Starting phenix.real_space_refine on Sun Feb 18 14:54:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dm1_27523/02_2024/8dm1_27523.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dm1_27523/02_2024/8dm1_27523.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dm1_27523/02_2024/8dm1_27523.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dm1_27523/02_2024/8dm1_27523.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dm1_27523/02_2024/8dm1_27523.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dm1_27523/02_2024/8dm1_27523.pdb" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.013 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 101 5.16 5 C 14181 2.51 5 N 3631 2.21 5 O 4363 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 22276 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 6641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 851, 6641 Classifications: {'peptide': 851} Link IDs: {'PTRANS': 43, 'TRANS': 807} Chain breaks: 8 Chain: "B" Number of atoms: 6650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 852, 6650 Classifications: {'peptide': 852} Link IDs: {'PTRANS': 43, 'TRANS': 808} Chain breaks: 8 Chain: "C" Number of atoms: 8215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1048, 8215 Classifications: {'peptide': 1048} Link IDs: {'PTRANS': 55, 'TRANS': 992} Chain breaks: 7 Chain: "D" 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: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 11.35, per 1000 atoms: 0.51 Number of scatterers: 22276 At special positions: 0 Unit cell: (138, 149, 173, 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 101 16.00 O 4363 8.00 N 3631 7.00 C 14181 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, 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 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=2.02 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 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=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " 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 D 1 " - " NAG D 2 " " 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 S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 165 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 709 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 165 " " NAG B1303 " - " ASN B 234 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 709 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 165 " " NAG C1303 " - " ASN C 234 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 331 " " NAG C1306 " - " ASN C 343 " " NAG C1307 " - " ASN C 709 " " NAG D 1 " - " ASN A 122 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1074 " " NAG H 1 " - " ASN A1098 " " NAG I 1 " - " ASN A1134 " " NAG J 1 " - " ASN B 122 " " NAG K 1 " - " ASN B 717 " " NAG L 1 " - " ASN B 801 " " NAG M 1 " - " ASN B1074 " " NAG N 1 " - " ASN B1098 " " NAG O 1 " - " ASN B1134 " " NAG P 1 " - " ASN C 122 " " NAG Q 1 " - " ASN C 717 " " NAG R 1 " - " ASN C 801 " " NAG S 1 " - " ASN C1074 " " NAG T 1 " - " ASN C1098 " " NAG U 1 " - " ASN C1134 " Time building additional restraints: 8.51 Conformation dependent library (CDL) restraints added in 4.3 seconds 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5168 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 41 sheets defined 26.9% alpha, 34.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.89 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 616 through 620 removed outlier: 4.022A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.598A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 849 through 856 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 3.880A 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 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 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 3.997A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.145A 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 616 through 620 removed outlier: 3.976A 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 removed outlier: 3.558A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 849 through 856 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 887 through 891 removed outlier: 3.698A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.930A 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 945 through 965 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 Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.156A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 4.044A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 386 through 389 Processing helix chain 'C' and resid 404 through 410 removed outlier: 3.926A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.841A 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 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.564A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 849 through 856 removed outlier: 3.730A pdb=" N ASN C 856 " --> pdb=" O ALA C 852 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 887 through 891 removed outlier: 3.752A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 3.936A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 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 1032 removed outlier: 4.052A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.197A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 30 removed outlier: 7.617A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 43 through 44 removed outlier: 6.553A pdb=" N PHE A 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.015A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.765A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.820A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.853A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 