Starting phenix.real_space_refine on Tue Nov 19 20:20:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xtz_33453/11_2024/7xtz_33453_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xtz_33453/11_2024/7xtz_33453.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xtz_33453/11_2024/7xtz_33453.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xtz_33453/11_2024/7xtz_33453.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xtz_33453/11_2024/7xtz_33453_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xtz_33453/11_2024/7xtz_33453_trim.cif" } resolution = 2.8 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= 0.006 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: 5 Type Number sf(0) Gaussians S 126 5.16 5 C 17100 2.51 5 N 4383 2.21 5 O 5259 1.98 5 H 25032 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 51900 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 16915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 16915 Classifications: {'peptide': 1097} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 50, 'TRANS': 1046} Chain breaks: 3 Chain: "B" Number of atoms: 16915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 16915 Classifications: {'peptide': 1097} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 50, 'TRANS': 1046} Chain breaks: 3 Chain: "C" Number of atoms: 16915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1097, 16915 Classifications: {'peptide': 1097} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 50, 'TRANS': 1046} Chain breaks: 3 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: "A" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 245 Unusual residues: {'BLA': 1, 'EIC': 1, 'NAG': 13} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 245 Unusual residues: {'BLA': 1, 'EIC': 1, 'NAG': 13} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 245 Unusual residues: {'BLA': 1, 'EIC': 1, 'NAG': 13} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Time building chain proxies: 23.87, per 1000 atoms: 0.46 Number of scatterers: 51900 At special positions: 0 Unit cell: (143.235, 152.784, 171.882, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 126 16.00 O 5259 8.00 N 4383 7.00 C 17100 6.00 H 25032 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, 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=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 427 " - pdb=" SG CYS B 987 " distance=2.02 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A 987 " - pdb=" SG CYS C 427 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 427 " - pdb=" SG CYS C 987 " distance=2.02 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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-ASN " NAG A1201 " - " ASN A 331 " " NAG A1202 " - " ASN A 603 " " NAG A1203 " - " ASN A 616 " " NAG A1204 " - " ASN A 657 " " NAG A1205 " - " ASN A 709 " " NAG A1206 " - " ASN A1074 " " NAG A1207 " - " ASN A1098 " " NAG A1208 " - " ASN A 165 " " NAG A1209 " - " ASN A 282 " " NAG A1210 " - " ASN A 343 " " NAG A1211 " - " ASN A 17 " " NAG A1212 " - " ASN A 61 " " NAG A1213 " - " ASN A 149 " " NAG B1602 " - " ASN B 331 " " NAG B1603 " - " ASN B 603 " " NAG B1604 " - " ASN B 616 " " NAG B1605 " - " ASN B 657 " " NAG B1606 " - " ASN B 709 " " NAG B1607 " - " ASN B1074 " " NAG B1608 " - " ASN B1098 " " NAG B1609 " - " ASN B 165 " " NAG B1610 " - " ASN B 282 " " NAG B1611 " - " ASN B 343 " " NAG B1612 " - " ASN B 17 " " NAG B1613 " - " ASN B 61 " " NAG B1614 " - " ASN B 149 " " NAG C1602 " - " ASN C 331 " " NAG C1603 " - " ASN C 603 " " NAG C1604 " - " ASN C 616 " " NAG C1605 " - " ASN C 657 " " NAG C1606 " - " ASN C 709 " " NAG C1607 " - " ASN C1074 " " NAG C1608 " - " ASN C1098 " " NAG C1609 " - " ASN C 165 " " NAG C1610 " - " ASN C 282 " " NAG C1611 " - " ASN C 343 " " NAG C1612 " - " ASN C 17 " " NAG C1613 " - " ASN C 61 " " NAG C1614 " - " ASN C 149 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN A 801 " " NAG F 1 " - " ASN A1134 " " NAG G 1 " - " ASN A 234 " " NAG H 1 " - " ASN A 122 " " NAG I 1 " - " ASN B 717 " " NAG J 1 " - " ASN B 801 " " NAG K 1 " - " ASN B1134 " " NAG L 1 " - " ASN B 234 " " NAG M 1 " - " ASN B 122 " " NAG N 1 " - " ASN C 717 " " NAG O 1 " - " ASN C 801 " " NAG P 1 " - " ASN C1134 " " NAG Q 1 " - " ASN C 234 " " NAG R 1 " - " ASN C 122 " Time building additional restraints: 12.96 Conformation dependent library (CDL) restraints added in 3.5 seconds 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6150 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 48 sheets defined 24.3% alpha, 28.