Starting phenix.real_space_refine on Thu Mar 21 09:25:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ws9_32751/03_2024/7ws9_32751.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ws9_32751/03_2024/7ws9_32751.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ws9_32751/03_2024/7ws9_32751.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ws9_32751/03_2024/7ws9_32751.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ws9_32751/03_2024/7ws9_32751.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ws9_32751/03_2024/7ws9_32751.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.052 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 140 5.16 5 C 18989 2.51 5 N 4887 2.21 5 O 5694 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A GLU 780": "OE1" <-> "OE2" Residue "A GLU 918": "OE1" <-> "OE2" Residue "B TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B GLU 309": "OE1" <-> "OE2" Residue "B GLU 702": "OE1" <-> "OE2" Residue "B GLU 1017": "OE1" <-> "OE2" Residue "B GLU 1092": "OE1" <-> "OE2" Residue "B GLU 1111": "OE1" <-> "OE2" Residue "C PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 661": "OE1" <-> "OE2" Residue "C GLU 702": "OE1" <-> "OE2" Residue "C GLU 773": "OE1" <-> "OE2" Residue "C GLU 780": "OE1" <-> "OE2" Residue "C GLU 868": "OE1" <-> "OE2" Residue "C GLU 988": "OE1" <-> "OE2" Residue "D GLU 227": "OE1" <-> "OE2" Residue "D GLU 231": "OE1" <-> "OE2" Residue "D PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 29710 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 8101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8101 Classifications: {'peptide': 1032} Link IDs: {'PTRANS': 57, 'TRANS': 974} Chain breaks: 8 Chain: "B" Number of atoms: 8096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8096 Classifications: {'peptide': 1032} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 57, 'TRANS': 974} Chain breaks: 8 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 8096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8096 Classifications: {'peptide': 1032} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 57, 'TRANS': 974} Chain breaks: 8 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 4857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4857 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 27, 'TRANS': 567} 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: "E" 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: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "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: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" 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: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" 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 Time building chain proxies: 15.34, per 1000 atoms: 0.52 Number of scatterers: 29710 At special positions: 0 Unit cell: (134.784, 143.936, 243.776, 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 140 16.00 O 5694 8.00 N 4887 7.00 C 18989 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " 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 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 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 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 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=2.04 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 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 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-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 709 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 709 " " NAG C1301 " - " ASN C 709 " " NAG D 701 " - " ASN D 53 " " NAG D 702 " - " ASN D 90 " " NAG D 703 " - " ASN D 103 " " NAG D 704 " - " ASN D 322 " " NAG D 705 " - " ASN D 432 " " NAG D 706 " - " ASN D 546 " " NAG E 1 " - " ASN B 801 " " NAG F 1 " - " ASN B1074 " " NAG G 1 " - " ASN B1098 " " NAG H 1 " - " ASN B1134 " " NAG I 1 " - " ASN C 717 " " NAG J 1 " - " ASN C 801 " " NAG K 1 " - " ASN C1074 " " NAG L 1 " - " ASN C1098 " " NAG M 1 " - " ASN C1134 " " NAG N 1 " - " ASN A 717 " " NAG O 1 " - " ASN B 717 " " NAG P 1 " - " ASN A 801 " " NAG Q 1 " - " ASN A1098 " " NAG R 1 " - " ASN A1134 " Time building additional restraints: 11.81 Conformation dependent library (CDL) restraints added in 5.3 seconds 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6946 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 49 sheets defined 32.2% alpha, 25.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.76 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: 3.768A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 389 removed outlier: 3.605A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.054A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.590A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.057A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 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 984 removed outlier: 3.648A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.321A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.462A 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 365 through 370 Processing helix chain 'B' and resid 384 through 388 removed outlier: 3.977A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 384 through 388' Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.623A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.520A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.038A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.005A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.123A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 removed outlier: 3.529A pdb=" N LEU B1145 " --> pdb=" O LEU B1141 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 384 