328 Processing sheet with id=AA8, first strand: chain 'A' and resid 551 through 554 removed outlier: 4.740A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.916A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.630A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.460A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.460A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.278A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 787 through 790 removed outlier: 3.676A pdb=" N LYS A 790 " --> pdb=" O ASN C 703 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB7, first strand: chain 'B' and resid 20 through 30 removed outlier: 7.695A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.926A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.849A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 8.805A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.803A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.238A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.827A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.448A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.506A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.506A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.318A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD1, first strand: chain 'C' and resid 20 through 30 removed outlier: 7.645A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.999A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD4, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.866A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 8.871A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.967A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.909A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.909A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AD9, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.746A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.957A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.441A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.478A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.478A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.431A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 1120 through 1122 1032 hydrogen bonds defined for protein. 2868 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: 10.11 Time building geometry restraints manager: 9.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6879 1.34 - 1.46: 5361 1.46 - 1.58: 10384 1.58 - 1.70: 0 1.70 - 1.82: 131 Bond restraints: 22755 Sorted by residual: bond pdb=" C PRO C 986 " pdb=" N PRO C 987 " ideal model delta sigma weight residual 1.335 1.417 -0.082 1.38e-02 5.25e+03 3.56e+01 bond pdb=" C1 NAG N 1 " pdb=" O5 NAG N 1 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.54e+00 bond pdb=" C1 NAG B1302 " pdb=" O5 NAG B1302 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.39e+00 bond pdb=" C1 NAG C1302 " pdb=" O5 NAG C1302 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.10e+00 bond pdb=" C1 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.87e+00 ... (remaining 22750 not shown) Histogram of bond angle deviations from ideal: 96.84 - 104.28: 393 104.28 - 111.72: 10653 111.72 - 119.16: 7776 119.16 - 126.59: 11873 126.59 - 134.03: 255 Bond angle restraints: 30950 Sorted by residual: angle pdb=" C ILE B 197 " pdb=" N ASP B 198 " pdb=" CA ASP B 198 " ideal model delta sigma weight residual 122.46 129.76 -7.30 1.41e+00 5.03e-01 2.68e+01 angle pdb=" C ILE C 197 " pdb=" N ASP C 198 " pdb=" CA ASP C 198 " ideal model delta sigma weight residual 122.46 129.55 -7.09 1.41e+00 5.03e-01 2.53e+01 angle pdb=" C ILE A 197 " pdb=" N ASP A 198 " pdb=" CA ASP A 198 " ideal model delta sigma weight residual 122.46 129.42 -6.96 1.41e+00 5.03e-01 2.44e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 115.96 -5.26 1.22e+00 6.72e-01 1.86e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 115.93 -5.23 1.22e+00 6.72e-01 1.84e+01 ... (remaining 30945 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 13181 17.92 - 35.83: 850 35.83 - 53.75: 200 53.75 - 71.67: 58 71.67 - 89.58: 23 Dihedral angle restraints: 14312 sinusoidal: 6305 harmonic: 8007 Sorted by residual: dihedral pdb=" CB CYS B 131 " pdb=" SG CYS B 131 " pdb=" SG CYS B 166 " pdb=" CB CYS B 166 " ideal model delta sinusoidal sigma weight residual -86.00 -55.09 -30.91 1 1.00e+01 1.00e-02 1.36e+01 dihedral pdb=" CB CYS C 131 " pdb=" SG CYS C 131 " pdb=" SG CYS C 166 " pdb=" CB CYS C 166 " ideal model delta sinusoidal sigma weight residual -86.00 -55.46 -30.54 1 1.00e+01 1.00e-02 1.33e+01 dihedral pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " pdb=" SG CYS A 166 " pdb=" CB CYS A 166 " ideal model delta sinusoidal sigma weight residual -86.00 -56.42 -29.58 1 1.00e+01 1.00e-02 1.25e+01 ... (remaining 14309 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 2471 0.047 - 0.095: 806 0.095 - 0.142: 362 0.142 - 0.189: 56 0.189 - 0.237: 8 Chirality restraints: 3703 Sorted by residual: chirality pdb=" CA ASP A 198 " pdb=" N ASP A 198 " pdb=" C ASP A 198 " pdb=" CB ASP A 198 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CB VAL B 227 " pdb=" CA VAL B 227 " pdb=" CG1 VAL B 227 " pdb=" CG2 VAL B 227 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA ASP B 198 " pdb=" N ASP B 198 " pdb=" C ASP B 198 " pdb=" CB ASP B 198 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 3700 not shown) Planarity restraints: 3957 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN C 953 " 0.019 2.00e-02 2.50e+03 3.80e-02 1.44e+01 pdb=" C ASN C 953 " -0.066 2.00e-02 2.50e+03 pdb=" O ASN C 953 " 0.025 2.00e-02 2.50e+03 pdb=" N HIS C 954 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 952 " -0.019 2.00e-02 2.50e+03 3.76e-02 1.42e+01 pdb=" C VAL B 