Starting phenix.real_space_refine on Thu Feb 22 08:58:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tca_25807/02_2024/7tca_25807.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tca_25807/02_2024/7tca_25807.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tca_25807/02_2024/7tca_25807.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tca_25807/02_2024/7tca_25807.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tca_25807/02_2024/7tca_25807.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tca_25807/02_2024/7tca_25807.pdb" } resolution = 3.85 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= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 148 5.16 5 C 21430 2.51 5 N 5554 2.21 5 O 6573 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 773": "OE1" <-> "OE2" Residue "A ASP 775": "OD1" <-> "OD2" Residue "A GLU 780": "OE1" <-> "OE2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 364": "OD1" <-> "OD2" Residue "B TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 773": "OE1" <-> "OE2" Residue "B PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 780": "OE1" <-> "OE2" Residue "C GLU 988": "OE1" <-> "OE2" Residue "C GLU 1031": "OE1" <-> "OE2" Residue "D TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 62": "OD1" <-> "OD2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 33705 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 8715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1114, 8715 Classifications: {'peptide': 1114} Link IDs: {'PTRANS': 56, 'TRANS': 1057} Chain breaks: 2 Chain: "B" Number of atoms: 8755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1118, 8755 Classifications: {'peptide': 1118} Link IDs: {'PTRANS': 57, 'TRANS': 1060} Chain breaks: 1 Chain: "C" Number of atoms: 8755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1118, 8755 Classifications: {'peptide': 1118} Link IDs: {'PTRANS': 57, 'TRANS': 1060} Chain breaks: 1 Chain: "D" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1749 Classifications: {'peptide': 231} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 218} Chain: "E" Number of atoms: 1599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1599 Classifications: {'peptide': 216} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 200} Chain: "H" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1749 Classifications: {'peptide': 231} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 218} Chain: "L" Number of atoms: 1599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1599 Classifications: {'peptide': 216} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 200} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 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: "C" 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: 18.37, per 1000 atoms: 0.55 Number of scatterers: 33705 At special positions: 0 Unit cell: (153.9, 216.315, 234.27, 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 148 16.00 O 6573 8.00 N 5554 7.00 C 21430 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 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 A 840 " - pdb=" SG CYS A 851 " distance=2.04 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 B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 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 B 840 " - pdb=" SG CYS B 851 " 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 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.05 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 153 " - pdb=" SG CYS D 209 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 90 " distance=2.03 Simple disulfide: pdb=" SG CYS E 138 " - pdb=" SG CYS E 197 " distance=2.03 Simple disulfide: pdb=" SG CYS H 153 " - pdb=" SG CYS H 209 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Simple disulfide: pdb=" SG CYS L 138 " - pdb=" SG CYS L 197 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A 709 " " NAG A1303 " - " ASN A1074 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 343 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 603 " " NAG B1301 " - " ASN B 709 " " NAG B1302 " - " ASN B1074 " " NAG B1303 " - " ASN B 61 " " NAG B1304 " - " ASN B 657 " " NAG B1305 " - " ASN B 616 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 282 " " NAG B1308 " - " ASN B 234 " " NAG B1309 " - " ASN B 122 " " NAG C1301 " - " ASN C 709 " " NAG C1302 " - " ASN C1074 " " NAG C1303 " - " ASN C 61 " " NAG C1304 " - " ASN C 657 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 603 " " NAG C1307 " - " ASN C 282 " " NAG C1308 " - " ASN C 234 " " NAG C1309 " - " ASN C 122 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A 801 " " NAG I 1 " - " ASN A1098 " " NAG J 1 " - " ASN A1134 " " NAG K 1 " - " ASN B 717 " " NAG M 1 " - " ASN B1098 " " NAG N 1 " - " ASN B1134 " " NAG O 1 " - " ASN B 331 " " NAG P 1 " - " ASN B 801 " " NAG Q 1 " - " ASN C 717 " " NAG R 1 " - " ASN C1098 " " NAG S 1 " - " ASN C1134 " " NAG T 1 " - " ASN C 331 " " NAG U 1 " - " ASN C 801 " Time building additional restraints: 14.39 Conformation dependent library (CDL) restraints added in 6.3 seconds 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7898 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 71 sheets defined 21.5% alpha, 26.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.61 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 383 through 387 removed outlier: 4.153A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 633 through 639 removed outlier: 3.519A pdb=" N TYR A 636 " --> pdb=" O TRP A 633 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR A 638 " --> pdb=" O VAL A 635 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY A 639 " --> pdb=" O TYR A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.572A pdb=" N CYS A 743 " --> pdb=" O THR A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 754 Processing helix chain 'A' and resid 758 through 783 removed outlier: 4.299A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 837 through 845 removed outlier: 6.482A pdb=" N GLY A 842 " --> pdb=" O ASP A 839 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N ASP A 843 " --> pdb=" O CYS A 840 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ILE A 844 " --> pdb=" O LEU A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 856 Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.533A pdb=" N ILE A 870 " --> pdb=" O THR A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.150A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.568A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.193A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 4.032A pdb=" N SER A 939 " --> pdb=" O GLN A 935 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N SER A 940 " --> pdb=" O ASP A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.062A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.217A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG A1014 " --> pdb=" O GLN A1010 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA A1015 " --> pdb=" O GLN A1011 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ALA A1016 " --> pdb=" O LEU A1012 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'A' and resid 1140 through 1145 removed outlier: 3.967A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LEU A1145 " --> pdb=" O LEU A1141 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1140 through 1145' Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 369 removed outlier: 3.570A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 408 