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.36 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.592A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.283A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 756 through 783 Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.713A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 843 Processing helix chain 'A' and resid 848 through 855 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: 4.165A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.650A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.555A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 5.337A pdb=" N VAL A 991 " --> pdb=" O CYS A 987 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 383 through 389 removed outlier: 3.583A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.282A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 756 through 783 Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.719A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 836 through 843 Processing helix chain 'B' and resid 848 through 855 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.172A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.645A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.561A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 5.332A pdb=" N VAL B 991 " --> pdb=" O CYS B 987 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 383 through 389 removed outlier: 3.599A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.282A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 756 through 783 Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.721A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 836 through 843 Processing helix chain 'C' and resid 848 through 855 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.166A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.653A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.548A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.335A pdb=" N VAL C 991 " --> pdb=" O CYS C 987 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.836A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.329A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.920A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.496A pdb=" N VAL A 126 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N VAL A 171 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ILE A 128 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLU A 169 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N VAL A 130 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLU A 132 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N ASN A 165 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N GLN A 134 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ALA A 163 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.649A pdb=" N CYS A 136 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N SER A 161 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ASP A 138 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL A 159 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N PHE A 140 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N PHE A 157 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N MET A 153 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 83 through 85 Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 315 removed outlier: 4.741A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 325 removed outlier: 6.831A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.507A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.937A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.558A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.477A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.936A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.518A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.117A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.449A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.679A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.834A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.899A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.483A pdb=" N VAL B 126 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N VAL B 171 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ILE B 128 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLU B 169 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLU B 132 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N ASN B 165 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N GLN B 134 