" <-> "OD2" Residue "E TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 29205 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1008, 7910 Classifications: {'peptide': 1008} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 53, 'TRANS': 954} Chain breaks: 8 Chain: "H" Number of atoms: 874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 874 Classifications: {'peptide': 115} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 111} Chain: "K" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 825 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "B" Number of atoms: 7910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1008, 7910 Classifications: {'peptide': 1008} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 53, 'TRANS': 954} Chain breaks: 8 Chain: "C" Number of atoms: 874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 874 Classifications: {'peptide': 115} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 111} Chain: "D" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 825 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "E" Number of atoms: 7910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1008, 7910 Classifications: {'peptide': 1008} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 53, 'TRANS': 954} Chain breaks: 8 Chain: "F" Number of atoms: 874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 874 Classifications: {'peptide': 115} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 111} Chain: "G" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 825 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "E" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 14.85, per 1000 atoms: 0.51 Number of scatterers: 29205 At special positions: 0 Unit cell: (154.23, 146.47, 210.49, 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 5631 8.00 N 4833 7.00 C 18603 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 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=2.03 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=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 96 " distance=2.04 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 166 " distance=2.04 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS E 538 " - pdb=" SG CYS E 590 " distance=2.04 Simple disulfide: pdb=" SG CYS E 617 " - pdb=" SG CYS E 649 " distance=2.03 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS E1082 " - pdb=" SG CYS E1126 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 96 " distance=2.04 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 63 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 603 " " NAG A1304 " - " ASN A 657 " " NAG A1305 " - " ASN A1074 " " NAG A1306 " - " ASN A 122 " " NAG A1307 " - " ASN A 165 " " NAG A1308 " - " ASN A 234 " " NAG A1309 " - " ASN A 331 " " NAG B1301 " - " ASN B 63 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 603 " " NAG B1304 " - " ASN B 657 " " NAG B1305 " - " ASN B1074 " " NAG B1306 " - " ASN B 122 " " NAG B1307 " - " ASN B 165 " " NAG B1308 " - " ASN B 234 " " NAG B1309 " - " ASN B 331 " " NAG E1301 " - " ASN E 63 " " NAG E1302 " - " ASN E 282 " " NAG E1303 " - " ASN E 603 " " NAG E1304 " - " ASN E 657 " " NAG E1305 " - " ASN E1074 " " NAG E1306 " - " ASN E 122 " " NAG E1307 " - " ASN E 165 " " NAG E1308 " - " ASN E 234 " " NAG E1309 " - " ASN E 331 " Time building additional restraints: 10.58 Conformation dependent library (CDL) restraints added in 4.8 seconds 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6870 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 54 sheets defined 21.5% alpha, 24.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.30 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 366 through 372 removed outlier: 3.850A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 388 removed outlier: 4.093A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.573A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.632A pdb=" N TYR A 421 " --> pdb=" O ASN A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.646A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 4.027A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA A 783 " --> pdb=" O GLN A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 800 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.731A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.260A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.781A pdb=" N SER A 939 " --> pdb=" O GLN A 935 " (cutoff:3.500A) 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 967 removed outlier: 3.860A pdb=" N SER A 967 " --> pdb=" O VAL A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.815A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.518A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 33 removed outlier: 3.895A pdb=" N ASN H 33 " --> pdb=" O VAL H 30 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 65 removed outlier: 3.671A pdb=" N ARG H 65 " --> pdb=" O ASP H 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 366 through 372 removed outlier: 3.850A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 388 removed outlier: 4.093A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.573A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.632A pdb=" N TYR B 421 " --> pdb=" O ASN B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.645A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 4.028A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA B 783 " --> pdb=" O GLN B 779 " (cutoff:3.500A) Processing helix chain 'B' and resid 796 through 800 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.732A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.260A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.781A pdb=" N SER B 939 " --> pdb=" O GLN B 935 " (cutoff:3.500A) 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 967 removed outlier: 3.860A pdb=" N SER B 967 " --> pdb=" O VAL B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.815A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.518A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 33 removed outlier: 3.895A pdb=" N ASN C 33 " --> pdb=" O VAL C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 65 removed outlier: 3.671A pdb=" N ARG C 65 " --> pdb=" O ASP C 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 304 Processing helix chain 'E' and resid 337 through 343 Processing helix chain 'E' and resid 366 through 372 removed outlier: 3.851A pdb=" N ASN E 370 " --> pdb=" O SER E 366 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE E 371 " --> pdb=" O VAL E 367 " (cutoff:3.500A) Processing helix chain 'E' and resid 384 through 388 removed outlier: 4.093A pdb=" N ASN E 388 " --> pdb=" O THR E 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 410 removed outlier: 4.573A pdb=" N SER E 408 " --> pdb=" O ASN E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 422 removed outlier: 3.632A pdb=" N TYR E 421 " --> pdb=" O ASN E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 737 through 742 Processing helix chain 'E' and resid 746 through 755 removed outlier: 3.646A pdb=" N GLN E 755 " --> pdb=" O ASN E 751 " (cutoff:3.500A) Processing helix chain 'E' and resid 758 through 783 removed outlier: 4.027A pdb=" N GLN E 762 " --> pdb=" O SER E 758 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR E 778 " --> pdb=" O GLN E 774 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL E 781 " --> pdb=" O ASN E 777 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA E 783 " --> pdb=" O GLN E 779 " (cutoff:3.500A) Processing helix chain 'E' and resid 796 through 800 Processing helix chain 'E' and resid 816 through 826 Processing helix chain 'E' and resid 866 through 884 Processing helix chain 'E' and resid 886 through 891 removed outlier: 3.730A pdb=" N ALA E 890 " --> pdb=" O TRP E 886 " (cutoff:3.500A) Processing helix chain 'E' and resid 897 through 910 Processing helix chain 'E' and resid 912 through 919 removed outlier: 4.260A pdb=" N LEU E 916 " --> pdb=" O THR E 912 " (cutoff:3.500A) Processing helix chain 'E' and resid 919 through 941 removed outlier: 3.781A pdb=" N SER E 939 " --> pdb=" O GLN E 935 " (cutoff:3.500A) 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 967 removed outlier: 3.860A pdb=" N SER E 967 " --> pdb=" O VAL E 963 " (cutoff:3.500A) Processing helix chain 'E' and resid 976 through 984 removed outlier: 3.815A pdb=" N ILE E 980 " --> pdb=" O VAL E 976 " (cutoff:3.500A) Processing helix chain 'E' and resid 985 through 1033 removed outlier: 4.518A pdb=" N VAL E 991 " --> pdb=" O PRO E 987 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 33 removed outlier: 3.895A pdb=" N ASN F 33 " --> pdb=" O VAL F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 65 removed outlier: 3.671A pdb=" N ARG F 65 " --> pdb=" O ASP F 62 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 32 removed outlier: 5.947A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 8.953A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL A 38 