removed outlier: 4.031A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 405 through 408' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 removed outlier: 3.694A pdb=" N HIS B 505 " --> pdb=" O GLY B 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 502 through 505' Processing helix chain 'B' and resid 568 through 572 removed outlier: 3.881A pdb=" N THR B 572 " --> pdb=" O ILE B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 628 removed outlier: 4.087A pdb=" N ALA B 623 " --> pdb=" O GLU B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 638 removed outlier: 4.297A pdb=" N TYR B 636 " --> pdb=" O THR B 632 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N SER B 637 " --> pdb=" O TRP B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.539A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.526A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.658A pdb=" N THR B 768 " --> pdb=" O LYS B 764 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY B 769 " --> pdb=" O ARG B 765 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE B 770 " --> pdb=" O ALA B 766 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ALA B 771 " --> pdb=" O LEU B 767 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 827 removed outlier: 3.743A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR B 827 " --> pdb=" O PHE B 823 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 855 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.598A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 913 through 918' Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 946 through 965 removed outlier: 3.549A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.552A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1034 removed outlier: 5.097A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA B1016 " --> pdb=" O LEU B1012 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU B1034 " --> pdb=" O SER B1030 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 366 through 370 Processing helix chain 'C' and resid 405 through 408 removed outlier: 4.323A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 405 through 408' Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 619 through 628 removed outlier: 3.670A pdb=" N ALA C 623 " --> pdb=" O GLU C 619 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 637 removed outlier: 3.695A pdb=" N ARG C 634 " --> pdb=" O THR C 630 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.511A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.662A pdb=" N THR C 768 " --> pdb=" O LYS C 764 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY C 769 " --> pdb=" O ARG C 765 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ILE C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ALA C 771 " --> pdb=" O LEU C 767 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 827 removed outlier: 3.507A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS C 825 " --> pdb=" O LEU C 821 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N THR C 827 " --> pdb=" O PHE C 823 " (cutoff:3.500A) Processing helix chain 'C' and resid 849 through 856 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.541A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.574A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.651A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.529A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 965 removed outlier: 3.610A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 983 removed outlier: 3.637A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1034 removed outlier: 4.741A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU C1034 " --> pdb=" O SER C1030 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 4.573A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU C1145 " --> pdb=" O LEU C1141 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1140 through 1145' Processing helix chain 'D' and resid 28 through 30 No H-bonds generated for 'chain 'D' and resid 28 through 30' Processing helix chain 'D' and resid 62 through 65 removed outlier: 3.745A pdb=" N LYS D 65 " --> pdb=" O ASP D 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 62 through 65' Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.538A pdb=" N THR D 91 " --> pdb=" O ALA D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 145 Processing helix chain 'D' and resid 169 through 171 No H-bonds generated for 'chain 'D' and resid 169 through 171' Processing helix chain 'D' and resid 200 through 202 No H-bonds generated for 'chain 'D' and resid 200 through 202' Processing helix chain 'E' and resid 30 through 34 Processing helix chain 'E' and resid 81 through 85 Processing helix chain 'E' and resid 125 through 130 Processing helix chain 'E' and resid 185 through 191 Processing helix chain 'E' and resid 211 through 216 removed outlier: 3.900A pdb=" N CYS E 215 " --> pdb=" O ALA E 211 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N SER E 216 " --> pdb=" O PRO E 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 211 through 216' Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 169 through 171 No H-bonds generated for 'chain 'H' and resid 169 through 171' Processing helix chain 'H' and resid 200 through 202 No H-bonds generated for 'chain 'H' and resid 200 through 202' Processing helix chain 'L' and resid 30 through 34 Processing helix chain 'L' and resid 81 through 85 removed outlier: 3.563A pdb=" N ASP L 84 " --> pdb=" O GLN L 81 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU L 85 " --> pdb=" O ALA L 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 81 through 85' Processing helix chain 'L' and resid 125 through 131 Processing helix chain 'L' and resid 185 through 191 Processing helix chain 'L' and resid 211 through 216 removed outlier: 3.928A pdb=" N CYS L 215 " --> pdb=" O ALA L 211 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER L 216 " --> pdb=" O PRO L 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 211 through 216' Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 3.540A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA A 263 " --> pdb=" O VAL A 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.681A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 93 through 94 Processing sheet with id=AA6, first strand: chain 'A' and resid 101 through 102 Processing sheet with id=AA7, first strand: chain 'A' and resid 116 through 117 removed outlier: 3.650A pdb=" N VAL A 130 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 193 through 197 removed outlier: 3.532A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 311 through 319 removed outlier: 3.573A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 325 through 326 removed outlier: 3.535A pdb=" N ILE A 326 " --> pdb=" O ASN A 540 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 356 through 357 Processing sheet with id=AB3, first strand: chain 'A' and resid 378 through 380 Processing sheet with id=AB4, first strand: chain 'A' and resid 453 through 454 Processing sheet with id=AB5, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB6, first strand: chain 'A' and resid 553 through 554 Processing sheet with id=AB7, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.579A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.615A pdb=" N ILE A 714 " --> pdb=" O LYS A1073 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 718 through 727 removed outlier: 3.921A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.324A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N