through 389 removed outlier: 3.638A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.699A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 506 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.772A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.531A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.515A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.030A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN C 919 " --> pdb=" O VAL C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.544A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (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 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.282A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 removed outlier: 3.519A pdb=" N LEU C1145 " --> pdb=" O LEU C1141 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 53 removed outlier: 3.503A pdb=" N HIS D 34 " --> pdb=" O ASP D 30 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 81 Processing helix chain 'D' and resid 90 through 101 removed outlier: 3.725A pdb=" N LYS D 94 " --> pdb=" O ASN D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 149 through 154 removed outlier: 3.544A pdb=" N ALA D 153 " --> pdb=" O ASN D 149 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN D 154 " --> pdb=" O GLU D 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 149 through 154' Processing helix chain 'D' and resid 157 through 194 removed outlier: 3.625A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) Proline residue: D 178 - end of helix removed outlier: 3.566A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 221 through 252 removed outlier: 4.380A pdb=" N GLU D 232 " --> pdb=" O HIS D 228 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE D 233 " --> pdb=" O THR D 229 " (cutoff:3.500A) Proline residue: D 235 - end of helix removed outlier: 3.645A pdb=" N HIS D 239 " --> pdb=" O PRO D 235 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASN D 250 " --> pdb=" O ALA D 246 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA D 251 " --> pdb=" O LYS D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 275 through 279 Processing helix chain 'D' and resid 293 through 300 removed outlier: 3.884A pdb=" N MET D 297 " --> pdb=" O VAL D 293 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL D 298 " --> pdb=" O THR D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 319 Processing helix chain 'D' and resid 325 through 331 removed outlier: 3.768A pdb=" N GLU D 329 " --> pdb=" O GLN D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.522A pdb=" N HIS D 378 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA D 384 " --> pdb=" O GLN D 380 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 413 removed outlier: 4.408A pdb=" N HIS D 401 " --> pdb=" O ASN D 397 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N GLU D 402 " --> pdb=" O GLU D 398 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 Processing helix chain 'D' and resid 432 through 447 removed outlier: 3.969A pdb=" N ASN D 437 " --> pdb=" O GLU D 433 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE D 438 " --> pdb=" O THR D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 466 removed outlier: 4.348A pdb=" N PHE D 452 " --> pdb=" O GLY D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 484 Processing helix chain 'D' and resid 499 through 503 Processing helix chain 'D' and resid 505 through 509 Processing helix chain 'D' and resid 512 through 533 removed outlier: 4.181A pdb=" N TYR D 516 " --> pdb=" O PHE D 512 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA D 528 " --> pdb=" O GLN D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 547 through 561 removed outlier: 3.519A pdb=" N GLY D 551 " --> pdb=" O SER D 547 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU D 560 " --> pdb=" O ASN D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 574 removed outlier: 3.769A pdb=" N VAL D 573 " --> pdb=" O ALA D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 588 removed outlier: 3.691A pdb=" N LEU D 585 " --> pdb=" O VAL D 581 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR D 587 " --> pdb=" O PRO D 583 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE D 588 " --> pdb=" O LEU D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 599 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.787A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA A 264 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE A 197 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.006A 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: 3.635A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 11.561A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 10.179A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.434A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.704A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.387A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 10.228A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 313 Processing sheet with id=AA5, first strand: chain 'A' and resid 317 through 319 Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 328 removed outlier: 3.998A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.570A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY A 431 " --> pdb=" O TYR A 380 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR A 380 " --> pdb=" O GLY A 431 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.863A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.504A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 553 through 554 removed outlier: 