952 " 0.065 2.00e-02 2.50e+03 pdb=" O VAL B 952 " -0.025 2.00e-02 2.50e+03 pdb=" N ASN B 953 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS B 954 " 0.018 2.00e-02 2.50e+03 3.69e-02 1.36e+01 pdb=" C HIS B 954 " -0.064 2.00e-02 2.50e+03 pdb=" O HIS B 954 " 0.024 2.00e-02 2.50e+03 pdb=" N ASN B 955 " 0.022 2.00e-02 2.50e+03 ... (remaining 3954 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 6584 2.82 - 3.34: 19060 3.34 - 3.86: 38323 3.86 - 4.38: 43747 4.38 - 4.90: 75829 Nonbonded interactions: 183543 Sorted by model distance: nonbonded pdb=" OG1 THR C 323 " pdb=" OE1 GLU C 324 " model vdw 2.305 2.440 nonbonded pdb=" OH TYR A 756 " pdb=" OD1 ASP A 994 " model vdw 2.332 2.440 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.335 2.440 nonbonded pdb=" OG1 THR A 618 " pdb=" OE1 GLU A 619 " model vdw 2.354 2.440 nonbonded pdb=" O GLY B 880 " pdb=" OG SER B 884 " model vdw 2.360 2.440 ... (remaining 183538 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 14 through 528 or resid 530 through 1147 or resid 1301 thr \ ough 1306)) } ncs_group { reference = chain 'D' selection = 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' selection = chain 'S' selection = chain 'T' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 5.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 14.520 Check model and map are aligned: 0.350 Set scattering table: 0.210 Process input model: 60.810 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 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 : 0.005 0.082 22755 Z= 0.350 Angle : 0.838 10.833 30950 Z= 0.467 Chirality : 0.056 0.237 3703 Planarity : 0.007 0.067 3920 Dihedral : 13.213 89.584 9042 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.54 % Allowed : 4.22 % Favored : 95.24 % 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: 0.41 (0.15), residues: 2699 helix: 1.91 (0.18), residues: 653 sheet: 0.66 (0.19), residues: 611 loop : -0.68 (0.15), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 64 HIS 0.018 0.002 HIS C 954 PHE 0.027 0.002 PHE C 371 TYR 0.032 0.002 TYR C1067 ARG 0.016 0.001 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 2417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 558 time to evaluate : 2.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 VAL cc_start: 0.8202 (t) cc_final: 0.7581 (p) REVERT: A 137 ASN cc_start: 0.7473 (m110) cc_final: 0.6782 (p0) REVERT: A 201 PHE cc_start: 0.7456 (t80) cc_final: 0.7053 (t80) REVERT: A 615 VAL cc_start: 0.7793 (t) cc_final: 0.7572 (t) REVERT: A 858 LEU cc_start: 0.8335 (mt) cc_final: 0.8115 (mt) REVERT: B 55 PHE cc_start: 0.8208 (m-80) cc_final: 0.7671 (m-80) REVERT: B 177 MET cc_start: 0.7796 (pmm) cc_final: 0.7350 (pmm) REVERT: B 200 TYR cc_start: 0.8266 (m-80) cc_final: 0.7829 (m-80) REVERT: B 202 LYS cc_start: 0.8478 (mttm) cc_final: 0.8004 (mppt) REVERT: B 223 LEU cc_start: 0.6495 (OUTLIER) cc_final: 0.6196 (mp) REVERT: B 226 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7840 (tp) REVERT: B 330 PRO cc_start: 0.8496 (Cg_exo) cc_final: 0.8003 (Cg_endo) REVERT: B 613 GLN cc_start: 0.8770 (mt0) cc_final: 0.8119 (mp10) REVERT: B 900 MET cc_start: 0.7762 (mtp) cc_final: 0.7457 (mtt) REVERT: B 902 MET cc_start: 0.8866 (tpp) cc_final: 0.8628 (tpt) REVERT: B 917 TYR cc_start: 0.7935 (m-80) cc_final: 0.7522 (m-80) REVERT: B 970 PHE cc_start: 0.8364 (m-80) cc_final: 0.8135 (m-10) REVERT: C 91 TYR cc_start: 0.7359 (t80) cc_final: 0.6899 (t80) REVERT: C 99 ASN cc_start: 0.7971 (p0) cc_final: 0.6938 (t0) REVERT: C 189 LEU cc_start: 0.9391 (tp) cc_final: 0.8578 (tp) REVERT: C 191 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7339 (mp0) REVERT: C 202 LYS cc_start: 0.8072 (mttm) cc_final: 0.7681 (mppt) REVERT: C 220 PHE cc_start: 0.4280 (m-80) cc_final: 0.3868 (m-80) REVERT: C 235 ILE cc_start: 0.6789 (mt) cc_final: 0.6449 (mt) REVERT: C 238 PHE cc_start: 0.5644 (p90) cc_final: 0.5091 (p90) REVERT: C 302 THR cc_start: 0.8788 (m) cc_final: 0.8286 (p) REVERT: C 351 TYR cc_start: 0.8643 (p90) cc_final: 0.8168 (p90) REVERT: C 392 PHE cc_start: 0.6575 (m-80) cc_final: 0.6279 (m-80) REVERT: C 574 ASP cc_start: 0.7487 (t0) cc_final: 0.7200 (t0) REVERT: C 585 LEU cc_start: 0.9024 (mt) cc_final: 0.8607 (mm) outliers start: 13 outliers final: 3 residues processed: 565 average time/residue: 0.3434 time to fit residues: 302.6852 Evaluate side-chains 302 residues out of total 2417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 297 time to evaluate : 2.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 231 optimal weight: 2.9990 chunk 207 optimal weight: 9.9990 chunk 115 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 140 optimal weight: 6.9990 chunk 110 optimal weight: 0.6980 chunk 214 optimal weight: 7.9990 chunk 83 optimal weight: 0.0870 chunk 130 optimal weight: 1.9990 chunk 159 optimal weight: 0.8980 chunk 248 optimal weight: 1.9990 overall best weight: 1.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 164 ASN A 218 GLN A 613 GLN A 710 ASN A 957 GLN B 115 GLN B 245 HIS ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 641 ASN B 901 GLN ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 954 HIS ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS C 115 GLN C 658 ASN C 926 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN C1011 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 22755 Z= 0.307 Angle : 0.705 19.464 30950 Z= 0.357 Chirality : 0.052 0.975 3703 Planarity : 0.005 0.078 3920 Dihedral : 6.966 59.306 4096 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 3.14 % Allowed : 11.92 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.15), residues: 2699 helix: 1.63 (0.19), residues: 665 sheet: 0.34 (0.19), residues: 601 loop : -0.42 (0.15), residues: 1433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 104 HIS 0.007 0.001 HIS C 954 PHE 0.030 0.002 PHE B 220 TYR 0.028 0.002 TYR A1067 ARG 0.012 0.001 ARG C1107 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 300 time to evaluate : 2.