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 57 removed outlier: 3.843A pdb=" N VAL A 49 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 169 through 172 removed outlier: 3.656A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.460A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 354 through 355 removed outlier: 3.585A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA7, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'A' and resid 538 through 543 removed outlier: 3.619A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE A 543 " --> pdb=" O LEU A 546 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 660 removed outlier: 5.971A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 8.645A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE A 664 " --> pdb=" O ALA A 672 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB2, first strand: chain 'A' and resid 712 through 728 removed outlier: 6.540A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.548A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 788 through 789 removed outlier: 5.518A pdb=" N ILE A 788 " --> pdb=" O ASN E 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB6, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB7, first strand: chain 'H' and resid 4 through 8 removed outlier: 3.884A pdb=" N GLN H 4 " --> pdb=" O SER H 26 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER H 22 " --> pdb=" O SER H 8 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 11 through 13 removed outlier: 6.178A pdb=" N GLY H 11 " --> pdb=" O THR H 115 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL H 114 " --> pdb=" O ALA H 92 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N TYR H 34 " --> pdb=" O ASP H 99 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N MET H 35 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N VAL H 51 " --> pdb=" O MET H 35 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N TRP H 37 " --> pdb=" O VAL H 49 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 4 through 6 removed outlier: 3.931A pdb=" N VAL K 19 " --> pdb=" O ILE K 75 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE K 71 " --> pdb=" O CYS K 23 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 45 through 48 removed outlier: 5.800A pdb=" N LEU K 46 " --> pdb=" O GLN K 37 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N GLN K 37 " --> pdb=" O LEU K 46 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 30 through 32 removed outlier: 5.947A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 8.953A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL B 38 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 49 through 57 removed outlier: 3.843A pdb=" N VAL B 49 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 169 through 172 removed outlier: 3.656A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.460A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 355 removed outlier: 3.584A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'B' and resid 538 through 543 removed outlier: 3.618A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE B 543 " --> pdb=" O LEU B 546 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 660 removed outlier: 5.971A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.645A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE B 664 " --> pdb=" O ALA B 672 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 702 through 703 Processing sheet with id=AD3, first strand: chain 'B' and resid 712 through 728 removed outlier: 6.539A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.548A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD6, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD7, first strand: chain 'C' and resid 4 through 8 removed outlier: 3.884A pdb=" N GLN C 4 " --> pdb=" O SER C 26 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER C 22 " --> pdb=" O SER C 8 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 11 through 13 removed outlier: 6.178A pdb=" N GLY C 11 " --> pdb=" O THR C 115 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL C 114 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N TYR C 34 " --> pdb=" O ASP C 99 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N MET C 35 " --> pdb=" O VAL C 51 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N VAL C 51 " --> pdb=" O MET C 35 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N TRP C 37 " --> pdb=" O VAL C 49 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 4 through 6 removed outlier: 3.931A pdb=" N VAL D 19 " --> pdb=" O ILE D 75 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE D 71 " --> pdb=" O CYS D 23 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 45 through 48 removed outlier: 5.800A pdb=" N LEU D 46 " --> pdb=" O GLN D 37 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N GLN D 37 " --> pdb=" O LEU D 46 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 30 through 32 removed outlier: 5.947A pdb=" N PHE E 201 " --> pdb=" O ASP E 228 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ASP E 228 " --> pdb=" O PHE E 201 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ILE E 203 " --> pdb=" O LEU E 226 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N HIS E 207 " --> pdb=" O ALA E 222 " (cutoff:3.500A) removed outlier: 8.954A pdb=" N ALA E 222 " --> pdb=" O HIS E 207 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL E 38 " --> pdb=" O LEU E 223 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 49 through 57 removed outlier: 3.842A pdb=" N VAL E 49 " --> pdb=" O TYR E 279 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ASP E 287 " --> pdb=" O LYS E 278 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 169 through 172 removed outlier: 3.656A pdb=" N SER E 172 " --> pdb=" O VAL E 126 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 311 through 319 removed outlier: 5.460A pdb=" N ILE E 312 " --> pdb=" O THR E 599 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N THR E 599 " --> pdb=" O ILE E 312 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N GLN E 314 " --> pdb=" O VAL E 597 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL E 597 " --> pdb=" O GLN E 314 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N SER E 316 " --> pdb=" O VAL E 595 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLY E 594 " --> pdb=" O GLN E 613 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 354 through 355 removed outlier: 3.584A pdb=" N ASN E 354 " --> pdb=" O SER E 399 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER E 399 " --> pdb=" O ASN E 354 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 391 through 392 Processing sheet with id=AE8, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AE9, first strand: chain 'E' and resid 538 through 543 removed outlier: 3.619A pdb=" N GLY E 550 " --> pdb=" O VAL E 539 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE E 543 " --> pdb=" O LEU E 546 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR E 553 " --> pdb=" O ASP E 586 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 654 through 660 removed outlier: 5.971A pdb=" N GLU E 654 " --> pdb=" O ALA E 694 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N THR E 696 " --> pdb=" O GLU E 654 " (cutoff:3.500A) removed outlier: 8.645A pdb=" N VAL E 656 " --> pdb=" O THR E 696 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER E 691 " --> pdb=" O GLN E 675 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE E 670 " --> pdb=" O ILE E 666 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE E 664 " --> pdb=" O ALA E 672 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 712 through 728 removed outlier: 6.540A pdb=" N ALA E 713 " --> pdb=" O ASN E1074 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ASN E1074 " --> pdb=" O ALA E 713 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLU E1072 " --> pdb=" O PRO E 715 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ASN E 717 " --> pdb=" O ALA E1070 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET E1050 " --> pdb=" O VAL E1065 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N TYR E1067 " --> pdb=" O HIS E1048 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N HIS E1048 " --> pdb=" O TYR E1067 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 733 through 736 removed outlier: 4.548A pdb=" N LYS E 733 " --> pdb=" O LEU E 861 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 1120 through 1122 Processing sheet with id=AF5, first strand: chain 'E' and resid 1094 through 1097 Processing sheet with id=AF6, first strand: chain 'F' and resid 4 through 8 removed outlier: 3.884A pdb=" N GLN F 4 " --> pdb=" O SER F 26 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER F 22 " --> pdb=" O SER F 8 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 11 through 13 removed outlier: 6.178A pdb=" N GLY F 11 " --> pdb=" O THR F 115 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL F 114 " --> pdb=" O ALA F 92 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N TYR F 34 " --> pdb=" O ASP F 99 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N MET F 35 " --> pdb=" O VAL F 51 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N VAL F 51 " --> pdb=" O MET F 35 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N TRP F 37 " --> pdb=" O VAL F 49 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'G' and resid 4 through 6 removed outlier: 3.932A pdb=" N VAL G 19 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE G 71 " --> pdb=" O CYS G 23 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'G' and resid 45 through 48 removed outlier: 5.800A pdb=" N LEU G 46 " --> pdb=" O GLN G 37 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N GLN G 37 " --> pdb=" O LEU G 46 " (cutoff:3.500A) 1052 hydrogen bonds defined for protein. 