3.574A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.897A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.944A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.801A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.801A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.905A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.902A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.579A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 10.003A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 9.146A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 9.966A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 9.394A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.337A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.558A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.620A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY B 431 " --> pdb=" O TYR B 380 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.116A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.984A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.487A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 701 through 704 removed outlier: 3.594A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.678A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.678A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.405A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD6, first strand: chain 'C' and resid 27 through 30 removed outlier: 7.969A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA C 264 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LYS C 202 " --> pdb=" O LYS C 195 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.156A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.687A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU C 118 " --> pdb=" O LYS C 129 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS C 129 " --> pdb=" O LEU C 118 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL C 120 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL C 127 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 133 through 142 removed outlier: 8.086A pdb=" N CYS C 136 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 10.060A pdb=" N SER C 162 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 9.988A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG C 158 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU C 156 " --> pdb=" O ASP C 142 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 316 removed outlier: 5.216A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 324 through 325 removed outlier: 6.991A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.655A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.578A pdb=" N GLY C 431 " --> pdb=" O TYR C 380 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N TYR C 380 " --> pdb=" O GLY C 431 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.518A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'C' and resid 448 through 454 removed outlier: 6.367A pdb=" N TYR C 449 " --> pdb=" O PHE C 497 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N PHE C 497 " --> pdb=" O TYR C 449 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N TYR C 451 " --> pdb=" O TYR C 495 " (cutoff:3.500A) 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 654 through 655 removed outlier: 5.918A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.680A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.680A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.095A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF3, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.708A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'D' and resid 347 through 352 removed outlier: 3.761A pdb=" N THR D 347 " --> pdb=" O LEU D 359 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) 1280 hydrogen bonds defined for protein. 3585 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 14.81 Time building geometry restraints manager: 12.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5099 1.32 - 1.45: 8403 1.45 - 1.58: 16727 1.58 - 1.70: 1 1.70 - 1.83: 188 Bond restraints: 30418 Sorted by residual: bond pdb=" N VAL A 595 " pdb=" CA VAL A 595 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.14e-02 7.69e+03 1.08e+01 bond pdb=" CA SER C 591 " pdb=" CB SER C 591 " ideal model delta sigma weight residual 1.530 1.480 0.051 1.62e-02 3.81e+03 9.85e+00 bond pdb=" N VAL B 367 " pdb=" CA VAL B 367 " ideal model delta sigma weight residual 1.462 1.494 -0.032 1.06e-02 8.90e+03 9.17e+00 bond pdb=" C PRO C 589 " pdb=" O PRO C 589 " ideal model delta sigma weight residual 1.233 1.198 0.035 1.21e-02 6.83e+03 8.27e+00 bond pdb=" CG1 ILE C 742 " pdb=" CD1 ILE C 742 " ideal model delta sigma weight residual 1.513 1.402 0.111 3.90e-02 6.57e+02 8.11e+00 ... (remaining 30413 not shown) Histogram of bond angle deviations from ideal: 97.99 - 105.20: 648 105.20 - 112.41: 15441 112.41 - 119.62: 9765 119.62 - 126.83: 15146 126.83 - 134.04: 372 Bond angle restraints: 41372 Sorted by residual: angle pdb=" CA PRO D 146 " pdb=" N PRO D 146 " pdb=" CD PRO D 146 " ideal model delta sigma weight residual 112.00 105.46 6.54 1.40e+00 5.10e-01 2.18e+01 angle pdb=" N PHE B 338 " pdb=" CA PHE B 338 " pdb=" C PHE B 338 " ideal model delta sigma weight residual 113.50 108.36 5.14 1.23e+00 6.61e-01 1.75e+01 angle pdb=" CA GLY C 594 " pdb=" C GLY C 594 " pdb=" O GLY C 594 " ideal model delta sigma weight residual 120.94 117.72 3.22 7.80e-01 1.64e+00 1.70e+01 angle pdb=" N LEU B 368 " pdb=" CA LEU B 368 " pdb=" C LEU B 368 " ideal model delta sigma weight residual 113.55 108.82 4.73 1.26e+00 6.30e-01 1.41e+01 angle pdb=" N CYS C 432 " pdb=" CA CYS C 432 " pdb=" C CYS C 432 " ideal model delta sigma weight residual 108.60 113.96 -5.36 1.46e+00 4.69e-01 1.35e+01 ... (remaining 41367 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.51: 17210 19.51 - 39.02: 1181 39.02 - 58.54: 196 58.54 - 78.05: 52 78.05 - 97.56: 22 Dihedral angle restraints: 18661 sinusoidal: 7886 harmonic: 10775 Sorted by residual: dihedral pdb=" CB CYS D 133 " pdb=" SG CYS D 133 " pdb=" SG CYS D 141 " pdb=" CB CYS D 141 " ideal model delta sinusoidal sigma weight residual 93.00 36.76 56.24 1 1.00e+01 1.00e-02 4.27e+01 dihedral pdb=" CA CYS C 617 " pdb=" C CYS C 617 " pdb=" N THR C 618 " pdb=" CA THR C 618 " ideal model delta harmonic sigma weight residual 180.00 152.31 27.69 0 5.00e+00 4.00e-02 3.07e+01 dihedral pdb=" CA CYS A 617 " pdb=" C CYS A 617 " pdb=" N THR A 618 " pdb=" CA THR A 618 " ideal model delta harmonic sigma weight residual 180.00 156.10 23.90 0 5.00e+00 4.00e-02 2.28e+01 ... (remaining 18658 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 4156 0.070 - 0.140: 571 0.140 - 0.211: 12 0.211 - 0.281: 2 0.281 - 0.351: 1 Chirality restraints: 4742 Sorted by residual: chirality pdb=" C1 NAG A1303 " pdb=" ND2 ASN A 709 " pdb=" C2 NAG A1303 " pdb=" O5 NAG A1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.08e+00 chirality pdb=" C1 NAG D 702 " pdb=" ND2 ASN D 90 " pdb=" C2 NAG D 702 " pdb=" O5 NAG D 702 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CA VAL A 320 " pdb=" N VAL A 320 " pdb=" C VAL A 320 " pdb=" CB VAL A 320 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 4739 not shown) Planarity restraints: 5322 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 461 " 0.023 2.00e-02 2.50e+03 2.39e-02 1.43e+01 pdb=" CG TRP D 461 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP D 461 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP D 461 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 461 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 461 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 461 " 0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 461 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 461 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP D 461 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 318 " 0.017 2.00e-02 2.50e+03 3.50e-02 1.22e+01 pdb=" C PHE A 318 " -0.061 2.00e-02 2.50e+03 pdb=" O PHE A 318 " 0.023 2.00e-02 2.50e+03 pdb=" N ARG A 319 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 90 " 0.002 2.00e-02 2.50e+03 2.91e-02 1.06e+01 pdb=" CG ASN D 90 " 0.032 2.00e-02 2.50e+03 pdb=" OD1 ASN D 90 " -0.035 2.00e-02 2.50e+03 pdb=" ND2 ASN D 90 " 0.032 2.00e-02 2.50e+03 pdb=" C1 NAG D 702 " -0.031 2.00e-02 2.50e+03 ... (remaining 5319 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.66: 444 2.66 - 3.22: 27296 3.22 - 3.78: 45741 3.78 - 4.34: 63478 4.34 - 4.90: 104141 Nonbonded interactions: 241100 Sorted by model distance: nonbonded pdb=" OG1 THR C 732 " pdb=" ND2 ASN C 955 " model vdw 2.095 2.520 nonbonded pdb=" OH TYR A 756 " pdb=" OD1 ASP A 994 " model vdw 2.151 2.440 nonbonded pdb=" O ASN C 439 " pdb=" OG SER C 443 " model vdw 2.161 2.440 nonbonded pdb=" OH TYR B 756 " pdb=" OD1 ASP B 994 " model vdw 2.168 2.440 nonbonded pdb=" OE1 GLU B 516 " pdb=" OH TYR C 200 " model vdw 2.174 2.440 ... (remaining 241095 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 518 or (resid 519 through 520 and (name N or na \ me CA or name C or name O or name CB )) or resid 521 through 1147 or resid 1301) \ ) selection = (chain 'B' and (resid 14 through 1147 or resid 1301)) selection = chain 'C' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } 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: 11.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 29.510 Check model and map are aligned: 0.470 Set scattering table: 0.290 Process input model: 81.420 Find NCS groups from input model: 2.080 Set up NCS constraints: 0.330 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:13.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 140.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.111 30418 Z= 0.242 Angle : 0.588 7.895 41372 Z= 0.329 Chirality : 0.045 0.351 4742 Planarity : 0.004 0.064 5296 Dihedral : 13.615 97.559 11589 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.31 % Favored : 97.52 % Rotamer: Outliers : 0.03 % Allowed : 0.68 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.14), residues: 3635 helix: 1.64 (0.17), residues: 1019 sheet: 0.34 (0.20), residues: 603 loop : -0.55 (0.13), residues: 2013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.001 TRP D 461 HIS 0.004 0.001 HIS C 505 PHE 0.031 0.001 PHE C 429 TYR 0.014 0.001 TYR B 453 ARG 0.007 0.000 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 3247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 221 time to evaluate : 3.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 82 MET cc_start: 0.7370 (mtp) cc_final: 0.7162 (mtp) REVERT: D 323 MET cc_start: -0.1217 (mtt) cc_final: -0.2688 (pmm) REVERT: D 360 MET cc_start: -0.1345 (mmp) cc_final: -0.1602 (mmp) REVERT: D 383 MET cc_start: 0.6603 (mpp) cc_final: 0.6379 (mpt) REVERT: D 523 PHE cc_start: 0.5535 (m-80) cc_final: 0.4593 (m-80) REVERT: D 579 MET cc_start: -0.0476 (mmt) cc_final: -0.2701 (ppp) outliers start: 1 outliers final: 1 residues processed: 222 average time/residue: 1.1250 time to fit residues: 305.2571 Evaluate side-chains 151 residues out of total 3247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 150 time to evaluate : 3.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 274 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 310 optimal weight: 20.0000 chunk 278 optimal weight: 5.9990 chunk 154 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 188 optimal weight: 5.9990 chunk 149 optimal weight: 7.9990 chunk 288 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 175 optimal weight: 5.9990 chunk 214 optimal weight: 7.9990 chunk 334 optimal weight: 30.