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ALA B 163 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.652A pdb=" N CYS B 136 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N SER B 161 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ASP B 138 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N VAL B 159 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N MET B 153 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 83 through 85 Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 315 removed outlier: 4.735A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.931A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.536A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL B 524 " --> pdb=" O PHE B 392 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.482A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.546A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.110A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.462A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 787 through 788 Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.667A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.846A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.881A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 83 through 85 removed outlier: 6.486A pdb=" N VAL C 126 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL C 171 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ILE C 128 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLU C 169 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N VAL C 130 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLU C 132 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N ASN C 165 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N GLN C 134 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ALA C 163 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N CYS C 136 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N SER C 161 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ASP C 138 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N VAL C 159 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N PHE C 140 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N PHE C 157 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N MET C 153 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 83 through 85 Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 315 removed outlier: 4.725A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 324 through 325 removed outlier: 6.846A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.937A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.552A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL C 524 " --> pdb=" O PHE C 392 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE7, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.474A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.543A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.120A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.454A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.683A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1114 hydrogen bonds defined for protein. 3054 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: 24.37 Time building geometry restraints manager: 15.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 25026 1.03 - 1.23: 350 1.23 - 1.43: 11150 1.43 - 1.63: 15818 1.63 - 1.82: 156 Bond restraints: 52500 Sorted by residual: bond pdb=" C4C BLA C1615 " pdb=" NC BLA C1615 " ideal model delta sigma weight residual 1.375 1.536 -0.161 2.00e-02 2.50e+03 6.51e+01 bond pdb=" C4C BLA A1214 " pdb=" NC BLA A1214 " ideal model delta sigma weight residual 1.375 1.536 -0.161 2.00e-02 2.50e+03 6.49e+01 bond pdb=" C4C BLA B1615 " pdb=" NC BLA B1615 " ideal model delta sigma weight residual 1.375 1.536 -0.161 2.00e-02 2.50e+03 6.49e+01 bond pdb=" C1C BLA A1214 " pdb=" NC BLA A1214 " ideal model delta sigma weight residual 1.368 1.528 -0.160 2.00e-02 2.50e+03 6.40e+01 bond pdb=" C1C BLA B1615 " pdb=" NC BLA B1615 " ideal model delta sigma weight residual 1.368 1.527 -0.159 2.00e-02 2.50e+03 6.35e+01 ... (remaining 52495 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.05: 93921 5.05 - 10.09: 90 10.09 - 15.14: 3 15.14 - 20.18: 0 20.18 - 25.23: 3 Bond angle restraints: 94017 Sorted by residual: angle pdb=" C11 EIC C1601 " pdb=" C10 EIC C1601 " pdb=" C9 EIC C1601 " ideal model delta sigma weight residual 127.32 102.09 25.23 3.00e+00 1.11e-01 7.07e+01 angle pdb=" C11 EIC B1601 " pdb=" C10 EIC B1601 " pdb=" C9 EIC B1601 " ideal model delta sigma