Starting phenix.real_space_refine on Fri Aug 9 00:17:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zb5_11145/08_2024/6zb5_11145.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zb5_11145/08_2024/6zb5_11145.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zb5_11145/08_2024/6zb5_11145.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zb5_11145/08_2024/6zb5_11145.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zb5_11145/08_2024/6zb5_11145.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zb5_11145/08_2024/6zb5_11145.cif" } resolution = 2.85 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 15646 2.51 5 N 4043 2.21 5 O 4696 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 111": "OD1" <-> "OD2" Residue "C ARG 158": "NH1" <-> "NH2" Residue "C PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 237": "NH1" <-> "NH2" Residue "C GLU 281": "OE1" <-> "OE2" Residue "C GLU 298": "OE1" <-> "OE2" Residue "C PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 389": "OD1" <-> "OD2" Residue "C ARG 403": "NH1" <-> "NH2" Residue "C GLU 406": "OE1" <-> "OE2" Residue "C ASP 420": "OD1" <-> "OD2" Residue "C GLU 516": "OE1" <-> "OE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 614": "OD1" <-> "OD2" Residue "C ARG 646": "NH1" <-> "NH2" Residue "C TYR 692": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 722": "OE1" <-> "OE2" Residue "C ASP 742": "OD1" <-> "OD2" Residue "C GLU 745": "OE1" <-> "OE2" Residue "C PHE 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 777": "OE1" <-> "OE2" Residue "C ASP 805": "OD1" <-> "OD2" Residue "C PHE 830": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 845": "OD1" <-> "OD2" Residue "C ASP 864": "OD1" <-> "OD2" Residue "C GLU 865": "OE1" <-> "OE2" Residue "C ASP 982": "OD1" <-> "OD2" Residue "C GLU 1028": "OE1" <-> "OE2" Residue "C ASP 1038": "OD1" <-> "OD2" Residue "C GLU 1069": "OE1" <-> "OE2" Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 111": "OD1" <-> "OD2" Residue "B ARG 158": "NH1" <-> "NH2" Residue "B PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 237": "NH1" <-> "NH2" Residue "B GLU 281": "OE1" <-> "OE2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 389": "OD1" <-> "OD2" Residue "B ARG 403": "NH1" <-> "NH2" Residue "B GLU 406": "OE1" <-> "OE2" Residue "B ASP 420": "OD1" <-> "OD2" Residue "B GLU 516": "OE1" <-> "OE2" Residue "B PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 614": "OD1" <-> "OD2" Residue "B ARG 646": "NH1" <-> "NH2" Residue "B TYR 692": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 722": "OE1" <-> "OE2" Residue "B ASP 742": "OD1" <-> "OD2" Residue "B GLU 745": "OE1" <-> "OE2" Residue "B PHE 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 777": "OE1" <-> "OE2" Residue "B ASP 805": "OD1" <-> "OD2" Residue "B PHE 830": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 845": "OD1" <-> "OD2" Residue "B ASP 864": "OD1" <-> "OD2" Residue "B GLU 865": "OE1" <-> "OE2" Residue "B ASP 982": "OD1" <-> "OD2" Residue "B GLU 1028": "OE1" <-> "OE2" Residue "B ASP 1038": "OD1" <-> "OD2" Residue "B GLU 1069": "OE1" <-> "OE2" Residue "A PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 111": "OD1" <-> "OD2" Residue "A ARG 158": "NH1" <-> "NH2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 237": "NH1" <-> "NH2" Residue "A GLU 281": "OE1" <-> "OE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 389": "OD1" <-> "OD2" Residue "A ARG 403": "NH1" <-> "NH2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A ASP 420": "OD1" <-> "OD2" Residue "A GLU 516": "OE1" <-> "OE2" Residue "A PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 614": "OD1" <-> "OD2" Residue "A ARG 646": "NH1" <-> "NH2" Residue "A TYR 692": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 722": "OE1" <-> "OE2" Residue "A ASP 742": "OD1" <-> "OD2" Residue "A GLU 745": "OE1" <-> "OE2" Residue "A PHE 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 777": "OE1" <-> "OE2" Residue "A ASP 805": "OD1" <-> "OD2" Residue "A PHE 830": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 845": "OD1" <-> "OD2" Residue "A ASP 864": "OD1" <-> "OD2" Residue "A GLU 865": "OE1" <-> "OE2" Residue "A ASP 982": "OD1" <-> "OD2" Residue "A GLU 1028": "OE1" <-> "OE2" Residue "A ASP 1038": "OD1" <-> "OD2" Residue "A GLU 1069": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 24499 Number of models: 1 Model: "" Number of chains: 9 Chain: "C" Number of atoms: 8025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8025 Classifications: {'peptide': 1032} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 47, 'TRANS': 984} Chain breaks: 11 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 8025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8025 Classifications: {'peptide': 1032} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 47, 'TRANS': 984} Chain breaks: 11 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 17 Chain: "A" Number of atoms: 8025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8025 Classifications: {'peptide': 1032} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 47, 'TRANS': 984} Chain breaks: 11 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 17 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: "C" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 104 Unusual residues: {'EIC': 1, 'NAG': 6} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 152 Unusual residues: {'EIC': 2, 'NAG': 8} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 12.92, per 1000 atoms: 0.53 Number of scatterers: 24499 At special positions: 0 Unit cell: (141.75, 135.45, 168, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 114 16.00 O 4696 8.00 N 4043 7.00 C 15646 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 746 " distance=2.03 Simple disulfide: pdb=" SG CYS C 837 " - pdb=" SG CYS C 848 " distance=2.04 Simple disulfide: pdb=" SG CYS C1029 " - pdb=" SG CYS C1040 " distance=2.03 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1123 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 746 " distance=2.03 Simple disulfide: pdb=" SG CYS B 837 " - pdb=" SG CYS B 848 " distance=2.04 Simple disulfide: pdb=" SG CYS B1029 " - pdb=" SG CYS B1040 " distance=2.03 Simple disulfide: pdb=" SG CYS B1079 " - pdb=" SG CYS B1123 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 746 " distance=2.03 Simple disulfide: pdb=" SG CYS A 837 " - pdb=" SG CYS A 848 " distance=2.04 Simple disulfide: pdb=" SG CYS A1029 " - pdb=" SG CYS A1040 " distance=2.03 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1123 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A2102 " - " ASN A 343 " " NAG A2104 " - " ASN A 616 " " NAG A2105 " - " ASN A 798 " " NAG B1301 " - " ASN B 798 " " NAG B1302 " - " ASN B 343 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 616 " " NAG B1306 " - " ASN B 282 " " NAG B1308 " - " ASN B 17 " " NAG C1401 " - " ASN C 343 " " NAG C1403 " - " ASN C 616 " " NAG C1404 " - " ASN C 798 " " NAG C1405 " - " ASN C1071 " " NAG F 1 " - " ASN A 714 " Time building additional restraints: 9.69 Conformation dependent library (CDL) restraints added in 4.6 seconds 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5778 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 48 sheets defined 24.5% alpha, 24.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.09 Creating SS restraints... Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.880A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 369 removed outlier: 3.983A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.707A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.528A pdb=" N TYR C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 734 through 740 Processing helix chain 'C' and resid 743 through 750 Processing helix chain 'C' and resid 754 through 780 removed outlier: 3.902A pdb=" N THR C 758 " --> pdb=" O GLY C 754 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASP C 772 " --> pdb=" O ALA C 768 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS C 773 " --> pdb=" O VAL C 769 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 821 Processing helix chain 'C' and resid 833 through 838 Processing helix chain 'C' and resid 846 through 852 Processing helix chain 'C' and resid 863 through 882 Processing helix chain 'C' and resid 894 through 905 removed outlier: 3.526A pdb=" N TYR C 901 " --> pdb=" O MET C 897 " (cutoff:3.500A) Processing helix chain 'C' and resid 909 through 916 removed outlier: 4.337A pdb=" N LEU C 913 " --> pdb=" O THR C 909 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 936 Processing helix chain 'C' and resid 943 through 962 removed outlier: 3.867A pdb=" N VAL C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 963 through 965 No H-bonds generated for 'chain 'C' and resid 963 through 965' Processing helix chain 'C' and resid 973 through 981 removed outlier: 3.593A pdb=" N ILE C 977 " --> pdb=" O VAL C 973 " (cutoff:3.500A) Processing helix chain 'C' and resid 982 through 1030 removed outlier: 3.578A pdb=" N GLU C 987 " --> pdb=" O LYS C 983 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N VAL C 988 " --> pdb=" O VAL C 984 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLN C 989 " --> pdb=" O GLU C 985 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA C1013 " --> pdb=" O LEU C1009 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLU C1014 " --> pdb=" O ILE C1010 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL C1030 " --> pdb=" O MET C1026 " (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 349 through 353 removed outlier: 3.882A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 369 removed outlier: 3.983A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.706A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.528A pdb=" N TYR B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 734 through 740 Processing helix chain 'B' and resid 743 through 750 Processing helix chain 'B' and resid 754 through 780 removed outlier: 3.902A pdb=" N THR B 758 " --> pdb=" O GLY B 754 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASP B 772 " --> pdb=" O ALA B 768 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS B 773 " --> pdb=" O VAL B 769 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 821 Processing helix chain 'B' and resid 833 through 838 Processing helix chain 'B' and resid 846 through 852 Processing helix chain 'B' and resid 863 through 882 Processing helix chain 'B' and resid 894 through 905 removed outlier: 3.525A pdb=" N TYR B 901 " --> pdb=" O MET B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 909 through 916 removed outlier: 4.337A pdb=" N LEU B 913 " --> pdb=" O THR B 909 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 936 Processing helix chain 'B' and resid 943 through 962 removed outlier: 3.866A pdb=" N VAL B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 963 through 965 No H-bonds generated for 'chain 'B' and resid 963 through 965' Processing helix chain 'B' and resid 973 through 981 removed outlier: 3.593A pdb=" N ILE B 977 " --> pdb=" O VAL B 973 " (cutoff:3.500A) Processing helix chain 'B' and resid 982 through 1030 removed outlier: 3.578A pdb=" N GLU B 987 " --> pdb=" O LYS B 983 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N VAL B 988 " --> pdb=" O VAL B 984 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLN B 989 " --> pdb=" O GLU B 985 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA B1013 " --> pdb=" O LEU B1009 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLU B1014 " --> pdb=" O ILE B1010 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL B1030 " --> pdb=" O MET B1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.881A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 369 removed outlier: 3.983A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.705A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.527A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 740 Processing helix chain 'A' and resid 743 through 750 Processing helix chain 'A' and resid 754 through 780 removed outlier: 3.903A pdb=" N THR A 758 " --> pdb=" O GLY A 754 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASP A 772 " --> pdb=" O ALA A 768 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS A 773 " --> pdb=" O VAL A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 821 Processing helix chain 'A' and resid 833 through 838 Processing helix chain 'A' and resid 846 through 852 Processing helix chain 'A' and resid 863 through 882 Processing helix chain 'A' and resid 894 through 905 removed outlier: 3.525A pdb=" N TYR A 901 " --> pdb=" O MET A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 916 removed outlier: 4.336A pdb=" N LEU A 913 " --> pdb=" O THR A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 936 Processing helix chain 'A' and resid 943 through 962 removed outlier: 3.867A pdb=" N VAL A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 965 No H-bonds generated for 'chain 'A' and resid 963 through 965' Processing helix chain 'A' and resid 973 through 981 removed outlier: 3.594A pdb=" N ILE A 977 " --> pdb=" O VAL A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 1030 removed outlier: 3.578A pdb=" N GLU A 987 " --> pdb=" O LYS A 983 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N VAL A 988 " --> pdb=" O VAL A 984 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLN A 989 " --> pdb=" O GLU A 985 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA A1013 " --> pdb=" O LEU A1009 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLU A1014 " --> pdb=" O ILE A1010 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL A1030 " --> pdb=" O MET A1026 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 28 through 31 removed outlier: 4.261A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.218A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.758A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 84 through 85 removed outlier: 12.958A pdb=" N PHE C 238 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 12.239A pdb=" N ASN C 137 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 9.139A pdb=" N THR C 240 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N LEU C 242 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU C 244 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 311 through 315 removed outlier: 4.733A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 324 through 328 removed outlier: 5.615A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.397A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AA9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.168A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 698 through 699 removed outlier: 6.255A pdb=" N ALA C 698 " --> pdb=" O ILE A 785 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 708 through 712 removed outlier: 3.566A pdb=" N THR C1073 " --> pdb=" O SER C1094 