2859 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: 11.89 Time building geometry restraints manager: 11.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7795 1.33 - 1.45: 6388 1.45 - 1.58: 15514 1.58 - 1.70: 0 1.70 - 1.82: 183 Bond restraints: 29880 Sorted by residual: bond pdb=" N ILE A 233 " pdb=" CA ILE A 233 " ideal model delta sigma weight residual 1.457 1.499 -0.042 1.35e-02 5.49e+03 9.83e+00 bond pdb=" N ILE E 233 " pdb=" CA ILE E 233 " ideal model delta sigma weight residual 1.457 1.499 -0.042 1.35e-02 5.49e+03 9.79e+00 bond pdb=" N ILE B 233 " pdb=" CA ILE B 233 " ideal model delta sigma weight residual 1.457 1.499 -0.042 1.35e-02 5.49e+03 9.76e+00 bond pdb=" N THR E 912 " pdb=" CA THR E 912 " ideal model delta sigma weight residual 1.453 1.491 -0.038 1.31e-02 5.83e+03 8.26e+00 bond pdb=" N THR A 912 " pdb=" CA THR A 912 " ideal model delta sigma weight residual 1.453 1.490 -0.037 1.31e-02 5.83e+03 8.09e+00 ... (remaining 29875 not shown) Histogram of bond angle deviations from ideal: 100.23 - 106.99: 908 106.99 - 113.75: 16320 113.75 - 120.51: 11061 120.51 - 127.27: 12081 127.27 - 134.03: 259 Bond angle restraints: 40629 Sorted by residual: angle pdb=" C PRO E 230 " pdb=" CA PRO E 230 " pdb=" CB PRO E 230 " ideal model delta sigma weight residual 112.97 103.85 9.12 1.43e+00 4.89e-01 4.07e+01 angle pdb=" C PRO A 230 " pdb=" CA PRO A 230 " pdb=" CB PRO A 230 " ideal model delta sigma weight residual 112.97 103.87 9.10 1.43e+00 4.89e-01 4.05e+01 angle pdb=" C PRO B 230 " pdb=" CA PRO B 230 " pdb=" CB PRO B 230 " ideal model delta sigma weight residual 112.97 103.88 9.09 1.43e+00 4.89e-01 4.04e+01 angle pdb=" N VAL E 159 " pdb=" CA VAL E 159 " pdb=" C VAL E 159 " ideal model delta sigma weight residual 113.53 109.45 4.08 9.80e-01 1.04e+00 1.73e+01 angle pdb=" N VAL A 159 " pdb=" CA VAL A 159 " pdb=" C VAL A 159 " ideal model delta sigma weight residual 113.53 109.47 4.06 9.80e-01 1.04e+00 1.72e+01 ... (remaining 40624 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.20: 16686 17.20 - 34.39: 1124 34.39 - 51.59: 239 51.59 - 68.78: 50 68.78 - 85.98: 15 Dihedral angle restraints: 18114 sinusoidal: 7401 harmonic: 10713 Sorted by residual: dihedral pdb=" CB CYS E 662 " pdb=" SG CYS E 662 " pdb=" SG CYS E 671 " pdb=" CB CYS E 671 " ideal model delta sinusoidal sigma weight residual -86.00 -0.02 -85.98 1 1.00e+01 1.00e-02 8.93e+01 dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual -86.00 -0.06 -85.94 1 1.00e+01 1.00e-02 8.92e+01 dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual -86.00 -0.08 -85.92 1 1.00e+01 1.00e-02 8.92e+01 ... (remaining 18111 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 3960 0.066 - 0.133: 620 0.133 - 0.199: 49 0.199 - 0.265: 3 0.265 - 0.331: 6 Chirality restraints: 4638 Sorted by residual: chirality pdb=" C1 NAG A1308 " pdb=" ND2 ASN A 234 " pdb=" C2 NAG A1308 " pdb=" O5 NAG A1308 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" C1 NAG B1308 " pdb=" ND2 ASN B 234 " pdb=" C2 NAG B1308 " pdb=" O5 NAG B1308 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.74e+00 chirality pdb=" C1 NAG E1308 " pdb=" ND2 ASN E 234 " pdb=" C2 NAG E1308 " pdb=" O5 NAG E1308 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.74e+00 ... (remaining 4635 not shown) Planarity restraints: 5241 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E1309 " 0.350 2.00e-02 2.50e+03 3.02e-01 1.14e+03 pdb=" C7 NAG E1309 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG E1309 " 0.116 2.00e-02 2.50e+03 pdb=" N2 NAG E1309 " -0.538 2.00e-02 2.50e+03 pdb=" O7 NAG E1309 " 0.157 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1309 " 0.349 2.00e-02 2.50e+03 3.02e-01 1.14e+03 pdb=" C7 NAG B1309 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG B1309 " 0.115 2.00e-02 2.50e+03 pdb=" N2 NAG B1309 " -0.538 2.00e-02 2.50e+03 pdb=" O7 NAG B1309 " 0.157 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1309 " -0.349 2.00e-02 2.50e+03 3.02e-01 1.14e+03 pdb=" C7 NAG A1309 " 0.084 2.00e-02 2.50e+03 pdb=" C8 NAG A1309 " -0.105 2.00e-02 2.50e+03 pdb=" N2 NAG A1309 " 0.537 2.00e-02 2.50e+03 pdb=" O7 NAG A1309 " -0.166 2.00e-02 2.50e+03 ... (remaining 5238 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3882 2.76 - 3.29: 27463 3.29 - 3.83: 44813 3.83 - 4.36: 52667 4.36 - 4.90: 94036 Nonbonded interactions: 222861 Sorted by model distance: nonbonded pdb=" OH TYR D 36 " pdb=" OE1 GLN D 89 " model vdw 2.220 2.440 nonbonded pdb=" OH TYR K 36 " pdb=" OE1 GLN K 89 " model vdw 2.220 2.440 nonbonded pdb=" OH TYR G 36 " pdb=" OE1 GLN G 89 " model vdw 2.220 2.440 nonbonded pdb=" O ILE B 742 " pdb=" NH1 ARG B1000 " model vdw 2.230 2.520 nonbonded pdb=" O ILE A 742 " pdb=" NH1 ARG A1000 " model vdw 2.230 2.520 ... (remaining 222856 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'K' } 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: 0.000 Normalize map: mean=0, sd=1: 2.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.200 Construct map_model_manager: 0.030 Extract box with map and model: 12.930 Check model and map are aligned: 0.420 Set scattering table: 0.260 Process input model: 74.370 Find NCS groups from input model: 1.700 Set up NCS constraints: 0.200 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:3.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6633 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 : 0.004 0.042 29880 Z= 0.266 Angle : 0.630 9.125 40629 Z= 0.379 Chirality : 0.047 0.331 4638 Planarity : 0.009 0.302 5214 Dihedral : 12.040 75.257 11109 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.09 % Allowed : 0.28 % Favored : 99.63 % 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 (0.14), residues: 3627 helix: 2.17 (0.21), residues: 648 sheet: -0.01 (0.17), residues: 996 loop : -1.25 (0.13), residues: 1983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 353 HIS 0.005 0.001 HIS F 100 PHE 0.017 0.001 PHE A 45 TYR 0.019 0.001 TYR E 396 ARG 0.005 0.000 ARG E 355 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 708 residues out of total 3213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 705 time to evaluate : 2.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 THR cc_start: 0.7048 (p) cc_final: 0.6845 (p) REVERT: A 121 ASN cc_start: 0.7684 (m-40) cc_final: 0.7378 (t0) REVERT: A 191 GLU cc_start: 0.7353 (mt-10) cc_final: 0.6908 (mt-10) REVERT: A 200 TYR cc_start: 0.6778 (m-80) cc_final: 0.6498 (m-80) REVERT: A 542 ASN cc_start: 0.7073 (t0) cc_final: 0.6840 (t0) REVERT: A 646 ARG cc_start: 0.6866 (ttt90) cc_final: 0.6621 (ttt90) REVERT: A 945 LEU cc_start: 0.7859 (mm) cc_final: 0.7514 (mp) REVERT: A 1084 ASP cc_start: 0.6998 (t0) cc_final: 0.6548 (t0) REVERT: B 190 ARG cc_start: 0.6965 (mpt180) cc_final: 0.6661 (mtt90) REVERT: B 227 VAL cc_start: 0.8139 (t) cc_final: 0.7931 (m) REVERT: B 239 GLN cc_start: 0.7101 (tt0) cc_final: 0.6669 (tt0) REVERT: B 531 THR cc_start: 0.8128 (m) cc_final: 0.7731 (p) REVERT: B 555 SER cc_start: 0.8174 (t) cc_final: 0.7764 (t) REVERT: B 583 GLU cc_start: 0.6402 (tp30) cc_final: 0.6105 (tp30) REVERT: B 584 ILE cc_start: 0.7992 (pt) cc_final: 0.7791 (pt) REVERT: B 586 ASP cc_start: 0.7205 (m-30) cc_final: 0.7003 (m-30) REVERT: B 587 ILE cc_start: 0.8064 (mm) cc_final: 0.7785 (mt) REVERT: B 646 ARG cc_start: 0.6730 (ttt90) cc_final: 0.6508 (ttt90) REVERT: B 674 TYR cc_start: 0.8312 (t80) cc_final: 0.7998 (t80) REVERT: B 704 SER cc_start: 0.8286 (t) cc_final: 0.8042 (m) REVERT: B 735 SER cc_start: 0.8249 (t) cc_final: 0.7826 (p) REVERT: B 1084 ASP cc_start: 0.6794 (t0) cc_final: 0.6438 (t0) REVERT: B 1139 ASP cc_start: 0.7286 (t0) cc_final: 0.6971 (t0) REVERT: D 92 ASN cc_start: 0.6331 (m-40) cc_final: 0.6091 (m-40) REVERT: E 121 ASN cc_start: 0.7676 (m-40) cc_final: 0.7362 (t0) REVERT: E 239 GLN cc_start: 0.6917 (tt0) cc_final: 0.6489 (tt0) REVERT: E 541 PHE cc_start: 0.7485 (p90) cc_final: 0.7245 (p90) REVERT: E 567 ARG cc_start: 0.7821 (ttm170) cc_final: 0.7549 (mtt180) REVERT: E 578 ASP cc_start: 0.6500 (p0) cc_final: 0.6297 (p0) REVERT: E 735 SER cc_start: 0.8335 (t) cc_final: 0.7881 (p) REVERT: E 784 GLN cc_start: 0.8503 (mt0) cc_final: 0.8284 (mt0) REVERT: E 883 THR cc_start: 0.8510 (m) cc_final: 0.7831 (p) REVERT: E 904 TYR cc_start: 0.7371 (m-10) cc_final: 0.6632 (m-10) REVERT: E 1084 ASP cc_start: 0.6841 (t0) cc_final: 0.6487 (t0) REVERT: E 1102 TRP cc_start: 0.8350 (m100) cc_final: 0.7958 (m100) REVERT: E 1136 THR cc_start: 0.8509 (p) cc_final: 0.8216 (p) REVERT: E 1139 ASP cc_start: 0.7538 (t0) cc_final: 0.7306 (t0) outliers start: 3 outliers final: 1 residues processed: 708 average time/residue: 0.4345 time to fit residues: 477.3569 Evaluate side-chains 592 residues out of total 3213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 591 time to evaluate : 3.