Starting phenix.real_space_refine on Thu Feb 22 12:48:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whb_32498/02_2024/7whb_32498.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whb_32498/02_2024/7whb_32498.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whb_32498/02_2024/7whb_32498.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whb_32498/02_2024/7whb_32498.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whb_32498/02_2024/7whb_32498.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7whb_32498/02_2024/7whb_32498.pdb" } resolution = 2.67 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 147 5.16 5 C 21677 2.51 5 N 5644 2.21 5 O 6741 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 773": "OE1" <-> "OE2" Residue "B GLU 780": "OE1" <-> "OE2" Residue "C GLU 471": "OE1" <-> "OE2" Residue "C GLU 780": "OE1" <-> "OE2" Residue "C TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 74": "OE1" <-> "OE2" Residue "G GLU 10": "OE1" <-> "OE2" Residue "G GLU 89": "OE1" <-> "OE2" Residue "J GLU 10": "OE1" <-> "OE2" Residue "J GLU 89": "OE1" <-> "OE2" 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: 34209 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 7863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1006, 7863 Classifications: {'peptide': 1006} Link IDs: {'PTRANS': 50, 'TRANS': 955} Chain breaks: 8 Chain: "B" Number of atoms: 7870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1007, 7870 Classifications: {'peptide': 1007} Link IDs: {'PTRANS': 49, 'TRANS': 957} Chain breaks: 8 Chain: "C" Number of atoms: 7853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1004, 7853 Classifications: {'peptide': 1004} Link IDs: {'PTRANS': 49, 'TRANS': 954} Chain breaks: 8 Chain: "D" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1646 Classifications: {'peptide': 224} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 211} Chain: "E" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1643 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 201} Chain: "G" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1646 Classifications: {'peptide': 224} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 211} Chain: "H" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1643 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 201} Chain: "J" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1646 Classifications: {'peptide': 224} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 211} Chain: "K" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1643 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 9, 'TRANS': 201} 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: "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: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" 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: "X" 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: "Y" 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: "Z" 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: 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: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 17.11, per 1000 atoms: 0.50 Number of scatterers: 34209 At special positions: 0 Unit cell: (166.881, 173.468, 248.125, 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 147 16.00 O 6741 8.00 N 5644 7.00 C 21677 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 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=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 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 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 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=2.05 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 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 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 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 148 " - pdb=" SG CYS D 204 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 134 " - pdb=" SG CYS E 194 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 148 " - pdb=" SG CYS G 204 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 134 " - pdb=" SG CYS H 194 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 148 " - pdb=" SG CYS J 204 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 134 " - pdb=" SG CYS K 194 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG I 1 " - " NAG I 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 122 " " NAG A1403 " - " ASN A 603 " " NAG A1404 " - " ASN A 616 " " NAG A1405 " - " ASN A 657 " " NAG A1406 " - " ASN A 709 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 282 " " NAG B1403 " - " ASN B 603 " " NAG B1404 " - " ASN B 616 " " NAG B1405 " - " ASN B 657 " " NAG C1201 " - " ASN A 282 " " NAG C1202 " - " ASN C 61 " " NAG C1203 " - " ASN C 122 " " NAG C1204 " - " ASN C 282 " " NAG C1205 " - " ASN C 603 " " NAG C1206 " - " ASN C 616 " " NAG C1207 " - " ASN C 657 " " NAG F 1 " - " ASN A 717 " " NAG I 1 " - " ASN A 801 " " NAG L 1 " - " ASN A1074 " " NAG M 1 " - " ASN A1098 " " NAG N 1 " - " ASN A1134 " " NAG O 1 " - " ASN B 331 " " NAG P 1 " - " ASN B 709 " " NAG Q 1 " - " ASN B 717 " " NAG R 1 " - " ASN B 801 " " NAG S 1 " - " ASN B1074 " " NAG T 1 " - " ASN B1098 " " NAG U 1 " - " ASN B1134 " " NAG V 1 " - " ASN C 709 " " NAG W 1 " - " ASN C 717 " " NAG X 1 " - " ASN C 801 " " NAG Y 1 " - " ASN C1074 " " NAG Z 1 " - " ASN C1098 " " NAG a 1 " - " ASN C1134 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 13.23 Conformation dependent library (CDL) restraints added in 6.1 seconds 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8054 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 78 sheets defined 18.4% alpha, 31.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.39 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.021A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 410 removed outlier: 5.203A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 removed outlier: 4.043A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.500A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 815 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 3.988A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.829A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.733A 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 988 through 1033 removed outlier: 3.615A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.853A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) 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 370 removed outlier: 4.037A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 5.108A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.511A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 939 removed outlier: 6.798A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.844A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.689A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 5.167A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1142 through 1146 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 341 removed outlier: 3.511A pdb=" N GLU C 340 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.050A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 removed outlier: 5.233A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.847A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 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: 3.683A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.610A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.841A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.083A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.666A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.692A 