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA C1075 " --> pdb=" O PHE C1092 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N PHE C1092 " --> pdb=" O ALA C1075 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL C1101 " --> pdb=" O GLN C1110 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N GLN C1103 " --> pdb=" O GLU C1108 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N GLU C1108 " --> pdb=" O GLN C1103 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 715 through 725 removed outlier: 5.962A pdb=" N TYR C1064 " --> pdb=" O HIS C1045 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N HIS C1045 " --> pdb=" O TYR C1064 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 731 through 733 Processing sheet with id=AB7, first strand: chain 'C' and resid 784 through 785 Processing sheet with id=AB8, first strand: chain 'C' and resid 1118 through 1119 Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 31 removed outlier: 4.261A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.218A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.759A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 12.958A pdb=" N PHE B 238 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 12.240A pdb=" N ASN B 137 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 9.138A pdb=" N THR B 240 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N LEU B 242 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU B 244 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 315 removed outlier: 4.733A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 324 through 328 removed outlier: 5.615A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.397A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 391 through 392 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: 6.168A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 708 through 712 removed outlier: 3.565A pdb=" N THR B1073 " --> pdb=" O SER B1094 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ALA B1075 " --> pdb=" O PHE B1092 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N PHE B1092 " --> pdb=" O ALA B1075 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL B1101 " --> pdb=" O GLN B1110 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N GLN B1103 " --> pdb=" O GLU B1108 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N GLU B1108 " --> pdb=" O GLN B1103 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 715 through 725 removed outlier: 5.961A pdb=" N TYR B1064 " --> pdb=" O HIS B1045 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N HIS B1045 " --> pdb=" O TYR B1064 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 731 through 733 Processing sheet with id=AD5, first strand: chain 'B' and resid 784 through 785 Processing sheet with id=AD6, first strand: chain 'B' and resid 1118 through 1119 Processing sheet with id=AD7, first strand: chain 'A' and resid 28 through 31 removed outlier: 4.261A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.218A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.759A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 84 through 85 removed outlier: 12.958A pdb=" N PHE A 238 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 12.240A pdb=" N ASN A 137 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 9.138A pdb=" N THR A 240 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N LEU A 242 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU A 244 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 311 through 315 removed outlier: 4.734A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 324 through 328 removed outlier: 5.615A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.397A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AE6, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AE7, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AE8, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.168A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'A' and resid 708 through 712 removed outlier: 3.566A pdb=" N THR A1073 " --> pdb=" O SER A1094 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ALA A1075 " --> pdb=" O PHE A1092 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N PHE A1092 " --> pdb=" O ALA A1075 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL A1101 " --> pdb=" O GLN A1110 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N GLN A1103 " --> pdb=" O GLU A1108 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N GLU A1108 " --> pdb=" O GLN A1103 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'A' and resid 715 through 725 removed outlier: 5.961A pdb=" N TYR A1064 " --> pdb=" O HIS A1045 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N HIS A1045 " --> pdb=" O TYR A1064 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'A' and resid 731 through 733 Processing sheet with id=AF3, first strand: chain 'A' and resid 1118 through 1119 953 hydrogen bonds defined for protein. 2571 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.76 Time building geometry restraints manager: 10.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3987 1.31 - 1.44: 7024 1.44 - 1.57: 13881 1.57 - 1.70: 0 1.70 - 1.82: 138 Bond restraints: 25030 Sorted by residual: bond pdb=" C7 NAG C1406 " pdb=" N2 NAG C1406 " ideal model delta sigma weight residual 1.346 1.465 -0.119 2.00e-02 2.50e+03 3.53e+01 bond pdb=" C7 NAG A2101 " pdb=" N2 NAG A2101 " ideal model delta sigma weight residual 1.346 1.463 -0.117 2.00e-02 2.50e+03 3.43e+01 bond pdb=" C1 NAG C1406 " pdb=" O5 NAG C1406 " ideal model delta sigma weight residual 1.406 1.498 -0.092 2.00e-02 2.50e+03 2.10e+01 bond pdb=" C1 NAG A2101 " pdb=" O5 NAG A2101 " ideal model delta sigma weight residual 1.406 1.497 -0.091 2.00e-02 2.50e+03 2.06e+01 bond pdb=" N ASN B 798 " pdb=" CA ASN B 798 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.27e-02 6.20e+03 9.77e+00 ... (remaining 25025 not shown) Histogram of bond angle deviations from ideal: 99.18 - 106.15: 470 106.15 - 113.12: 13493 113.12 - 120.09: 8324 120.09 - 127.06: 11530 127.06 - 134.04: 199 Bond angle restraints: 34016 Sorted by residual: angle pdb=" CA ASN B 798 " pdb=" CB ASN B 798 " pdb=" CG ASN B 798 " ideal model delta sigma weight residual 112.60 128.02 -15.42 1.00e+00 1.00e+00 2.38e+02 angle pdb=" CB ASN B 798 " pdb=" CG ASN B 798 " pdb=" ND2 ASN B 798 " ideal model delta sigma weight residual 116.40 124.84 -8.44 1.50e+00 4.44e-01 3.17e+01 angle pdb=" N GLY B 311 " pdb=" CA GLY B 311 " pdb=" C GLY B 311 " ideal model delta sigma weight residual 110.38 116.82 -6.44 1.28e+00 6.10e-01 2.53e+01 angle pdb=" N GLY C 311 " pdb=" CA GLY C 311 " pdb=" C GLY C 311 " ideal model delta sigma weight residual 110.38 116.81 -6.43 1.28e+00 6.10e-01 2.52e+01 angle pdb=" C ASN B 798 " pdb=" CA ASN B 798 " pdb=" CB ASN B 798 " ideal model delta sigma weight residual 110.79 102.61 8.18 1.63e+00 3.76e-01 2.52e+01 ... (remaining 34011 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.04: 14084 27.04 - 54.08: 918 54.08 - 81.12: 128 81.12 - 108.16: 23 108.16 - 135.19: 15 Dihedral angle restraints: 15168 sinusoidal: 6192 harmonic: 8976 Sorted by residual: dihedral pdb=" CA TYR B 704 " pdb=" C TYR B 704 " pdb=" N SER B 705 " pdb=" CA SER B 705 " ideal model delta harmonic sigma weight residual 180.00 153.78 26.22 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" CA TYR C 704 " pdb=" C TYR C 704 " pdb=" N SER C 705 " pdb=" CA SER C 705 " ideal model delta harmonic