weight residual 127.32 105.09 22.23 3.00e+00 1.11e-01 5.49e+01 angle pdb=" C11 EIC A1215 " pdb=" C10 EIC A1215 " pdb=" C9 EIC A1215 " ideal model delta sigma weight residual 127.32 106.40 20.92 3.00e+00 1.11e-01 4.86e+01 angle pdb=" CB LYS A 786 " pdb=" CG LYS A 786 " pdb=" CD LYS A 786 " ideal model delta sigma weight residual 111.30 120.21 -8.91 2.30e+00 1.89e-01 1.50e+01 angle pdb=" CB LYS C 786 " pdb=" CG LYS C 786 " pdb=" CD LYS C 786 " ideal model delta sigma weight residual 111.30 120.18 -8.88 2.30e+00 1.89e-01 1.49e+01 ... (remaining 94012 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 23808 17.65 - 35.31: 1727 35.31 - 52.96: 478 52.96 - 70.62: 144 70.62 - 88.27: 36 Dihedral angle restraints: 26193 sinusoidal: 14673 harmonic: 11520 Sorted by residual: dihedral pdb=" CB CYS C 291 " pdb=" SG CYS C 291 " pdb=" SG CYS C 301 " pdb=" CB CYS C 301 " ideal model delta sinusoidal sigma weight residual 93.00 154.16 -61.16 1 1.00e+01 1.00e-02 4.97e+01 dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual 93.00 154.05 -61.05 1 1.00e+01 1.00e-02 4.95e+01 dihedral pdb=" CB CYS B 291 " pdb=" SG CYS B 291 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual 93.00 153.97 -60.97 1 1.00e+01 1.00e-02 4.94e+01 ... (remaining 26190 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 3848 0.080 - 0.160: 525 0.160 - 0.240: 13 0.240 - 0.320: 0 0.320 - 0.400: 6 Chirality restraints: 4392 Sorted by residual: chirality pdb=" C1 NAG C1613 " pdb=" ND2 ASN C 61 " pdb=" C2 NAG C1613 " pdb=" O5 NAG C1613 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 4.01e+00 chirality pdb=" C1 NAG A1212 " pdb=" ND2 ASN A 61 " pdb=" C2 NAG A1212 " pdb=" O5 NAG A1212 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 4.01e+00 chirality pdb=" C1 NAG B1613 " pdb=" ND2 ASN B 61 " pdb=" C2 NAG B1613 " pdb=" O5 NAG B1613 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 4.00e+00 ... (remaining 4389 not shown) Planarity restraints: 7917 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" ND BLA B1615 " -0.067 2.00e-02 2.50e+03 8.19e-02 1.68e+02 pdb=" C1A BLA B1615 " 0.186 2.00e-02 2.50e+03 pdb=" C1D BLA B1615 " -0.014 2.00e-02 2.50e+03 pdb=" C2D BLA B1615 " 0.015 2.00e-02 2.50e+03 pdb=" C3D BLA B1615 " -0.018 2.00e-02 2.50e+03 pdb=" C4D BLA B1615 " -0.070 2.00e-02 2.50e+03 pdb=" CAD BLA B1615 " 0.010 2.00e-02 2.50e+03 pdb=" CHA BLA B1615 " -0.123 2.00e-02 2.50e+03 pdb=" CHD BLA B1615 " -0.003 2.00e-02 2.50e+03 pdb=" CMD BLA B1615 " 0.084 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" ND BLA C1615 " -0.066 2.00e-02 2.50e+03 8.17e-02 1.67e+02 pdb=" C1A BLA C1615 " 0.186 2.00e-02 2.50e+03 pdb=" C1D BLA C1615 " -0.014 2.00e-02 2.50e+03 pdb=" C2D BLA C1615 " 0.016 2.00e-02 2.50e+03 pdb=" C3D BLA C1615 " -0.018 2.00e-02 2.50e+03 pdb=" C4D BLA C1615 " -0.069 2.00e-02 2.50e+03 pdb=" CAD BLA C1615 " 0.010 2.00e-02 2.50e+03 pdb=" CHA BLA C1615 " -0.123 2.00e-02 2.50e+03 pdb=" CHD BLA C1615 " -0.004 2.00e-02 2.50e+03 pdb=" CMD BLA C1615 " 0.084 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" ND BLA A1214 " -0.067 2.00e-02 2.50e+03 8.17e-02 1.67e+02 pdb=" C1A BLA A1214 " 0.185 2.00e-02 2.50e+03 pdb=" C1D BLA A1214 " -0.015 2.00e-02 2.50e+03 pdb=" C2D BLA A1214 " 0.016 2.00e-02 2.50e+03 pdb=" C3D BLA A1214 " -0.019 2.00e-02 2.50e+03 pdb=" C4D BLA A1214 " -0.069 2.00e-02 2.50e+03 pdb=" CAD BLA A1214 " 0.010 2.00e-02 2.50e+03 pdb=" CHA BLA A1214 " -0.123 2.00e-02 2.50e+03 pdb=" CHD BLA A1214 " -0.003 2.00e-02 2.50e+03 pdb=" CMD BLA A1214 " 0.084 2.00e-02 2.50e+03 ... (remaining 7914 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.27: 6969 2.27 - 2.85: 113239 2.85 - 3.43: 130934 3.43 - 4.02: 192693 4.02 - 4.60: 286532 Nonbonded interactions: 730367 Sorted by model distance: nonbonded pdb=" HG1 THR C1077 " pdb=" O PHE C1095 " model vdw 1.686 2.450 nonbonded pdb=" HG1 THR B1077 " pdb=" O PHE B1095 " model vdw 1.689 2.450 nonbonded pdb=" HG1 THR A1077 " pdb=" O PHE A1095 " model vdw 1.689 2.450 nonbonded pdb=" HH TYR C 37 " pdb=" O LEU C 54 " model vdw 1.697 2.450 nonbonded pdb=" HH TYR B 37 " pdb=" O LEU B 54 " model vdw 1.697 2.450 ... (remaining 730362 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 1141 or resid 1202 through 1213)) selection = (chain 'B' and (resid 14 through 1141 or resid 1602 through 1613)) selection = (chain 'C' and (resid 14 through 1141 or resid 1602 through 1613)) } 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' } 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=0.00 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: 3.