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 984 removed outlier: 3.576A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.058A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 Processing helix chain 'D' and resid 62 through 65 removed outlier: 3.575A pdb=" N GLN D 65 " --> pdb=" O GLN D 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 62 through 65' Processing helix chain 'D' and resid 164 through 166 No H-bonds generated for 'chain 'D' and resid 164 through 166' Processing helix chain 'D' and resid 193 through 197 Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.896A pdb=" N PHE E 83 " --> pdb=" O PRO E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 183 through 188 Processing helix chain 'G' and resid 87 through 91 removed outlier: 3.952A pdb=" N THR G 91 " --> pdb=" O SER G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 193 through 197 Processing helix chain 'H' and resid 79 through 83 removed outlier: 3.938A pdb=" N PHE H 83 " --> pdb=" O PRO H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 187 Processing helix chain 'J' and resid 87 through 91 removed outlier: 3.902A pdb=" N THR J 91 " --> pdb=" O SER J 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 193 through 197 Processing helix chain 'K' and resid 79 through 83 removed outlier: 3.942A pdb=" N PHE K 83 " --> pdb=" O PRO K 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 183 through 188 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 6.670A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 9.638A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.198A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.854A pdb=" N ILE A 105 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N VAL A 126 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N VAL A 171 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE A 128 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N GLU A 169 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL A 130 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLU A 132 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N ASN A 165 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.556A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.690A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER A 514 " --> pdb=" O TYR A 396 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA7, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA9, first strand: chain 'A' and resid 538 through 539 removed outlier: 5.012A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 542 through 543 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.162A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.679A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 704 removed outlier: 3.576A pdb=" N LYS B 790 " --> pdb=" O ASN A 703 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.444A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.444A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.458A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.338A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.728A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 31 Processing sheet with id=AC1, first strand: chain 'B' and resid 36 through 37 removed outlier: 6.966A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.254A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE B 194 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 49 through 51 removed outlier: 6.864A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 54 through 55 removed outlier: 3.507A pdb=" N GLN B 271 " --> pdb=" O PHE B 55 " (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 311 through 319 removed outlier: 5.539A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY B 593 " --> pdb=" O PHE B 318 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.759A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC9, first strand: chain 'B' and resid 538 through 543 removed outlier: 5.009A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N THR B 573 " --> pdb=" O ASP B 568 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASP B 568 " --> pdb=" O THR B 573 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.094A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.561A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 702 through 704 removed outlier: 3.628A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.685A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 5.866A 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 711 through 728 removed outlier: 6.685A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (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 1122 Processing sheet with id=AD7, first strand: chain 'C' and resid 28 through 31 Processing sheet with id=AD8, first strand: chain 'C' and resid 36 through 37 removed outlier: 7.009A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 8.749A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL C 90 " --> pdb=" O PHE C 194 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 50 through 51 removed outlier: 3.620A pdb=" N LEU C 276 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 54 through 55 Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.553A pdb=" N SER C 116 " --> pdb=" O CYS C 131 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.561A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.811A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AE6, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE7, first strand: chain 'C' and resid 538 through 543 removed outlier: 5.050A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N THR C 573 " --> pdb=" O ASP C 568 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ASP C 568 " --> pdb=" O THR C 573 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.944A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.605A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.704A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.875A 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: 6.704A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (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 1120 through 1122 Processing sheet with id=AF4, first strand: chain 'D' and resid 3 through 6 removed outlier: 3.872A pdb=" N GLN D 3 " --> pdb=" O SER D 25 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 57 through 60 removed outlier: 3.505A pdb=" N ASN D 59 " --> pdb=" O ARG D 50 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N VAL D 110 " --> pdb=" O LYS D 98 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 57 through 60 removed outlier: 3.505A pdb=" N ASN D 59 " --> pdb=" O ARG D 50 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR D 94 " --> pdb=" O THR D 115 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 128 through 132 removed outlier: 3.670A pdb=" N LYS D 151 " --> pdb=" O SER D 128 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER D 188 " --> pdb=" O CYS D 148 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 128 through 132 removed outlier: 3.670A pdb=" N LYS D 151 " --> pdb=" O SER D 128 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N LYS D 151 " --> pdb=" O LEU D 186 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N LEU D 186 " --> pdb=" O LYS D 151 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 161 through 162 removed outlier: 3.595A pdb=" N VAL D 215 " --> pdb=" O VAL D 206 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 5 through 7 removed outlier: 3.509A pdb=" N ARG E 24 " --> pdb=" O THR E 5 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N CYS E 23 " --> pdb=" O PHE E 71 