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 317 ASN ** A 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN B 901 GLN B 907 ASN C 282 ASN C 417 ASN C 955 ASN D 96 GLN D 175 GLN D 580 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.070 30418 Z= 0.574 Angle : 0.702 11.325 41372 Z= 0.364 Chirality : 0.051 0.271 4742 Planarity : 0.005 0.052 5296 Dihedral : 6.903 75.646 4800 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.54 % Allowed : 7.27 % Favored : 91.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.13), residues: 3635 helix: 1.42 (0.16), residues: 1021 sheet: 0.34 (0.18), residues: 703 loop : -0.79 (0.13), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP D 461 HIS 0.014 0.002 HIS D 241 PHE 0.026 0.002 PHE A 275 TYR 0.028 0.002 TYR C1067 ARG 0.010 0.001 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 3247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 169 time to evaluate : 3.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.7320 (t80) cc_final: 0.7070 (t80) REVERT: A 237 ARG cc_start: 0.7101 (ptm-80) cc_final: 0.6335 (ttt-90) REVERT: A 239 GLN cc_start: 0.6422 (OUTLIER) cc_final: 0.5923 (mm-40) REVERT: A 1010 GLN cc_start: 0.8015 (OUTLIER) cc_final: 0.7183 (mp10) REVERT: D 82 MET cc_start: 0.7281 (mtp) cc_final: 0.7028 (mtp) REVERT: D 139 GLN cc_start: 0.0857 (pm20) cc_final: 0.0012 (mt0) REVERT: D 225 ASP cc_start: 0.2233 (m-30) cc_final: 0.1521 (m-30) REVERT: D 243 TYR cc_start: 0.5067 (t80) cc_final: 0.4620 (m-80) REVERT: D 323 MET cc_start: -0.0605 (mtt) cc_final: -0.2711 (pmm) REVERT: D 383 MET cc_start: 0.6685 (mpp) cc_final: 0.6438 (mmm) REVERT: D 579 MET cc_start: -0.0387 (mmt) cc_final: -0.2742 (ppp) outliers start: 50 outliers final: 23 residues processed: 202 average time/residue: 1.1351 time to fit residues: 281.2607 Evaluate side-chains 169 residues out of total 3247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 144 time to evaluate : 3.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain D residue 274 PHE Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain D residue 555 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 185 optimal weight: 1.9990 chunk 103 optimal weight: 20.0000 chunk 278 optimal weight: 0.8980 chunk 227 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 334 optimal weight: 20.0000 chunk 361 optimal weight: 8.9990 chunk 298 optimal weight: 0.7980 chunk 331 optimal weight: 20.0000 chunk 114 optimal weight: 4.9990 chunk 268 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 542 ASN A1002 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN C 81 ASN C 314 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30418 Z= 0.212 Angle : 0.535 8.888 41372 Z= 0.274 Chirality : 0.044 0.274 4742 Planarity : 0.004 0.050 5296 Dihedral : 5.842 54.465 4800 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.48 % Allowed : 9.98 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.13), residues: 3635 helix: 1.90 (0.16), residues: 1005 sheet: 0.60 (0.19), residues: 682 loop : -0.69 (0.13), residues: 1948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 461 HIS 0.009 0.001 HIS D 241 PHE 0.014 0.001 PHE C 106 TYR 0.020 0.001 TYR B1067 ARG 0.009 0.000 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 3247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 167 time to evaluate : 3.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.7313 (t80) cc_final: 0.7053 (t80) REVERT: A 237 ARG cc_start: 0.7131 (ptm-80) cc_final: 0.6334 (mtm110) REVERT: A 794 ILE cc_start: 0.9044 (OUTLIER) cc_final: 0.8742 (pp) REVERT: A 1010 GLN cc_start: 0.7983 (OUTLIER) cc_final: 0.7213 (mp10) REVERT: B 200 TYR cc_start: 0.7878 (m-80) cc_final: 0.7651 (m-80) REVERT: B 983 ARG cc_start: 0.8466 (ttp80) cc_final: 0.8098 (ttp80) REVERT: C 752 LEU cc_start: 0.9006 (mp) cc_final: 0.8677 (mp) REVERT: D 82 MET cc_start: 0.7242 (mtp) cc_final: 0.6984 (mtp) REVERT: D 139 GLN cc_start: 0.0905 (pm20) cc_final: 0.0085 (tt0) REVERT: D 243 TYR cc_start: 0.5151 (t80) cc_final: 0.4713 (m-80) REVERT: D 297 MET cc_start: -0.1689 (OUTLIER) cc_final: -0.2037 (mmt) REVERT: D 323 MET cc_start: -0.0070 (mtt) cc_final: -0.2506 (pmm) REVERT: D 360 MET cc_start: -0.1418 (mmp) cc_final: -0.1622 (mmp) REVERT: D 383 MET cc_start: 0.6707 (mpp) cc_final: 0.6504 (mmm) REVERT: D 445 THR cc_start: 0.6286 (OUTLIER) cc_final: 0.6067 (p) REVERT: D 579 MET cc_start: -0.0332 (mmt) cc_final: -0.2558 (ppp) outliers start: 48 outliers final: 21 residues processed: 200 average time/residue: 1.1718 time to fit residues: 287.0975 Evaluate side-chains 167 residues out of total 3247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 142 time to evaluate : 3.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 542 ASN Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1142 GLN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain D residue 297 MET Chi-restraints excluded: chain D residue 445 THR Chi-restraints excluded: chain D residue 555 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 330 optimal weight: 20.0000 chunk 251 optimal weight: 10.0000 chunk 173 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 224 optimal weight: 3.9990 chunk 335 optimal weight: 0.2980 chunk 355 optimal weight: 30.0000 chunk 175 optimal weight: 3.9990 chunk 318 optimal weight: 10.0000 chunk 95 optimal weight: 0.7980 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN A1002 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN D 535 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 30418 Z= 0.258 Angle : 0.533 8.897 41372 Z= 0.273 Chirality : 0.044 0.300 4742 Planarity : 0.004 0.048 5296 Dihedral : 5.299 53.175 4798 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.82 % Allowed : 11.00 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.14), residues: 3635 helix: 1.99 (0.16), residues: 1012 sheet: 0.56 (0.18), residues: 700 loop : -0.66 (0.13), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 461 HIS 0.008 0.001 HIS D 241 PHE 0.021 0.001 PHE A 168 TYR 0.021 0.001 TYR B1067 ARG 0.007 0.000 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 3247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 156 time to evaluate : 3.