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7683 (m-90) cc_final: 0.7473 (m-90) REVERT: A 137 ASN cc_start: 0.7640 (m110) cc_final: 0.6947 (p0) REVERT: A 201 PHE cc_start: 0.8026 (t80) cc_final: 0.7663 (t80) REVERT: A 273 ARG cc_start: 0.7207 (mmm-85) cc_final: 0.6792 (mmm-85) REVERT: A 314 GLN cc_start: 0.8663 (tm-30) cc_final: 0.8069 (tm-30) REVERT: B 55 PHE cc_start: 0.8358 (m-80) cc_final: 0.7662 (m-80) REVERT: B 160 TYR cc_start: 0.7177 (p90) cc_final: 0.6820 (p90) REVERT: B 177 MET cc_start: 0.7553 (pmm) cc_final: 0.7264 (pmm) REVERT: B 200 TYR cc_start: 0.8139 (m-80) cc_final: 0.7871 (m-80) REVERT: B 955 ASN cc_start: 0.8197 (m-40) cc_final: 0.7843 (t0) REVERT: B 970 PHE cc_start: 0.8897 (m-80) cc_final: 0.8612 (m-80) REVERT: C 189 LEU cc_start: 0.9263 (tp) cc_final: 0.8456 (tp) REVERT: C 191 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7480 (mp0) REVERT: C 238 PHE cc_start: 0.6806 (p90) cc_final: 0.6339 (p90) REVERT: C 351 TYR cc_start: 0.8657 (p90) cc_final: 0.8191 (p90) REVERT: C 434 ILE cc_start: 0.3502 (OUTLIER) cc_final: 0.3299 (mt) REVERT: C 574 ASP cc_start: 0.7713 (t0) cc_final: 0.7443 (t0) REVERT: C 598 ILE cc_start: 0.9307 (mp) cc_final: 0.9081 (mp) REVERT: C 950 ASP cc_start: 0.8333 (m-30) cc_final: 0.7920 (m-30) REVERT: C 957 GLN cc_start: 0.8338 (tt0) cc_final: 0.8112 (tt0) REVERT: C 994 ASP cc_start: 0.8584 (m-30) cc_final: 0.8130 (m-30) REVERT: C 1047 TYR cc_start: 0.9071 (m-80) cc_final: 0.8827 (m-80) outliers start: 76 outliers final: 38 residues processed: 350 average time/residue: 0.3234 time to fit residues: 180.9160 Evaluate side-chains 262 residues out of total 2417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 223 time to evaluate : 2.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1125 ASN Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1051 SER Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 138 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 207 optimal weight: 9.9990 chunk 169 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 249 optimal weight: 0.8980 chunk 269 optimal weight: 1.9990 chunk 221 optimal weight: 0.4980 chunk 247 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 199 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1011 GLN C 658 ASN C 804 GLN C 926 GLN C 935 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.4301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 22755 Z= 0.206 Angle : 0.539 8.805 30950 Z= 0.280 Chirality : 0.044 0.190 3703 Planarity : 0.004 0.067 3920 Dihedral : 6.058 58.312 4087 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.57 % Allowed : 13.36 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.16), residues: 2699 helix: 2.22 (0.20), residues: 666 sheet: 0.43 (0.19), residues: 632 loop : -0.28 (0.16), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 104 HIS 0.006 0.001 HIS C 954 PHE 0.030 0.001 PHE A 592 TYR 0.022 0.001 TYR A1067 ARG 0.003 0.000 ARG B 567 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 230 time to evaluate : 2.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.7746 (m-90) cc_final: 0.7522 (m-90) REVERT: A 990 GLU cc_start: 0.8445 (pp20) cc_final: 0.8207 (pp20) REVERT: B 55 PHE cc_start: 0.8133 (m-80) cc_final: 0.7602 (m-80) REVERT: B 177 MET cc_start: 0.7448 (pmm) cc_final: 0.6980 (pmm) REVERT: B 224 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7902 (mp0) REVERT: B 242 LEU cc_start: 0.8047 (mm) cc_final: 0.7716 (mm) REVERT: B 309 GLU cc_start: 0.8622 (mp0) cc_final: 0.8420 (mp0) REVERT: B 330 PRO cc_start: 0.8544 (Cg_exo) cc_final: 0.8245 (Cg_endo) REVERT: B 902 MET cc_start: 0.9071 (tpt) cc_final: 0.8777 (tpt) REVERT: B 945 LEU cc_start: 0.9260 (mt) cc_final: 0.9023 (mp) REVERT: B 955 ASN cc_start: 0.8094 (m110) cc_final: 0.7822 (t0) REVERT: B 970 PHE cc_start: 0.8886 (m-80) cc_final: 0.8682 (m-80) REVERT: C 52 GLN cc_start: 0.8022 (tm-30) cc_final: 0.7476 (tp40) REVERT: C 189 LEU cc_start: 0.9225 (tp) cc_final: 0.8348 (tp) REVERT: C 191 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7508 (mp0) REVERT: C 238 PHE cc_start: 0.6842 (p90) cc_final: 0.6393 (p90) REVERT: C 351 TYR cc_start: 0.8668 (p90) cc_final: 0.8155 (p90) REVERT: C 434 ILE cc_start: 0.3692 (OUTLIER) cc_final: 0.3449 (mt) REVERT: C 586 ASP cc_start: 0.7716 (t70) cc_final: 0.7400 (t0) REVERT: C 855 PHE cc_start: 0.8091 (m-80) cc_final: 0.7604 (m-80) REVERT: C 933 LYS cc_start: 0.8405 (mmtm) cc_final: 0.8032 (mttm) REVERT: C 950 ASP cc_start: 0.8426 (m-30) cc_final: 0.7920 (m-30) outliers start: 62 outliers final: 43 residues processed: 278 average time/residue: 0.3159 time to fit residues: 140.6479 Evaluate side-chains 242 residues out of total 2417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 197 time to evaluate : 2.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1051 SER Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 246 optimal weight: 0.0010 chunk 187 optimal weight: 0.0070 chunk 129 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 118 optimal weight: 0.6980 chunk 167 optimal weight: 0.9990 chunk 250 optimal weight: 2.9990 chunk 264 optimal weight: 0.0770 chunk 130 optimal weight: 1.9990 chunk 237 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 overall best weight: 0.