CYS A1082 " --> pdb=" O VAL A1133 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.848A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA B 264 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU B 189 " --> pdb=" O THR B 208 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.562A pdb=" N THR B 51 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE B 275 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS B 278 " --> pdb=" O ASP B 287 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC5, first strand: chain 'B' and resid 142 through 146 removed outlier: 3.711A pdb=" N HIS B 146 " --> pdb=" O LEU B 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.499A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLN B 613 " --> pdb=" O GLY B 594 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL B 610 " --> pdb=" O ILE B 651 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 324 through 326 Processing sheet with id=AC8, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.734A pdb=" N ILE B 358 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER B 514 " --> pdb=" O TYR B 396 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASP B 398 " --> pdb=" O VAL B 512 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 660 removed outlier: 3.836A pdb=" N GLU B 654 " --> pdb=" O ILE B 692 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ASN B 658 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 713 removed outlier: 3.651A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR B1105 " --> pdb=" O VAL B1094 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 717 through 719 removed outlier: 3.803A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 722 through 728 removed outlier: 3.534A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 3.896A pdb=" N SER B1123 " --> pdb=" O ALA B1087 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N CYS B1082 " --> pdb=" O VAL B1133 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 27 through 28 Processing sheet with id=AD8, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.552A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS C 278 " --> pdb=" O ASP C 287 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.823A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 93 through 96 removed outlier: 3.505A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 118 through 120 Processing sheet with id=AE3, first strand: chain 'C' and resid 156 through 157 removed outlier: 3.737A pdb=" N GLU C 156 " --> pdb=" O ASP C 142 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ASP C 142 " --> pdb=" O GLU C 156 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.190A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN C 613 " --> pdb=" O GLY C 594 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 324 through 327 removed outlier: 3.558A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.940A pdb=" N ILE C 358 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASP C 398 " --> pdb=" O VAL C 512 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLY C 431 " --> pdb=" O TYR C 380 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N TYR C 380 " --> pdb=" O GLY C 431 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL C 433 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.494A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.756A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.463A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU C 725 " --> pdb=" O PHE C1062 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE C1052 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.463A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU C 725 " --> pdb=" O PHE C1062 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF3, first strand: chain 'C' and resid 1081 through 1083 Processing sheet with id=AF4, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AF5, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.913A pdb=" N VAL D 12 " --> pdb=" O THR D 123 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLY D 33 " --> pdb=" O GLY D 99 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N MET D 34 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VAL D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N TYR D 59 " --> pdb=" O VAL D 50 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.913A pdb=" N VAL D 12 " --> pdb=" O THR D 123 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL D 115 " --> pdb=" O ARG D 98 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 133 through 137 removed outlier: 3.713A pdb=" N GLY D 152 " --> pdb=" O LEU D 137 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N TYR D 189 " --> pdb=" O ASP D 157 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL D 194 " --> pdb=" O HIS D 177 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N HIS D 177 " --> pdb=" O VAL D 194 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 133 through 137 removed outlier: 3.713A pdb=" N GLY D 152 " --> pdb=" O LEU D 137 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N TYR D 189 " --> pdb=" O ASP D 157 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER D 190 " --> pdb=" O VAL D 182 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL D 182 " --> pdb=" O SER D 190 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 164 through 167 removed outlier: 3.564A pdb=" N VAL D 211 " --> pdb=" O VAL D 220 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N VAL D 220 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N HIS D 213 " --> pdb=" O THR D 218 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR D 218 " --> pdb=" O HIS D 213 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 4 through 6 Processing sheet with id=AG2, first strand: chain 'E' and resid 9 through 12 removed outlier: 5.894A pdb=" N PHE E 10 " --> pdb=" O THR E 108 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N GLN E 39 " --> pdb=" O THR E 48 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N THR E 48 " --> pdb=" O GLN E 39 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR E 55 " --> pdb=" O TYR E 51 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 9 through 12 removed outlier: 5.894A pdb=" N PHE E 10 " --> pdb=" O THR E 108 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU E 92 " --> pdb=" O VAL E 100 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE E 98 " --> pdb=" O MET E 94 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'E' and resid 118 through 122 removed outlier: 3.503A pdb=" N SER E 141 " --> pdb=" O SER E 118 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL E 137 " --> pdb=" O PHE E 122 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N TYR E 176 " --> pdb=" O ASP E 142 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'E' and resid 118 through 122 removed outlier: 3.503A pdb=" N SER E 141 " --> pdb=" O SER E 118 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL E 137 " --> pdb=" O PHE E 122 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N TYR E 176 " --> pdb=" O ASP E 142 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'E' and resid 157 through 159 removed outlier: 4.764A pdb=" N TRP E 152 " --> pdb=" O VAL E 159 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS E 153 " --> pdb=" O SER E 196 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER E 196 " --> pdb=" O LYS E 153 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL E 199 " --> pdb=" O VAL E 206 