sigma weight residual 180.00 153.78 26.22 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" CA TYR A 704 " pdb=" C TYR A 704 " pdb=" N SER A 705 " pdb=" CA SER A 705 " ideal model delta harmonic sigma weight residual 180.00 153.82 26.18 0 5.00e+00 4.00e-02 2.74e+01 ... (remaining 15165 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.142: 3902 0.142 - 0.283: 21 0.283 - 0.425: 2 0.425 - 0.566: 3 0.566 - 0.708: 6 Chirality restraints: 3934 Sorted by residual: chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-02 2.50e+03 5.13e+02 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.82 0.42 2.00e-02 2.50e+03 4.45e+02 chirality pdb=" C1 NAG B1302 " pdb=" ND2 ASN B 343 " pdb=" C2 NAG B1302 " pdb=" O5 NAG B1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.69 -0.71 2.00e-01 2.50e+01 1.25e+01 ... (remaining 3931 not shown) Planarity restraints: 4372 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1301 " 0.357 2.00e-02 2.50e+03 3.07e-01 1.18e+03 pdb=" C7 NAG B1301 " -0.087 2.00e-02 2.50e+03 pdb=" C8 NAG B1301 " 0.138 2.00e-02 2.50e+03 pdb=" N2 NAG B1301 " -0.545 2.00e-02 2.50e+03 pdb=" O7 NAG B1301 " 0.137 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1302 " -0.341 2.00e-02 2.50e+03 2.96e-01 1.09e+03 pdb=" C7 NAG B1302 " 0.077 2.00e-02 2.50e+03 pdb=" C8 NAG B1302 " -0.074 2.00e-02 2.50e+03 pdb=" N2 NAG B1302 " 0.524 2.00e-02 2.50e+03 pdb=" O7 NAG B1302 " -0.186 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A2102 " 0.334 2.00e-02 2.50e+03 2.90e-01 1.05e+03 pdb=" C7 NAG A2102 " -0.075 2.00e-02 2.50e+03 pdb=" C8 NAG A2102 " 0.057 2.00e-02 2.50e+03 pdb=" N2 NAG A2102 " -0.511 2.00e-02 2.50e+03 pdb=" O7 NAG A2102 " 0.195 2.00e-02 2.50e+03 ... (remaining 4369 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 160 2.57 - 3.15: 18216 3.15 - 3.73: 33041 3.73 - 4.32: 50383 4.32 - 4.90: 86371 Nonbonded interactions: 188171 Sorted by model distance: nonbonded pdb=" OD2 ASP A 568 " pdb=" OG1 THR A 572 " model vdw 1.985 3.040 nonbonded pdb=" OD2 ASP B 568 " pdb=" OG1 THR B 572 " model vdw 1.985 3.040 nonbonded pdb=" OD2 ASP C 568 " pdb=" OG1 THR C 572 " model vdw 1.986 3.040 nonbonded pdb=" ND2 ASN C 165 " pdb=" O5 NAG C1402 " model vdw 2.008 3.120 nonbonded pdb=" ND2 ASN B 714 " pdb=" C1 NAG E 1 " model vdw 2.055 3.550 ... (remaining 188166 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' selection = (chain 'B' and (resid 15 through 1136 or resid 1301 through 1306)) selection = (chain 'C' and (resid 15 through 1136 or resid 1401 through 1406)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.870 Check model and map are aligned: 0.150 Set scattering table: 0.220 Process input model: 68.200 Find NCS groups from input model: 1.290 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 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 : 0.009 0.119 25030 Z= 0.584 Angle : 0.769 15.419 34016 Z= 0.412 Chirality : 0.060 0.708 3934 Planarity : 0.015 0.307 4358 Dihedral : 18.164 135.194 9291 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 3.76 % Allowed : 20.56 % Favored : 75.69 % Cbeta Deviations : 0.03 % 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: -3.22 (0.13), residues: 3024 helix: -1.71 (0.16), residues: 681 sheet: -0.38 (0.18), residues: 693 loop : -3.27 (0.12), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.006 0.001 HIS A1061 PHE 0.016 0.002 PHE A 592 TYR 0.021 0.002 TYR A 704 ARG 0.007 0.000 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 317 time to evaluate : 2.520 Fit side-chains revert: symmetry clash REVERT: C 187 LYS cc_start: 0.5084 (OUTLIER) cc_final: 0.4316 (ttmt) REVERT: C 207 HIS cc_start: 0.7542 (t-90) cc_final: 0.7156 (m90) REVERT: C 298 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.7170 (tt0) REVERT: C 493 GLN cc_start: 0.7806 (mt0) cc_final: 0.7595 (mt0) REVERT: C 801 GLN cc_start: 0.7931 (mt0) cc_final: 0.7592 (mm110) REVERT: B 97 LYS cc_start: 0.6532 (OUTLIER) cc_final: 0.6256 (pttm) REVERT: B 207 HIS cc_start: 0.7546 (t-90) cc_final: 0.7124 (m90) REVERT: B 567 ARG cc_start: 0.8264 (mmt90) cc_final: 0.7993 (mmt90) REVERT: B 801 GLN cc_start: 0.8096 (mt0) cc_final: 0.7775 (mm110) REVERT: A 128 ILE cc_start: 0.6955 (OUTLIER) cc_final: 0.6653 (mp) REVERT: A 207 HIS cc_start: 0.7568 (t-90) cc_final: 0.7247 (m90) REVERT: A 346 ARG cc_start: 0.7512 (ttp80) cc_final: 0.7232 (tmt170) REVERT: A 567 ARG cc_start: 0.8352 (mmt90) cc_final: 0.7981 (mmt180) REVERT: A 947 ASP cc_start: 0.7498 (m-30) cc_final: 0.7189 (m-30) REVERT: A 1070 LYS cc_start: 0.7411 (mtpp) cc_final: 0.7205 (tttm) outliers start: 100 outliers final: 31 residues processed: 406 average time/residue: 1.0613 time to fit residues: 510.1852 Evaluate side-chains 289 residues out of total 2691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 254 time to evaluate : 3.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 713 THR Chi-restraints excluded: chain C residue 1136 ASP Chi-restraints excluded: chain B residue 45 SER Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 798 ASN Chi-restraints excluded: chain B residue 1120 SER Chi-restraints excluded: chain B residue 1136 ASP Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 359 SER Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1136 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 260 optimal weight: 3.9990 chunk 234 optimal weight: 0.0070 chunk 129 optimal weight: 10.0000 chunk 80 optimal weight: 2.9990 chunk 157 optimal weight: 0.8980 chunk 125 optimal weight: 1.9990 chunk 242 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 147 optimal weight: 2.9990 chunk 180 optimal weight: 2.9990 chunk 280 optimal weight: 3.9990 overall best weight: 1.3804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 125 ASN C 137 ASN C 164 ASN C 370 ASN C 540 ASN C 606 ASN C 675 GLN C 916 ASN C 946 GLN C 951 GLN B 125 ASN B 137 ASN B 164 ASN B 603 ASN B 606 ASN B 675 GLN B 687 GLN B 916 ASN B1071 ASN B1098 HIS A 125 ASN A 137 ASN A 606 ASN A 675 GLN A 916 ASN A 951 GLN A1002 GLN A1007 GLN A1071 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 25030 Z= 0.172 Angle : 0.592 11.203 34016 Z= 0.304 Chirality : 0.047 0.272 3934 Planarity : 0.005 0.060 4358 Dihedral : 10.324 116.156 3939 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.38 % Allowed : 20.22 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.14), residues: 3024 helix: 0.25 (0.19), residues: 699 sheet: 0.00 (0.19), residues: 669 loop : -2.68 (0.12), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.004 0.001 HIS B1098 PHE 0.019 0.001 PHE B 799 TYR 0.015 0.001 TYR B1064 ARG 0.005 0.000 ARG C1104 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 253 time to evaluate : 2.884 Fit side-chains REVERT: C 207 HIS cc_start: 0.7593 (t-90) cc_final: 0.7216 (m90) REVERT: C 493 GLN cc_start: 0.7823 (mt0) cc_final: 0.7609 (mt0) REVERT: C 613 GLN cc_start: 0.8328 (OUTLIER) cc_final: 0.7269 (mt0) REVERT: C 801 GLN cc_start: 0.7999 (mt0) cc_final: 0.7635 (mm110) REVERT: C 999 GLN cc_start: 0.8059 (OUTLIER) cc_final: 0.7807 (tm-30) REVERT: C 1007 GLN cc_start: 0.8184 (mm-40) cc_final: 0.7924 (mm-40) REVERT: B 118 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8182 (tp) REVERT: B 207 HIS cc_start: 0.7598 (t-90) cc_final: 0.7167 (m90) REVERT: B 321 GLN cc_start: 0.8062 (mm-40) cc_final: 0.7818 (mm110) REVERT: B 357 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.7089 (ttm170) REVERT: B 567 ARG cc_start: 0.8294 (mmt90) cc_final: 0.8080 (mmt90) REVERT: B 613 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.7319 (mt0) REVERT: B 801 GLN cc_start: 0.8080 (mt0) cc_final: 0.7729 (mm110) REVERT: B 947 ASP cc_start: 0.7350 (m-30) cc_final: 0.7023 (m-30) REVERT: B 1007 GLN cc_start: 0.7979 (OUTLIER) cc_final: 0.7668 (mt0) REVERT: A 202 LYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8750 (mttp) REVERT: A 207 HIS cc_start: 0.7582 (t-90) cc_final: 0.7268 (m90) REVERT: A 346 ARG cc_start: 0.7538 (ttp80) cc_final: 0.7219 (tmt170) REVERT: A 567 ARG cc_start: 0.8304 (mmt90) cc_final: 0.8050 (mmt90) REVERT: A 947 ASP cc_start: 0.7447 (m-30) cc_final: 0.7112 (m-30) REVERT: A 1110 GLN cc_start: 0.8296 (OUTLIER) cc_final: 0.7982 (mm110) outliers start: 90 outliers final: 42 residues processed: 318 average time/residue: 1.0359 time to fit residues: 394.6346 Evaluate side-chains 283 residues out of total 2691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 233 time to evaluate : 2.