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.850 Extract box with map and model: 2.030 Check model and map are aligned: 0.330 Set scattering table: 0.480 Process input model: 105.890 Find NCS groups from input model: 2.340 Set up NCS constraints: 0.250 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:10.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 126.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 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 : 0.012 0.161 27468 Z= 0.813 Angle : 0.905 25.230 37362 Z= 0.407 Chirality : 0.053 0.400 4392 Planarity : 0.005 0.082 4740 Dihedral : 13.646 88.273 10965 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 0.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.42 % Allowed : 0.38 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.29 (0.14), residues: 3267 helix: 1.17 (0.20), residues: 714 sheet: 0.62 (0.18), residues: 711 loop : -1.12 (0.14), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 152 HIS 0.002 0.000 HIS A1048 PHE 0.034 0.002 PHE C 823 TYR 0.022 0.001 TYR B 365 ARG 0.006 0.001 ARG C 646 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 163 time to evaluate : 3.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 902 MET cc_start: 0.8429 (tpp) cc_final: 0.8195 (tpp) outliers start: 12 outliers final: 3 residues processed: 166 average time/residue: 2.6562 time to fit residues: 526.9536 Evaluate side-chains 117 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 114 time to evaluate : 4.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain C residue 227 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 276 optimal weight: 0.8980 chunk 247 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 167 optimal weight: 0.5980 chunk 132 optimal weight: 9.9990 chunk 256 optimal weight: 0.5980 chunk 99 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 190 optimal weight: 1.9990 chunk 296 optimal weight: 4.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 GLN A 901 GLN B 901 GLN C 901 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.0816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 27468 Z= 0.271 Angle : 0.531 5.917 37362 Z= 0.278 Chirality : 0.046 0.403 4392 Planarity : 0.004 0.042 4740 Dihedral : 8.495 88.947 5118 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 0.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.70 % Allowed : 3.84 % Favored : 95.46 % 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: -0.23 (0.14), residues: 3267 helix: 1.42 (0.20), residues: 717 sheet: 0.50 (0.18), residues: 738 loop : -1.11 (0.14), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 152 HIS 0.003 0.001 HIS A1088 PHE 0.013 0.001 PHE A 32 TYR 0.017 0.001 TYR B 365 ARG 0.003 0.000 ARG B1107 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 3.887 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 1050 MET cc_start: 0.8725 (OUTLIER) cc_final: 0.8497 (ptm) REVERT: B 153 MET cc_start: 0.7632 (ptt) cc_final: 0.7381 (ptt) REVERT: C 780 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7576 (mt-10) outliers start: 20 outliers final: 5 residues processed: 135 average time/residue: 2.5374 time to fit residues: 415.0136 Evaluate side-chains 117 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 110 time to evaluate : 4.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 780 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 165 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 247 optimal weight: 1.9990 chunk 202 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 297 optimal weight: 3.9990 chunk 321 optimal weight: 0.8980 chunk 264 optimal weight: 0.9980 chunk 295 optimal weight: 2.9990 chunk 101 optimal weight: 0.0980 chunk 238 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 ASN A 901 GLN B1005 GLN C 66 HIS ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 27468 Z= 0.258 Angle : 0.505 5.957 37362 Z= 0.265 Chirality : 0.045 0.373 4392 Planarity : 0.003 0.036 4740 Dihedral : 7.585 86.053 5118 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 0.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.94 % Allowed : 4.51 % Favored : 94.55 % 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: -0.26 (0.14), residues: 3267 helix: 1.36 (0.20), residues: 732 sheet: 0.48 (0.18), residues: 753 loop : -1.15 (0.14), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 152 HIS 0.005 0.001 HIS A 146 PHE 0.014 0.001 PHE A 32 TYR 0.015 0.001 TYR B 365 ARG 0.002 0.000 ARG C1107 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 116 time to evaluate : 4.