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 306 optimal weight: 7.9990 chunk 275 optimal weight: 0.4980 chunk 152 optimal weight: 0.5980 chunk 93 optimal weight: 2.9990 chunk 185 optimal weight: 7.9990 chunk 146 optimal weight: 0.7980 chunk 284 optimal weight: 0.9980 chunk 110 optimal weight: 3.9990 chunk 173 optimal weight: 0.9980 chunk 211 optimal weight: 0.8980 chunk 329 optimal weight: 0.1980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 ASN ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS A 239 GLN A 417 ASN A 544 ASN A 762 GLN A 774 GLN A 853 GLN H 100 HIS K 38 GLN K 55 GLN ** K 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN B 207 HIS B 417 ASN B 564 GLN B 658 ASN B 762 GLN B 774 GLN B 784 GLN B 853 GLN B 913 GLN C 100 HIS D 55 GLN E 115 GLN ** E 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 196 ASN E 207 HIS E 417 ASN E 658 ASN E 762 GLN E 774 GLN E 853 GLN F 100 HIS G 55 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6716 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 29880 Z= 0.217 Angle : 0.580 12.589 40629 Z= 0.298 Chirality : 0.046 0.353 4638 Planarity : 0.005 0.061 5214 Dihedral : 6.556 54.477 4550 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.28 % Allowed : 8.00 % Favored : 90.73 % 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 (0.14), residues: 3627 helix: 2.20 (0.21), residues: 651 sheet: 0.44 (0.18), residues: 885 loop : -1.28 (0.12), residues: 2091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 48 HIS 0.012 0.001 HIS H 100 PHE 0.031 0.001 PHE E 497 TYR 0.022 0.001 TYR E 170 ARG 0.007 0.001 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 645 residues out of total 3213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 604 time to evaluate : 3.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 PHE cc_start: 0.7523 (t80) cc_final: 0.7188 (t80) REVERT: A 190 ARG cc_start: 0.6878 (mpt180) cc_final: 0.6598 (mtt90) REVERT: A 200 TYR cc_start: 0.6670 (m-80) cc_final: 0.6396 (m-80) REVERT: A 229 LEU cc_start: 0.8033 (mt) cc_final: 0.7752 (mp) REVERT: A 567 ARG cc_start: 0.7692 (ttm170) cc_final: 0.7422 (ttm170) REVERT: A 574 ASP cc_start: 0.6833 (t0) cc_final: 0.6559 (t0) REVERT: A 646 ARG cc_start: 0.6859 (ttt90) cc_final: 0.6607 (ttt90) REVERT: A 779 GLN cc_start: 0.7916 (tp40) cc_final: 0.7632 (tm-30) REVERT: A 1031 GLU cc_start: 0.7607 (mt-10) cc_final: 0.7310 (mt-10) REVERT: A 1084 ASP cc_start: 0.7036 (t0) cc_final: 0.6463 (t0) REVERT: B 190 ARG cc_start: 0.7003 (mpt180) cc_final: 0.6729 (mtt90) REVERT: B 239 GLN cc_start: 0.7061 (tt0) cc_final: 0.6640 (tt0) REVERT: B 531 THR cc_start: 0.8133 (m) cc_final: 0.7734 (p) REVERT: B 583 GLU cc_start: 0.6402 (tp30) cc_final: 0.6079 (tp30) REVERT: B 585 LEU cc_start: 0.7516 (OUTLIER) cc_final: 0.6944 (pp) REVERT: B 587 ILE cc_start: 0.8137 (mm) cc_final: 0.7907 (mt) REVERT: B 646 ARG cc_start: 0.6731 (ttt90) cc_final: 0.6527 (ttt90) REVERT: B 779 GLN cc_start: 0.8034 (tp40) cc_final: 0.7720 (tm-30) REVERT: B 804 GLN cc_start: 0.8017 (mm-40) cc_final: 0.7548 (mm-40) REVERT: B 1084 ASP cc_start: 0.6920 (t0) cc_final: 0.6454 (t0) REVERT: E 121 ASN cc_start: 0.7663 (m-40) cc_final: 0.7419 (t0) REVERT: E 239 GLN cc_start: 0.6856 (tt0) cc_final: 0.6429 (tt0) REVERT: E 425 LEU cc_start: 0.7417 (mt) cc_final: 0.7214 (mt) REVERT: E 559 PHE cc_start: 0.7713 (m-10) cc_final: 0.7421 (m-10) REVERT: E 723 THR cc_start: 0.8213 (p) cc_final: 0.7954 (m) REVERT: E 784 GLN cc_start: 0.8471 (mt0) cc_final: 0.8264 (mt0) REVERT: E 859 THR cc_start: 0.8141 (p) cc_final: 0.7896 (t) REVERT: E 904 TYR cc_start: 0.7721 (m-10) cc_final: 0.7155 (m-10) REVERT: E 1084 ASP cc_start: 0.6928 (t0) cc_final: 0.6482 (t0) REVERT: E 1114 ILE cc_start: 0.7919 (mm) cc_final: 0.7694 (mt) REVERT: E 1139 ASP cc_start: 0.7543 (t0) cc_final: 0.7340 (t0) outliers start: 41 outliers final: 16 residues processed: 622 average time/residue: 0.4901 time to fit residues: 480.8904 Evaluate side-chains 582 residues out of total 3213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 565 time to evaluate : 3.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain H residue 95 TYR Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain B residue 55 ASP Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 177 MET Chi-restraints excluded: chain E residue 304 LYS Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain F residue 95 TYR Chi-restraints excluded: chain G residue 30 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 183 optimal weight: 0.6980 chunk 102 optimal weight: 3.9990 chunk 274 optimal weight: 1.9990 chunk 224 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 330 optimal weight: 0.6980 chunk 356 optimal weight: 4.9990 chunk 294 optimal weight: 0.7980 chunk 327 optimal weight: 0.9990 chunk 112 optimal weight: 0.7980 chunk 264 optimal weight: 1.9990 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 115 GLN ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS A 542 ASN A 544 ASN A 774 GLN A 784 GLN K 37 GLN B 115 GLN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 542 ASN B 658 ASN B 774 GLN ** D 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 ASN ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 ASN E 207 HIS E 450 ASN E 460 ASN E 564 GLN E 658 ASN E 690 GLN E 774 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6760 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 29880 Z= 0.247 Angle : 0.572 15.141 40629 Z= 0.294 Chirality : 0.045 0.344 4638 Planarity : 0.005 0.054 5214 Dihedral : 6.124 54.557 4548 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.90 % Allowed : 11.27 % Favored : 86.83 % 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: -0.28 (0.14), residues: 3627 helix: 2.38 (0.21), residues: 627 sheet: 0.25 (0.17), residues: 957 loop : -1.29 (0.12), residues: 2043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 35 HIS 0.007 0.001 HIS G 90 PHE 0.018 0.001 PHE A 592 TYR 0.023 0.002 TYR B 266 ARG 0.008 0.001 ARG E 357 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 3213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 590 time to evaluate : 3.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 PHE cc_start: 0.7444 (t80) cc_final: 0.7186 (t80) REVERT: A 190 ARG cc_start: 0.6908 (mpt180) cc_final: 0.6541 (mtt90) REVERT: A 200 TYR cc_start: 0.6667 (m-80) cc_final: 0.6398 (m-80) REVERT: A 205 SER cc_start: 0.8202 (p) cc_final: 0.7981 (t) REVERT: A 229 LEU cc_start: 0.8001 (mt) cc_final: 0.7760 (mp) REVERT: A 266 TYR cc_start: 0.7271 (m-10) cc_final: 0.6934 (m-80) REVERT: A 338 PHE cc_start: 0.7884 (m-80) cc_final: 0.7591 (m-80) REVERT: A 567 ARG cc_start: 0.7749 (ttm170) cc_final: 0.7291 (mtt90) REVERT: A 574 ASP cc_start: 0.6800 (t0) cc_final: 0.6549 (t0) REVERT: A 646 ARG cc_start: 0.6858 (ttt90) cc_final: 0.6605 (ttt90) REVERT: A 779 GLN cc_start: 0.7930 (tp40) cc_final: 0.7686 (tm-30) REVERT: A 945 LEU cc_start: 0.8259 (mt) cc_final: 0.8024 (mp) REVERT: A 1031 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7254 (mt-10) REVERT: A 1084 ASP cc_start: 0.7079 (t0) cc_final: 0.6505 (t0) REVERT: B 188 ASN cc_start: 0.6877 (p0) cc_final: 0.6436 (p0) REVERT: B 190 ARG cc_start: 0.6992 (mpt180) cc_final: 0.6412 (mtt90) REVERT: B 239 GLN cc_start: 0.6990 (tt0) cc_final: 0.6641 (tt0) REVERT: B 298 GLU cc_start: 0.7625 (mt-10) cc_final: 0.7251 (mt-10) REVERT: B 425 LEU cc_start: 0.7652 (mt) cc_final: 0.7334 (mt) REVERT: B 567 ARG cc_start: 0.7805 (ttm170) cc_final: 0.7474 (mtt90) REVERT: B 583 GLU cc_start: 0.6484 (tp30) cc_final: 0.6057 (tp30) REVERT: B 585 LEU cc_start: 0.7550 (OUTLIER) cc_final: 0.7008 (pp) REVERT: B 587 ILE cc_start: 0.8074 (mm) cc_final: 0.7845 (mt) REVERT: B 740 MET cc_start: 0.7507 (mmm) cc_final: 0.7126 (mmm) REVERT: B 749 CYS cc_start: 0.5420 (OUTLIER) cc_final: 0.5162 (t) REVERT: B 779 GLN cc_start: 0.8019 (tp40) cc_final: 0.7734 (tm-30) REVERT: B 804 GLN cc_start: 0.8086 (mm-40) cc_final: 0.7647 (mm-40) REVERT: B 1002 GLN cc_start: 0.7407 (mm110) cc_final: 0.7184 (mm-40) REVERT: B 1031 GLU cc_start: 0.7610 (mt-10) cc_final: 0.7229 (mt-10) REVERT: B 1084 ASP cc_start: 0.7029 (t0) cc_final: 0.6441 (t0) REVERT: E 121 ASN cc_start: 0.7713 (m-40) cc_final: 0.7331 (t0) REVERT: E 129 LYS cc_start: 0.7809 (ptmt) cc_final: 0.7351 (ptmm) REVERT: E 239 GLN cc_start: 0.6959 (tt0) cc_final: 0.6509 (tt0) REVERT: E 784 GLN cc_start: 0.8484 (mt0) cc_final: 0.8253 (mt0) REVERT: E 804 GLN cc_start: 0.8101 (mm-40) cc_final: 0.7621 (mm-40) REVERT: E 856 ASN cc_start: 0.7320 (m-40) cc_final: 0.7105 (m-40) REVERT: E 859 THR cc_start: 0.8143 (p) cc_final: 0.7928 (t) REVERT: E 869 MET cc_start: 0.7935 (mtt) cc_final: 0.7623 (mtt) REVERT: E 894 LEU cc_start: 0.8707 (mt) cc_final: 0.8449 (mt) REVERT: E 904 TYR cc_start: 0.7818 (m-10) cc_final: 0.7191 (m-10) REVERT: E 1084 ASP cc_start: 0.7087 (t0) cc_final: 0.6612 (t0) REVERT: E 1102 TRP cc_start: 0.8426 (m100) cc_final: 0.8093 (m100) outliers start: 61 outliers final: 38 residues processed: 624 average time/residue: 0.4452 time to fit residues: 432.7119 Evaluate side-chains 601 residues out of total 3213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 561 time to evaluate : 3.