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 702 VAL Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 999 GLN Chi-restraints excluded: chain C residue 1034 SER Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1123 CYS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 1007 GLN Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain B residue 1123 CYS Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 632 THR Chi-restraints excluded: chain A residue 737 MET Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1110 GLN Chi-restraints excluded: chain A residue 1123 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 155 optimal weight: 10.0000 chunk 87 optimal weight: 7.9990 chunk 233 optimal weight: 10.0000 chunk 191 optimal weight: 7.9990 chunk 77 optimal weight: 6.9990 chunk 281 optimal weight: 10.0000 chunk 303 optimal weight: 0.9990 chunk 250 optimal weight: 1.9990 chunk 278 optimal weight: 9.9990 chunk 95 optimal weight: 5.9990 chunk 225 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 370 ASN C 904 ASN C 951 GLN B 603 ASN ** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1098 HIS A 165 ASN A 474 GLN A 951 GLN A1002 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 25030 Z= 0.357 Angle : 0.696 11.849 34016 Z= 0.367 Chirality : 0.050 0.246 3934 Planarity : 0.005 0.072 4358 Dihedral : 9.516 111.149 3899 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 4.02 % Allowed : 19.09 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.14), residues: 3024 helix: 0.38 (0.20), residues: 696 sheet: 0.09 (0.19), residues: 687 loop : -2.52 (0.12), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 353 HIS 0.009 0.001 HIS B1098 PHE 0.016 0.002 PHE B 592 TYR 0.023 0.002 TYR C 704 ARG 0.005 0.001 ARG C 997 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 238 time to evaluate : 2.583 Fit side-chains REVERT: C 128 ILE cc_start: 0.7373 (OUTLIER) cc_final: 0.7058 (mt) REVERT: C 207 HIS cc_start: 0.7700 (t-90) cc_final: 0.7433 (m90) REVERT: C 554 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7481 (mm-30) REVERT: C 613 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.7420 (mt0) REVERT: C 801 GLN cc_start: 0.7976 (mt0) cc_final: 0.7632 (mm110) REVERT: C 999 GLN cc_start: 0.8122 (OUTLIER) cc_final: 0.7860 (tm-30) REVERT: C 1007 GLN cc_start: 0.8189 (mm-40) cc_final: 0.7746 (mt0) REVERT: C 1110 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.7788 (mm110) REVERT: B 118 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8122 (tp) REVERT: B 207 HIS cc_start: 0.7586 (t-90) cc_final: 0.7251 (m90) REVERT: B 244 LEU cc_start: 0.6368 (OUTLIER) cc_final: 0.6043 (pp) REVERT: B 357 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.7350 (ttm170) REVERT: B 567 ARG cc_start: 0.8305 (mmt90) cc_final: 0.8049 (mmt90) REVERT: B 613 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.7418 (mt0) REVERT: B 801 GLN cc_start: 0.8071 (mt0) cc_final: 0.7792 (mm110) REVERT: B 947 ASP cc_start: 0.7426 (m-30) cc_final: 0.7018 (m-30) REVERT: B 1007 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7810 (mt0) REVERT: B 1110 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.8033 (mm-40) REVERT: A 52 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.7705 (tt0) REVERT: A 207 HIS cc_start: 0.7663 (t-90) cc_final: 0.7377 (m90) REVERT: A 244 LEU cc_start: 0.6300 (OUTLIER) cc_final: 0.6011 (pp) REVERT: A 303 LEU cc_start: 0.8630 (mt) cc_final: 0.8424 (mt) REVERT: A 465 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7961 (tt0) REVERT: A 567 ARG cc_start: 0.8369 (mmt90) cc_final: 0.8157 (mmt90) REVERT: A 613 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.7686 (mt0) REVERT: A 730 LYS cc_start: 0.9095 (OUTLIER) cc_final: 0.8803 (mtpt) REVERT: A 875 LEU cc_start: 0.8982 (mm) cc_final: 0.8721 (mt) REVERT: A 947 ASP cc_start: 0.7522 (m-30) cc_final: 0.7114 (m-30) REVERT: A 1110 GLN cc_start: 0.8349 (OUTLIER) cc_final: 0.8002 (mm110) outliers start: 107 outliers final: 56 residues processed: 320 average time/residue: 1.1687 time to fit residues: 440.8424 Evaluate side-chains 304 residues out of total 2691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 231 time to evaluate : 3.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 637 SER Chi-restraints excluded: chain C residue 999 GLN Chi-restraints excluded: chain C residue 1034 SER Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1110 GLN Chi-restraints excluded: chain C residue 1123 CYS Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 965 SER Chi-restraints excluded: chain B residue 984 VAL Chi-restraints excluded: chain B residue 1007 GLN Chi-restraints excluded: chain B residue 1069 GLU Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1110 GLN Chi-restraints excluded: chain B residue 1123 CYS Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 730 LYS Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain A residue 1025 LYS Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1110 GLN Chi-restraints excluded: chain A residue 1123 CYS Chi-restraints excluded: chain A residue 1125 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 277 optimal weight: 4.9990 chunk 211 optimal weight: 1.9990 chunk 145 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 134 optimal weight: 20.0000 chunk 188 optimal weight: 0.9990 chunk 282 optimal weight: 5.9990 chunk 298 optimal weight: 0.9980 chunk 147 optimal weight: 0.9990 chunk 267 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 ASN C 234 ASN C 370 ASN C 675 GLN C 951 GLN B 234 ASN B 603 ASN B 687 GLN B1071 ASN B1098 HIS A 234 ASN A 946 GLN A 951 GLN A1071 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 25030 Z= 0.150 Angle : 0.522 9.341 34016 Z= 0.277 Chirality : 0.044 0.294 3934 Planarity : 0.004 0.059 4358 Dihedral : 8.404 115.409 3896 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.67 % Allowed : 20.71 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.14), residues: 3024 helix: 1.05 (0.20), residues: 696 sheet: 0.20 (0.19), residues: 705 loop : -2.31 (0.13), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.007 0.001 HIS B1098 PHE 0.013 0.001 PHE A 32 TYR 0.013 0.001 TYR A 901 ARG 0.003 0.000 ARG C1104 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 247 time to evaluate : 2.721 Fit side-chains revert: symmetry clash REVERT: C 207 HIS cc_start: 0.7664 (t-90) cc_final: 0.7356 (m90) REVERT: C 493 GLN cc_start: 0.7798 (mm-40) cc_final: 0.7593 (mt0) REVERT: C 613 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.7332 (mt0) REVERT: C 801 GLN cc_start: 0.7944 (mt0) cc_final: 0.7620 (mm110) REVERT: C 947 ASP cc_start: 0.7266 (m-30) cc_final: 0.7045 (m-30) REVERT: C 999 GLN cc_start: 0.8084 (OUTLIER) cc_final: 0.7846 (tm-30) REVERT: C 1007 GLN cc_start: 0.8117 (mm-40) cc_final: 0.7897 (mm-40) REVERT: C 1110 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.7814 (mm110) REVERT: B 207 HIS cc_start: 0.7522 (t-90) cc_final: 0.7235 (m90) REVERT: B 321 GLN cc_start: 0.8055 (mm-40) cc_final: 0.7845 (mm110) REVERT: B 357 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.7142 (ttm170) REVERT: B 458 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.8053 (mttp) REVERT: B 465 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7403 (mt-10) REVERT: B 567 ARG cc_start: 0.8251 (mmt90) cc_final: 0.8010 (mmt90) REVERT: B 801 GLN cc_start: 0.8073 (mt0) cc_final: 0.7799 (mm110) REVERT: B 947 ASP cc_start: 0.7186 (m-30) cc_final: 0.6790 (m-30) REVERT: B 1007 GLN cc_start: 0.7993 (OUTLIER) cc_final: 0.7690 (mt0) REVERT: B 1047 MET cc_start: 0.8463 (ptm) cc_final: 0.8235 (ptm) REVERT: A 207 HIS cc_start: 0.7598 (t-90) cc_final: 0.7360 (m90) REVERT: A 567 ARG cc_start: 0.8274 (mmt90) cc_final: 0.8040 (mmt90) REVERT: A 613 GLN cc_start: 0.8569 (OUTLIER) cc_final: 0.7520 (mt0) REVERT: A 755 SER cc_start: 0.6748 (OUTLIER) cc_final: 0.6391 (p) REVERT: A 947 ASP cc_start: 0.7300 (m-30) cc_final: 0.6849 (m-30) outliers start: 71 outliers final: 29 residues processed: 298 average time/residue: 1.1515 time to fit residues: 405.8840 Evaluate side-chains 266 residues out of total 2691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 228 time to evaluate : 2.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 999 GLN Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1110 GLN Chi-restraints excluded: chain C residue 1123 CYS Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 965 SER Chi-restraints excluded: chain B residue 1007 GLN Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1123 CYS Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1123 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 248 optimal weight: 7.9990 chunk 169 optimal weight: 0.9990 chunk 4 optimal weight: 8.9990 chunk 222 optimal weight: 8.9990 chunk 123 optimal weight: 9.9990 chunk 254 optimal weight: 6.9990 chunk 206 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 152 optimal weight: 6.9990 chunk 268 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 164 ASN C 951 GLN B 603 ASN B1098 HIS A 603 ASN A 951 GLN A1002 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 25030 Z= 0.339 Angle : 0.655 9.355 34016 Z= 0.349 Chirality : 0.049 0.315 3934 Planarity : 0.005 0.069 4358 Dihedral : 8.371 120.663 3893 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 1.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 4.13 % Allowed : 19.43 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.14), residues: 3024 helix: 0.70 (0.20), residues: 696 sheet: 0.23 (0.19), residues: 705 loop : -2.36 (0.13), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 353 HIS 0.008 0.001 HIS B1098 PHE 0.016 0.002 PHE A 32 TYR 0.021 0.002 TYR C 704 ARG 0.006 0.001 ARG C1104 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 239 time to evaluate : 2.812 Fit side-chains revert: symmetry clash REVERT: C 128 ILE cc_start: 0.7343 (OUTLIER) cc_final: 0.7127 (mp) REVERT: C 207 HIS cc_start: 0.7721 (t-90) cc_final: 0.7439 (m90) REVERT: C 357 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.7336 (ttm170) REVERT: C 465 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7509 (mt-10) REVERT: C 493 GLN cc_start: 0.7922 (mm-40) cc_final: 0.7701 (mt0) REVERT: C 613 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.7409 (mt0) REVERT: C 801 GLN cc_start: 0.7981 (mt0) cc_final: 0.7628 (mm110) REVERT: C 999 GLN cc_start: 0.8122 (OUTLIER) cc_final: 0.7864 (tm-30) REVERT: C 1007 GLN cc_start: 0.8150 (mm-40) cc_final: 0.7920 (mm-40) REVERT: C 1110 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.7804 (mm110) REVERT: B 118 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8140 (tp) REVERT: B 207 HIS cc_start: 0.7558 (t-90) cc_final: 0.7280 (m90) REVERT: B 239 GLN cc_start: 0.8706 (tt0) cc_final: 0.8447 (tt0) REVERT: B 244 LEU cc_start: 0.6275 (OUTLIER) cc_final: 0.5936 (pp) REVERT: B 357 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.7351 (ttm170) REVERT: B 458 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8163 (mttp) REVERT: B 465 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7406 (mt-10) REVERT: B 567 ARG cc_start: 0.8296 (mmt90) cc_final: 0.8087 (mmt90) REVERT: B 613 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.7465 (mt0) REVERT: B 730 LYS cc_start: 0.9100 (OUTLIER) cc_final: 0.8454 (mtmt) REVERT: B 801 GLN cc_start: 0.8029 (mt0) cc_final: 0.7765 (mm110) REVERT: B 947 ASP cc_start: 0.7559 (m-30) cc_final: 0.7162 (m-30) REVERT: B 1007 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.7838 (mt0) REVERT: B 1047 MET cc_start: 0.8712 (ptm) cc_final: 0.8424 (ptm) REVERT: B 1110 GLN cc_start: 0.8318 (OUTLIER) cc_final: 0.7977 (mm-40) REVERT: A 207 HIS cc_start: 0.7604 (t-90) cc_final: 0.7327 (m90) REVERT: A 244 LEU cc_start: 0.6427 (OUTLIER) cc_final: 0.6199 (pp) REVERT: A 465 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7957 (tt0) REVERT: A 613 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.7660 (mt0) REVERT: A 755 SER cc_start: 0.7272 (OUTLIER) cc_final: 0.6767 (p) REVERT: A 947 ASP cc_start: 0.7499 (m-30) cc_final: 0.7044 (m-30) REVERT: A 1110 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.7995 (mm110) outliers start: 110 outliers final: 60 residues processed: 323 average time/residue: 1.1809 time to fit residues: 447.3057 Evaluate side-chains 310 residues out of total 2691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 230 time to evaluate : 2.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 637 SER Chi-restraints excluded: chain C residue 999 GLN Chi-restraints excluded: chain C residue 1034 SER Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1110 GLN Chi-restraints excluded: chain C residue 1123 CYS Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 458 LYS Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 730 LYS Chi-restraints excluded: chain B residue 904 ASN Chi-restraints excluded: chain B residue 965 SER Chi-restraints excluded: chain B residue 1007 GLN Chi-restraints excluded: chain B residue 1025 LYS Chi-restraints excluded: chain B residue 1069 GLU Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1110 GLN Chi-restraints excluded: chain B residue 1123 CYS Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1025 LYS Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1110 GLN Chi-restraints excluded: chain A residue 1123 CYS Chi-restraints excluded: chain A residue 1125 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 100 optimal weight: 7.9990 chunk 268 optimal weight: 2.9990 chunk 59 optimal weight: 8.9990 chunk 175 optimal weight: 10.0000 chunk 73 optimal weight: 9.9990 chunk 298 optimal weight: 2.9990 chunk 248 optimal weight: 6.9990 chunk 138 optimal weight: 8.9990 chunk 24 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 156 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 675 GLN C 687 GLN C 904 ASN C 951 GLN B 603 ASN B1098 HIS A 603 ASN A 675 GLN A 951 GLN A1002 GLN A1071 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 25030 Z= 0.372 Angle : 0.688 9.343 34016 Z= 0.368 