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N PHE E 71 " --> pdb=" O CYS E 23 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 53 through 54 removed outlier: 6.518A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 114 through 118 removed outlier: 5.894A pdb=" N TYR E 173 " --> pdb=" O ASN E 138 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'E' and resid 153 through 155 removed outlier: 4.577A pdb=" N TRP E 148 " --> pdb=" O GLN E 155 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'G' and resid 3 through 6 removed outlier: 3.952A pdb=" N GLN G 3 " --> pdb=" O SER G 25 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.917A pdb=" N GLY G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN G 59 " --> pdb=" O ARG G 50 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'G' and resid 10 through 12 removed outlier: 4.164A pdb=" N VAL G 110 " --> pdb=" O LYS G 98 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'G' and resid 128 through 132 removed outlier: 3.715A pdb=" N LYS G 151 " --> pdb=" O SER G 128 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER G 188 " --> pdb=" O CYS G 148 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'G' and resid 128 through 132 removed outlier: 3.715A pdb=" N LYS G 151 " --> pdb=" O SER G 128 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N LYS G 151 " --> pdb=" O LEU G 186 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N LEU G 186 " --> pdb=" O LYS G 151 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'G' and resid 158 through 162 removed outlier: 3.660A pdb=" N THR G 159 " --> pdb=" O ASN G 207 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS G 217 " --> pdb=" O CYS G 204 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL G 215 " --> pdb=" O VAL G 206 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N HIS G 208 " --> pdb=" O THR G 213 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'H' and resid 5 through 7 removed outlier: 3.705A pdb=" N SER H 7 " --> pdb=" O SER H 22 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER H 22 " --> pdb=" O SER H 7 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N CYS H 23 " --> pdb=" O PHE H 71 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N PHE H 71 " --> pdb=" O CYS H 23 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASP H 70 " --> pdb=" O SER H 67 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER H 67 " --> pdb=" O ASP H 70 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'H' and resid 53 through 54 removed outlier: 6.527A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'H' and resid 114 through 118 removed outlier: 5.900A pdb=" N TYR H 173 " --> pdb=" O ASN H 138 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'H' and resid 153 through 155 removed outlier: 4.582A pdb=" N TRP H 148 " --> pdb=" O GLN H 155 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'J' and resid 3 through 6 removed outlier: 3.964A pdb=" N GLN J 3 " --> pdb=" O SER J 25 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.685A pdb=" N TYR J 94 " --> pdb=" O THR J 115 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY J 49 " --> pdb=" O TRP J 36 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.685A pdb=" N TYR J 94 " --> pdb=" O THR J 115 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N VAL J 110 " --> pdb=" O LYS J 98 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'J' and resid 128 through 132 removed outlier: 3.558A pdb=" N LYS J 151 " --> pdb=" O SER J 128 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER J 188 " --> pdb=" O CYS J 148 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'J' and resid 128 through 132 removed outlier: 3.558A pdb=" N LYS J 151 " --> pdb=" O SER J 128 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N LYS J 151 " --> pdb=" O LEU J 186 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N LEU J 186 " --> pdb=" O LYS J 151 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'J' and resid 158 through 162 removed outlier: 3.764A pdb=" N THR J 159 " --> pdb=" O ASN J 207 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN J 207 " --> pdb=" O THR J 159 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS J 217 " --> pdb=" O CYS J 204 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL J 215 " --> pdb=" O VAL J 206 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'K' and resid 5 through 7 removed outlier: 3.791A pdb=" N CYS K 23 " --> pdb=" O PHE K 71 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N PHE K 71 " --> pdb=" O CYS K 23 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASP K 70 " --> pdb=" O SER K 67 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER K 67 " --> pdb=" O ASP K 70 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'K' and resid 53 through 54 removed outlier: 6.541A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'K' and resid 114 through 118 removed outlier: 5.892A pdb=" N TYR K 173 " --> pdb=" O ASN K 138 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'K' and resid 153 through 155 removed outlier: 4.309A pdb=" N TRP K 148 " --> pdb=" O GLN K 155 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLN K 147 " --> pdb=" O GLU K 195 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU K 195 " --> pdb=" O GLN K 147 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA K 193 " --> pdb=" O LYS K 149 " (cutoff:3.500A) 1313 hydrogen bonds defined for protein. 3426 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: 18.00 Time building geometry restraints manager: 14.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 10928 1.35 - 1.47: 8827 1.47 - 1.59: 15013 1.59 - 1.72: 0 1.72 - 1.84: 183 Bond restraints: 34951 Sorted by residual: bond pdb=" C1 NAG S 1 " pdb=" O5 NAG S 1 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.65e+00 bond pdb=" C1 NAG T 2 " pdb=" O5 NAG T 2 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.55e+00 bond pdb=" C PRO A 986 " pdb=" N PRO A 987 " ideal model delta sigma weight residual 1.334 1.374 -0.040 2.34e-02 1.83e+03 2.93e+00 bond pdb=" C1 NAG A1403 " pdb=" O5 NAG A1403 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.73e+00 bond pdb=" C1 NAG C1203 " pdb=" O5 NAG C1203 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.53e+00 ... (remaining 34946 not shown) Histogram of bond angle deviations from ideal: 98.89 - 105.92: 802 105.92 - 112.96: 19032 112.96 - 119.99: 11359 119.99 - 127.03: 16007 127.03 - 134.06: 330 Bond angle restraints: 47530 Sorted by residual: angle pdb=" N ILE C 418 " pdb=" CA ILE C 418 " pdb=" C ILE C 418 " ideal model delta sigma weight residual 113.47 108.63 4.84 1.01e+00 9.80e-01 2.30e+01 angle pdb=" N ILE C 100 " pdb=" CA ILE C 100 " pdb=" C ILE C 100 " ideal model delta sigma weight residual 113.43 108.85 4.58 1.09e+00 8.42e-01 1.76e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 115.74 -5.04 1.22e+00 6.72e-01 1.71e+01 angle pdb=" C PHE A 86 " pdb=" N ASN A 87 " pdb=" CA ASN A 87 " ideal model delta sigma weight residual 121.54 129.36 -7.82 1.91e+00 2.74e-01 1.68e+01 angle pdb=" N GLU C 281 " pdb=" CA GLU C 281 " pdb=" C GLU C 281 " ideal model delta sigma weight residual 114.75 109.99 4.76 1.26e+00 6.30e-01 1.43e+01 ... (remaining 47525 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 19628 17.98 - 35.96: 1541 35.96 - 53.94: 285 53.94 - 71.92: 66 71.92 - 89.90: 63 Dihedral angle restraints: 21583 sinusoidal: 9051 harmonic: 12532 Sorted by residual: dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -0.65 -85.35 1 1.00e+01 1.00e-02 8.82e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -5.04 -80.96 1 1.00e+01 1.00e-02 8.09e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -8.49 -77.51 1 