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 542 ASN Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 55 ASP Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 100 HIS Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 188 ASN Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain E residue 551 VAL Chi-restraints excluded: chain E residue 786 LYS Chi-restraints excluded: chain E residue 961 THR Chi-restraints excluded: chain E residue 1055 SER Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 100 HIS Chi-restraints excluded: chain G residue 30 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 326 optimal weight: 7.9990 chunk 248 optimal weight: 3.9990 chunk 171 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 157 optimal weight: 4.9990 chunk 221 optimal weight: 8.9990 chunk 331 optimal weight: 0.9990 chunk 350 optimal weight: 2.9990 chunk 173 optimal weight: 0.6980 chunk 314 optimal weight: 0.0170 chunk 94 optimal weight: 0.8980 overall best weight: 0.7020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 ASN A 207 HIS A 542 ASN A 544 ASN A 774 GLN ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 ASN B 115 GLN B 125 ASN B 207 HIS B 542 ASN B 544 ASN D 37 GLN ** D 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 ASN ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 207 HIS E 460 ASN E 564 GLN E 658 ASN E 774 GLN ** F 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6768 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 29880 Z= 0.226 Angle : 0.562 12.663 40629 Z= 0.286 Chirality : 0.045 0.360 4638 Planarity : 0.004 0.052 5214 Dihedral : 6.081 59.985 4548 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.74 % Allowed : 13.79 % Favored : 84.47 % 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: -0.27 (0.13), residues: 3627 helix: 2.41 (0.21), residues: 627 sheet: 0.32 (0.17), residues: 900 loop : -1.29 (0.12), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 35 HIS 0.008 0.001 HIS D 90 PHE 0.016 0.001 PHE A 592 TYR 0.019 0.001 TYR B1067 ARG 0.005 0.000 ARG E 357 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 3213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 579 time to evaluate : 3.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.6908 (mpt180) cc_final: 0.6521 (mtt90) REVERT: A 200 TYR cc_start: 0.6658 (m-80) cc_final: 0.6390 (m-80) REVERT: A 205 SER cc_start: 0.8211 (p) cc_final: 0.7995 (t) REVERT: A 229 LEU cc_start: 0.7949 (mt) cc_final: 0.7742 (mp) REVERT: A 266 TYR cc_start: 0.7222 (m-10) cc_final: 0.6897 (m-80) REVERT: A 558 LYS cc_start: 0.7782 (mmmm) cc_final: 0.7539 (mmmm) REVERT: A 646 ARG cc_start: 0.6857 (ttt90) cc_final: 0.6598 (ttt90) REVERT: A 779 GLN cc_start: 0.7916 (tp40) cc_final: 0.7675 (tm-30) REVERT: A 1031 GLU cc_start: 0.7612 (mt-10) cc_final: 0.7322 (mt-10) REVERT: A 1084 ASP cc_start: 0.7117 (t0) cc_final: 0.6552 (t0) REVERT: B 110 LEU cc_start: 0.7347 (mm) cc_final: 0.7145 (mm) REVERT: B 239 GLN cc_start: 0.6974 (tt0) cc_final: 0.6627 (tt0) REVERT: B 567 ARG cc_start: 0.7785 (ttm170) cc_final: 0.7531 (mtt90) REVERT: B 583 GLU cc_start: 0.6524 (tp30) cc_final: 0.6096 (tp30) REVERT: B 585 LEU cc_start: 0.7539 (OUTLIER) cc_final: 0.7024 (pp) REVERT: B 616 ASN cc_start: 0.7757 (m-40) cc_final: 0.7556 (m-40) REVERT: B 740 MET cc_start: 0.7492 (mmm) cc_final: 0.7092 (mmm) REVERT: B 779 GLN cc_start: 0.8002 (tp40) cc_final: 0.7724 (tm-30) REVERT: B 804 GLN cc_start: 0.8067 (mm-40) cc_final: 0.7674 (mm-40) REVERT: B 1002 GLN cc_start: 0.7400 (mm110) cc_final: 0.7112 (mm-40) REVERT: B 1084 ASP cc_start: 0.7050 (t0) cc_final: 0.6469 (t0) REVERT: E 129 LYS cc_start: 0.7772 (ptmt) cc_final: 0.7400 (ptmm) REVERT: E 239 GLN cc_start: 0.6967 (tt0) cc_final: 0.6520 (tt0) REVERT: E 338 PHE cc_start: 0.7993 (m-80) cc_final: 0.7748 (m-10) REVERT: E 675 GLN cc_start: 0.6877 (tt0) cc_final: 0.6661 (mt0) REVERT: E 784 GLN cc_start: 0.8465 (mt0) cc_final: 0.8230 (mt0) REVERT: E 804 GLN cc_start: 0.8076 (mm-40) cc_final: 0.7405 (mm-40) REVERT: E 856 ASN cc_start: 0.7334 (m-40) cc_final: 0.7118 (m-40) REVERT: E 869 MET cc_start: 0.7942 (mtt) cc_final: 0.7642 (mtt) REVERT: E 904 TYR cc_start: 0.7849 (m-10) cc_final: 0.7185 (m-10) REVERT: E 1084 ASP cc_start: 0.7117 (t0) cc_final: 0.6640 (t0) outliers start: 56 outliers final: 36 residues processed: 613 average time/residue: 0.4825 time to fit residues: 469.3758 Evaluate side-chains 598 residues out of total 3213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 561 time to evaluate : 3.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 100 HIS Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 100 HIS Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain E residue 551 VAL Chi-restraints excluded: chain E residue 749 CYS Chi-restraints excluded: chain E residue 786 LYS Chi-restraints excluded: chain E residue 961 THR Chi-restraints excluded: chain E residue 1055 SER Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 100 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 292 optimal weight: 1.9990 chunk 199 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 261 optimal weight: 0.8980 chunk 144 optimal weight: 1.9990 chunk 299 optimal weight: 1.9990 chunk 242 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 179 optimal weight: 1.9990 chunk 314 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 ASN A 207 HIS A 544 ASN A 853 GLN ** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 ASN B 207 HIS B 542 ASN B 774 GLN B 853 GLN ** D 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 ASN ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 ASN E 207 HIS E 460 ASN E 564 GLN E 658 ASN E 774 GLN ** F 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 37 GLN ** G 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6802 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 29880 Z= 0.291 Angle : 0.592 13.329 40629 Z= 0.302 Chirality : 0.046 0.343 4638 Planarity : 0.005 0.053 5214 Dihedral : 6.163 58.283 4548 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.37 % Allowed : 14.41 % Favored : 83.22 % 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: -0.31 (0.13), residues: 3627 helix: 2.31 (0.21), residues: 627 sheet: 0.20 (0.17), residues: 924 loop : -1.26 (0.12), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 35 HIS 0.007 0.001 HIS D 90 PHE 0.019 0.002 PHE A 45 TYR 0.019 0.002 TYR B 266 ARG 0.008 0.001 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 3213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 572 time to evaluate : 2.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.7017 (mpt180) cc_final: 0.6672 (mtt90) REVERT: A 200 TYR cc_start: 0.6671 (m-80) cc_final: 0.6395 (m-80) REVERT: A 205 SER cc_start: 0.8253 (p) cc_final: 0.8031 (t) REVERT: A 542 ASN cc_start: 0.7313 (t0) cc_final: 0.7083 (t0) REVERT: A 558 LYS cc_start: 0.7797 (mmmm) cc_final: 0.7531 (mmmm) REVERT: A 646 ARG cc_start: 0.6868 (ttt90) cc_final: 0.6612 (ttt90) REVERT: A 776 LYS cc_start: 0.8154 (ttpt) cc_final: 0.7856 (tttt) REVERT: A 779 GLN cc_start: 0.8000 (tp40) cc_final: 0.7754 (tm-30) REVERT: A 790 LYS cc_start: 0.8006 (mttt) cc_final: 0.7683 (mttp) REVERT: A 1031 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7379 (mt-10) REVERT: A 1084 ASP cc_start: 0.7167 (t0) cc_final: 0.6611 (t0) REVERT: H 5 LEU cc_start: 0.7678 (mp) cc_final: 0.7272 (mp) REVERT: B 239 GLN cc_start: 0.6990 (tt0) cc_final: 0.6639 (tt0) REVERT: B 583 GLU cc_start: 0.6566 (tp30) cc_final: 0.6183 (tp30) REVERT: B 585 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.7173 (pp) REVERT: B 740 MET cc_start: 0.7603 (mmm) cc_final: 0.7194 (mmm) REVERT: B 743 CYS cc_start: 0.6741 (OUTLIER) cc_final: 0.6505 (p) REVERT: B 779 GLN cc_start: 0.8026 (tp40) cc_final: 0.7789 (tm-30) REVERT: B 804 GLN cc_start: 0.8109 (mm-40) cc_final: 0.7745 (mm-40) REVERT: B 1002 GLN cc_start: 0.7444 (mm110) cc_final: 0.7116 (mm-40) REVERT: B 1084 ASP cc_start: 0.7139 (t0) cc_final: 0.6573 (t0) REVERT: B 1102 TRP cc_start: 0.8473 (m100) cc_final: 0.8227 (m100) REVERT: E 129 LYS cc_start: 0.7891 (ptmt) cc_final: 0.7511 (ptmm) REVERT: E 239 GLN cc_start: 0.6899 (tt0) cc_final: 0.6494 (tt0) REVERT: E 675 GLN cc_start: 0.6943 (tt0) cc_final: 0.6741 (mt0) REVERT: E 735 SER cc_start: 0.8399 (t) cc_final: 0.7884 (p) REVERT: E 784 GLN cc_start: 0.8493 (mt0) cc_final: 0.8238 (mt0) REVERT: E 804 GLN cc_start: 0.8079 (mm-40) cc_final: 0.7421 (mm-40) REVERT: E 856 ASN cc_start: 0.7333 (m-40) cc_final: 0.7116 (m-40) REVERT: E 869 MET cc_start: 0.7989 (mtt) cc_final: 0.7667 (mtt) REVERT: E 904 TYR cc_start: 0.7876 (m-10) cc_final: 0.7212 (m-10) REVERT: E 1084 ASP cc_start: 0.7224 (t0) cc_final: 0.6752 (t0) REVERT: G 55 GLN cc_start: 0.6952 (OUTLIER) cc_final: 0.6742 (tm130) outliers start: 76 outliers final: 50 residues processed: 614 average time/residue: 0.4263 time to fit residues: 410.0394 Evaluate side-chains 615 residues out of total 3213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 562 time to evaluate : 3.