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN C 935 GLN C1002 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.4571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 22755 Z= 0.143 Angle : 0.502 8.826 30950 Z= 0.262 Chirality : 0.043 0.188 3703 Planarity : 0.004 0.041 3920 Dihedral : 5.689 59.293 4087 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.61 % Allowed : 13.82 % Favored : 83.57 % 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: 0.89 (0.16), residues: 2699 helix: 2.44 (0.20), residues: 658 sheet: 0.47 (0.19), residues: 627 loop : -0.20 (0.16), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 104 HIS 0.006 0.001 HIS C 505 PHE 0.027 0.001 PHE C 220 TYR 0.021 0.001 TYR A1067 ARG 0.005 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 224 time to evaluate : 2.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 990 GLU cc_start: 0.8422 (pp20) cc_final: 0.8203 (pp20) REVERT: B 55 PHE cc_start: 0.8198 (m-80) cc_final: 0.7624 (m-80) REVERT: B 177 MET cc_start: 0.7397 (pmm) cc_final: 0.6947 (pmm) REVERT: B 242 LEU cc_start: 0.8089 (mm) cc_final: 0.7744 (mm) REVERT: B 330 PRO cc_start: 0.8510 (Cg_exo) cc_final: 0.8204 (Cg_endo) REVERT: B 853 GLN cc_start: 0.7044 (OUTLIER) cc_final: 0.6741 (mp10) REVERT: B 902 MET cc_start: 0.9114 (tpt) cc_final: 0.8780 (tpt) REVERT: B 945 LEU cc_start: 0.9264 (mt) cc_final: 0.9045 (mp) REVERT: C 52 GLN cc_start: 0.8023 (tm-30) cc_final: 0.7510 (tp40) REVERT: C 238 PHE cc_start: 0.6860 (p90) cc_final: 0.6386 (p90) REVERT: C 351 TYR cc_start: 0.8713 (p90) cc_final: 0.8186 (p90) REVERT: C 434 ILE cc_start: 0.3712 (OUTLIER) cc_final: 0.3499 (mt) REVERT: C 855 PHE cc_start: 0.8052 (m-80) cc_final: 0.7764 (m-80) REVERT: C 856 ASN cc_start: 0.9187 (m110) cc_final: 0.8898 (m-40) REVERT: C 868 GLU cc_start: 0.8035 (mp0) cc_final: 0.7828 (mp0) REVERT: C 900 MET cc_start: 0.8360 (mtp) cc_final: 0.8032 (mtm) REVERT: C 933 LYS cc_start: 0.8392 (mmtm) cc_final: 0.8048 (mttm) REVERT: C 950 ASP cc_start: 0.8414 (m-30) cc_final: 0.7892 (m-30) REVERT: C 957 GLN cc_start: 0.8286 (tt0) cc_final: 0.8060 (tt0) outliers start: 63 outliers final: 46 residues processed: 269 average time/residue: 0.2935 time to fit residues: 128.7882 Evaluate side-chains 246 residues out of total 2417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 198 time to evaluate : 2.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 853 GLN Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1018 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 220 optimal weight: 8.9990 chunk 150 optimal weight: 0.8980 chunk 3 optimal weight: 6.9990 chunk 197 optimal weight: 5.9990 chunk 109 optimal weight: 10.0000 chunk 226 optimal weight: 0.8980 chunk 183 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 135 optimal weight: 2.9990 chunk 237 optimal weight: 0.4980 chunk 66 optimal weight: 2.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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** A 824 ASN A1005 GLN A1142 GLN B 23 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 824 ASN ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B1058 HIS C 394 ASN C 450 ASN C 824 ASN C 856 ASN C 926 GLN C 960 ASN C1002 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.6156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 22755 Z= 0.337 Angle : 0.612 9.774 30950 Z= 0.319 Chirality : 0.047 0.193 3703 Planarity : 0.004 0.045 3920 Dihedral : 5.569 57.118 4085 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.19 % Allowed : 14.03 % Favored : 82.79 % 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: 0.55 (0.16), residues: 2699 helix: 1.94 (0.19), residues: 659 sheet: 0.21 (0.19), residues: 642 loop : -0.27 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 104 HIS 0.008 0.002 HIS A1058 PHE 0.027 0.002 PHE B 823 TYR 0.024 0.002 TYR A1067 ARG 0.005 0.001 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 209 time to evaluate : 2.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ASN cc_start: 0.7364 (m-40) cc_final: 0.6698 (p0) REVERT: A 157 PHE cc_start: 0.7621 (m-10) cc_final: 0.7394 (m-10) REVERT: A 170 TYR cc_start: 0.8062 (t80) cc_final: 0.7844 (t80) REVERT: A 200 TYR cc_start: 0.7816 (m-80) cc_final: 0.7595 (m-80) REVERT: A 201 PHE cc_start: 0.8290 (t80) cc_final: 0.7904 (t80) REVERT: B 55 PHE cc_start: 0.8251 (m-80) cc_final: 0.7789 (m-80) REVERT: B 177 MET cc_start: 0.7392 (pmm) cc_final: 0.6890 (pmm) REVERT: B 224 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7723 (mp0) REVERT: B 242 LEU cc_start: 0.8035 (mm) cc_final: 0.7668 (mm) REVERT: B 313 TYR cc_start: 0.8796 (m-80) cc_final: 0.8445 (m-80) REVERT: B 853 GLN cc_start: 0.7151 (OUTLIER) cc_final: 0.6824 (mp10) REVERT: B 868 GLU cc_start: 0.8375 (mp0) cc_final: 0.8054 (mp0) REVERT: B 955 ASN cc_start: 0.8450 (m110) cc_final: 0.8176 (t0) REVERT: C 50 SER cc_start: 0.9482 (p) cc_final: 0.9262 (m) REVERT: C 52 GLN cc_start: 0.8432 (tm-30) cc_final: 0.8221 (tm-30) REVERT: C 238 PHE cc_start: 0.7142 (p90) cc_final: 0.6940 (p90) REVERT: C 351 TYR cc_start: 0.8744 (p90) cc_final: 0.8267 (p90) REVERT: C 434 ILE cc_start: 0.4049 (OUTLIER) cc_final: 0.3827 (mt) REVERT: C 512 VAL cc_start: 0.8229 (OUTLIER) cc_final: 0.7745 (p) REVERT: C 572 THR cc_start: 0.7849 (m) cc_final: 0.7527 (p) REVERT: C 758 SER cc_start: 0.8950 (OUTLIER) cc_final: 0.8746 (p) REVERT: C 773 GLU cc_start: 0.8239 (tt0) cc_final: 0.7896 (tt0) REVERT: C 855 PHE cc_start: 0.8130 (m-80) cc_final: 0.7889 (m-80) REVERT: C 856 ASN cc_start: 0.9203 (m-40) cc_final: 0.8929 (m-40) REVERT: C 950 ASP cc_start: 0.8490 (m-30) cc_final: 0.7903 (m-30) REVERT: C 957 GLN cc_start: 0.8432 (tt0) cc_final: 0.8227 (tt0) outliers start: 77 outliers final: 45 residues processed: 269 average time/residue: 0.3144 time to fit residues: 139.5856 Evaluate side-chains 235 residues out of total 2417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 185 time to evaluate : 2.