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 794 ILE cc_start: 0.9038 (OUTLIER) cc_final: 0.8739 (pp) REVERT: A 1010 GLN cc_start: 0.7961 (OUTLIER) cc_final: 0.7140 (mp10) REVERT: B 371 LEU cc_start: 0.2409 (OUTLIER) cc_final: 0.1444 (tm) REVERT: B 983 ARG cc_start: 0.8490 (ttp80) cc_final: 0.8104 (ttp80) REVERT: B 1040 VAL cc_start: 0.9222 (OUTLIER) cc_final: 0.8901 (m) REVERT: C 326 ILE cc_start: 0.8388 (OUTLIER) cc_final: 0.8127 (pt) REVERT: D 82 MET cc_start: 0.7237 (mtp) cc_final: 0.6971 (mtp) REVERT: D 139 GLN cc_start: 0.0925 (pm20) cc_final: 0.0092 (tt0) REVERT: D 297 MET cc_start: -0.1731 (OUTLIER) cc_final: -0.2083 (mmt) REVERT: D 323 MET cc_start: -0.0463 (mtt) cc_final: -0.2616 (ptm) REVERT: D 519 THR cc_start: 0.4685 (OUTLIER) cc_final: 0.3951 (p) REVERT: D 579 MET cc_start: -0.0283 (mmt) cc_final: -0.2492 (ppp) outliers start: 59 outliers final: 27 residues processed: 201 average time/residue: 1.1712 time to fit residues: 287.0873 Evaluate side-chains 179 residues out of total 3247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 145 time to evaluate : 3.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1142 GLN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain D residue 274 PHE Chi-restraints excluded: chain D residue 297 MET Chi-restraints excluded: chain D residue 519 THR Chi-restraints excluded: chain D residue 555 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 296 optimal weight: 0.8980 chunk 201 optimal weight: 0.6980 chunk 5 optimal weight: 8.9990 chunk 264 optimal weight: 0.0970 chunk 146 optimal weight: 9.9990 chunk 303 optimal weight: 0.9980 chunk 245 optimal weight: 0.6980 chunk 0 optimal weight: 20.0000 chunk 181 optimal weight: 0.5980 chunk 319 optimal weight: 20.0000 chunk 89 optimal weight: 0.6980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN A1002 GLN C 314 GLN C 804 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 30418 Z= 0.154 Angle : 0.508 14.555 41372 Z= 0.255 Chirality : 0.043 0.315 4742 Planarity : 0.003 0.048 5296 Dihedral : 4.759 55.081 4798 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.48 % Allowed : 12.11 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.14), residues: 3635 helix: 2.16 (0.17), residues: 1011 sheet: 0.65 (0.19), residues: 688 loop : -0.54 (0.13), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 461 HIS 0.008 0.001 HIS D 241 PHE 0.025 0.001 PHE A 168 TYR 0.026 0.001 TYR A 170 ARG 0.003 0.000 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 3247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 161 time to evaluate : 3.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.6835 (ptm-80) cc_final: 0.6595 (ttt-90) REVERT: B 371 LEU cc_start: 0.2595 (OUTLIER) cc_final: 0.1634 (tm) REVERT: B 983 ARG cc_start: 0.8424 (ttp80) cc_final: 0.8067 (ttp80) REVERT: C 1010 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7003 (mp10) REVERT: D 82 MET cc_start: 0.7218 (mtp) cc_final: 0.6947 (mtp) REVERT: D 243 TYR cc_start: 0.5268 (t80) cc_final: 0.4800 (m-80) REVERT: D 297 MET cc_start: -0.1815 (OUTLIER) cc_final: -0.2059 (mmt) REVERT: D 323 MET cc_start: -0.0833 (mtt) cc_final: -0.2473 (ptm) REVERT: D 462 MET cc_start: 0.4464 (ttt) cc_final: 0.3724 (mmt) REVERT: D 579 MET cc_start: -0.0092 (mmt) cc_final: -0.2335 (ppp) outliers start: 48 outliers final: 25 residues processed: 193 average time/residue: 1.1920 time to fit residues: 281.6199 Evaluate side-chains 170 residues out of total 3247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 142 time to evaluate : 3.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1142 GLN Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain D residue 274 PHE Chi-restraints excluded: chain D residue 297 MET Chi-restraints excluded: chain D residue 360 MET Chi-restraints excluded: chain D residue 597 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 119 optimal weight: 4.9990 chunk 320 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 208 optimal weight: 4.9990 chunk 87 optimal weight: 0.8980 chunk 356 optimal weight: 0.9990 chunk 295 optimal weight: 0.5980 chunk 164 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 117 optimal weight: 8.9990 chunk 186 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1142 GLN D 580 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 30418 Z= 0.174 Angle : 0.511 13.147 41372 Z= 0.256 Chirality : 0.043 0.448 4742 Planarity : 0.003 0.047 5296 Dihedral : 4.523 53.885 4798 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.76 % Allowed : 12.70 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.14), residues: 3635 helix: 2.20 (0.17), residues: 1013 sheet: 0.71 (0.19), residues: 697 loop : -0.50 (0.14), residues: 1925 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 461 HIS 0.007 0.001 HIS D 241 PHE 0.024 0.001 PHE A 168 TYR 0.026 0.001 TYR A 170 ARG 0.005 0.000 ARG D 273 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 3247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 149 time to evaluate : 3.