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 100 HIS Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 121 ASN Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 100 HIS Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 188 ASN Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 551 VAL Chi-restraints excluded: chain E residue 584 ILE Chi-restraints excluded: chain E residue 585 LEU Chi-restraints excluded: chain E residue 786 LYS Chi-restraints excluded: chain E residue 961 THR Chi-restraints excluded: chain E residue 1055 SER Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 100 HIS Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 55 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 118 optimal weight: 9.9990 chunk 315 optimal weight: 0.0020 chunk 69 optimal weight: 0.5980 chunk 206 optimal weight: 0.7980 chunk 86 optimal weight: 0.7980 chunk 351 optimal weight: 5.9990 chunk 291 optimal weight: 0.0010 chunk 162 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 116 optimal weight: 0.0270 chunk 184 optimal weight: 0.9980 overall best weight: 0.2852 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 ASN A 207 HIS A 544 ASN A 774 GLN A 856 ASN B 32 ASN B 207 HIS B 317 ASN B 542 ASN D 92 ASN E 32 ASN ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 ASN E 188 ASN E 207 HIS E 460 ASN E 564 GLN E 690 GLN ** F 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6762 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.075 29880 Z= 0.162 Angle : 0.553 13.767 40629 Z= 0.278 Chirality : 0.045 0.418 4638 Planarity : 0.004 0.076 5214 Dihedral : 5.933 59.125 4548 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.18 % Allowed : 15.28 % Favored : 82.54 % 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: -0.18 (0.14), residues: 3627 helix: 2.55 (0.21), residues: 627 sheet: 0.22 (0.17), residues: 942 loop : -1.19 (0.12), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP K 35 HIS 0.007 0.001 HIS D 90 PHE 0.018 0.001 PHE C 68 TYR 0.017 0.001 TYR B1067 ARG 0.007 0.000 ARG E 190 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 3213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 564 time to evaluate : 3.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLN cc_start: 0.6439 (OUTLIER) cc_final: 0.6130 (mm-40) REVERT: A 266 TYR cc_start: 0.7148 (m-10) cc_final: 0.6815 (m-80) REVERT: A 466 ARG cc_start: 0.6752 (ttp80) cc_final: 0.6551 (ttp80) REVERT: A 542 ASN cc_start: 0.7293 (t0) cc_final: 0.7063 (t0) REVERT: A 558 LYS cc_start: 0.7707 (mmmm) cc_final: 0.7469 (mmmm) REVERT: A 646 ARG cc_start: 0.6842 (ttt90) cc_final: 0.6586 (ttt90) REVERT: A 776 LYS cc_start: 0.8118 (ttpt) cc_final: 0.7813 (tttp) REVERT: A 779 GLN cc_start: 0.7888 (tp40) cc_final: 0.7640 (tm-30) REVERT: A 790 LYS cc_start: 0.8047 (mttt) cc_final: 0.7540 (mttm) REVERT: A 980 ILE cc_start: 0.8450 (OUTLIER) cc_final: 0.8162 (mp) REVERT: A 1031 GLU cc_start: 0.7588 (mt-10) cc_final: 0.7333 (mt-10) REVERT: A 1084 ASP cc_start: 0.7142 (t0) cc_final: 0.6583 (t0) REVERT: B 239 GLN cc_start: 0.6976 (tt0) cc_final: 0.6624 (tt0) REVERT: B 298 GLU cc_start: 0.7578 (mt-10) cc_final: 0.7283 (mt-10) REVERT: B 583 GLU cc_start: 0.6499 (tp30) cc_final: 0.6140 (tp30) REVERT: B 585 LEU cc_start: 0.7531 (OUTLIER) cc_final: 0.6956 (pp) REVERT: B 592 PHE cc_start: 0.8481 (p90) cc_final: 0.8088 (p90) REVERT: B 740 MET cc_start: 0.7470 (mmm) cc_final: 0.7096 (mmm) REVERT: B 743 CYS cc_start: 0.6857 (OUTLIER) cc_final: 0.6540 (p) REVERT: B 749 CYS cc_start: 0.5653 (OUTLIER) cc_final: 0.5304 (t) REVERT: B 779 GLN cc_start: 0.7951 (tp40) cc_final: 0.7724 (tm-30) REVERT: B 804 GLN cc_start: 0.8043 (mm-40) cc_final: 0.7700 (mm-40) REVERT: B 868 GLU cc_start: 0.6662 (mp0) cc_final: 0.6357 (mp0) REVERT: B 980 ILE cc_start: 0.8382 (OUTLIER) cc_final: 0.8137 (mp) REVERT: B 1084 ASP cc_start: 0.7103 (t0) cc_final: 0.6537 (t0) REVERT: B 1102 TRP cc_start: 0.8399 (m100) cc_final: 0.8143 (m100) REVERT: E 129 LYS cc_start: 0.7700 (ptmt) cc_final: 0.7331 (ptmm) REVERT: E 239 GLN cc_start: 0.6986 (tt0) cc_final: 0.6577 (tt0) REVERT: E 586 ASP cc_start: 0.7500 (m-30) cc_final: 0.7250 (m-30) REVERT: E 675 GLN cc_start: 0.6913 (tt0) cc_final: 0.6710 (mt0) REVERT: E 784 GLN cc_start: 0.8416 (mt0) cc_final: 0.8208 (mt0) REVERT: E 790 LYS cc_start: 0.8240 (mttm) cc_final: 0.7889 (mttm) REVERT: E 804 GLN cc_start: 0.8008 (mm-40) cc_final: 0.7320 (mm-40) REVERT: E 856 ASN cc_start: 0.7275 (m-40) cc_final: 0.7044 (m-40) REVERT: E 869 MET cc_start: 0.7916 (mtt) cc_final: 0.7579 (mtt) REVERT: E 904 TYR cc_start: 0.7854 (m-10) cc_final: 0.7244 (m-10) REVERT: E 980 ILE cc_start: 0.8395 (OUTLIER) cc_final: 0.8114 (mp) REVERT: E 1084 ASP cc_start: 0.7215 (t0) cc_final: 0.6730 (t0) outliers start: 70 outliers final: 45 residues processed: 607 average time/residue: 0.4455 time to fit residues: 424.1880 Evaluate side-chains 603 residues out of total 3213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 551 time to evaluate : 3.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 95 TYR Chi-restraints excluded: chain H residue 100 HIS Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 55 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 743 CYS Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 100 HIS Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 188 ASN Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 585 LEU Chi-restraints excluded: chain E residue 749 CYS Chi-restraints excluded: chain E residue 763 LEU Chi-restraints excluded: chain E residue 980 ILE Chi-restraints excluded: chain E residue 1055 SER Chi-restraints excluded: chain E residue 1072 GLU Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 100 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 338 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 200 optimal weight: 0.8980 chunk 256 optimal weight: 0.8980 chunk 198 optimal weight: 0.7980 chunk 295 optimal weight: 0.9980 chunk 196 optimal weight: 1.9990 chunk 349 optimal weight: 10.0000 chunk 218 optimal weight: 0.7980 chunk 213 optimal weight: 1.9990 chunk 161 optimal weight: 10.0000 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 ASN A 207 HIS A 544 ASN A1002 GLN B 207 HIS B 317 ASN B 542 ASN B 774 GLN ** C 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 GLN E 188 ASN E 207 HIS E 460 ASN ** F 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6800 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 29880 Z= 0.260 Angle : 0.577 12.893 40629 Z= 0.293 Chirality : 0.045 0.342 4638 Planarity : 0.004 0.052 5214 Dihedral : 5.965 59.807 4548 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.33 % Allowed : 15.90 % Favored : 81.76 % 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: -0.21 (0.13), residues: 3627 helix: 2.42 (0.21), residues: 627 sheet: 0.28 (0.17), residues: 921 loop : -1.20 (0.12), residues: 2079 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP K 35 HIS 0.005 0.001 HIS A1058 PHE 0.019 0.001 PHE A 45 TYR 0.019 0.001 TYR B1067 ARG 0.007 0.001 ARG B 498 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 627 residues out of total 3213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 552 time to evaluate : 3.