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 215 ASP Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 853 GLN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 758 SER Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 89 optimal weight: 3.9990 chunk 238 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 155 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 265 optimal weight: 0.6980 chunk 220 optimal weight: 0.9980 chunk 122 optimal weight: 0.6980 chunk 22 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 139 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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** A1005 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN C 245 HIS C 926 GLN C 960 ASN C1002 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.6373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22755 Z= 0.191 Angle : 0.518 10.414 30950 Z= 0.268 Chirality : 0.044 0.173 3703 Planarity : 0.004 0.038 3920 Dihedral : 5.306 56.408 4085 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.57 % Allowed : 14.85 % Favored : 82.58 % 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: 0.78 (0.16), residues: 2699 helix: 2.30 (0.20), residues: 665 sheet: 0.20 (0.19), residues: 674 loop : -0.15 (0.17), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 104 HIS 0.007 0.001 HIS C 245 PHE 0.026 0.001 PHE B 823 TYR 0.024 0.001 TYR B 170 ARG 0.005 0.000 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 197 time to evaluate : 2.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ASN cc_start: 0.7309 (m-40) cc_final: 0.6548 (p0) REVERT: A 157 PHE cc_start: 0.7633 (m-10) cc_final: 0.7432 (m-10) REVERT: A 200 TYR cc_start: 0.7757 (m-80) cc_final: 0.7442 (m-80) REVERT: A 902 MET cc_start: 0.8995 (tpp) cc_final: 0.8784 (tpt) REVERT: A 995 ARG cc_start: 0.8828 (mtp-110) cc_final: 0.8141 (mtp85) REVERT: B 55 PHE cc_start: 0.8275 (m-80) cc_final: 0.7659 (m-80) REVERT: B 177 MET cc_start: 0.7426 (pmm) cc_final: 0.6942 (pmm) REVERT: B 242 LEU cc_start: 0.8088 (mm) cc_final: 0.7481 (mp) REVERT: B 745 ASP cc_start: 0.8124 (p0) cc_final: 0.7812 (p0) REVERT: B 853 GLN cc_start: 0.7195 (OUTLIER) cc_final: 0.6887 (mp10) REVERT: B 868 GLU cc_start: 0.8315 (mp0) cc_final: 0.7974 (mp0) REVERT: B 955 ASN cc_start: 0.8431 (m110) cc_final: 0.8199 (t0) REVERT: C 52 GLN cc_start: 0.8403 (tm-30) cc_final: 0.7823 (tp40) REVERT: C 238 PHE cc_start: 0.7141 (p90) cc_final: 0.6914 (p90) REVERT: C 351 TYR cc_start: 0.8838 (p90) cc_final: 0.8428 (p90) REVERT: C 434 ILE cc_start: 0.4172 (OUTLIER) cc_final: 0.3863 (mt) REVERT: C 512 VAL cc_start: 0.8224 (OUTLIER) cc_final: 0.7998 (m) REVERT: C 773 GLU cc_start: 0.8182 (tt0) cc_final: 0.7900 (tt0) REVERT: C 855 PHE cc_start: 0.8182 (m-80) cc_final: 0.7890 (m-80) REVERT: C 900 MET cc_start: 0.8404 (mtp) cc_final: 0.8191 (mtm) REVERT: C 950 ASP cc_start: 0.8511 (m-30) cc_final: 0.7971 (m-30) REVERT: C 957 GLN cc_start: 0.8461 (tt0) cc_final: 0.8178 (tt0) outliers start: 62 outliers final: 37 residues processed: 240 average time/residue: 0.3147 time to fit residues: 125.9428 Evaluate side-chains 213 residues out of total 2417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 173 time to evaluate : 2.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 823 PHE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 853 GLN Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 745 ASP Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1017 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 255 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 151 optimal weight: 3.9990 chunk 193 optimal weight: 1.9990 chunk 149 optimal weight: 0.8980 chunk 223 optimal weight: 4.9990 chunk 148 optimal weight: 0.9990 chunk 264 optimal weight: 2.9990 chunk 165 optimal weight: 0.8980 chunk 161 optimal weight: 0.7980 chunk 121 optimal weight: 0.0670 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN C 23 GLN C 394 ASN ** C 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 GLN C 960 ASN C1002 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.6597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22755 Z= 0.188 Angle : 0.519 10.491 30950 Z= 0.266 Chirality : 0.043 0.167 3703 Planarity : 0.004 0.039 3920 Dihedral : 5.007 54.681 4085 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.28 % Allowed : 15.14 % Favored : 82.58 % 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: 0.89 (0.16), residues: 2699 helix: 2.41 (0.20), residues: 665 sheet: 0.25 (0.19), residues: 669 loop : -0.08 (0.17), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 104 HIS 0.004 0.001 HIS C 954 PHE 0.024 0.001 PHE B 823 TYR 0.021 0.001 TYR A1067 ARG 0.005 0.000 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 193 time to evaluate : 2.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ASN cc_start: 0.8241 (m-40) cc_final: 0.7682 (p0) REVERT: A 137 ASN cc_start: 0.7287 (m-40) cc_final: 0.6625 (p0) REVERT: A 200 TYR cc_start: 0.7829 (m-80) cc_final: 0.7471 (m-80) REVERT: A 201 PHE cc_start: 0.8171 (t80) cc_final: 0.7812 (t80) REVERT: B 55 PHE cc_start: 0.8130 (m-80) cc_final: 0.7655 (m-80) REVERT: B 177 MET cc_start: 0.7398 (pmm) cc_final: 0.6926 (pmm) REVERT: B 242 LEU cc_start: 0.8048 (mm) cc_final: 0.7454 (mp) REVERT: B 269 TYR cc_start: 0.7501 (m-80) cc_final: 0.7194 (m-10) REVERT: B 745 ASP cc_start: 0.8196 (p0) cc_final: 0.7876 (p0) REVERT: B 853 GLN cc_start: 0.7384 (OUTLIER) cc_final: 0.7105 (mp10) REVERT: B 868 GLU cc_start: 0.8307 (mp0) cc_final: 0.7977 (mp0) REVERT: B 955 ASN cc_start: 0.8436 (m110) cc_final: 0.8218 (t0) REVERT: C 52 GLN cc_start: 0.8495 (tm-30) cc_final: 0.7900 (tp40) REVERT: C 351 TYR cc_start: 0.8828 (p90) cc_final: 0.8407 (p90) REVERT: C 434 ILE cc_start: 0.4083 (OUTLIER) cc_final: 0.3793 (mt) REVERT: C 773 GLU cc_start: 0.8177 (tt0) cc_final: 0.7904 (tt0) REVERT: C 855 PHE cc_start: 0.8200 (m-80) cc_final: 0.7943 (m-80) REVERT: C 900 MET cc_start: 0.8471 (mtp) cc_final: 0.8208 (mtm) REVERT: C 950 ASP cc_start: 0.8459 (m-30) cc_final: 0.7916 (m-30) REVERT: C 957 GLN cc_start: 0.8426 (tt0) cc_final: 0.8152 (tt0) outliers start: 55 outliers final: 44 residues processed: 238 average time/residue: 0.2943 time to fit residues: 116.7713 Evaluate side-chains 228 residues out of total 2417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 182 time to evaluate : 2.