Chirality : 0.051 0.331 3934 Planarity : 0.005 0.073 4358 Dihedral : 8.480 124.388 3893 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 4.13 % Allowed : 19.77 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.14), residues: 3024 helix: 0.46 (0.20), residues: 696 sheet: 0.22 (0.19), residues: 705 loop : -2.39 (0.13), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 353 HIS 0.010 0.001 HIS B1098 PHE 0.017 0.002 PHE A1118 TYR 0.023 0.002 TYR A 704 ARG 0.005 0.001 ARG C1104 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 243 time to evaluate : 2.780 Fit side-chains revert: symmetry clash REVERT: C 128 ILE cc_start: 0.7398 (OUTLIER) cc_final: 0.7140 (mp) REVERT: C 326 ILE cc_start: 0.8134 (OUTLIER) cc_final: 0.7655 (mp) REVERT: C 357 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.7349 (ttm170) REVERT: C 493 GLN cc_start: 0.7927 (mm-40) cc_final: 0.7675 (mt0) REVERT: C 613 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.7445 (mt0) REVERT: C 801 GLN cc_start: 0.8006 (mt0) cc_final: 0.7659 (mm110) REVERT: C 1007 GLN cc_start: 0.8154 (mm-40) cc_final: 0.7736 (mt0) REVERT: C 1110 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.7788 (mm110) REVERT: B 207 HIS cc_start: 0.7527 (t-90) cc_final: 0.7315 (m90) REVERT: B 239 GLN cc_start: 0.8715 (tt0) cc_final: 0.8453 (tt0) REVERT: B 244 LEU cc_start: 0.6270 (OUTLIER) cc_final: 0.5927 (pp) REVERT: B 321 GLN cc_start: 0.8129 (mm-40) cc_final: 0.7912 (mm110) REVERT: B 357 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.7333 (ttm170) REVERT: B 465 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7393 (mt-10) REVERT: B 613 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.7520 (mt0) REVERT: B 730 LYS cc_start: 0.9094 (OUTLIER) cc_final: 0.8469 (mtmt) REVERT: B 801 GLN cc_start: 0.8029 (mt0) cc_final: 0.7767 (mm110) REVERT: B 947 ASP cc_start: 0.7493 (m-30) cc_final: 0.7089 (m-30) REVERT: B 1007 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.7891 (mt0) REVERT: B 1047 MET cc_start: 0.8763 (ptm) cc_final: 0.8479 (ptm) REVERT: B 1110 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.7983 (mm-40) REVERT: A 52 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.7678 (tt0) REVERT: A 207 HIS cc_start: 0.7619 (t-90) cc_final: 0.7349 (m90) REVERT: A 244 LEU cc_start: 0.6439 (OUTLIER) cc_final: 0.6204 (pp) REVERT: A 465 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7918 (tt0) REVERT: A 613 GLN cc_start: 0.8675 (OUTLIER) cc_final: 0.7671 (mt0) REVERT: A 755 SER cc_start: 0.7439 (OUTLIER) cc_final: 0.6857 (p) REVERT: A 793 ASP cc_start: 0.6485 (t0) cc_final: 0.6196 (t0) REVERT: A 875 LEU cc_start: 0.8986 (mm) cc_final: 0.8733 (mt) REVERT: A 947 ASP cc_start: 0.7537 (m-30) cc_final: 0.7115 (m-30) REVERT: A 1110 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.8012 (mm110) outliers start: 110 outliers final: 63 residues processed: 321 average time/residue: 1.2069 time to fit residues: 455.2340 Evaluate side-chains 314 residues out of total 2691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 233 time to evaluate : 2.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 637 SER Chi-restraints excluded: chain C residue 755 SER Chi-restraints excluded: chain C residue 1034 SER Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1110 GLN Chi-restraints excluded: chain C residue 1123 CYS Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 730 LYS Chi-restraints excluded: chain B residue 904 ASN Chi-restraints excluded: chain B residue 965 SER Chi-restraints excluded: chain B residue 1007 GLN Chi-restraints excluded: chain B residue 1025 LYS Chi-restraints excluded: chain B residue 1069 GLU Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1110 GLN Chi-restraints excluded: chain B residue 1123 CYS Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 1025 LYS Chi-restraints excluded: chain A residue 1069 GLU Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1110 GLN Chi-restraints excluded: chain A residue 1123 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 288 optimal weight: 8.9990 chunk 33 optimal weight: 0.8980 chunk 170 optimal weight: 3.9990 chunk 218 optimal weight: 9.9990 chunk 169 optimal weight: 4.9990 chunk 251 optimal weight: 2.9990 chunk 166 optimal weight: 1.9990 chunk 297 optimal weight: 0.9990 chunk 186 optimal weight: 9.9990 chunk 181 optimal weight: 9.9990 chunk 137 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 188 ASN C 207 HIS C 370 ASN C 951 GLN B 603 ASN B1098 HIS A 603 ASN A 675 GLN A 951 GLN A1071 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25030 Z= 0.174 Angle : 0.536 9.430 34016 Z= 0.288 Chirality : 0.045 0.323 3934 Planarity : 0.005 0.064 4358 Dihedral : 7.870 114.494 3893 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.27 % Allowed : 20.74 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.14), residues: 3024 helix: 0.98 (0.20), residues: 696 sheet: 0.27 (0.19), residues: 705 loop : -2.25 (0.13), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 436 HIS 0.009 0.001 HIS B1098 PHE 0.013 0.001 PHE A 32 TYR 0.020 0.001 TYR A 901 ARG 0.006 0.000 ARG C1104 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 243 time to evaluate : 2.662 Fit side-chains revert: symmetry clash REVERT: C 207 HIS cc_start: 0.7613 (t-90) cc_final: 0.7227 (m90) REVERT: C 326 ILE cc_start: 0.8096 (OUTLIER) cc_final: 0.7647 (mp) REVERT: C 357 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.7332 (ttm170) REVERT: C 613 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.7423 (mt0) REVERT: C 801 GLN cc_start: 0.7965 (mt0) cc_final: 0.7626 (mm110) REVERT: C 1007 GLN cc_start: 0.8100 (mm-40) cc_final: 0.7887 (mm-40) REVERT: C 1110 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.7799 (mm110) REVERT: B 118 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8058 (tp) REVERT: B 207 HIS cc_start: 0.7523 (t-90) cc_final: 0.7254 (m90) REVERT: B 239 GLN cc_start: 0.8627 (tt0) cc_final: 0.8338 (tt0) REVERT: B 244 LEU cc_start: 0.6277 (OUTLIER) cc_final: 0.5879 (pp) REVERT: B 321 GLN cc_start: 0.8199 (mm-40) cc_final: 0.7958 (mm110) REVERT: B 357 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.7186 (ttm170) REVERT: B 465 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7379 (mt-10) REVERT: B 801 GLN cc_start: 0.8008 (mt0) cc_final: 0.7760 (mm110) REVERT: B 947 ASP cc_start: 0.7293 (m-30) cc_final: 0.6885 (m-30) REVERT: B 1007 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.7752 (mt0) REVERT: B 1047 MET cc_start: 0.8600 (ptm) cc_final: 0.8207 (ptm) REVERT: B 1110 GLN cc_start: 0.8306 (OUTLIER) cc_final: 0.7960 (mm-40) REVERT: A 207 HIS cc_start: 0.7602 (t-90) cc_final: 0.7328 (m90) REVERT: A 244 LEU cc_start: 0.6403 (OUTLIER) cc_final: 0.6192 (pp) REVERT: A 613 GLN cc_start: 0.8619 (OUTLIER) cc_final: 0.7584 (mt0) REVERT: A 755 SER cc_start: 0.6831 (OUTLIER) cc_final: 0.6537 (p) REVERT: A 947 ASP cc_start: 0.7304 (m-30) cc_final: 0.6827 (m-30) REVERT: A 1110 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.7990 (mm110) outliers start: 87 outliers final: 48 residues processed: 305 average time/residue: 1.1515 time to fit residues: 415.1077 Evaluate side-chains 291 residues out of total 2691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 229 time to evaluate : 2.