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL E 206 " --> pdb=" O VAL E 199 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AG8, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.309A pdb=" N GLY H 33 " --> pdb=" O GLY H 99 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL H 50 " --> pdb=" O TYR H 59 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N TYR H 59 " --> pdb=" O VAL H 50 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.959A pdb=" N VAL H 115 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'H' and resid 133 through 137 removed outlier: 3.551A pdb=" N CYS H 153 " --> pdb=" O SER H 193 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N TYR H 189 " --> pdb=" O ASP H 157 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'H' and resid 164 through 167 removed outlier: 4.045A pdb=" N TYR H 207 " --> pdb=" O VAL H 224 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'L' and resid 4 through 6 removed outlier: 3.526A pdb=" N GLY L 23 " --> pdb=" O THR L 5 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'L' and resid 55 through 56 removed outlier: 6.616A pdb=" N TRP L 37 " --> pdb=" O LEU L 49 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'L' and resid 55 through 56 removed outlier: 6.616A pdb=" N TRP L 37 " --> pdb=" O LEU L 49 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'L' and resid 118 through 122 removed outlier: 3.513A pdb=" N VAL L 137 " --> pdb=" O PHE L 122 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR L 181 " --> pdb=" O GLU L 164 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU L 164 " --> pdb=" O TYR L 181 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'L' and resid 118 through 122 removed outlier: 3.513A pdb=" N VAL L 137 " --> pdb=" O PHE L 122 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N TYR L 176 " --> pdb=" O ASP L 142 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'L' and resid 157 through 159 removed outlier: 4.259A pdb=" N TRP L 152 " --> pdb=" O VAL L 159 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS L 153 " --> pdb=" O SER L 196 " (cutoff:3.500A) 1138 hydrogen bonds defined for protein. 3012 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: 15.40 Time building geometry restraints manager: 15.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10699 1.34 - 1.47: 8696 1.47 - 1.59: 14917 1.59 - 1.71: 1 1.71 - 1.84: 186 Bond restraints: 34499 Sorted by residual: bond pdb=" C1 NAG B1308 " pdb=" O5 NAG B1308 " ideal model delta sigma weight residual 1.406 1.491 -0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" C1 NAG C1304 " pdb=" O5 NAG C1304 " ideal model delta sigma weight residual 1.406 1.486 -0.080 2.00e-02 2.50e+03 1.60e+01 bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.474 -0.068 2.00e-02 2.50e+03 1.15e+01 bond pdb=" C1 NAG A1306 " pdb=" O5 NAG A1306 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 7.11e+00 bond pdb=" C1 NAG N 1 " pdb=" O5 NAG N 1 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.25e+00 ... (remaining 34494 not shown) Histogram of bond angle deviations from ideal: 97.91 - 105.12: 677 105.12 - 112.34: 17686 112.34 - 119.56: 10636 119.56 - 126.77: 17546 126.77 - 133.99: 433 Bond angle restraints: 46978 Sorted by residual: angle pdb=" CA CYS C 391 " pdb=" CB CYS C 391 " pdb=" SG CYS C 391 " ideal model delta sigma weight residual 114.40 132.29 -17.89 2.30e+00 1.89e-01 6.05e+01 angle pdb=" CA CYS C 525 " pdb=" CB CYS C 525 " pdb=" SG CYS C 525 " ideal model delta sigma weight residual 114.40 131.75 -17.35 2.30e+00 1.89e-01 5.69e+01 angle pdb=" C LEU C 390 " pdb=" N CYS C 391 " pdb=" CA CYS C 391 " ideal model delta sigma weight residual 122.44 113.50 8.94 1.45e+00 4.76e-01 3.80e+01 angle pdb=" N THR A 76 " pdb=" CA THR A 76 " pdb=" C THR A 76 " ideal model delta sigma weight residual 114.56 108.65 5.91 1.27e+00 6.20e-01 2.17e+01 angle pdb=" C GLY C 526 " pdb=" N PRO C 527 " pdb=" CD PRO C 527 " ideal model delta sigma weight residual 125.00 106.92 18.08 4.10e+00 5.95e-02 1.94e+01 ... (remaining 46973 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.37: 20156 25.37 - 50.75: 957 50.75 - 76.12: 118 76.12 - 101.49: 32 101.49 - 126.87: 6 Dihedral angle restraints: 21269 sinusoidal: 8943 harmonic: 12326 Sorted by residual: dihedral pdb=" CA CYS C 525 " pdb=" C CYS C 525 " pdb=" N GLY C 526 " pdb=" CA GLY C 526 " ideal model delta harmonic sigma weight residual -180.00 -126.83 -53.17 0 5.00e+00 4.00e-02 1.13e+02 dihedral pdb=" CB CYS C 391 " pdb=" SG CYS C 391 " pdb=" SG CYS C 525 " pdb=" CB CYS C 525 " ideal model delta sinusoidal sigma weight residual -86.00 1.31 -87.31 1 1.00e+01 1.00e-02 9.15e+01 dihedral pdb=" CB CYS A 840 " pdb=" SG CYS A 840 " pdb=" SG CYS A 851 " pdb=" CB CYS A 851 " ideal model delta sinusoidal sigma weight residual 93.00 172.75 -79.75 1 1.00e+01 1.00e-02 7.89e+01 ... (remaining 21266 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 5410 0.123 - 0.246: 49 0.246 - 0.369: 4 0.369 - 0.492: 1 0.492 - 0.615: 2 Chirality restraints: 5466 Sorted by residual: chirality pdb=" C1 NAG B1304 " pdb=" ND2 ASN B 657 " pdb=" C2 NAG B1304 " pdb=" O5 NAG B1304 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-01 2.50e+01 9.45e+00 chirality pdb=" C1 NAG C1308 " pdb=" ND2 ASN C 234 " pdb=" C2 NAG C1308 " pdb=" O5 NAG C1308 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-01 2.50e+01 9.24e+00 chirality pdb=" C1 NAG T 1 " pdb=" ND2 ASN C 331 " pdb=" C2 NAG T 1 " pdb=" O5 NAG T 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.79e+00 ... (remaining 5463 not shown) Planarity restraints: 6028 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 526 " -0.112 5.00e-02 4.00e+02 1.70e-01 4.65e+01 pdb=" N PRO C 527 " 0.295 5.00e-02 4.00e+02 pdb=" CA PRO C 527 " -0.102 5.00e-02 4.00e+02 pdb=" CD PRO C 527 " -0.081 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 717 " 0.050 2.00e-02 2.50e+03 4.68e-02 2.74e+01 pdb=" CG ASN A 717 " -0.054 2.00e-02 2.50e+03 pdb=" OD1 ASN A 717 " 0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN A 717 " -0.054 2.00e-02 2.50e+03 pdb=" C1 NAG F 1 " 0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 717 " 0.049 2.00e-02 2.50e+03 4.54e-02 2.57e+01 pdb=" CG ASN B 717 " -0.048 2.00e-02 2.50e+03 pdb=" OD1 ASN B 717 " 0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN B 717 " -0.054 2.00e-02 2.50e+03 pdb=" C1 NAG K 1 " 0.052 2.00e-02 2.50e+03 ... (remaining 6025 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 871 2.69 - 3.24: 33208 3.24 - 3.79: 50915 3.79 - 4.35: 64785 4.35 - 4.90: 106320 Nonbonded interactions: 256099 Sorted by model distance: nonbonded pdb=" OG1 THR B 323 " pdb=" OE1 GLU B 324 " model vdw 2.132 2.440 nonbonded pdb=" O THR C 208 " pdb=" NH2 ARG C 214 " model vdw 2.191 2.520 nonbonded pdb=" O THR B 208 " pdb=" NH1 ARG B 214 " model vdw 2.202 2.520 nonbonded pdb=" OE1 GLN D 184 " pdb=" OG SER D 190 " model vdw 2.205 2.440 nonbonded pdb=" O CYS C 15 " pdb=" N ASN C 17 " model vdw 2.206 2.520 ... (remaining 256094 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 676 or resid 689 through 1145 or resid 1301 thr \ ough 1309)) selection = (chain 'B' and (resid 14 through 213 or resid 215 through 676 or resid 689 throu \ gh 1145 or resid 1301 through 1309)) selection = (chain 'C' and (resid 14 through 213 or resid 215 through 676 or resid 689 throu \ gh 1145 or resid 1301 through 1309)) } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'L' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 27.430 Check model and map are aligned: 0.590 Set scattering table: 0.350 Process input model: 93.280 Find NCS groups from input model: 2.540 Set up NCS constraints: 0.400 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: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 134.