1.00e+01 1.00e-02 7.52e+01 ... (remaining 21580 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.136: 5534 0.136 - 0.272: 26 0.272 - 0.409: 0 0.409 - 0.545: 0 0.545 - 0.681: 1 Chirality restraints: 5561 Sorted by residual: chirality pdb=" C1 NAG L 1 " pdb=" ND2 ASN A1074 " pdb=" C2 NAG L 1 " pdb=" O5 NAG L 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.72 -0.68 2.00e-01 2.50e+01 1.16e+01 chirality pdb=" C1 NAG C1204 " pdb=" ND2 ASN C 282 " pdb=" C2 NAG C1204 " pdb=" O5 NAG C1204 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" C1 NAG T 1 " pdb=" ND2 ASN B1098 " pdb=" C2 NAG T 1 " pdb=" O5 NAG T 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 9.99e-01 ... (remaining 5558 not shown) Planarity restraints: 6108 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 985 " -0.029 5.00e-02 4.00e+02 4.31e-02 2.97e+00 pdb=" N PRO A 986 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 986 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 986 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU G 156 " 0.028 5.00e-02 4.00e+02 4.27e-02 2.91e+00 pdb=" N PRO G 157 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO G 157 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO G 157 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 983 " -0.127 9.50e-02 1.11e+02 5.72e-02 2.66e+00 pdb=" NE ARG B 983 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG B 983 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG B 983 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG B 983 " 0.000 2.00e-02 2.50e+03 ... (remaining 6105 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 2232 2.73 - 3.28: 33511 3.28 - 3.82: 54324 3.82 - 4.36: 63317 4.36 - 4.90: 111731 Nonbonded interactions: 265115 Sorted by model distance: nonbonded pdb=" OH TYR C 674 " pdb=" N GLN C 690 " model vdw 2.193 2.520 nonbonded pdb=" NH1 ARG D 50 " pdb=" OE2 GLU D 99 " model vdw 2.200 2.520 nonbonded pdb=" CZ TYR C 674 " pdb=" N GLN C 690 " model vdw 2.220 3.340 nonbonded pdb=" O THR A 676 " pdb=" OG SER A 691 " model vdw 2.226 2.440 nonbonded pdb=" NH1 ARG J 50 " pdb=" OE2 GLU J 99 " model vdw 2.252 2.520 ... (remaining 265110 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 27 through 620 or resid 641 through 939 or resid 944 throu \ gh 1146 or resid 1401 through 1405)) selection = (chain 'B' and (resid 27 through 620 or resid 641 through 826 or resid 855 throu \ gh 1146 or resid 1401 through 1405)) selection = (chain 'C' and (resid 27 through 826 or resid 855 through 1146 or resid 1201 thr \ ough 1205)) } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'J' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'K' } ncs_group { reference = chain 'F' selection = chain 'I' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 11.480 Check model and map are aligned: 0.540 Set scattering table: 0.330 Process input model: 92.370 Find NCS groups from input model: 2.600 Set up NCS constraints: 0.520 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 123.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 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 0.043 34951 Z= 0.214 Angle : 0.601 9.900 47530 Z= 0.312 Chirality : 0.045 0.681 5561 Planarity : 0.004 0.057 6072 Dihedral : 13.908 89.897 13376 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.78 % Favored : 93.20 % Rotamer: Outliers : 0.27 % Allowed : 0.29 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.13), residues: 4265 helix: 2.02 (0.21), residues: 674 sheet: -0.59 (0.15), residues: 1314 loop : -1.54 (0.13), residues: 2277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 64 HIS 0.002 0.000 HIS A 49 PHE 0.019 0.001 PHE C 906 TYR 0.023 0.001 TYR E 49 ARG 0.014 0.000 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 3748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 316 time to evaluate : 4.039 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.8691 (p90) cc_final: 0.8349 (p90) REVERT: A 340 GLU cc_start: 0.8295 (pt0) cc_final: 0.8086 (pp20) REVERT: A 773 GLU cc_start: 0.7878 (tt0) cc_final: 0.7658 (tt0) REVERT: B 269 TYR cc_start: 0.8579 (m-80) cc_final: 0.8317 (m-80) REVERT: B 651 ILE cc_start: 0.9275 (pt) cc_final: 0.9013 (pp) REVERT: B 776 LYS cc_start: 0.9079 (ttpt) cc_final: 0.8505 (ttpt) REVERT: B 780 GLU cc_start: 0.8374 (mt-10) cc_final: 0.7949 (mp0) REVERT: B 983 ARG cc_start: 0.8477 (mtm110) cc_final: 0.8270 (mtm110) REVERT: B 1002 GLN cc_start: 0.8930 (tp40) cc_final: 0.8638 (tm-30) REVERT: B 1092 GLU cc_start: 0.7622 (tm-30) cc_final: 0.7361 (pp20) REVERT: C 153 MET cc_start: 0.4122 (tpp) cc_final: 0.3600 (tpp) REVERT: C 780 GLU cc_start: 0.8378 (mt-10) cc_final: 0.8079 (mp0) REVERT: C 814 LYS cc_start: 0.7740 (OUTLIER) cc_final: 0.7513 (mmmt) REVERT: D 125 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8506 (tptp) REVERT: E 172 THR cc_start: 0.8626 (p) cc_final: 0.8282 (p) REVERT: E 210 ASN cc_start: 0.7705 (p0) cc_final: 0.7315 (p0) REVERT: H 210 ASN cc_start: 0.7779 (p0) cc_final: 0.7523 (p0) REVERT: K 210 ASN cc_start: 0.7932 (p0) cc_final: 0.7631 (p0) outliers start: 10 outliers final: 8 residues processed: 326 average time/residue: 1.2054 time to fit residues: 489.8636 Evaluate side-chains 248 residues out of total 3748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 238 time to evaluate : 3.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 979 ASP Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 125 LYS Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 121 SER Chi-restraints excluded: chain J residue 128 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 362 optimal weight: 6.9990 chunk 325 optimal weight: 2.9990 chunk 180 optimal weight: 6.9990 chunk 111 optimal weight: 0.9990 chunk 219 optimal weight: 2.9990 chunk 173 optimal weight: 4.9990 chunk 336 optimal weight: 4.9990 chunk 130 optimal weight: 0.0170 chunk 204 optimal weight: 0.6980 chunk 250 optimal weight: 0.9990 chunk 389 optimal weight: 0.9990 overall best weight: 0.7424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 343 ASN A1005 GLN C 343 ASN C 388 ASN C 658 ASN C1002 GLN C1005 GLN ** E 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 166 GLN H 138 ASN ** H 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.0976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 34951 Z= 0.171 Angle : 0.605 13.184 47530 Z= 0.302 Chirality : 0.045 0.450 5561 Planarity : 0.004 0.048 6072 Dihedral : 7.162 109.733 5777 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.71 % Favored : 93.27 % Rotamer: Outliers : 0.72 % Allowed : 7.52 % Favored : 91.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.13), residues: 4265 helix: 2.18 (0.21), residues: 678 sheet: -0.38 (0.15), residues: 1284 loop : -1.45 (0.13), residues: 2303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 104 HIS 0.002 0.001 HIS J 208 PHE 0.015 0.001 PHE A 86 TYR 0.022 0.001 TYR A1067 ARG 0.009 0.000 ARG K 18 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 3748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 287 time to evaluate : 3.