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 780 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7499 (mt-10) REVERT: B 153 MET cc_start: 0.7790 (ptt) cc_final: 0.7508 (ptt) REVERT: C 780 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7534 (mt-10) outliers start: 27 outliers final: 8 residues processed: 138 average time/residue: 2.3029 time to fit residues: 390.7417 Evaluate side-chains 121 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 3.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 1123 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 293 optimal weight: 0.4980 chunk 223 optimal weight: 4.9990 chunk 154 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 199 optimal weight: 1.9990 chunk 298 optimal weight: 2.9990 chunk 316 optimal weight: 1.9990 chunk 155 optimal weight: 0.8980 chunk 282 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 ASN B 856 ASN B1005 GLN C 66 HIS ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 27468 Z= 0.315 Angle : 0.513 5.838 37362 Z= 0.270 Chirality : 0.046 0.366 4392 Planarity : 0.003 0.038 4740 Dihedral : 7.084 84.330 5118 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 1.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.80 % Allowed : 5.66 % Favored : 93.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.14), residues: 3267 helix: 1.36 (0.20), residues: 732 sheet: 0.45 (0.18), residues: 756 loop : -1.15 (0.13), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.003 0.000 HIS A 146 PHE 0.015 0.001 PHE A 32 TYR 0.017 0.001 TYR B 365 ARG 0.002 0.000 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 109 time to evaluate : 3.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 780 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7547 (mt-10) REVERT: B 153 MET cc_start: 0.7815 (ptt) cc_final: 0.7463 (ptt) REVERT: C 212 LEU cc_start: 0.7355 (OUTLIER) cc_final: 0.7063 (tp) REVERT: C 780 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7467 (mt-10) outliers start: 23 outliers final: 11 residues processed: 130 average time/residue: 2.4791 time to fit residues: 394.8049 Evaluate side-chains 119 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 3.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 1123 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 263 optimal weight: 3.9990 chunk 179 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 235 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 269 optimal weight: 0.0670 chunk 218 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 161 optimal weight: 1.9990 chunk 283 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 ASN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.133 27468 Z= 0.222 Angle : 0.491 8.736 37362 Z= 0.261 Chirality : 0.045 0.349 4392 Planarity : 0.003 0.030 4740 Dihedral : 6.767 84.943 5118 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 1.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.70 % Allowed : 6.46 % Favored : 92.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.14), residues: 3267 helix: 1.51 (0.20), residues: 732 sheet: 0.45 (0.18), residues: 753 loop : -1.10 (0.14), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.032 0.001 HIS C 66 PHE 0.013 0.001 PHE A 32 TYR 0.013 0.001 TYR B 365 ARG 0.002 0.000 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 4.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 780 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7514 (mt-10) REVERT: B 153 MET cc_start: 0.7808 (ptt) cc_final: 0.7439 (ptt) REVERT: C 780 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7474 (mt-10) outliers start: 20 outliers final: 9 residues processed: 133 average time/residue: 2.5096 time to fit residues: 408.4858 Evaluate side-chains 119 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 108 time to evaluate : 4.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 780 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 106 optimal weight: 1.9990 chunk 284 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 185 optimal weight: 7.9990 chunk 78 optimal weight: 3.9990 chunk 316 optimal weight: 1.9990 chunk 262 optimal weight: 0.9980 chunk 146 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 104 optimal weight: 2.9990 chunk 166 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 ASN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 27468 Z= 0.261 Angle : 0.499 7.692 37362 Z= 0.263 Chirality : 0.045 0.347 4392 Planarity : 0.003 0.056 4740 Dihedral : 6.620 87.996 5118 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 1.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.70 % Allowed : 6.67 % Favored : 92.