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 794 ILE cc_start: 0.9033 (OUTLIER) cc_final: 0.8732 (pp) REVERT: B 371 LEU cc_start: 0.2752 (OUTLIER) cc_final: 0.1723 (tm) REVERT: B 468 ILE cc_start: 0.3316 (OUTLIER) cc_final: 0.2998 (mt) REVERT: B 981 PHE cc_start: 0.8215 (m-80) cc_final: 0.8006 (m-80) REVERT: B 983 ARG cc_start: 0.8358 (ttp80) cc_final: 0.8008 (ttp80) REVERT: B 1040 VAL cc_start: 0.9204 (OUTLIER) cc_final: 0.8900 (m) REVERT: C 326 ILE cc_start: 0.8379 (OUTLIER) cc_final: 0.8123 (pt) REVERT: C 1010 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.6955 (mp10) REVERT: D 82 MET cc_start: 0.7247 (mtp) cc_final: 0.6978 (mtp) REVERT: D 243 TYR cc_start: 0.5105 (t80) cc_final: 0.4727 (m-80) REVERT: D 323 MET cc_start: -0.0800 (mtt) cc_final: -0.2435 (ptm) REVERT: D 579 MET cc_start: -0.0129 (mmt) cc_final: -0.2357 (ppp) outliers start: 57 outliers final: 26 residues processed: 190 average time/residue: 1.1929 time to fit residues: 279.2206 Evaluate side-chains 171 residues out of total 3247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 139 time to evaluate : 3.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain D residue 360 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 343 optimal weight: 20.0000 chunk 40 optimal weight: 10.0000 chunk 202 optimal weight: 0.7980 chunk 260 optimal weight: 2.9990 chunk 201 optimal weight: 0.6980 chunk 299 optimal weight: 0.8980 chunk 198 optimal weight: 1.9990 chunk 354 optimal weight: 20.0000 chunk 221 optimal weight: 8.9990 chunk 216 optimal weight: 4.9990 chunk 163 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 ASN B1142 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30418 Z= 0.197 Angle : 0.515 14.051 41372 Z= 0.258 Chirality : 0.043 0.273 4742 Planarity : 0.003 0.047 5296 Dihedral : 4.399 53.389 4798 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.79 % Allowed : 13.19 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.14), residues: 3635 helix: 2.24 (0.17), residues: 1012 sheet: 0.69 (0.19), residues: 704 loop : -0.48 (0.14), residues: 1919 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 461 HIS 0.007 0.001 HIS D 241 PHE 0.013 0.001 PHE A 220 TYR 0.021 0.001 TYR C 473 ARG 0.006 0.000 ARG B 498 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 3247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 146 time to evaluate : 3.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 794 ILE cc_start: 0.9030 (OUTLIER) cc_final: 0.8729 (pp) REVERT: B 371 LEU cc_start: 0.2942 (OUTLIER) cc_final: 0.1842 (tm) REVERT: B 468 ILE cc_start: 0.3172 (OUTLIER) cc_final: 0.2834 (mt) REVERT: B 983 ARG cc_start: 0.8352 (ttp80) cc_final: 0.8061 (ttp80) REVERT: C 326 ILE cc_start: 0.8380 (OUTLIER) cc_final: 0.8107 (pt) REVERT: C 1010 GLN cc_start: 0.8190 (OUTLIER) cc_final: 0.6955 (mp10) REVERT: C 1145 LEU cc_start: 0.8367 (mp) cc_final: 0.8052 (tt) REVERT: D 82 MET cc_start: 0.7338 (mtp) cc_final: 0.7043 (mtp) REVERT: D 243 TYR cc_start: 0.5158 (t80) cc_final: 0.4839 (m-80) REVERT: D 323 MET cc_start: -0.0783 (mtt) cc_final: -0.2414 (ptm) REVERT: D 579 MET cc_start: -0.0235 (mmt) cc_final: -0.2371 (ppp) outliers start: 58 outliers final: 29 residues processed: 187 average time/residue: 1.1525 time to fit residues: 264.5971 Evaluate side-chains 173 residues out of total 3247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 139 time to evaluate : 3.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 574 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 219 optimal weight: 10.0000 chunk 141 optimal weight: 20.0000 chunk 211 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 chunk 69 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 225 optimal weight: 6.9990 chunk 241 optimal weight: 9.9990 chunk 175 optimal weight: 4.9990 chunk 33 optimal weight: 9.9990 chunk 278 optimal weight: 1.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 388 ASN A 907 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1142 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 30418 Z= 0.377 Angle : 0.593 14.912 41372 Z= 0.299 Chirality : 0.046 0.293 4742 Planarity : 0.004 0.047 5296 Dihedral : 4.725 51.501 4798 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.60 % Allowed : 13.59 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.56 (0.14), residues: 3635 helix: 2.01 (0.16), residues: 1028 sheet: 0.48 (0.19), residues: 724 loop : -0.60 (0.14), residues: 1883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 886 HIS 0.007 0.001 HIS D 241 PHE 0.017 0.002 PHE A 220 TYR 0.023 0.002 TYR C 473 ARG 0.005 0.000 ARG B 995 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 3247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 150 time to evaluate : 3.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.7313 (ttt90) cc_final: 0.6534 (mtp85) REVERT: A 239 GLN cc_start: 0.6724 (mm-40) cc_final: 0.6393 (mm-40) REVERT: A 794 ILE cc_start: 0.9053 (OUTLIER) cc_final: 0.8748 (pp) REVERT: B 468 ILE cc_start: 0.3132 (OUTLIER) cc_final: 0.2798 (mt) REVERT: B 983 ARG cc_start: 0.8474 (ttp80) cc_final: 0.8071 (ttp80) REVERT: C 229 LEU cc_start: 0.7876 (tp) cc_final: 0.7438 (tp) REVERT: C 326 ILE cc_start: 0.8442 (OUTLIER) cc_final: 0.8163 (pt) REVERT: D 82 MET cc_start: 0.7423 (mtp) cc_final: 0.7164 (mtp) REVERT: D 297 MET cc_start: -0.1782 (OUTLIER) cc_final: -0.2008 (mmt) REVERT: D 579 MET cc_start: -0.0057 (mmt) cc_final: -0.2344 (ppp) outliers start: 52 outliers final: 27 residues processed: 188 average time/residue: 1.1746 time to fit residues: 270.7234 Evaluate side-chains 174 residues out of total 3247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 143 time to evaluate : 3.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 763 LEU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 297 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 322 optimal weight: 30.0000 chunk 339 optimal weight: 9.9990 chunk 310 optimal weight: 20.0000 chunk 330 optimal weight: 2.9990 chunk 198 optimal weight: 0.9980 chunk 143 optimal weight: 2.9990 chunk 259 optimal weight: 0.8980 chunk 101 optimal weight: 0.8980 chunk 298 optimal weight: 2.9990 chunk 312 optimal weight: 40.0000 chunk 329 optimal weight: 6.