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.8702 (p90) cc_final: 0.8373 (p90) REVERT: A 740 MET cc_start: 0.6887 (ttt) cc_final: 0.6144 (tmt) REVERT: A 983 ARG cc_start: 0.8794 (ttp80) cc_final: 0.8469 (tmm-80) REVERT: B 421 TYR cc_start: 0.7677 (OUTLIER) cc_final: 0.6369 (p90) REVERT: B 651 ILE cc_start: 0.8955 (pt) cc_final: 0.8662 (pp) REVERT: B 776 LYS cc_start: 0.9047 (ttpt) cc_final: 0.8509 (ttpt) REVERT: B 780 GLU cc_start: 0.8341 (mt-10) cc_final: 0.7997 (mp0) REVERT: B 1002 GLN cc_start: 0.8986 (tp40) cc_final: 0.8672 (tm-30) REVERT: C 88 ASP cc_start: 0.8950 (OUTLIER) cc_final: 0.8622 (p0) REVERT: C 135 PHE cc_start: 0.8215 (m-80) cc_final: 0.8011 (m-80) REVERT: C 153 MET cc_start: 0.4143 (tpp) cc_final: 0.3508 (tpp) REVERT: C 780 GLU cc_start: 0.8360 (mt-10) cc_final: 0.8159 (mp0) REVERT: C 1050 MET cc_start: 0.8667 (ptm) cc_final: 0.8320 (ptm) REVERT: E 134 CYS cc_start: 0.5994 (t) cc_final: 0.5426 (t) REVERT: E 172 THR cc_start: 0.8792 (p) cc_final: 0.8579 (p) REVERT: E 210 ASN cc_start: 0.7814 (p0) cc_final: 0.7305 (p0) REVERT: H 10 THR cc_start: 0.8218 (t) cc_final: 0.7295 (t) REVERT: H 122 ASP cc_start: 0.8617 (p0) cc_final: 0.8049 (p0) REVERT: H 210 ASN cc_start: 0.8145 (p0) cc_final: 0.7655 (p0) REVERT: J 188 SER cc_start: 0.8790 (t) cc_final: 0.8545 (t) REVERT: K 27 GLN cc_start: 0.7697 (mp10) cc_final: 0.7496 (mp-120) REVERT: K 210 ASN cc_start: 0.8182 (p0) cc_final: 0.7744 (p0) outliers start: 27 outliers final: 11 residues processed: 305 average time/residue: 1.2783 time to fit residues: 480.0021 Evaluate side-chains 247 residues out of total 3748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 234 time to evaluate : 4.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 207 ASN Chi-restraints excluded: chain J residue 118 THR Chi-restraints excluded: chain K residue 152 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 216 optimal weight: 0.0970 chunk 120 optimal weight: 0.8980 chunk 324 optimal weight: 6.9990 chunk 265 optimal weight: 4.9990 chunk 107 optimal weight: 20.0000 chunk 390 optimal weight: 5.9990 chunk 421 optimal weight: 2.9990 chunk 347 optimal weight: 4.9990 chunk 387 optimal weight: 0.7980 chunk 133 optimal weight: 4.9990 chunk 313 optimal weight: 4.9990 overall best weight: 1.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 ASN A 540 ASN ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN ** E 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 200 GLN ** H 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 34951 Z= 0.300 Angle : 0.612 10.280 47530 Z= 0.308 Chirality : 0.045 0.486 5561 Planarity : 0.004 0.053 6072 Dihedral : 6.478 57.443 5760 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.22 % Favored : 92.75 % Rotamer: Outliers : 1.28 % Allowed : 10.73 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.13), residues: 4265 helix: 2.15 (0.21), residues: 687 sheet: -0.38 (0.14), residues: 1326 loop : -1.49 (0.13), residues: 2252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 104 HIS 0.004 0.001 HIS D 208 PHE 0.015 0.001 PHE B 106 TYR 0.027 0.002 TYR E 49 ARG 0.010 0.001 ARG K 18 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 3748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 243 time to evaluate : 4.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 VAL cc_start: 0.9204 (t) cc_final: 0.8967 (m) REVERT: A 140 PHE cc_start: 0.8700 (p90) cc_final: 0.8354 (p90) REVERT: A 740 MET cc_start: 0.7086 (ttt) cc_final: 0.6113 (tmt) REVERT: A 983 ARG cc_start: 0.8804 (ttp80) cc_final: 0.8445 (ttp80) REVERT: B 92 PHE cc_start: 0.8244 (t80) cc_final: 0.7895 (t80) REVERT: B 100 ILE cc_start: 0.8310 (pt) cc_final: 0.7884 (mp) REVERT: B 153 MET cc_start: 0.6164 (pp-130) cc_final: 0.5937 (ppp) REVERT: B 421 TYR cc_start: 0.7959 (OUTLIER) cc_final: 0.6267 (p90) REVERT: B 651 ILE cc_start: 0.9030 (pt) cc_final: 0.8708 (pp) REVERT: B 776 LYS cc_start: 0.9064 (ttpt) cc_final: 0.8419 (ttpt) REVERT: B 780 GLU cc_start: 0.8409 (mt-10) cc_final: 0.8012 (mp0) REVERT: B 1002 GLN cc_start: 0.9010 (tp40) cc_final: 0.8711 (tm-30) REVERT: B 1092 GLU cc_start: 0.7999 (tp30) cc_final: 0.7636 (pp20) REVERT: C 88 ASP cc_start: 0.8943 (OUTLIER) cc_final: 0.8635 (p0) REVERT: C 153 MET cc_start: 0.4051 (tpp) cc_final: 0.3431 (tpp) REVERT: C 780 GLU cc_start: 0.8389 (mt-10) cc_final: 0.8165 (mp0) REVERT: E 134 CYS cc_start: 0.5969 (t) cc_final: 0.5510 (t) REVERT: E 210 ASN cc_start: 0.7912 (p0) cc_final: 0.7341 (p0) REVERT: G 48 MET cc_start: 0.7683 (mtt) cc_final: 0.7472 (mtt) REVERT: G 82 GLU cc_start: 0.7874 (tm-30) cc_final: 0.7578 (tm-30) REVERT: H 134 CYS cc_start: 0.5900 (t) cc_final: 0.5567 (t) REVERT: H 210 ASN cc_start: 0.8287 (p0) cc_final: 0.7752 (p0) REVERT: K 210 ASN cc_start: 0.8272 (p0) cc_final: 0.7838 (p0) outliers start: 48 outliers final: 21 residues processed: 281 average time/residue: 1.2053 time to fit residues: 424.7149 Evaluate side-chains 255 residues out of total 3748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 232 time to evaluate : 4.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 207 ASN Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain H residue 152 ASN Chi-restraints excluded: chain H residue 177 SER Chi-restraints excluded: chain J residue 118 THR Chi-restraints excluded: chain J residue 148 CYS Chi-restraints excluded: chain K residue 152 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 385 optimal weight: 3.9990 chunk 293 optimal weight: 1.9990 chunk 202 optimal weight: 9.9990 chunk 43 optimal weight: 0.7980 chunk 186 optimal weight: 0.7980 chunk 262 optimal weight: 0.6980 chunk 391 optimal weight: 0.6980 chunk 414 optimal weight: 0.9980 chunk 204 optimal weight: 8.9990 chunk 371 optimal weight: 8.9990 chunk 111 optimal weight: 7.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1005 GLN B 239 GLN C1002 GLN ** E 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 34951 Z= 0.163 Angle : 0.573 11.674 47530 Z= 0.284 Chirality : 0.044 0.453 5561 Planarity : 0.004 0.047 6072 Dihedral : 6.013 56.562 5759 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.26 % Favored : 93.72 % Rotamer: Outliers : 1.84 % Allowed : 12.09 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.13), residues: 4265 helix: 2.19 (0.21), residues: 699 sheet: -0.32 (0.14), residues: 1326 loop : -1.45 (0.13), residues: 2240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 104 HIS 0.002 0.000 HIS J 208 PHE 0.014 0.001 PHE A 135 TYR 0.028 0.001 TYR J 153 ARG 0.009 0.000 ARG K 18 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 3748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 265 time to evaluate : 4.365 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 120 VAL cc_start: 0.9201 (t) cc_final: 0.8977 (m) REVERT: A 140 PHE cc_start: 0.8710 (p90) cc_final: 0.8398 (p90) REVERT: A 740 MET cc_start: 0.6971 (ttt) cc_final: 0.6100 (tmt) REVERT: B 92 PHE cc_start: 0.8134 (t80) cc_final: 0.7772 (t80) REVERT: B 100 ILE cc_start: 0.8294 (pt) cc_final: 0.7867 (mp) REVERT: B 421 TYR cc_start: 0.7867 (OUTLIER) cc_final: 0.6208 (p90) REVERT: B 651 ILE cc_start: 0.8988 (pt) cc_final: 0.8671 (pp) REVERT: B 776 LYS cc_start: 0.9038 (ttpt) cc_final: 0.8500 (ttpt) REVERT: B 780 GLU cc_start: 0.8298 (mt-10) cc_final: 0.7976 (mp0) REVERT: B 866 THR cc_start: 0.8785 (OUTLIER) cc_final: 0.8209 (p) REVERT: B 902 MET cc_start: 0.9059 (mmm) cc_final: 0.8787 (tpp) REVERT: B 1002 GLN cc_start: 0.8976 (tp40) cc_final: 0.8660 (tm-30) REVERT: C 153 MET cc_start: 0.3985 (tpp) cc_final: 0.3416 (tpp) REVERT: C 1002 GLN cc_start: 0.8863 (OUTLIER) cc_final: 0.8398 (tm-30) REVERT: E 134 CYS cc_start: 0.5873 (t) cc_final: 0.5420 (t) REVERT: E 210 ASN cc_start: 0.7990 (p0) cc_final: 0.7409 (p0) REVERT: G 82 GLU cc_start: 0.7914 (tm-30) cc_final: 0.7623 (tm-30) REVERT: H 210 ASN cc_start: 0.8312 (p0) cc_final: 0.7732 (p0) REVERT: K 27 GLN cc_start: 0.7823 (mp10) cc_final: 0.7505 (mp-120) REVERT: K 210 ASN cc_start: 0.8287 (p0) cc_final: 0.7832 (p0) outliers start: 69 outliers final: 28 residues processed: 319 average time/residue: 1.1116 time to fit residues: 448.8274 Evaluate side-chains 262 residues out of total 3748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 231 time to evaluate : 3.