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.14), residues: 3267 helix: 1.53 (0.20), residues: 732 sheet: 0.45 (0.18), residues: 753 loop : -1.13 (0.14), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.006 0.001 HIS C 66 PHE 0.014 0.001 PHE A 32 TYR 0.016 0.001 TYR B 365 ARG 0.007 0.000 ARG C1091 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 4.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 780 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7513 (mt-10) REVERT: B 153 MET cc_start: 0.7843 (ptt) cc_final: 0.7462 (ptt) REVERT: C 137 ASN cc_start: 0.7960 (t0) cc_final: 0.7558 (t0) REVERT: C 780 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7466 (mt-10) outliers start: 20 outliers final: 10 residues processed: 129 average time/residue: 2.6401 time to fit residues: 410.7628 Evaluate side-chains 124 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 3.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 780 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 305 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 180 optimal weight: 1.9990 chunk 231 optimal weight: 0.9980 chunk 179 optimal weight: 0.9990 chunk 266 optimal weight: 0.0980 chunk 176 optimal weight: 1.9990 chunk 315 optimal weight: 1.9990 chunk 197 optimal weight: 0.7980 chunk 192 optimal weight: 1.9990 chunk 145 optimal weight: 0.5980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 ASN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 27468 Z= 0.193 Angle : 0.471 7.003 37362 Z= 0.248 Chirality : 0.044 0.331 4392 Planarity : 0.003 0.054 4740 Dihedral : 6.340 89.398 5118 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.59 % Allowed : 7.20 % Favored : 92.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.14), residues: 3267 helix: 1.62 (0.20), residues: 732 sheet: 0.31 (0.18), residues: 726 loop : -1.05 (0.14), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.005 0.001 HIS C 66 PHE 0.013 0.001 PHE A 32 TYR 0.013 0.001 TYR B 365 ARG 0.007 0.000 ARG A1091 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 3.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 731 MET cc_start: 0.9277 (ptt) cc_final: 0.9000 (ptt) REVERT: B 153 MET cc_start: 0.7852 (ptt) cc_final: 0.7489 (ptt) REVERT: B 1050 MET cc_start: 0.8607 (ptm) cc_final: 0.8338 (pmm) REVERT: C 137 ASN cc_start: 0.8017 (t0) cc_final: 0.7646 (t0) REVERT: C 780 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7458 (mt-10) outliers start: 17 outliers final: 11 residues processed: 137 average time/residue: 2.4869 time to fit residues: 417.2035 Evaluate side-chains 125 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 113 time to evaluate : 4.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 780 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 194 optimal weight: 1.9990 chunk 125 optimal weight: 5.9990 chunk 188 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 200 optimal weight: 1.9990 chunk 214 optimal weight: 0.8980 chunk 155 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 247 optimal weight: 0.9980 chunk 286 optimal weight: 0.4980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 481 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 27468 Z= 0.217 Angle : 0.478 7.921 37362 Z= 0.252 Chirality : 0.044 0.332 4392 Planarity : 0.003 0.058 4740 Dihedral : 6.220 84.300 5118 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 1.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.70 % Allowed : 7.48 % Favored : 91.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.16 (0.14), residues: 3267 helix: 1.61 (0.20), residues: 732 sheet: 0.35 (0.18), residues: 726 loop : -1.05 (0.14), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.003 0.000 HIS C 66 PHE 0.013 0.001 PHE A 32 TYR 0.015 0.001 TYR C1138 ARG 0.008 0.000 ARG A1091 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 3.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 731 MET cc_start: 0.9273 (ptt) cc_final: 0.8996 (ptt) REVERT: A 902 MET cc_start: 0.8896 (tpp) cc_final: 0.8591 (mmt) REVERT: B 153 MET cc_start: 0.7881 (ptt) cc_final: 0.7551 (ptt) REVERT: C 780 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7454 (mt-10) outliers start: 20 outliers final: 11 residues processed: 131 average time/residue: 2.5314 time to fit residues: 401.1761 Evaluate side-chains 121 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 3.