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 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 : 0.003 0.107 34499 Z= 0.205 Angle : 0.638 18.082 46978 Z= 0.318 Chirality : 0.048 0.615 5466 Planarity : 0.005 0.170 5988 Dihedral : 14.116 126.868 13227 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.43 % Allowed : 7.03 % Favored : 92.54 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.68 % Cis-general : 0.00 % Twisted Proline : 0.45 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.13), residues: 4222 helix: 1.69 (0.21), residues: 728 sheet: -0.13 (0.17), residues: 958 loop : -1.62 (0.12), residues: 2536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 258 HIS 0.004 0.000 HIS H 35 PHE 0.032 0.001 PHE A 238 TYR 0.017 0.001 TYR L 38 ARG 0.006 0.000 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 3667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 4.003 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: A 490 PHE cc_start: 0.8642 (t80) cc_final: 0.8226 (t80) REVERT: C 177 MET cc_start: 0.6535 (mpp) cc_final: 0.6226 (mmm) REVERT: C 988 GLU cc_start: 0.8906 (mm-30) cc_final: 0.8607 (mp0) REVERT: E 170 LYS cc_start: 0.7497 (pttt) cc_final: 0.7272 (mttt) REVERT: L 94 MET cc_start: 0.9008 (mmp) cc_final: 0.8530 (mmm) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.5274 time to fit residues: 107.9918 Evaluate side-chains 77 residues out of total 3667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 3.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 355 optimal weight: 0.0870 chunk 319 optimal weight: 8.9990 chunk 177 optimal weight: 0.8980 chunk 109 optimal weight: 3.9990 chunk 215 optimal weight: 0.9990 chunk 170 optimal weight: 7.9990 chunk 329 optimal weight: 7.9990 chunk 127 optimal weight: 20.0000 chunk 200 optimal weight: 4.9990 chunk 245 optimal weight: 30.0000 chunk 382 optimal weight: 20.0000 overall best weight: 2.1964 ------------------------------------------------------------------------------- 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 394 ASN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 35 HIS ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 44 GLN ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 54 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 34499 Z= 0.204 Angle : 0.616 18.811 46978 Z= 0.310 Chirality : 0.044 0.331 5466 Planarity : 0.005 0.171 5988 Dihedral : 8.785 116.205 5747 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.44 % Favored : 92.18 % Rotamer: Outliers : 0.35 % Allowed : 6.57 % Favored : 93.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.13), residues: 4222 helix: 1.86 (0.21), residues: 724 sheet: -0.05 (0.17), residues: 979 loop : -1.59 (0.12), residues: 2519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 633 HIS 0.008 0.001 HIS C 146 PHE 0.019 0.001 PHE A 400 TYR 0.017 0.001 TYR L 51 ARG 0.009 0.000 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 3667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 78 time to evaluate : 3.952 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 490 PHE cc_start: 0.8626 (t80) cc_final: 0.8257 (t80) REVERT: A 1050 MET cc_start: 0.7788 (ptp) cc_final: 0.7437 (mtm) REVERT: C 118 LEU cc_start: 0.9487 (mm) cc_final: 0.8953 (mp) REVERT: C 177 MET cc_start: 0.6528 (mpp) cc_final: 0.6189 (mmm) REVERT: C 988 GLU cc_start: 0.8956 (mm-30) cc_final: 0.8653 (mp0) REVERT: L 94 MET cc_start: 0.8987 (mmp) cc_final: 0.8512 (mmm) REVERT: L 207 GLU cc_start: 0.7332 (mm-30) cc_final: 0.6947 (tt0) outliers start: 13 outliers final: 5 residues processed: 88 average time/residue: 0.5110 time to fit residues: 75.4246 Evaluate side-chains 72 residues out of total 3667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 67 time to evaluate : 4.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 717 ASN Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 822 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 212 optimal weight: 8.9990 chunk 118 optimal weight: 20.0000 chunk 318 optimal weight: 5.9990 chunk 260 optimal weight: 6.9990 chunk 105 optimal weight: 10.0000 chunk 383 optimal weight: 8.9990 chunk 413 optimal weight: 50.0000 chunk 341 optimal weight: 30.0000 chunk 379 optimal weight: 30.0000 chunk 130 optimal weight: 8.9990 chunk 307 optimal weight: 5.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- 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 394 ASN ** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1083 HIS A1106 GLN A1108 ASN B 52 GLN ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN ** C 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1088 HIS C1101 HIS C1106 GLN D 57 ASN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 71 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.105 34499 Z= 0.559 Angle : 0.883 19.904 46978 Z= 0.448 Chirality : 0.048 0.305 5466 Planarity : 0.006 0.173 5988 Dihedral : 8.905 114.289 5747 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 27.30 Ramachandran Plot: Outliers : 0.38 % Allowed : 10.37 % Favored : 89.25 % Rotamer: Outliers : 1.64 % Allowed : 12.60 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.13), residues: 4222 helix: 0.51 (0.19), residues: 723 sheet: -0.55 (0.16), residues: 956 loop : -1.71 (0.12), residues: 2543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 633 HIS 0.012 0.002 HIS C 146 PHE 0.027 0.003 PHE A 802 TYR 0.042 0.002 TYR B 269 ARG 0.012 0.001 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 3667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 74 time to evaluate : 4.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 490 PHE cc_start: 0.8388 (t80) cc_final: 0.7873 (t80) REVERT: A 553 THR cc_start: 0.9297 (OUTLIER) cc_final: 0.9077 (p) REVERT: A 833 PHE cc_start: 0.6961 (m-80) cc_final: 0.6758 (m-10) REVERT: B 408 ARG cc_start: 0.9347 (OUTLIER) cc_final: 0.8737 (pmt-80) REVERT: C 331 ASN cc_start: 0.8904 (OUTLIER) cc_final: 0.8680 (m-40) REVERT: C 740 MET cc_start: 0.8289 (tpt) cc_final: 0.7922 (tpp) REVERT: C 847 ARG cc_start: 0.3259 (OUTLIER) cc_final: 0.2622 (pmt-80) REVERT: C 1018 ILE cc_start: 0.9503 (OUTLIER) cc_final: 0.9235 (mm) REVERT: C 1050 MET cc_start: 0.8693 (pmm) cc_final: 0.8156 (pmm) REVERT: H 113 MET cc_start: 0.6347 (tmm) cc_final: 0.5516 (tmm) REVERT: L 94 MET cc_start: 0.8860 (mmp) cc_final: 0.8447 (mmm) REVERT: L 207 GLU cc_start: 0.7171 (mm-30) cc_final: 0.6886 (tt0) outliers start: 60 outliers final: 24 residues processed: 127 average time/residue: 0.4775 time to fit residues: 102.0497 Evaluate side-chains 89 residues out of total 3667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 60 time to evaluate : 3.