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 207 ASN Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 32 TYR Chi-restraints excluded: chain J residue 108 MET Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain J residue 148 CYS Chi-restraints excluded: chain K residue 152 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 345 optimal weight: 7.9990 chunk 235 optimal weight: 0.7980 chunk 6 optimal weight: 5.9990 chunk 308 optimal weight: 4.9990 chunk 171 optimal weight: 9.9990 chunk 353 optimal weight: 2.9990 chunk 286 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 211 optimal weight: 8.9990 chunk 372 optimal weight: 4.9990 chunk 104 optimal weight: 20.0000 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 ASN B 239 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 GLN ** E 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.065 34951 Z= 0.537 Angle : 0.720 14.601 47530 Z= 0.363 Chirality : 0.048 0.503 5561 Planarity : 0.005 0.047 6072 Dihedral : 6.289 58.147 5759 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.82 % Favored : 91.16 % Rotamer: Outliers : 2.43 % Allowed : 14.09 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.13), residues: 4265 helix: 1.95 (0.20), residues: 696 sheet: -0.55 (0.14), residues: 1402 loop : -1.63 (0.13), residues: 2167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 104 HIS 0.007 0.001 HIS J 208 PHE 0.021 0.002 PHE B 906 TYR 0.029 0.002 TYR E 49 ARG 0.011 0.001 ARG K 18 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 3748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 235 time to evaluate : 3.920 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 120 VAL cc_start: 0.9312 (t) cc_final: 0.9085 (m) REVERT: A 140 PHE cc_start: 0.8713 (p90) cc_final: 0.8369 (p90) REVERT: A 740 MET cc_start: 0.7246 (ttt) cc_final: 0.6528 (tmt) REVERT: A 1002 GLN cc_start: 0.8900 (tm-30) cc_final: 0.8063 (tm-30) REVERT: B 92 PHE cc_start: 0.8193 (t80) cc_final: 0.7877 (t80) REVERT: B 133 PHE cc_start: 0.7407 (m-80) cc_final: 0.6647 (m-80) REVERT: B 231 ILE cc_start: 0.9193 (OUTLIER) cc_final: 0.8910 (mm) REVERT: B 240 THR cc_start: 0.8446 (OUTLIER) cc_final: 0.8149 (t) REVERT: B 651 ILE cc_start: 0.9103 (pt) cc_final: 0.8787 (pp) REVERT: B 776 LYS cc_start: 0.9103 (ttpt) cc_final: 0.8383 (ttpt) REVERT: B 780 GLU cc_start: 0.8460 (mt-10) cc_final: 0.8016 (mp0) REVERT: B 866 THR cc_start: 0.8896 (OUTLIER) cc_final: 0.8322 (p) REVERT: B 1002 GLN cc_start: 0.9056 (tp40) cc_final: 0.8668 (tm-30) REVERT: C 153 MET cc_start: 0.3872 (tpp) cc_final: 0.3473 (tpp) REVERT: C 191 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.7986 (mp0) REVERT: C 780 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7751 (mp0) REVERT: C 856 ASN cc_start: 0.8562 (OUTLIER) cc_final: 0.8254 (p0) REVERT: C 1002 GLN cc_start: 0.9036 (OUTLIER) cc_final: 0.8770 (tm-30) REVERT: D 203 ILE cc_start: 0.9461 (mp) cc_final: 0.9103 (mm) REVERT: E 134 CYS cc_start: 0.6129 (t) cc_final: 0.5713 (t) REVERT: E 210 ASN cc_start: 0.8118 (p0) cc_final: 0.7450 (p0) REVERT: G 82 GLU cc_start: 0.7973 (tm-30) cc_final: 0.7681 (tm-30) REVERT: H 210 ASN cc_start: 0.8479 (p0) cc_final: 0.7856 (p0) REVERT: K 210 ASN cc_start: 0.8329 (p0) cc_final: 0.7813 (p0) outliers start: 91 outliers final: 48 residues processed: 312 average time/residue: 1.0811 time to fit residues: 428.8123 Evaluate side-chains 280 residues out of total 3748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 225 time to evaluate : 4.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 988 GLU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 152 ASN Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain H residue 152 ASN Chi-restraints excluded: chain H residue 177 SER Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 108 MET Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain K residue 63 ILE Chi-restraints excluded: chain K residue 82 ASP Chi-restraints excluded: chain K residue 152 ASN Chi-restraints excluded: chain K residue 177 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 139 optimal weight: 2.9990 chunk 373 optimal weight: 0.8980 chunk 81 optimal weight: 5.9990 chunk 243 optimal weight: 0.9990 chunk 102 optimal weight: 5.9990 chunk 415 optimal weight: 0.9990 chunk 344 optimal weight: 6.9990 chunk 192 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 137 optimal weight: 0.9990 chunk 217 optimal weight: 5.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN C 115 GLN ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 34951 Z= 0.220 Angle : 0.621 15.720 47530 Z= 0.307 Chirality : 0.046 0.655 5561 Planarity : 0.004 0.047 6072 Dihedral : 5.945 56.575 5759 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 2.05 % Allowed : 15.10 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.13), residues: 4265 helix: 2.13 (0.21), residues: 696 sheet: -0.42 (0.14), residues: 1373 loop : -1.56 (0.13), residues: 2196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 104 HIS 0.003 0.000 HIS J 208 PHE 0.014 0.001 PHE B 65 TYR 0.025 0.001 TYR E 49 ARG 0.011 0.000 ARG K 18 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 3748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 243 time to evaluate : 3.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 VAL cc_start: 0.9295 (t) cc_final: 0.9078 (m) REVERT: A 140 PHE cc_start: 0.8716 (p90) cc_final: 0.8381 (p90) REVERT: A 740 MET cc_start: 0.7175 (ttt) cc_final: 0.6461 (tmt) REVERT: A 1002 GLN cc_start: 0.8859 (tm-30) cc_final: 0.8117 (tm-30) REVERT: A 1005 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.8530 (mt0) REVERT: B 92 PHE cc_start: 0.8157 (t80) cc_final: 0.7886 (t80) REVERT: B 133 PHE cc_start: 0.7320 (m-80) cc_final: 0.6540 (m-80) REVERT: B 153 MET cc_start: 0.5742 (pp-130) cc_final: 0.5484 (ppp) REVERT: B 421 TYR cc_start: 0.7923 (OUTLIER) cc_final: 0.6031 (p90) REVERT: B 651 ILE cc_start: 0.9014 (pt) cc_final: 0.8740 (pp) REVERT: B 776 LYS cc_start: 0.9026 (ttpt) cc_final: 0.8358 (ttpt) REVERT: B 780 GLU cc_start: 0.8422 (mt-10) cc_final: 0.8068 (mp0) REVERT: B 866 THR cc_start: 0.8886 (OUTLIER) cc_final: 0.8311 (p) REVERT: B 1002 GLN cc_start: 0.9003 (tp40) cc_final: 0.8668 (tm-30) REVERT: C 153 MET cc_start: 0.3821 (tpp) cc_final: 0.3460 (tpp) REVERT: C 191 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8009 (mp0) REVERT: C 269 TYR cc_start: 0.8772 (m-80) cc_final: 0.8562 (m-80) REVERT: C 780 GLU cc_start: 0.8194 (mp0) cc_final: 0.7755 (mp0) REVERT: C 1002 GLN cc_start: 0.8963 (tp40) cc_final: 0.8492 (tm-30) REVERT: D 203 ILE cc_start: 0.9472 (mp) cc_final: 0.9254 (mm) REVERT: D 216 ASP cc_start: 0.7935 (t0) cc_final: 0.7638 (t0) REVERT: E 134 CYS cc_start: 0.5993 (t) cc_final: 0.5545 (t) REVERT: E 210 ASN cc_start: 0.8083 (p0) cc_final: 0.7448 (p0) REVERT: G 82 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7562 (tm-30) REVERT: H 210 ASN cc_start: 0.8435 (p0) cc_final: 0.7802 (p0) REVERT: K 210 ASN cc_start: 0.8338 (p0) cc_final: 0.7499 (p0) outliers start: 77 outliers final: 48 residues processed: 309 average time/residue: 1.1154 time to fit residues: 436.3693 Evaluate side-chains 278 residues out of total 3748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 226 time to evaluate : 3.