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 780 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 301 optimal weight: 0.7980 chunk 275 optimal weight: 0.9980 chunk 293 optimal weight: 0.9990 chunk 176 optimal weight: 0.9980 chunk 127 optimal weight: 1.9990 chunk 230 optimal weight: 4.9990 chunk 90 optimal weight: 0.8980 chunk 265 optimal weight: 0.9980 chunk 277 optimal weight: 0.8980 chunk 292 optimal weight: 0.8980 chunk 192 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 481 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 27468 Z= 0.222 Angle : 0.476 5.970 37362 Z= 0.252 Chirality : 0.044 0.330 4392 Planarity : 0.003 0.054 4740 Dihedral : 6.149 78.341 5118 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 1.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.52 % Allowed : 7.69 % Favored : 91.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.15 (0.14), residues: 3267 helix: 1.62 (0.20), residues: 732 sheet: 0.37 (0.19), residues: 726 loop : -1.05 (0.14), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.003 0.000 HIS C 66 PHE 0.013 0.001 PHE A 32 TYR 0.017 0.001 TYR B 365 ARG 0.006 0.000 ARG C1091 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 4.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 902 MET cc_start: 0.8888 (tpp) cc_final: 0.8543 (mmt) REVERT: B 153 MET cc_start: 0.7853 (ptt) cc_final: 0.7552 (ptt) REVERT: C 780 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7448 (mt-10) outliers start: 15 outliers final: 12 residues processed: 127 average time/residue: 2.5677 time to fit residues: 397.6770 Evaluate side-chains 125 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 3.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 780 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 310 optimal weight: 1.9990 chunk 189 optimal weight: 2.9990 chunk 147 optimal weight: 0.8980 chunk 215 optimal weight: 0.7980 chunk 325 optimal weight: 4.9990 chunk 299 optimal weight: 0.9990 chunk 259 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 200 optimal weight: 0.9980 chunk 159 optimal weight: 0.2980 chunk 206 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 481 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 27468 Z= 0.207 Angle : 0.474 8.186 37362 Z= 0.250 Chirality : 0.044 0.327 4392 Planarity : 0.003 0.052 4740 Dihedral : 6.061 71.026 5118 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.52 % Allowed : 7.65 % Favored : 91.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.14), residues: 3267 helix: 1.64 (0.20), residues: 732 sheet: 0.38 (0.19), residues: 726 loop : -1.05 (0.14), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.003 0.000 HIS C 66 PHE 0.013 0.001 PHE A 32 TYR 0.016 0.001 TYR B 365 ARG 0.006 0.000 ARG A1091 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 4.050 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 902 MET cc_start: 0.8884 (tpp) cc_final: 0.8546 (mmt) REVERT: B 153 MET cc_start: 0.7855 (ptt) cc_final: 0.7554 (ptt) outliers start: 15 outliers final: 12 residues processed: 124 average time/residue: 2.6427 time to fit residues: 399.0760 Evaluate side-chains 121 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 3.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 PHE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 827 THR Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 569 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 276 optimal weight: 0.0050 chunk 79 optimal weight: 0.7980 chunk 239 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 259 optimal weight: 1.9990 chunk 108 optimal weight: 0.6980 chunk 266 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 228 optimal weight: 1.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 ASN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.101310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.074019 restraints weight = 113654.783| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 2.21 r_work: 0.2750 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2607 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 27468 Z= 0.175 Angle : 0.462 8.045 37362 Z= 0.245 Chirality : 0.044 0.321 4392 Planarity : 0.003 0.109 4740 Dihedral : 5.906 60.317 5118 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.52 % Allowed : 7.72 % Favored : 91.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.00 (0.14), residues: 3267 helix: 1.87 (0.20), residues: 714 sheet: 0.40 (0.19), residues: 726 loop : -0.96 (0.14), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 152 HIS 0.002 0.000 HIS C 66 PHE 0.012 0.001 PHE A 32 TYR 0.014 0.001 TYR B 365 ARG 0.019 0.000 ARG C1091 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10669.52 seconds wall clock time: 188 minutes 8.24 seconds (11288.24 seconds total)