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 717 ASN Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 847 ARG Chi-restraints excluded: chain C residue 1008 VAL Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain L residue 51 TYR Chi-restraints excluded: chain L residue 109 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 378 optimal weight: 8.9990 chunk 287 optimal weight: 3.9990 chunk 198 optimal weight: 0.8980 chunk 42 optimal weight: 20.0000 chunk 182 optimal weight: 0.8980 chunk 257 optimal weight: 3.9990 chunk 384 optimal weight: 6.9990 chunk 406 optimal weight: 7.9990 chunk 200 optimal weight: 0.9990 chunk 364 optimal weight: 50.0000 chunk 109 optimal weight: 0.8980 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 394 ASN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 HIS B 134 GLN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 784 GLN ** B 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 ASN ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 57 ASN E 6 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 GLN ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 54 ASN L 71 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 34499 Z= 0.179 Angle : 0.610 17.715 46978 Z= 0.305 Chirality : 0.044 0.299 5466 Planarity : 0.005 0.167 5988 Dihedral : 8.000 115.783 5747 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.89 % Favored : 92.73 % Rotamer: Outliers : 1.04 % Allowed : 14.56 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.13), residues: 4222 helix: 1.51 (0.20), residues: 732 sheet: -0.37 (0.17), residues: 974 loop : -1.53 (0.12), residues: 2516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 633 HIS 0.005 0.001 HIS H 35 PHE 0.021 0.001 PHE A 400 TYR 0.017 0.001 TYR D 109 ARG 0.006 0.000 ARG C 78 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 3667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 65 time to evaluate : 4.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 490 PHE cc_start: 0.8494 (t80) cc_final: 0.7959 (t80) REVERT: A 1050 MET cc_start: 0.7748 (ptp) cc_final: 0.7537 (mtm) REVERT: B 408 ARG cc_start: 0.9342 (OUTLIER) cc_final: 0.8591 (pmt-80) REVERT: B 414 GLN cc_start: 0.8070 (OUTLIER) cc_final: 0.6046 (pm20) REVERT: C 177 MET cc_start: 0.6828 (mpp) cc_final: 0.6590 (mmm) REVERT: C 740 MET cc_start: 0.8243 (tpt) cc_final: 0.7900 (tpp) REVERT: C 1050 MET cc_start: 0.8454 (pmm) cc_final: 0.7943 (pmm) REVERT: H 113 MET cc_start: 0.6879 (tmm) cc_final: 0.6163 (tmm) REVERT: L 94 MET cc_start: 0.8686 (mmp) cc_final: 0.8111 (mmm) REVERT: L 207 GLU cc_start: 0.6999 (mm-30) cc_final: 0.6704 (tt0) outliers start: 38 outliers final: 18 residues processed: 100 average time/residue: 0.4762 time to fit residues: 82.7128 Evaluate side-chains 79 residues out of total 3667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 59 time to evaluate : 4.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 717 ASN Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain B residue 833 PHE Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 54 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 338 optimal weight: 20.0000 chunk 231 optimal weight: 20.0000 chunk 5 optimal weight: 6.9990 chunk 302 optimal weight: 20.0000 chunk 167 optimal weight: 10.0000 chunk 347 optimal weight: 40.0000 chunk 281 optimal weight: 4.9990 chunk 0 optimal weight: 30.0000 chunk 207 optimal weight: 3.9990 chunk 365 optimal weight: 20.0000 chunk 102 optimal weight: 4.9990 overall best weight: 6.1992 ------------------------------------------------------------------------------- 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 394 ASN A 675 GLN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 784 GLN ** B 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 ASN ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN ** C 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 GLN D 57 ASN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.092 34499 Z= 0.433 Angle : 0.730 18.152 46978 Z= 0.368 Chirality : 0.044 0.275 5466 Planarity : 0.005 0.168 5988 Dihedral : 8.085 114.108 5747 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 22.26 Ramachandran Plot: Outliers : 0.38 % Allowed : 9.73 % Favored : 89.89 % Rotamer: Outliers : 1.99 % Allowed : 16.14 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.13), residues: 4222 helix: 1.13 (0.20), residues: 727 sheet: -0.61 (0.17), residues: 942 loop : -1.63 (0.12), residues: 2553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 633 HIS 0.007 0.001 HIS C 146 PHE 0.016 0.002 PHE A 802 TYR 0.022 0.002 TYR B 269 ARG 0.011 0.001 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 3667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 61 time to evaluate : 4.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 490 PHE cc_start: 0.8301 (t80) cc_final: 0.7685 (t80) REVERT: A 492 LEU cc_start: 0.9062 (mp) cc_final: 0.8607 (mp) REVERT: B 414 GLN cc_start: 0.8197 (OUTLIER) cc_final: 0.6879 (pm20) REVERT: C 331 ASN cc_start: 0.8800 (OUTLIER) cc_final: 0.8541 (m-40) REVERT: C 740 MET cc_start: 0.8317 (tpt) cc_final: 0.7984 (tpp) REVERT: C 847 ARG cc_start: 0.2837 (OUTLIER) cc_final: 0.2423 (pmt-80) REVERT: C 1029 MET cc_start: 0.8951 (tpp) cc_final: 0.8729 (tpp) REVERT: C 1050 MET cc_start: 0.8644 (pmm) cc_final: 0.7872 (pmm) REVERT: H 113 MET cc_start: 0.7268 (tmm) cc_final: 0.6589 (tmm) REVERT: L 207 GLU cc_start: 0.6921 (mm-30) cc_final: 0.6608 (tt0) outliers start: 73 outliers final: 39 residues processed: 130 average time/residue: 0.4163 time to fit residues: 97.2598 Evaluate side-chains 101 residues out of total 3667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 59 time to evaluate : 4.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 717 ASN Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 847 ARG Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain L residue 54 ASN Chi-restraints excluded: chain L residue 101 PHE Chi-restraints excluded: chain L residue 109 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 136 optimal weight: 0.9990 chunk 366 optimal weight: 40.0000 chunk 80 optimal weight: 20.0000 chunk 238 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 407 optimal weight: 10.0000 chunk 338 optimal weight: 10.0000 chunk 188 optimal weight: 0.6980 chunk 33 optimal weight: 20.0000 chunk 134 optimal weight: 30.0000 chunk 213 optimal weight: 5.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- 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 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 ASN A 919 ASN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 784 GLN ** B 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 14 GLN C 49 HIS C 245 HIS ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN ** C 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 34499 Z= 0.265 Angle : 0.633 17.696 46978 Z= 0.317 Chirality : 0.044 0.281 5466 Planarity : 0.005 0.167 5988 Dihedral : 7.736 115.022 5747 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 19.04 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.05 % Favored : 91.59 % Rotamer: Outliers : 1.64 % Allowed : 17.15 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.13), residues: 4222 helix: 1.44 (0.20), residues: 727 sheet: -0.54 (0.17), residues: 914 loop : -1.57 (0.12), residues: 2581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 633 HIS 0.005 0.001 HIS C 146 PHE 0.017 0.001 PHE A 400 TYR 0.018 0.001 TYR D 109 ARG 0.008 0.000 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 3667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 63 time to evaluate : 3.