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 207 ASN Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 32 TYR Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 108 MET Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 148 CYS Chi-restraints excluded: chain J residue 207 ASN Chi-restraints excluded: chain K residue 152 ASN Chi-restraints excluded: chain K residue 177 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 400 optimal weight: 9.9990 chunk 46 optimal weight: 0.9980 chunk 236 optimal weight: 4.9990 chunk 303 optimal weight: 0.6980 chunk 234 optimal weight: 4.9990 chunk 349 optimal weight: 7.9990 chunk 231 optimal weight: 3.9990 chunk 413 optimal weight: 0.4980 chunk 258 optimal weight: 7.9990 chunk 252 optimal weight: 0.3980 chunk 190 optimal weight: 0.0980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 ASN ** H 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 34951 Z= 0.158 Angle : 0.605 14.669 47530 Z= 0.297 Chirality : 0.045 0.532 5561 Planarity : 0.004 0.045 6072 Dihedral : 5.697 56.277 5759 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 1.87 % Allowed : 15.88 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.13), residues: 4265 helix: 2.20 (0.21), residues: 700 sheet: -0.27 (0.14), residues: 1319 loop : -1.46 (0.13), residues: 2246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 104 HIS 0.002 0.000 HIS A 49 PHE 0.012 0.001 PHE A 86 TYR 0.044 0.001 TYR G 32 ARG 0.014 0.000 ARG K 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 3748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 251 time to evaluate : 3.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.8695 (p90) cc_final: 0.8397 (p90) REVERT: A 740 MET cc_start: 0.7127 (ttt) cc_final: 0.6293 (tmt) REVERT: A 902 MET cc_start: 0.8895 (tpp) cc_final: 0.8691 (mmt) REVERT: A 1005 GLN cc_start: 0.8907 (OUTLIER) cc_final: 0.8525 (mt0) REVERT: B 92 PHE cc_start: 0.8166 (t80) cc_final: 0.7840 (t80) REVERT: B 100 ILE cc_start: 0.8369 (pt) cc_final: 0.7905 (mp) REVERT: B 131 CYS cc_start: 0.4545 (OUTLIER) cc_final: 0.2111 (p) REVERT: B 133 PHE cc_start: 0.7429 (m-80) cc_final: 0.6533 (m-80) REVERT: B 153 MET cc_start: 0.5853 (pp-130) cc_final: 0.5630 (ppp) REVERT: B 421 TYR cc_start: 0.7932 (OUTLIER) cc_final: 0.5898 (p90) REVERT: B 776 LYS cc_start: 0.9024 (ttpt) cc_final: 0.8393 (ttpt) REVERT: B 780 GLU cc_start: 0.8355 (mt-10) cc_final: 0.8029 (mp0) REVERT: B 866 THR cc_start: 0.8862 (OUTLIER) cc_final: 0.8284 (p) REVERT: B 1002 GLN cc_start: 0.8981 (tp40) cc_final: 0.8649 (tm-30) REVERT: C 153 MET cc_start: 0.3559 (tpp) cc_final: 0.3135 (tpp) REVERT: C 269 TYR cc_start: 0.8699 (m-80) cc_final: 0.8295 (m-80) REVERT: C 780 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7950 (mt-10) REVERT: C 1002 GLN cc_start: 0.8941 (tp40) cc_final: 0.8456 (tm-30) REVERT: D 203 ILE cc_start: 0.9470 (mp) cc_final: 0.9257 (mm) REVERT: D 216 ASP cc_start: 0.7901 (t0) cc_final: 0.7647 (t0) REVERT: E 134 CYS cc_start: 0.5841 (t) cc_final: 0.5430 (t) REVERT: E 210 ASN cc_start: 0.8095 (p0) cc_final: 0.7451 (p0) REVERT: G 82 GLU cc_start: 0.7894 (tm-30) cc_final: 0.7585 (tm-30) REVERT: H 210 ASN cc_start: 0.8418 (p0) cc_final: 0.7779 (p0) REVERT: K 82 ASP cc_start: 0.7743 (m-30) cc_final: 0.7535 (m-30) outliers start: 70 outliers final: 41 residues processed: 310 average time/residue: 1.0538 time to fit residues: 417.9817 Evaluate side-chains 278 residues out of total 3748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 232 time to evaluate : 3.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain H residue 63 ILE Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 32 TYR Chi-restraints excluded: chain J residue 108 MET Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 148 CYS Chi-restraints excluded: chain K residue 152 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 255 optimal weight: 10.0000 chunk 165 optimal weight: 0.9980 chunk 246 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 81 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 chunk 262 optimal weight: 3.9990 chunk 281 optimal weight: 3.9990 chunk 204 optimal weight: 0.1980 chunk 38 optimal weight: 4.9990 chunk 325 optimal weight: 2.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 ASN C 360 ASN ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 34951 Z= 0.308 Angle : 0.643 16.232 47530 Z= 0.318 Chirality : 0.046 0.571 5561 Planarity : 0.004 0.061 6072 Dihedral : 5.794 56.954 5759 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 1.97 % Allowed : 16.36 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.13), residues: 4265 helix: 2.16 (0.21), residues: 696 sheet: -0.37 (0.14), residues: 1381 loop : -1.51 (0.13), residues: 2188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 104 HIS 0.003 0.001 HIS J 208 PHE 0.015 0.001 PHE A 86 TYR 0.041 0.002 TYR J 32 ARG 0.012 0.001 ARG E 24 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 3748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 240 time to evaluate : 3.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.8722 (p90) cc_final: 0.8424 (p90) REVERT: A 740 MET cc_start: 0.7198 (ttt) cc_final: 0.6370 (tmt) REVERT: A 1002 GLN cc_start: 0.8776 (tm-30) cc_final: 0.8127 (tm-30) REVERT: A 1005 GLN cc_start: 0.8939 (OUTLIER) cc_final: 0.8567 (mt0) REVERT: B 92 PHE cc_start: 0.8204 (t80) cc_final: 0.7860 (t80) REVERT: B 131 CYS cc_start: 0.4770 (OUTLIER) cc_final: 0.3361 (p) REVERT: B 133 PHE cc_start: 0.7396 (m-80) cc_final: 0.6539 (m-80) REVERT: B 153 MET cc_start: 0.6045 (pp-130) cc_final: 0.5793 (ppp) REVERT: B 421 TYR cc_start: 0.7953 (OUTLIER) cc_final: 0.6045 (p90) REVERT: B 776 LYS cc_start: 0.9030 (ttpt) cc_final: 0.8379 (ttpt) REVERT: B 780 GLU cc_start: 0.8414 (mt-10) cc_final: 0.8016 (mp0) REVERT: B 866 THR cc_start: 0.8883 (OUTLIER) cc_final: 0.8299 (p) REVERT: B 1002 GLN cc_start: 0.9010 (tp40) cc_final: 0.8663 (tm-30) REVERT: C 191 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.7943 (mp0) REVERT: C 269 TYR cc_start: 0.8719 (m-80) cc_final: 0.8363 (m-80) REVERT: C 780 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7765 (mp0) REVERT: C 1002 GLN cc_start: 0.8962 (tp40) cc_final: 0.8478 (tm-30) REVERT: E 134 CYS cc_start: 0.5946 (t) cc_final: 0.5533 (t) REVERT: E 210 ASN cc_start: 0.8156 (p0) cc_final: 0.7492 (p0) REVERT: G 81 MET cc_start: 0.8368 (tpp) cc_final: 0.7997 (tpp) REVERT: G 82 GLU cc_start: 0.7908 (tm-30) cc_final: 0.7598 (tm-30) REVERT: H 79 GLU cc_start: 0.8283 (mp0) cc_final: 0.7977 (mp0) REVERT: H 210 ASN cc_start: 0.8455 (p0) cc_final: 0.7328 (p0) REVERT: K 172 THR cc_start: 0.9064 (p) cc_final: 0.8812 (p) outliers start: 74 outliers final: 48 residues processed: 302 average time/residue: 1.2257 time to fit residues: 471.5277 Evaluate side-chains 279 residues out of total 3748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 225 time to evaluate : 3.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 108 MET Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 148 CYS Chi-restraints excluded: chain K residue 152 ASN Chi-restraints excluded: chain K residue 177 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 376 optimal weight: 3.9990 chunk 396 optimal weight: 0.0570 chunk 361 optimal weight: 3.9990 chunk 385 optimal weight: 0.3980 chunk 231 optimal weight: 4.9990 chunk 167 optimal weight: 0.0970 chunk 302 optimal weight: 1.9990 chunk 118 optimal weight: 8.9990 chunk 348 optimal weight: 0.9990 chunk 364 optimal weight: 0.7980 chunk 383 optimal weight: 7.9990 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 ASN K 90 GLN ** K 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 34951 Z= 0.156 Angle : 0.620 16.748 47530 Z= 0.303 Chirality : 0.045 0.508 5561 Planarity : 0.004 0.054 6072 Dihedral : 5.562 56.119 5759 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 1.60 % Allowed : 17.02 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.13), residues: 4265 helix: 2.12 (0.21), residues: 705 sheet: -0.20 (0.14), residues: 1328 loop : -1.41 (0.13), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP C 104 HIS 0.002 0.000 HIS B 49 PHE 0.013 0.001 PHE B 106 TYR 0.021 0.001 TYR H 49 ARG 0.012 0.000 ARG E 24 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 3748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 249 time to evaluate : 3.