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1142 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 30418 Z= 0.296 Angle : 0.565 15.113 41372 Z= 0.281 Chirality : 0.045 0.248 4742 Planarity : 0.004 0.050 5296 Dihedral : 4.658 53.238 4798 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.51 % Allowed : 14.11 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.57 (0.14), residues: 3635 helix: 2.07 (0.17), residues: 1022 sheet: 0.49 (0.19), residues: 723 loop : -0.61 (0.14), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 886 HIS 0.007 0.001 HIS D 241 PHE 0.017 0.001 PHE A 220 TYR 0.027 0.001 TYR A 170 ARG 0.005 0.000 ARG C1039 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 3247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 151 time to evaluate : 6.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.7360 (ttt90) cc_final: 0.6586 (mtp85) REVERT: A 355 ARG cc_start: 0.8256 (mmm-85) cc_final: 0.7847 (mmm-85) REVERT: A 794 ILE cc_start: 0.9027 (OUTLIER) cc_final: 0.8722 (pp) REVERT: B 468 ILE cc_start: 0.3120 (OUTLIER) cc_final: 0.2795 (mt) REVERT: C 229 LEU cc_start: 0.7927 (tp) cc_final: 0.7498 (tp) REVERT: C 326 ILE cc_start: 0.8378 (OUTLIER) cc_final: 0.8072 (pt) REVERT: D 82 MET cc_start: 0.7474 (mtp) cc_final: 0.7208 (mtp) REVERT: D 297 MET cc_start: -0.1881 (OUTLIER) cc_final: -0.2133 (mmt) REVERT: D 323 MET cc_start: -0.0835 (mtt) cc_final: -0.2369 (ptm) REVERT: D 579 MET cc_start: -0.0086 (mmt) cc_final: -0.2364 (ppp) outliers start: 49 outliers final: 28 residues processed: 188 average time/residue: 1.2716 time to fit residues: 295.6739 Evaluate side-chains 175 residues out of total 3247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 143 time to evaluate : 3.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 297 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 217 optimal weight: 3.9990 chunk 349 optimal weight: 0.1980 chunk 213 optimal weight: 0.6980 chunk 165 optimal weight: 0.4980 chunk 242 optimal weight: 0.0970 chunk 366 optimal weight: 20.0000 chunk 337 optimal weight: 10.0000 chunk 291 optimal weight: 3.9990 chunk 30 optimal weight: 20.0000 chunk 225 optimal weight: 5.9990 chunk 179 optimal weight: 0.1980 overall best weight: 0.3378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 ASN B1142 GLN C 314 GLN C 901 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 30418 Z= 0.138 Angle : 0.520 14.806 41372 Z= 0.257 Chirality : 0.043 0.256 4742 Planarity : 0.004 0.050 5296 Dihedral : 4.337 55.636 4798 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.99 % Allowed : 15.04 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.14), residues: 3635 helix: 2.27 (0.17), residues: 1020 sheet: 0.61 (0.19), residues: 707 loop : -0.45 (0.14), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 594 HIS 0.007 0.001 HIS D 241 PHE 0.012 0.001 PHE B1121 TYR 0.023 0.001 TYR B 170 ARG 0.006 0.000 ARG B 983 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7270 Ramachandran restraints generated. 3635 Oldfield, 0 Emsley, 3635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 3247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 162 time to evaluate : 3.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.7326 (ttt90) cc_final: 0.6836 (mtp85) REVERT: A 239 GLN cc_start: 0.6638 (mm-40) cc_final: 0.6279 (mm110) REVERT: A 318 PHE cc_start: 0.7336 (p90) cc_final: 0.5811 (t80) REVERT: A 529 LYS cc_start: 0.8461 (mmtt) cc_final: 0.8089 (mmtm) REVERT: B 468 ILE cc_start: 0.3145 (OUTLIER) cc_final: 0.2820 (mt) REVERT: B 983 ARG cc_start: 0.7918 (tmm-80) cc_final: 0.7512 (ttp-170) REVERT: B 1040 VAL cc_start: 0.9178 (OUTLIER) cc_final: 0.8878 (m) REVERT: C 229 LEU cc_start: 0.7905 (tp) cc_final: 0.7499 (tp) REVERT: C 326 ILE cc_start: 0.8314 (OUTLIER) cc_final: 0.7965 (pt) REVERT: C 1145 LEU cc_start: 0.8353 (mp) cc_final: 0.8089 (tt) REVERT: D 82 MET cc_start: 0.7543 (mtp) cc_final: 0.7288 (mtp) REVERT: D 297 MET cc_start: -0.1902 (OUTLIER) cc_final: -0.2141 (mmt) REVERT: D 323 MET cc_start: -0.1057 (mtt) cc_final: -0.2133 (ptm) REVERT: D 462 MET cc_start: 0.4429 (ttt) cc_final: 0.3632 (mmp) REVERT: D 579 MET cc_start: -0.0169 (mmt) cc_final: -0.2361 (ppp) outliers start: 32 outliers final: 20 residues processed: 183 average time/residue: 1.2066 time to fit residues: 268.8326 Evaluate side-chains 169 residues out of total 3247 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 145 time to evaluate : 3.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain D residue 152 MET Chi-restraints excluded: chain D residue 297 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 231 optimal weight: 3.9990 chunk 310 optimal weight: 20.0000 chunk 89 optimal weight: 0.7980 chunk 269 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 292 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 300 optimal weight: 0.5980 chunk 37 optimal weight: 10.0000 chunk 53 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.166448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.098869 restraints weight = 55350.140| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 3.73 r_work: 0.3060 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30418 Z= 0.177 Angle : 0.526 15.004 41372 Z= 0.260 Chirality : 0.043 0.258 4742 Planarity : 0.004 0.050 5296 Dihedral : 4.266 53.795 4798 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.02 % Allowed : 15.29 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.14), residues: 3635 helix: 2.28 (0.17), residues: 1024 sheet: 0.60 (0.19), residues: 722 loop : -0.45 (0.14), residues: 1889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 353 HIS 0.007 0.001 HIS D 241 PHE 0.021 0.001 PHE B 168 TYR 0.023 0.001 TYR A 170 ARG 0.007 0.000 ARG A 355 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9196.21 seconds wall clock time: 165 minutes 6.27 seconds (9906.27 seconds total)