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 490 PHE cc_start: 0.8337 (t80) cc_final: 0.7734 (t80) REVERT: A 492 LEU cc_start: 0.9029 (mp) cc_final: 0.8583 (mp) REVERT: A 1050 MET cc_start: 0.7870 (ptp) cc_final: 0.7558 (mtm) REVERT: B 182 LYS cc_start: 0.7469 (mttt) cc_final: 0.7152 (mtmt) REVERT: B 408 ARG cc_start: 0.9387 (OUTLIER) cc_final: 0.8681 (pmt-80) REVERT: B 414 GLN cc_start: 0.8054 (OUTLIER) cc_final: 0.5954 (pm20) REVERT: C 331 ASN cc_start: 0.8665 (OUTLIER) cc_final: 0.8397 (m-40) REVERT: C 740 MET cc_start: 0.8231 (tpt) cc_final: 0.7910 (tpp) REVERT: C 847 ARG cc_start: 0.2472 (OUTLIER) cc_final: 0.1264 (pmt-80) REVERT: C 1018 ILE cc_start: 0.9526 (OUTLIER) cc_final: 0.9297 (mm) REVERT: C 1050 MET cc_start: 0.8582 (pmm) cc_final: 0.8097 (pmm) REVERT: H 113 MET cc_start: 0.7227 (tmm) cc_final: 0.6624 (tmm) REVERT: L 207 GLU cc_start: 0.6792 (mm-30) cc_final: 0.6481 (tt0) outliers start: 60 outliers final: 36 residues processed: 119 average time/residue: 0.4616 time to fit residues: 95.8093 Evaluate side-chains 102 residues out of total 3667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 61 time to evaluate : 4.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 717 ASN Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 710 ASN Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 847 ARG Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain L residue 101 PHE Chi-restraints excluded: chain L residue 109 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 392 optimal weight: 40.0000 chunk 45 optimal weight: 20.0000 chunk 232 optimal weight: 8.9990 chunk 297 optimal weight: 6.9990 chunk 230 optimal weight: 7.9990 chunk 342 optimal weight: 50.0000 chunk 227 optimal weight: 10.0000 chunk 405 optimal weight: 6.9990 chunk 253 optimal weight: 0.9980 chunk 247 optimal weight: 9.9990 chunk 187 optimal weight: 0.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 ASN A 784 GLN A 919 ASN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 ASN ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 HIS ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN ** C 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 34499 Z= 0.348 Angle : 0.682 17.985 46978 Z= 0.343 Chirality : 0.044 0.273 5466 Planarity : 0.005 0.167 5988 Dihedral : 7.752 113.971 5747 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 21.82 Ramachandran Plot: Outliers : 0.36 % Allowed : 9.55 % Favored : 90.10 % Rotamer: Outliers : 2.40 % Allowed : 17.26 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.13), residues: 4222 helix: 1.26 (0.20), residues: 722 sheet: -0.69 (0.17), residues: 921 loop : -1.62 (0.12), residues: 2579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 633 HIS 0.008 0.001 HIS C 245 PHE 0.036 0.002 PHE E 10 TYR 0.020 0.001 TYR D 109 ARG 0.010 0.001 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 3667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 62 time to evaluate : 3.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8800 (pp) REVERT: A 490 PHE cc_start: 0.8259 (t80) cc_final: 0.7716 (t80) REVERT: A 808 ASP cc_start: 0.7798 (OUTLIER) cc_final: 0.6872 (p0) REVERT: B 182 LYS cc_start: 0.7563 (mttt) cc_final: 0.7247 (mtmt) REVERT: B 408 ARG cc_start: 0.9425 (OUTLIER) cc_final: 0.8734 (pmt-80) REVERT: B 414 GLN cc_start: 0.8033 (OUTLIER) cc_final: 0.5903 (pm20) REVERT: B 528 LYS cc_start: 0.5927 (OUTLIER) cc_final: 0.5494 (mtmm) REVERT: C 331 ASN cc_start: 0.8795 (OUTLIER) cc_final: 0.8485 (m-40) REVERT: C 432 CYS cc_start: 0.7863 (OUTLIER) cc_final: 0.7286 (p) REVERT: C 740 MET cc_start: 0.8256 (tpt) cc_final: 0.7943 (tpp) REVERT: C 1050 MET cc_start: 0.8626 (pmm) cc_final: 0.8032 (pmm) REVERT: H 113 MET cc_start: 0.7244 (tmm) cc_final: 0.6694 (tmm) REVERT: L 207 GLU cc_start: 0.6818 (mm-30) cc_final: 0.6462 (tt0) outliers start: 88 outliers final: 58 residues processed: 146 average time/residue: 0.4617 time to fit residues: 117.8031 Evaluate side-chains 123 residues out of total 3667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 58 time to evaluate : 3.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 717 ASN Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 808 ASP Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 710 ASN Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 49 HIS Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain L residue 51 TYR Chi-restraints excluded: chain L residue 101 PHE Chi-restraints excluded: chain L residue 109 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 251 optimal weight: 4.9990 chunk 162 optimal weight: 20.0000 chunk 242 optimal weight: 20.0000 chunk 122 optimal weight: 10.0000 chunk 79 optimal weight: 0.5980 chunk 78 optimal weight: 4.9990 chunk 257 optimal weight: 9.9990 chunk 276 optimal weight: 1.9990 chunk 200 optimal weight: 0.7980 chunk 37 optimal weight: 8.9990 chunk 318 optimal weight: 0.5980 overall best weight: 1.7984 ------------------------------------------------------------------------------- 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 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 ASN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1023 ASN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 34499 Z= 0.177 Angle : 0.603 17.487 46978 Z= 0.300 Chirality : 0.044 0.282 5466 Planarity : 0.004 0.166 5988 Dihedral : 7.330 114.723 5747 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 16.80 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.11 % Favored : 92.56 % Rotamer: Outliers : 1.58 % Allowed : 18.24 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.13), residues: 4222 helix: 1.66 (0.21), residues: 727 sheet: -0.67 (0.17), residues: 932 loop : -1.52 (0.12), residues: 2563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 633 HIS 0.020 0.001 HIS C 49 PHE 0.018 0.001 PHE A 400 TYR 0.016 0.001 TYR D 109 ARG 0.007 0.000 ARG C 847 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 3667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 65 time to evaluate : 4.176 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: A 490 PHE cc_start: 0.8294 (t80) cc_final: 0.7769 (t80) REVERT: A 571 ASP cc_start: 0.7885 (p0) cc_final: 0.7684 (p0) REVERT: B 182 LYS cc_start: 0.7495 (mttt) cc_final: 0.7179 (mtmt) REVERT: B 414 GLN cc_start: 0.7828 (OUTLIER) cc_final: 0.6399 (pm20) REVERT: C 331 ASN cc_start: 0.8660 (OUTLIER) cc_final: 0.8388 (m-40) REVERT: C 432 CYS cc_start: 0.8157 (OUTLIER) cc_final: 0.7435 (p) REVERT: C 740 MET cc_start: 0.8236 (tpt) cc_final: 0.7951 (tpp) REVERT: C 1050 MET cc_start: 0.8482 (pmm) cc_final: 0.8235 (pmm) REVERT: D 113 MET cc_start: 0.8108 (tmm) cc_final: 0.7743 (tmm) REVERT: H 113 MET cc_start: 0.7425 (tmm) cc_final: 0.6911 (tmm) REVERT: L 94 MET cc_start: 0.8770 (mmp) cc_final: 0.8263 (mmm) REVERT: L 207 GLU cc_start: 0.6797 (mm-30) cc_final: 0.6492 (tt0) REVERT: L 208 LYS cc_start: 0.5357 (tptp) cc_final: 0.4545 (ptmm) outliers start: 58 outliers final: 44 residues processed: 119 average time/residue: 0.4379 time to fit residues: 92.1023 Evaluate side-chains 108 residues out of total 3667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 61 time to evaluate : 3.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 717 ASN Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain L residue 101 PHE Chi-restraints excluded: chain L residue 109 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 369 optimal weight: 50.0000 chunk 388 optimal weight: 9.9990 chunk 354 optimal weight: 20.0000 chunk 378 optimal weight: 7.9990 chunk 227 optimal weight: 10.0000 chunk 164 optimal weight: 6.9990 chunk 296 optimal weight: 0.7980 chunk 116 optimal weight: 10.0000 chunk 341 optimal weight: 7.9990 chunk 357 optimal weight: 5.9990 chunk 376 optimal weight: 40.0000 overall best weight: 5.9588 ------------------------------------------------------------------------------- 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 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 ASN ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1023 ASN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN ** C 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 34499 Z= 0.423 Angle : 0.726 18.185 46978 Z= 0.365 Chirality : 0.044 0.263 5466 Planarity : 0.005 0.168 5988 Dihedral : 7.640 113.211 5747 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 23.65 Ramachandran Plot: Outliers : 0.36 % Allowed : 9.85 % Favored : 89.79 % Rotamer: Outliers : 2.05 % Allowed : 18.38 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.13), residues: 4222 helix: 1.16 (0.20), residues: 727 sheet: -0.83 (0.17), residues: 923 loop : -1.61 (0.12), residues: 2572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 633 HIS 0.009 0.002 HIS C 245 PHE 0.016 0.002 PHE B1075 TYR 0.035 0.002 TYR B 269 ARG 0.012 0.001 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 3667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 59 time to evaluate : 3.