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 853 GLN Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 963 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 163 optimal weight: 2.9990 chunk 105 optimal weight: 6.9990 chunk 157 optimal weight: 0.6980 chunk 79 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 chunk 167 optimal weight: 0.7980 chunk 179 optimal weight: 5.9990 chunk 130 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 207 optimal weight: 0.9990 chunk 240 optimal weight: 0.0070 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 GLN C 960 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.6753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22755 Z= 0.166 Angle : 0.515 11.900 30950 Z= 0.262 Chirality : 0.043 0.169 3703 Planarity : 0.004 0.052 3920 Dihedral : 4.874 55.113 4085 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.36 % Allowed : 15.64 % Favored : 82.00 % 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: 0.96 (0.16), residues: 2699 helix: 2.52 (0.20), residues: 665 sheet: 0.23 (0.19), residues: 668 loop : -0.03 (0.17), residues: 1366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 104 HIS 0.003 0.001 HIS C 954 PHE 0.022 0.001 PHE B 823 TYR 0.030 0.001 TYR B 170 ARG 0.004 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 196 time to evaluate : 2.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8533 (tm-30) cc_final: 0.8327 (tm-30) REVERT: A 99 ASN cc_start: 0.8267 (m-40) cc_final: 0.7710 (p0) REVERT: A 200 TYR cc_start: 0.7776 (m-80) cc_final: 0.7503 (m-80) REVERT: B 55 PHE cc_start: 0.8154 (m-80) cc_final: 0.7678 (m-80) REVERT: B 177 MET cc_start: 0.7264 (pmm) cc_final: 0.6816 (pmm) REVERT: B 242 LEU cc_start: 0.8187 (mm) cc_final: 0.7665 (mp) REVERT: B 269 TYR cc_start: 0.7540 (m-80) cc_final: 0.7291 (m-10) REVERT: B 745 ASP cc_start: 0.8193 (p0) cc_final: 0.7874 (p0) REVERT: B 853 GLN cc_start: 0.7479 (OUTLIER) cc_final: 0.7005 (pm20) REVERT: B 868 GLU cc_start: 0.8289 (mp0) cc_final: 0.7961 (mp0) REVERT: B 955 ASN cc_start: 0.8431 (m110) cc_final: 0.8213 (t0) REVERT: B 995 ARG cc_start: 0.8695 (ttm-80) cc_final: 0.8422 (ptm160) REVERT: C 52 GLN cc_start: 0.8513 (tm-30) cc_final: 0.7900 (tp40) REVERT: C 53 ASP cc_start: 0.7577 (t0) cc_final: 0.7232 (t0) REVERT: C 351 TYR cc_start: 0.8843 (p90) cc_final: 0.8437 (p90) REVERT: C 434 ILE cc_start: 0.4153 (OUTLIER) cc_final: 0.3859 (mt) REVERT: C 756 TYR cc_start: 0.9031 (m-80) cc_final: 0.8628 (m-80) REVERT: C 773 GLU cc_start: 0.8187 (tt0) cc_final: 0.7923 (tt0) REVERT: C 855 PHE cc_start: 0.8156 (m-10) cc_final: 0.7933 (m-80) REVERT: C 900 MET cc_start: 0.8437 (mtp) cc_final: 0.8197 (mtm) REVERT: C 950 ASP cc_start: 0.8448 (m-30) cc_final: 0.7975 (m-30) REVERT: C 957 GLN cc_start: 0.8444 (tt0) cc_final: 0.8192 (tt0) REVERT: C 994 ASP cc_start: 0.8416 (m-30) cc_final: 0.8180 (t70) outliers start: 57 outliers final: 41 residues processed: 240 average time/residue: 0.3141 time to fit residues: 123.7538 Evaluate side-chains 224 residues out of total 2417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 181 time to evaluate : 2.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 853 GLN Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 515 PHE 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 961 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 253 optimal weight: 3.9990 chunk 230 optimal weight: 1.9990 chunk 246 optimal weight: 0.0470 chunk 252 optimal weight: 0.9980 chunk 148 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 193 optimal weight: 0.9980 chunk 75 optimal weight: 0.6980 chunk 222 optimal weight: 0.0270 chunk 232 optimal weight: 4.9990 chunk 245 optimal weight: 5.9990 overall best weight: 0.5536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 GLN B 207 HIS ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 978 ASN ** C 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 GLN C 960 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.6895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22755 Z= 0.164 Angle : 0.517 11.582 30950 Z= 0.263 Chirality : 0.043 0.182 3703 Planarity : 0.004 0.059 3920 Dihedral : 4.754 54.498 4085 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.15 % Allowed : 15.89 % Favored : 81.96 % 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: 0.99 (0.16), residues: 2699 helix: 2.70 (0.20), residues: 647 sheet: 0.18 (0.18), residues: 668 loop : -0.02 (0.17), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 104 HIS 0.003 0.001 HIS C 954 PHE 0.023 0.001 PHE B 823 TYR 0.023 0.001 TYR B 170 ARG 0.007 0.000 ARG A1019 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 204 time to evaluate : 2.