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.7099 (mpt180) cc_final: 0.6665 (mtt90) REVERT: A 266 TYR cc_start: 0.7187 (m-10) cc_final: 0.6940 (m-80) REVERT: A 466 ARG cc_start: 0.6879 (ttp80) cc_final: 0.6630 (ttp80) REVERT: A 542 ASN cc_start: 0.7297 (t0) cc_final: 0.7062 (t0) REVERT: A 558 LYS cc_start: 0.7721 (mmmm) cc_final: 0.7481 (mmmm) REVERT: A 564 GLN cc_start: 0.7598 (mm-40) cc_final: 0.7322 (mm-40) REVERT: A 646 ARG cc_start: 0.6867 (ttt90) cc_final: 0.6608 (ttt90) REVERT: A 776 LYS cc_start: 0.8150 (ttpt) cc_final: 0.7844 (tttp) REVERT: A 779 GLN cc_start: 0.7933 (tp40) cc_final: 0.7688 (tm-30) REVERT: A 980 ILE cc_start: 0.8446 (OUTLIER) cc_final: 0.8152 (mp) REVERT: A 1031 GLU cc_start: 0.7608 (mt-10) cc_final: 0.7358 (mt-10) REVERT: A 1084 ASP cc_start: 0.7175 (t0) cc_final: 0.6617 (t0) REVERT: B 190 ARG cc_start: 0.6866 (mpt180) cc_final: 0.6473 (mtt90) REVERT: B 239 GLN cc_start: 0.7036 (tt0) cc_final: 0.6662 (tt0) REVERT: B 294 ASP cc_start: 0.6581 (OUTLIER) cc_final: 0.6300 (p0) REVERT: B 298 GLU cc_start: 0.7531 (mt-10) cc_final: 0.7233 (mt-10) REVERT: B 583 GLU cc_start: 0.6550 (tp30) cc_final: 0.6162 (tp30) REVERT: B 585 LEU cc_start: 0.7620 (OUTLIER) cc_final: 0.7238 (pp) REVERT: B 740 MET cc_start: 0.7563 (mmm) cc_final: 0.7177 (mmm) REVERT: B 779 GLN cc_start: 0.8026 (tp40) cc_final: 0.7792 (tm-30) REVERT: B 804 GLN cc_start: 0.8077 (mm-40) cc_final: 0.7749 (mm-40) REVERT: B 980 ILE cc_start: 0.8387 (OUTLIER) cc_final: 0.8159 (mp) REVERT: B 1084 ASP cc_start: 0.7146 (t0) cc_final: 0.6585 (t0) REVERT: E 129 LYS cc_start: 0.7802 (ptmt) cc_final: 0.7420 (ptmm) REVERT: E 239 GLN cc_start: 0.6988 (tt0) cc_final: 0.6604 (tt0) REVERT: E 586 ASP cc_start: 0.7503 (m-30) cc_final: 0.7259 (m-30) REVERT: E 784 GLN cc_start: 0.8453 (mt0) cc_final: 0.8197 (mt0) REVERT: E 790 LYS cc_start: 0.8232 (mttm) cc_final: 0.7933 (mttm) REVERT: E 804 GLN cc_start: 0.8061 (mm-40) cc_final: 0.7425 (mm-40) REVERT: E 856 ASN cc_start: 0.7306 (m-40) cc_final: 0.7058 (m-40) REVERT: E 869 MET cc_start: 0.7971 (mtt) cc_final: 0.7617 (mtt) REVERT: E 904 TYR cc_start: 0.7895 (m-10) cc_final: 0.7290 (m-10) REVERT: E 980 ILE cc_start: 0.8402 (OUTLIER) cc_final: 0.8122 (mp) REVERT: E 1084 ASP cc_start: 0.7298 (t0) cc_final: 0.6823 (t0) outliers start: 75 outliers final: 61 residues processed: 601 average time/residue: 0.4332 time to fit residues: 409.4600 Evaluate side-chains 611 residues out of total 3213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 545 time to evaluate : 3.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 95 TYR Chi-restraints excluded: chain H residue 100 HIS Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 100 HIS Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 188 ASN Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 294 ASP Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 584 ILE Chi-restraints excluded: chain E residue 585 LEU Chi-restraints excluded: chain E residue 749 CYS Chi-restraints excluded: chain E residue 763 LEU Chi-restraints excluded: chain E residue 961 THR Chi-restraints excluded: chain E residue 980 ILE Chi-restraints excluded: chain E residue 996 LEU Chi-restraints excluded: chain E residue 1055 SER Chi-restraints excluded: chain E residue 1072 GLU Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 100 HIS Chi-restraints excluded: chain G residue 30 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 216 optimal weight: 0.0050 chunk 139 optimal weight: 0.9980 chunk 208 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 67 optimal weight: 0.5980 chunk 222 optimal weight: 5.9990 chunk 238 optimal weight: 10.0000 chunk 172 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 275 optimal weight: 0.0370 overall best weight: 0.3872 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 ASN A 207 HIS B 207 HIS B 774 GLN ** C 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 ASN E 188 ASN E 207 HIS E 460 ASN E 564 GLN E 690 GLN E 774 GLN ** F 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6773 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 29880 Z= 0.171 Angle : 0.553 13.400 40629 Z= 0.278 Chirality : 0.045 0.364 4638 Planarity : 0.004 0.053 5214 Dihedral : 5.888 59.806 4548 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.18 % Allowed : 16.43 % Favored : 81.39 % 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: -0.13 (0.14), residues: 3627 helix: 2.56 (0.21), residues: 627 sheet: 0.24 (0.16), residues: 942 loop : -1.14 (0.13), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP K 35 HIS 0.004 0.001 HIS A 207 PHE 0.020 0.001 PHE A 168 TYR 0.022 0.001 TYR E 501 ARG 0.007 0.000 ARG E 466 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 3213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 552 time to evaluate : 3.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 TYR cc_start: 0.7112 (m-10) cc_final: 0.6719 (m-80) REVERT: A 466 ARG cc_start: 0.6785 (ttp80) cc_final: 0.6540 (ttp80) REVERT: A 542 ASN cc_start: 0.7278 (t0) cc_final: 0.7057 (t0) REVERT: A 558 LYS cc_start: 0.7615 (mmmm) cc_final: 0.7390 (mmmm) REVERT: A 646 ARG cc_start: 0.6850 (ttt90) cc_final: 0.6596 (ttt90) REVERT: A 776 LYS cc_start: 0.8132 (ttpt) cc_final: 0.7832 (tttp) REVERT: A 779 GLN cc_start: 0.7883 (tp40) cc_final: 0.7631 (tm-30) REVERT: A 980 ILE cc_start: 0.8438 (OUTLIER) cc_final: 0.8145 (mp) REVERT: A 1031 GLU cc_start: 0.7595 (mt-10) cc_final: 0.7330 (mt-10) REVERT: A 1084 ASP cc_start: 0.7160 (t0) cc_final: 0.6596 (t0) REVERT: B 190 ARG cc_start: 0.6830 (mpt180) cc_final: 0.6424 (mtt90) REVERT: B 239 GLN cc_start: 0.7017 (tt0) cc_final: 0.6645 (tt0) REVERT: B 294 ASP cc_start: 0.6515 (OUTLIER) cc_final: 0.6242 (p0) REVERT: B 298 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7271 (mt-10) REVERT: B 583 GLU cc_start: 0.6506 (tp30) cc_final: 0.6118 (tp30) REVERT: B 585 LEU cc_start: 0.7596 (OUTLIER) cc_final: 0.7070 (pp) REVERT: B 592 PHE cc_start: 0.8473 (p90) cc_final: 0.8116 (p90) REVERT: B 702 GLU cc_start: 0.7306 (tp30) cc_final: 0.6984 (tp30) REVERT: B 740 MET cc_start: 0.7455 (mmm) cc_final: 0.7073 (mmm) REVERT: B 779 GLN cc_start: 0.7961 (tp40) cc_final: 0.7724 (tm-30) REVERT: B 804 GLN cc_start: 0.8043 (mm-40) cc_final: 0.7724 (mm-40) REVERT: B 980 ILE cc_start: 0.8379 (OUTLIER) cc_final: 0.8152 (mp) REVERT: B 1084 ASP cc_start: 0.7133 (t0) cc_final: 0.6584 (t0) REVERT: E 129 LYS cc_start: 0.7714 (ptmt) cc_final: 0.7355 (ptmm) REVERT: E 239 GLN cc_start: 0.6965 (tt0) cc_final: 0.6580 (tt0) REVERT: E 537 LYS cc_start: 0.8081 (mtpt) cc_final: 0.7839 (mtmt) REVERT: E 586 ASP cc_start: 0.7455 (m-30) cc_final: 0.7255 (m-30) REVERT: E 784 GLN cc_start: 0.8407 (mt0) cc_final: 0.8188 (mt0) REVERT: E 790 LYS cc_start: 0.8226 (mttm) cc_final: 0.7844 (mttm) REVERT: E 804 GLN cc_start: 0.8006 (mm-40) cc_final: 0.7371 (mt0) REVERT: E 856 ASN cc_start: 0.7252 (m-40) cc_final: 0.7019 (m-40) REVERT: E 869 MET cc_start: 0.7912 (mtt) cc_final: 0.7565 (mtt) REVERT: E 904 TYR cc_start: 0.7874 (m-10) cc_final: 0.7231 (m-10) REVERT: E 980 ILE cc_start: 0.8396 (OUTLIER) cc_final: 0.8112 (mp) REVERT: E 1084 ASP cc_start: 0.7282 (t0) cc_final: 0.6808 (t0) outliers start: 70 outliers final: 53 residues processed: 597 average time/residue: 0.4282 time to fit residues: 402.6693 Evaluate side-chains 601 residues out of total 3213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 543 time to evaluate : 2.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 95 TYR Chi-restraints excluded: chain H residue 100 HIS Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 100 HIS Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 188 ASN Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 294 ASP Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 585 LEU Chi-restraints excluded: chain E residue 749 CYS Chi-restraints excluded: chain E residue 763 LEU Chi-restraints excluded: chain E residue 980 ILE Chi-restraints excluded: chain E residue 996 LEU Chi-restraints excluded: chain E residue 1055 SER Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 100 HIS Chi-restraints excluded: chain G residue 30 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 318 optimal weight: 0.7980 chunk 335 optimal weight: 1.9990 chunk 305 optimal weight: 1.9990 chunk 326 optimal weight: 5.9990 chunk 196 optimal weight: 0.9980 chunk 142 optimal weight: 0.6980 chunk 256 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 294 optimal weight: 0.6980 chunk 308 optimal weight: 1.9990 chunk 324 optimal weight: 0.8980 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 115 GLN ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 ASN A 207 HIS A 774 GLN B 32 ASN B 207 HIS B 542 ASN B 774 GLN E 188 ASN E 207 HIS E 460 ASN ** F 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6799 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 29880 Z= 0.242 Angle : 0.575 13.857 40629 Z= 0.291 Chirality : 0.046 0.352 4638 Planarity : 0.004 0.052 5214 Dihedral : 5.991 59.711 4548 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.27 % Allowed : 16.62 % Favored : 81.11 % 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: -0.17 (0.13), residues: 3627 helix: 2.49 (0.21), residues: 627 sheet: 0.27 (0.17), residues: 927 loop : -1.18 (0.12), residues: 2073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP K 35 HIS 0.005 0.001 HIS A 207 PHE 0.028 0.001 PHE A 374 TYR 0.019 0.001 TYR E 660 ARG 0.007 0.001 ARG E 466 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 3213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 547 time to evaluate : 3.