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.8668 (p90) cc_final: 0.8379 (p90) REVERT: A 740 MET cc_start: 0.7129 (ttt) cc_final: 0.6231 (tmt) REVERT: A 902 MET cc_start: 0.8870 (tpp) cc_final: 0.8670 (mmt) REVERT: A 1002 GLN cc_start: 0.8765 (tm-30) cc_final: 0.8126 (tm-30) REVERT: A 1005 GLN cc_start: 0.8894 (OUTLIER) cc_final: 0.8483 (mt0) REVERT: B 66 HIS cc_start: 0.3188 (OUTLIER) cc_final: 0.2221 (p90) REVERT: B 92 PHE cc_start: 0.8220 (t80) cc_final: 0.7909 (t80) REVERT: B 100 ILE cc_start: 0.8475 (pt) cc_final: 0.8063 (mp) REVERT: B 131 CYS cc_start: 0.4640 (OUTLIER) cc_final: 0.2069 (p) REVERT: B 133 PHE cc_start: 0.7451 (m-80) cc_final: 0.6605 (m-80) REVERT: B 421 TYR cc_start: 0.7916 (OUTLIER) cc_final: 0.5930 (p90) REVERT: B 776 LYS cc_start: 0.9015 (ttpt) cc_final: 0.8489 (ttpt) REVERT: B 780 GLU cc_start: 0.8297 (mt-10) cc_final: 0.7866 (mp0) REVERT: B 866 THR cc_start: 0.8868 (OUTLIER) cc_final: 0.8292 (p) REVERT: B 1002 GLN cc_start: 0.8953 (tp40) cc_final: 0.8622 (tm-30) REVERT: B 1092 GLU cc_start: 0.7870 (tp30) cc_final: 0.7585 (pp20) REVERT: C 191 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.8023 (mp0) REVERT: C 269 TYR cc_start: 0.8693 (m-80) cc_final: 0.8218 (m-80) REVERT: C 780 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7772 (mp0) REVERT: C 1002 GLN cc_start: 0.8924 (tp40) cc_final: 0.8436 (tm-30) REVERT: E 134 CYS cc_start: 0.5788 (t) cc_final: 0.5378 (t) REVERT: E 210 ASN cc_start: 0.8106 (p0) cc_final: 0.7458 (p0) REVERT: G 82 GLU cc_start: 0.7898 (tm-30) cc_final: 0.7675 (tm-30) REVERT: H 82 ASP cc_start: 0.8099 (m-30) cc_final: 0.7823 (m-30) REVERT: H 122 ASP cc_start: 0.8370 (p0) cc_final: 0.7588 (p0) REVERT: H 210 ASN cc_start: 0.8231 (p0) cc_final: 0.7833 (p0) REVERT: J 203 ILE cc_start: 0.9544 (mp) cc_final: 0.9319 (mp) REVERT: K 82 ASP cc_start: 0.7740 (m-30) cc_final: 0.7528 (m-30) outliers start: 60 outliers final: 48 residues processed: 300 average time/residue: 1.1085 time to fit residues: 419.0790 Evaluate side-chains 291 residues out of total 3748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 236 time to evaluate : 4.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain D residue 32 TYR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 63 ILE Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 108 MET Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 148 CYS Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 152 ASN Chi-restraints excluded: chain K residue 177 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 253 optimal weight: 1.9990 chunk 407 optimal weight: 3.9990 chunk 248 optimal weight: 5.9990 chunk 193 optimal weight: 7.9990 chunk 283 optimal weight: 9.9990 chunk 427 optimal weight: 10.0000 chunk 393 optimal weight: 5.9990 chunk 340 optimal weight: 6.9990 chunk 35 optimal weight: 0.9990 chunk 262 optimal weight: 0.9990 chunk 208 optimal weight: 8.9990 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 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 ASN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 34951 Z= 0.401 Angle : 0.687 16.344 47530 Z= 0.342 Chirality : 0.047 0.556 5561 Planarity : 0.004 0.072 6072 Dihedral : 5.795 57.207 5759 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 1.76 % Allowed : 17.13 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.13), residues: 4265 helix: 2.08 (0.21), residues: 695 sheet: -0.40 (0.14), residues: 1395 loop : -1.49 (0.13), residues: 2175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 104 HIS 0.004 0.001 HIS J 208 PHE 0.020 0.001 PHE J 103 TYR 0.030 0.002 TYR D 32 ARG 0.012 0.001 ARG E 24 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8530 Ramachandran restraints generated. 4265 Oldfield, 0 Emsley, 4265 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 3748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 231 time to evaluate : 4.473 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.8717 (p90) cc_final: 0.8437 (p90) REVERT: A 740 MET cc_start: 0.7250 (ttt) cc_final: 0.6356 (tmt) REVERT: A 1002 GLN cc_start: 0.8819 (tm-30) cc_final: 0.8138 (tm-30) REVERT: A 1005 GLN cc_start: 0.8942 (OUTLIER) cc_final: 0.8550 (mt0) REVERT: B 66 HIS cc_start: 0.3096 (OUTLIER) cc_final: 0.2128 (p90) REVERT: B 92 PHE cc_start: 0.8292 (t80) cc_final: 0.7999 (t80) REVERT: B 131 CYS cc_start: 0.5047 (OUTLIER) cc_final: 0.3930 (p) REVERT: B 133 PHE cc_start: 0.7494 (m-80) cc_final: 0.6680 (m-80) REVERT: B 421 TYR cc_start: 0.8046 (OUTLIER) cc_final: 0.6047 (p90) REVERT: B 776 LYS cc_start: 0.9044 (ttpt) cc_final: 0.8360 (ttpt) REVERT: B 780 GLU cc_start: 0.8430 (mt-10) cc_final: 0.8004 (mp0) REVERT: B 866 THR cc_start: 0.8899 (OUTLIER) cc_final: 0.8316 (p) REVERT: B 1002 GLN cc_start: 0.9022 (tp40) cc_final: 0.8660 (tm-30) REVERT: C 191 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.7983 (mp0) REVERT: C 269 TYR cc_start: 0.8693 (m-80) cc_final: 0.8297 (m-80) REVERT: C 780 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7787 (mp0) REVERT: C 1002 GLN cc_start: 0.8984 (tp40) cc_final: 0.8480 (tm-30) REVERT: D 216 ASP cc_start: 0.8001 (t0) cc_final: 0.7682 (t0) REVERT: E 134 CYS cc_start: 0.5985 (t) cc_final: 0.5597 (t) REVERT: E 210 ASN cc_start: 0.8108 (p0) cc_final: 0.7428 (p0) REVERT: G 82 GLU cc_start: 0.7898 (tm-30) cc_final: 0.7605 (tm-30) REVERT: G 184 TYR cc_start: 0.7960 (m-10) cc_final: 0.7685 (m-10) REVERT: H 210 ASN cc_start: 0.8219 (p0) cc_final: 0.7826 (p0) REVERT: J 203 ILE cc_start: 0.9579 (mp) cc_final: 0.9286 (mp) REVERT: J 216 ASP cc_start: 0.8377 (t0) cc_final: 0.8163 (t0) outliers start: 66 outliers final: 51 residues processed: 286 average time/residue: 1.0920 time to fit residues: 399.1407 Evaluate side-chains 286 residues out of total 3748 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 228 time to evaluate : 3.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain D residue 32 TYR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain E residue 177 SER Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 63 ILE Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 104 LEU Chi-restraints excluded: chain J residue 108 MET Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 148 CYS Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain K residue 152 ASN Chi-restraints excluded: chain K residue 177 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 270 optimal weight: 0.8980 chunk 362 optimal weight: 4.9990 chunk 104 optimal weight: 6.9990 chunk 313 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 340 optimal weight: 5.9990 chunk 142 optimal weight: 0.0010 chunk 350 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 360 ASN G 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.094231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.071777 restraints weight = 98805.323| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 3.91 r_work: 0.3126 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 34951 Z= 0.173 Angle : 0.634 16.545 47530 Z= 0.310 Chirality : 0.045 0.506 5561 Planarity : 0.004 0.056 6072 Dihedral : 5.590 55.882 5759 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 1.71 % Allowed : 17.16 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.13), residues: 4265 helix: 2.06 (0.21), residues: 704 sheet: -0.22 (0.14), residues: 1326 loop : -1.40 (0.13), residues: 2235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP C 104 HIS 0.002 0.000 HIS A 49 PHE 0.018 0.001 PHE J 103 TYR 0.026 0.001 TYR H 49 ARG 0.013 0.001 ARG E 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10016.60 seconds wall clock time: 180 minutes 51.81 seconds (10851.81 seconds total)