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8773 (pp) REVERT: A 490 PHE cc_start: 0.8155 (t80) cc_final: 0.7617 (t80) REVERT: A 697 MET cc_start: 0.8823 (pmm) cc_final: 0.8552 (pmm) REVERT: A 895 GLN cc_start: 0.8969 (OUTLIER) cc_final: 0.8707 (pp30) REVERT: B 182 LYS cc_start: 0.7585 (mttt) cc_final: 0.7263 (mtmt) REVERT: B 414 GLN cc_start: 0.7912 (OUTLIER) cc_final: 0.6514 (pm20) REVERT: B 528 LYS cc_start: 0.6023 (OUTLIER) cc_final: 0.5508 (mtmm) REVERT: B 900 MET cc_start: 0.8859 (mmm) cc_final: 0.8548 (mmm) REVERT: C 331 ASN cc_start: 0.8862 (OUTLIER) cc_final: 0.8549 (m-40) REVERT: C 432 CYS cc_start: 0.8167 (OUTLIER) cc_final: 0.7626 (p) REVERT: C 740 MET cc_start: 0.8348 (tpt) cc_final: 0.8068 (tpp) REVERT: C 1050 MET cc_start: 0.8667 (pmm) cc_final: 0.7888 (pmm) REVERT: D 113 MET cc_start: 0.8225 (tmm) cc_final: 0.7843 (tmm) REVERT: H 113 MET cc_start: 0.7435 (tmm) cc_final: 0.6894 (tmm) REVERT: L 94 MET cc_start: 0.8832 (mmp) cc_final: 0.8226 (mmp) REVERT: L 207 GLU cc_start: 0.6673 (mm-30) cc_final: 0.6296 (tt0) REVERT: L 208 LYS cc_start: 0.5664 (tptp) cc_final: 0.5008 (ptmm) outliers start: 75 outliers final: 55 residues processed: 130 average time/residue: 0.4300 time to fit residues: 98.4090 Evaluate side-chains 119 residues out of total 3667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 58 time to evaluate : 3.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 717 ASN Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 710 ASN Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain L residue 101 PHE Chi-restraints excluded: chain L residue 109 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 248 optimal weight: 0.9990 chunk 399 optimal weight: 0.9990 chunk 244 optimal weight: 3.9990 chunk 189 optimal weight: 3.9990 chunk 277 optimal weight: 10.0000 chunk 419 optimal weight: 5.9990 chunk 386 optimal weight: 40.0000 chunk 333 optimal weight: 20.0000 chunk 34 optimal weight: 20.0000 chunk 257 optimal weight: 5.9990 chunk 204 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 919 ASN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN ** C 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.3922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 34499 Z= 0.226 Angle : 0.624 17.971 46978 Z= 0.310 Chirality : 0.044 0.273 5466 Planarity : 0.005 0.168 5988 Dihedral : 7.329 113.956 5747 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 18.94 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.86 % Favored : 91.78 % Rotamer: Outliers : 1.83 % Allowed : 18.60 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.13), residues: 4222 helix: 1.42 (0.20), residues: 734 sheet: -0.74 (0.17), residues: 910 loop : -1.56 (0.12), residues: 2578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 633 HIS 0.006 0.001 HIS C 245 PHE 0.017 0.001 PHE A 400 TYR 0.020 0.001 TYR B 269 ARG 0.007 0.000 ARG C 357 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8444 Ramachandran restraints generated. 4222 Oldfield, 0 Emsley, 4222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 3667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 59 time to evaluate : 4.118 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: A 118 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8811 (pp) REVERT: A 490 PHE cc_start: 0.8188 (t80) cc_final: 0.7659 (t80) REVERT: B 182 LYS cc_start: 0.7507 (mttt) cc_final: 0.7187 (mtmt) REVERT: B 414 GLN cc_start: 0.7741 (OUTLIER) cc_final: 0.6282 (pm20) REVERT: B 528 LYS cc_start: 0.5922 (OUTLIER) cc_final: 0.5234 (mtmm) REVERT: C 331 ASN cc_start: 0.8731 (OUTLIER) cc_final: 0.8457 (m-40) REVERT: C 432 CYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7697 (p) REVERT: C 697 MET cc_start: 0.8622 (mmm) cc_final: 0.7941 (mmm) REVERT: C 740 MET cc_start: 0.8300 (tpt) cc_final: 0.8029 (tpp) REVERT: C 1050 MET cc_start: 0.8573 (pmm) cc_final: 0.8200 (pmm) REVERT: D 113 MET cc_start: 0.8118 (tmm) cc_final: 0.7730 (tmm) REVERT: H 113 MET cc_start: 0.7439 (tmm) cc_final: 0.6932 (tmm) REVERT: L 94 MET cc_start: 0.8763 (mmp) cc_final: 0.8128 (mmp) REVERT: L 207 GLU cc_start: 0.6675 (mm-30) cc_final: 0.6232 (tt0) outliers start: 67 outliers final: 54 residues processed: 122 average time/residue: 0.4347 time to fit residues: 93.4565 Evaluate side-chains 118 residues out of total 3667 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 59 time to evaluate : 3.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 717 ASN Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 767 LEU Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 132 GLU Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 844 ILE Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain L residue 101 PHE Chi-restraints excluded: chain L residue 109 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 421 random chunks: chunk 265 optimal weight: 30.0000 chunk 355 optimal weight: 20.0000 chunk 102 optimal weight: 2.9990 chunk 307 optimal weight: 6.9990 chunk 49 optimal weight: 10.0000 chunk 92 optimal weight: 9.9990 chunk 334 optimal weight: 0.5980 chunk 139 optimal weight: 4.9990 chunk 343 optimal weight: 1.9990 chunk 42 optimal weight: 0.0670 chunk 61 optimal weight: 6.9990 overall best weight: 2.1324 ------------------------------------------------------------------------------- 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 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 ASN A 556 ASN A 919 ASN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.056759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.036704 restraints weight = 259342.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.037307 restraints weight = 179585.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.037700 restraints weight = 145239.308| |-----------------------------------------------------------------------------| r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.3957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 34499 Z= 0.191 Angle : 0.599 17.998 46978 Z= 0.297 Chirality : 0.043 0.272 5466 Planarity : 0.004 0.168 5988 Dihedral : 6.943 112.237 5747 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.20 % Favored : 91.45 % Rotamer: Outliers : 1.69 % Allowed : 18.73 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.13), residues: 4222 helix: 1.63 (0.21), residues: 731 sheet: -0.74 (0.17), residues: 928 loop : -1.51 (0.12), residues: 2563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 633 HIS 0.006 0.001 HIS C 245 PHE 0.015 0.001 PHE A 400 TYR 0.020 0.001 TYR D 109 ARG 0.006 0.000 ARG C 357 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5270.52 seconds wall clock time: 99 minutes 43.15 seconds (5983.15 seconds total)