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8573 (tm-30) cc_final: 0.8355 (tm-30) REVERT: A 99 ASN cc_start: 0.8280 (m-40) cc_final: 0.7771 (p0) REVERT: A 200 TYR cc_start: 0.7834 (m-80) cc_final: 0.7520 (m-80) REVERT: A 201 PHE cc_start: 0.8171 (t80) cc_final: 0.7866 (t80) REVERT: A 239 GLN cc_start: 0.7816 (tt0) cc_final: 0.7395 (tp40) REVERT: B 55 PHE cc_start: 0.8176 (m-80) cc_final: 0.7668 (m-80) REVERT: B 177 MET cc_start: 0.7077 (pmm) cc_final: 0.6837 (pmm) REVERT: B 242 LEU cc_start: 0.8146 (mm) cc_final: 0.7627 (mp) REVERT: B 755 GLN cc_start: 0.8873 (mt0) cc_final: 0.8610 (tt0) REVERT: B 853 GLN cc_start: 0.7445 (OUTLIER) cc_final: 0.6986 (pm20) REVERT: B 868 GLU cc_start: 0.8255 (mp0) cc_final: 0.7939 (mp0) REVERT: C 52 GLN cc_start: 0.8558 (tm-30) cc_final: 0.8327 (tm-30) REVERT: C 351 TYR cc_start: 0.8836 (p90) cc_final: 0.8425 (p90) REVERT: C 434 ILE cc_start: 0.4117 (OUTLIER) cc_final: 0.3815 (mt) REVERT: C 756 TYR cc_start: 0.8993 (m-80) cc_final: 0.8738 (m-80) REVERT: C 773 GLU cc_start: 0.8194 (tt0) cc_final: 0.7935 (tt0) REVERT: C 855 PHE cc_start: 0.8140 (m-10) cc_final: 0.7847 (m-80) REVERT: C 900 MET cc_start: 0.8454 (mtp) cc_final: 0.8191 (mtm) REVERT: C 923 ILE cc_start: 0.9508 (OUTLIER) cc_final: 0.9264 (mp) REVERT: C 950 ASP cc_start: 0.8440 (m-30) cc_final: 0.7963 (m-30) REVERT: C 957 GLN cc_start: 0.8459 (tt0) cc_final: 0.8226 (tt0) REVERT: C 1017 GLU cc_start: 0.8373 (tt0) cc_final: 0.8068 (tt0) outliers start: 52 outliers final: 41 residues processed: 247 average time/residue: 0.3008 time to fit residues: 121.3663 Evaluate side-chains 230 residues out of total 2417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 186 time to evaluate : 2.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 853 GLN Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 934 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 161 optimal weight: 2.9990 chunk 260 optimal weight: 1.9990 chunk 158 optimal weight: 0.5980 chunk 123 optimal weight: 6.9990 chunk 180 optimal weight: 6.9990 chunk 272 optimal weight: 0.4980 chunk 251 optimal weight: 1.9990 chunk 217 optimal weight: 0.0980 chunk 22 optimal weight: 5.9990 chunk 167 optimal weight: 0.3980 chunk 133 optimal weight: 0.8980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN C 926 GLN C 935 GLN C 957 GLN C 960 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.7010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 22755 Z= 0.160 Angle : 0.532 12.214 30950 Z= 0.269 Chirality : 0.043 0.177 3703 Planarity : 0.004 0.063 3920 Dihedral : 4.700 54.596 4085 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.03 % Allowed : 16.30 % Favored : 81.67 % 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: 0.98 (0.16), residues: 2699 helix: 2.71 (0.20), residues: 648 sheet: 0.12 (0.18), residues: 678 loop : -0.01 (0.17), residues: 1373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 104 HIS 0.003 0.001 HIS C 954 PHE 0.024 0.001 PHE B 823 TYR 0.028 0.001 TYR B 170 ARG 0.006 0.000 ARG A1019 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5398 Ramachandran restraints generated. 2699 Oldfield, 0 Emsley, 2699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 196 time to evaluate : 2.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8537 (tm-30) cc_final: 0.8325 (tm-30) REVERT: A 99 ASN cc_start: 0.8279 (m-40) cc_final: 0.7805 (p0) REVERT: A 200 TYR cc_start: 0.7812 (m-80) cc_final: 0.7502 (m-80) REVERT: A 201 PHE cc_start: 0.8197 (t80) cc_final: 0.7894 (t80) REVERT: A 995 ARG cc_start: 0.8861 (mtp-110) cc_final: 0.8362 (mtp85) REVERT: B 55 PHE cc_start: 0.8196 (m-80) cc_final: 0.7699 (m-80) REVERT: B 177 MET cc_start: 0.7048 (pmm) cc_final: 0.6613 (pmm) REVERT: B 242 LEU cc_start: 0.8147 (mm) cc_final: 0.7604 (mp) REVERT: B 269 TYR cc_start: 0.7573 (m-10) cc_final: 0.7170 (m-10) REVERT: B 755 GLN cc_start: 0.8902 (mt0) cc_final: 0.8623 (tt0) REVERT: B 853 GLN cc_start: 0.7546 (OUTLIER) cc_final: 0.7125 (pm20) REVERT: B 868 GLU cc_start: 0.8243 (mp0) cc_final: 0.7934 (mp0) REVERT: C 52 GLN cc_start: 0.8531 (tm-30) cc_final: 0.8290 (tm-30) REVERT: C 351 TYR cc_start: 0.8842 (p90) cc_final: 0.8448 (p90) REVERT: C 434 ILE cc_start: 0.4189 (OUTLIER) cc_final: 0.3903 (mt) REVERT: C 773 GLU cc_start: 0.8193 (tt0) cc_final: 0.7940 (tt0) REVERT: C 855 PHE cc_start: 0.8055 (m-10) cc_final: 0.7799 (m-80) REVERT: C 900 MET cc_start: 0.8445 (mtp) cc_final: 0.8183 (mtm) REVERT: C 923 ILE cc_start: 0.9501 (OUTLIER) cc_final: 0.9257 (mp) REVERT: C 950 ASP cc_start: 0.8440 (m-30) cc_final: 0.8012 (m-30) REVERT: C 957 GLN cc_start: 0.8490 (tt0) cc_final: 0.8244 (tt0) REVERT: C 1017 GLU cc_start: 0.8344 (tt0) cc_final: 0.8072 (tt0) outliers start: 49 outliers final: 41 residues processed: 237 average time/residue: 0.2956 time to fit residues: 116.0534 Evaluate side-chains 231 residues out of total 2417 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 187 time to evaluate : 2.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 853 GLN Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 923 ILE Chi-restraints excluded: chain C residue 934 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 172 optimal weight: 1.9990 chunk 231 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 200 optimal weight: 10.0000 chunk 32 optimal weight: 8.9990 chunk 60 optimal weight: 0.5980 chunk 217 optimal weight: 0.0470 chunk 91 optimal weight: 0.9990 chunk 223 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 overall best weight: 0.6880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN C 926 GLN C 935 GLN C 960 ASN C1010 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.107093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.070266 restraints weight = 53348.960| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 3.24 r_work: 0.3018 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.7109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22755 Z= 0.182 Angle : 0.537 11.860 30950 Z= 0.272 Chirality : 0.044 0.210 3703 Planarity : 0.004 0.062 3920 Dihedral : 4.690 54.317 4085 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.11 % Allowed : 16.34 % Favored : 81.55 % 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: 1.00 (0.16), residues: 2699 helix: 2.73 (0.20), residues: 647 sheet: 0.18 (0.19), residues: 666 loop : -0.03 (0.17), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 104 HIS 0.007 0.001 HIS C 207 PHE 0.024 0.001 PHE B 823 TYR 0.022 0.001 TYR B 170 ARG 0.006 0.000 ARG A1019 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5048.93 seconds wall clock time: 92 minutes 19.58 seconds (5539.58 seconds total)