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.7095 (mpt180) cc_final: 0.6681 (mtt90) REVERT: A 266 TYR cc_start: 0.7146 (m-10) cc_final: 0.6938 (m-80) REVERT: A 434 ILE cc_start: 0.7590 (mt) cc_final: 0.7346 (mt) REVERT: A 542 ASN cc_start: 0.7290 (t0) cc_final: 0.7076 (t0) REVERT: A 558 LYS cc_start: 0.7681 (mmmm) cc_final: 0.7466 (mmmm) REVERT: A 646 ARG cc_start: 0.6866 (ttt90) cc_final: 0.6606 (ttt90) REVERT: A 776 LYS cc_start: 0.8154 (ttpt) cc_final: 0.7851 (tttp) REVERT: A 779 GLN cc_start: 0.7906 (tp40) cc_final: 0.7666 (tm-30) REVERT: A 980 ILE cc_start: 0.8447 (OUTLIER) cc_final: 0.8155 (mp) REVERT: A 1031 GLU cc_start: 0.7604 (mt-10) cc_final: 0.7349 (mt-10) REVERT: A 1084 ASP cc_start: 0.7162 (t0) cc_final: 0.6612 (t0) REVERT: B 239 GLN cc_start: 0.7118 (tt0) cc_final: 0.6760 (tt0) REVERT: B 294 ASP cc_start: 0.6566 (OUTLIER) cc_final: 0.6293 (p0) REVERT: B 298 GLU cc_start: 0.7542 (mt-10) cc_final: 0.7246 (mt-10) REVERT: B 498 ARG cc_start: 0.7297 (mmp80) cc_final: 0.7014 (mmp-170) REVERT: B 583 GLU cc_start: 0.6540 (tp30) cc_final: 0.6155 (tp30) REVERT: B 585 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.7294 (pp) REVERT: B 592 PHE cc_start: 0.8475 (p90) cc_final: 0.8109 (p90) REVERT: B 702 GLU cc_start: 0.7323 (tp30) cc_final: 0.6980 (tp30) REVERT: B 740 MET cc_start: 0.7509 (mmm) cc_final: 0.7122 (mmm) REVERT: B 779 GLN cc_start: 0.8014 (tp40) cc_final: 0.7782 (tm-30) REVERT: B 804 GLN cc_start: 0.8073 (mm-40) cc_final: 0.7763 (mm-40) REVERT: B 980 ILE cc_start: 0.8380 (OUTLIER) cc_final: 0.8160 (mp) REVERT: B 1084 ASP cc_start: 0.7158 (t0) cc_final: 0.6606 (t0) REVERT: E 129 LYS cc_start: 0.7761 (ptmt) cc_final: 0.7388 (ptmm) REVERT: E 239 GLN cc_start: 0.6990 (tt0) cc_final: 0.6644 (tt0) REVERT: E 537 LYS cc_start: 0.8131 (mtpt) cc_final: 0.7879 (mtmt) REVERT: E 784 GLN cc_start: 0.8439 (mt0) cc_final: 0.8188 (mt0) REVERT: E 790 LYS cc_start: 0.8214 (mttm) cc_final: 0.7800 (mttm) REVERT: E 804 GLN cc_start: 0.8018 (mm-40) cc_final: 0.7379 (mm-40) REVERT: E 856 ASN cc_start: 0.7277 (m-40) cc_final: 0.7030 (m-40) REVERT: E 869 MET cc_start: 0.7957 (mtt) cc_final: 0.7601 (mtt) REVERT: E 904 TYR cc_start: 0.7895 (m-10) cc_final: 0.7283 (m-10) REVERT: E 980 ILE cc_start: 0.8393 (OUTLIER) cc_final: 0.8094 (mp) REVERT: E 1084 ASP cc_start: 0.7367 (t0) cc_final: 0.6880 (t0) outliers start: 73 outliers final: 57 residues processed: 596 average time/residue: 0.4354 time to fit residues: 407.2871 Evaluate side-chains 601 residues out of total 3213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 539 time to evaluate : 3.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain B residue 55 ASP Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 100 HIS Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 188 ASN Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 294 ASP Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 551 VAL Chi-restraints excluded: chain E residue 585 LEU Chi-restraints excluded: chain E residue 723 THR Chi-restraints excluded: chain E residue 749 CYS Chi-restraints excluded: chain E residue 980 ILE Chi-restraints excluded: chain E residue 996 LEU Chi-restraints excluded: chain E residue 1055 SER Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 100 HIS Chi-restraints excluded: chain G residue 30 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 214 optimal weight: 0.6980 chunk 344 optimal weight: 5.9990 chunk 210 optimal weight: 0.6980 chunk 163 optimal weight: 3.9990 chunk 239 optimal weight: 2.9990 chunk 361 optimal weight: 6.9990 chunk 332 optimal weight: 1.9990 chunk 287 optimal weight: 0.7980 chunk 29 optimal weight: 7.9990 chunk 222 optimal weight: 7.9990 chunk 176 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 ASN A 207 HIS B 32 ASN B 207 HIS ** B 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 ASN B 774 GLN E 188 ASN E 207 HIS E 460 ASN E 853 GLN ** F 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6846 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 29880 Z= 0.379 Angle : 0.637 15.113 40629 Z= 0.327 Chirality : 0.048 0.400 4638 Planarity : 0.005 0.052 5214 Dihedral : 6.162 58.635 4548 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.02 % Allowed : 16.84 % Favored : 81.14 % 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: 3627 helix: 2.23 (0.21), residues: 627 sheet: 0.27 (0.17), residues: 918 loop : -1.28 (0.12), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP A 353 HIS 0.009 0.001 HIS A1058 PHE 0.028 0.002 PHE A 374 TYR 0.023 0.002 TYR B 266 ARG 0.007 0.001 ARG A 466 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 638 residues out of total 3213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 573 time to evaluate : 3.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.7026 (mpt180) cc_final: 0.6597 (mtt90) REVERT: A 200 TYR cc_start: 0.6687 (m-80) cc_final: 0.6422 (m-80) REVERT: A 434 ILE cc_start: 0.7655 (mt) cc_final: 0.7441 (mt) REVERT: A 542 ASN cc_start: 0.7338 (t0) cc_final: 0.7137 (t0) REVERT: A 558 LYS cc_start: 0.7748 (mmmm) cc_final: 0.7516 (mmmm) REVERT: A 646 ARG cc_start: 0.6903 (ttt90) cc_final: 0.6651 (ttt90) REVERT: A 776 LYS cc_start: 0.8167 (ttpt) cc_final: 0.7877 (tttt) REVERT: A 779 GLN cc_start: 0.8012 (tp40) cc_final: 0.7770 (tm-30) REVERT: A 980 ILE cc_start: 0.8486 (OUTLIER) cc_final: 0.8178 (mp) REVERT: A 1084 ASP cc_start: 0.7189 (t0) cc_final: 0.6634 (t0) REVERT: B 115 GLN cc_start: 0.7004 (OUTLIER) cc_final: 0.6494 (mm-40) REVERT: B 239 GLN cc_start: 0.7162 (tt0) cc_final: 0.6778 (tt0) REVERT: B 294 ASP cc_start: 0.6644 (OUTLIER) cc_final: 0.6357 (p0) REVERT: B 583 GLU cc_start: 0.6546 (tp30) cc_final: 0.6171 (tp30) REVERT: B 585 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7423 (pp) REVERT: B 702 GLU cc_start: 0.7349 (tp30) cc_final: 0.6950 (tt0) REVERT: B 740 MET cc_start: 0.7769 (mmm) cc_final: 0.7375 (mmm) REVERT: B 804 GLN cc_start: 0.8099 (mm-40) cc_final: 0.7794 (mm-40) REVERT: B 1084 ASP cc_start: 0.7219 (t0) cc_final: 0.6669 (t0) REVERT: E 129 LYS cc_start: 0.7869 (ptmt) cc_final: 0.7482 (ptmm) REVERT: E 239 GLN cc_start: 0.6974 (tt0) cc_final: 0.6606 (tt0) REVERT: E 305 SER cc_start: 0.8450 (t) cc_final: 0.8068 (p) REVERT: E 537 LYS cc_start: 0.8225 (mtpt) cc_final: 0.7962 (mtmt) REVERT: E 784 GLN cc_start: 0.8506 (mt0) cc_final: 0.8298 (mt0) REVERT: E 790 LYS cc_start: 0.8226 (mttm) cc_final: 0.7795 (mttm) REVERT: E 804 GLN cc_start: 0.8068 (mm-40) cc_final: 0.7425 (mm-40) REVERT: E 856 ASN cc_start: 0.7350 (m-40) cc_final: 0.7088 (m-40) REVERT: E 869 MET cc_start: 0.8005 (mtt) cc_final: 0.7642 (mtt) REVERT: E 904 TYR cc_start: 0.7912 (m-10) cc_final: 0.7257 (m-10) REVERT: E 980 ILE cc_start: 0.8403 (OUTLIER) cc_final: 0.8108 (mp) REVERT: E 1084 ASP cc_start: 0.7393 (t0) cc_final: 0.6916 (t0) outliers start: 65 outliers final: 56 residues processed: 615 average time/residue: 0.4329 time to fit residues: 418.2505 Evaluate side-chains 621 residues out of total 3213 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 560 time to evaluate : 3.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain B residue 32 ASN Chi-restraints excluded: chain B residue 55 ASP Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 100 HIS Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 188 ASN Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain E residue 294 ASP Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 551 VAL Chi-restraints excluded: chain E residue 584 ILE Chi-restraints excluded: chain E residue 585 LEU Chi-restraints excluded: chain E residue 723 THR Chi-restraints excluded: chain E residue 749 CYS Chi-restraints excluded: chain E residue 980 ILE Chi-restraints excluded: chain E residue 996 LEU Chi-restraints excluded: chain E residue 1055 SER Chi-restraints excluded: chain E residue 1072 GLU Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 100 HIS Chi-restraints excluded: chain G residue 30 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 228 optimal weight: 8.9990 chunk 306 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 265 optimal weight: 0.5980 chunk 42 optimal weight: 5.9990 chunk 80 optimal weight: 0.4980 chunk 288 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 chunk 296 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 53 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS B 32 ASN B 207 HIS ** B 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1023 ASN ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 207 HIS ** F 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.165351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.130701 restraints weight = 46084.971| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 2.74 r_work: 0.3596 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.112 29880 Z= 0.329 Angle : 0.752 59.200 40629 Z= 0.418 Chirality : 0.047 0.481 4638 Planarity : 0.005 0.118 5214 Dihedral : 6.189 58.768 4548 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.05 % Allowed : 17.21 % Favored : 80.73 % Cbeta Deviations : 0.06 % 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: -0.33 (0.13), residues: 3627 helix: 2.24 (0.21), residues: 627 sheet: 0.25 (0.17), residues: 918 loop : -1.28 (0.12), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP A 353 HIS 0.007 0.001 HIS A1058 PHE 0.026 0.002 PHE E 456 TYR 0.031 0.002 TYR G 36 ARG 0.007 0.001 ARG A 466 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8282.17 seconds wall clock time: 150 minutes 36.84 seconds (9036.84 seconds total)