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 637 SER Chi-restraints excluded: chain C residue 1034 SER Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1110 GLN Chi-restraints excluded: chain C residue 1123 CYS Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 965 SER Chi-restraints excluded: chain B residue 1007 GLN Chi-restraints excluded: chain B residue 1025 LYS Chi-restraints excluded: chain B residue 1034 SER Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1110 GLN Chi-restraints excluded: chain B residue 1123 CYS Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1110 GLN Chi-restraints excluded: chain A residue 1123 CYS Chi-restraints excluded: chain A residue 1125 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 184 optimal weight: 1.9990 chunk 118 optimal weight: 8.9990 chunk 177 optimal weight: 9.9990 chunk 89 optimal weight: 10.0000 chunk 58 optimal weight: 6.9990 chunk 57 optimal weight: 8.9990 chunk 189 optimal weight: 8.9990 chunk 202 optimal weight: 10.0000 chunk 147 optimal weight: 8.9990 chunk 27 optimal weight: 10.0000 chunk 234 optimal weight: 0.8980 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 951 GLN B 603 ASN B1098 HIS A 951 GLN A1002 GLN A1071 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 25030 Z= 0.440 Angle : 0.732 9.479 34016 Z= 0.391 Chirality : 0.052 0.344 3934 Planarity : 0.006 0.076 4358 Dihedral : 8.486 124.612 3893 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 1.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 3.95 % Allowed : 20.07 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.14), residues: 3024 helix: 0.43 (0.20), residues: 696 sheet: 0.25 (0.19), residues: 705 loop : -2.38 (0.13), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 353 HIS 0.012 0.002 HIS B1098 PHE 0.019 0.003 PHE A1118 TYR 0.027 0.003 TYR B 901 ARG 0.007 0.001 ARG C1104 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 237 time to evaluate : 2.532 Fit side-chains REVERT: C 128 ILE cc_start: 0.7472 (OUTLIER) cc_final: 0.7174 (mt) REVERT: C 207 HIS cc_start: 0.7743 (t-90) cc_final: 0.7382 (m90) REVERT: C 326 ILE cc_start: 0.8182 (OUTLIER) cc_final: 0.7677 (mp) REVERT: C 357 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.7340 (ttm170) REVERT: C 465 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7510 (mt-10) REVERT: C 613 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.7487 (mt0) REVERT: C 801 GLN cc_start: 0.8031 (mt0) cc_final: 0.7676 (mm110) REVERT: C 1007 GLN cc_start: 0.8173 (mm-40) cc_final: 0.7758 (mt0) REVERT: C 1110 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.7788 (mm110) REVERT: B 118 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8055 (tp) REVERT: B 207 HIS cc_start: 0.7514 (t-90) cc_final: 0.7293 (m90) REVERT: B 239 GLN cc_start: 0.8716 (tt0) cc_final: 0.8443 (tt0) REVERT: B 244 LEU cc_start: 0.6265 (OUTLIER) cc_final: 0.5866 (pp) REVERT: B 357 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.7330 (ttm170) REVERT: B 465 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7401 (mt-10) REVERT: B 613 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.7495 (mt0) REVERT: B 730 LYS cc_start: 0.9089 (OUTLIER) cc_final: 0.8429 (mtmt) REVERT: B 801 GLN cc_start: 0.8037 (mt0) cc_final: 0.7764 (mm110) REVERT: B 947 ASP cc_start: 0.7512 (m-30) cc_final: 0.7110 (m-30) REVERT: B 1007 GLN cc_start: 0.8254 (OUTLIER) cc_final: 0.7913 (mt0) REVERT: B 1110 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.7984 (mm-40) REVERT: A 52 GLN cc_start: 0.8374 (OUTLIER) cc_final: 0.7666 (tt0) REVERT: A 113 LYS cc_start: 0.8304 (OUTLIER) cc_final: 0.7639 (mttt) REVERT: A 207 HIS cc_start: 0.7662 (t-90) cc_final: 0.7383 (m90) REVERT: A 244 LEU cc_start: 0.6449 (OUTLIER) cc_final: 0.6190 (pp) REVERT: A 465 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7975 (tt0) REVERT: A 613 GLN cc_start: 0.8689 (OUTLIER) cc_final: 0.7695 (mt0) REVERT: A 875 LEU cc_start: 0.8995 (mm) cc_final: 0.8646 (mt) REVERT: A 947 ASP cc_start: 0.7577 (m-30) cc_final: 0.7151 (m-30) REVERT: A 1104 ARG cc_start: 0.8163 (mtt90) cc_final: 0.7870 (mtt180) REVERT: A 1110 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.8046 (mm110) outliers start: 105 outliers final: 65 residues processed: 311 average time/residue: 1.1907 time to fit residues: 435.8956 Evaluate side-chains 314 residues out of total 2691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 229 time to evaluate : 2.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 597 VAL Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 637 SER Chi-restraints excluded: chain C residue 744 THR Chi-restraints excluded: chain C residue 1034 SER Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1110 GLN Chi-restraints excluded: chain C residue 1123 CYS Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 730 LYS Chi-restraints excluded: chain B residue 965 SER Chi-restraints excluded: chain B residue 1007 GLN Chi-restraints excluded: chain B residue 1025 LYS Chi-restraints excluded: chain B residue 1034 SER Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1110 GLN Chi-restraints excluded: chain B residue 1123 CYS Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1110 GLN Chi-restraints excluded: chain A residue 1123 CYS Chi-restraints excluded: chain A residue 1125 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 270 optimal weight: 0.8980 chunk 285 optimal weight: 0.9980 chunk 260 optimal weight: 5.9990 chunk 277 optimal weight: 0.9990 chunk 167 optimal weight: 6.9990 chunk 120 optimal weight: 6.9990 chunk 217 optimal weight: 7.9990 chunk 85 optimal weight: 2.9990 chunk 250 optimal weight: 3.9990 chunk 262 optimal weight: 5.9990 chunk 276 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 951 GLN B 603 ASN B1098 HIS A 234 ASN A 675 GLN A 951 GLN A1002 GLN A1071 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25030 Z= 0.163 Angle : 0.535 9.455 34016 Z= 0.288 Chirality : 0.045 0.319 3934 Planarity : 0.005 0.065 4358 Dihedral : 7.816 113.715 3893 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.78 % Allowed : 21.31 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.14), residues: 3024 helix: 0.98 (0.20), residues: 696 sheet: 0.32 (0.19), residues: 705 loop : -2.20 (0.13), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 436 HIS 0.012 0.001 HIS B1098 PHE 0.016 0.001 PHE C 830 TYR 0.026 0.001 TYR B 901 ARG 0.006 0.000 ARG C1104 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 237 time to evaluate : 2.724 Fit side-chains revert: symmetry clash REVERT: C 207 HIS cc_start: 0.7669 (t-90) cc_final: 0.7258 (m90) REVERT: C 326 ILE cc_start: 0.8075 (OUTLIER) cc_final: 0.7618 (mp) REVERT: C 357 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.7329 (ttm170) REVERT: C 465 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7492 (mt-10) REVERT: C 613 GLN cc_start: 0.8503 (OUTLIER) cc_final: 0.7407 (mt0) REVERT: C 801 GLN cc_start: 0.7979 (mt0) cc_final: 0.7624 (mm110) REVERT: C 1110 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.7827 (mm110) REVERT: B 207 HIS cc_start: 0.7515 (t-90) cc_final: 0.7259 (m90) REVERT: B 239 GLN cc_start: 0.8598 (tt0) cc_final: 0.8337 (tt0) REVERT: B 321 GLN cc_start: 0.8229 (mm-40) cc_final: 0.7957 (mm110) REVERT: B 357 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.7159 (ttm170) REVERT: B 465 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7262 (mt-10) REVERT: B 801 GLN cc_start: 0.8011 (mt0) cc_final: 0.7750 (mm110) REVERT: B 947 ASP cc_start: 0.7292 (m-30) cc_final: 0.6876 (m-30) REVERT: B 1007 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7741 (mt0) REVERT: B 1047 MET cc_start: 0.8680 (ptm) cc_final: 0.8301 (ptm) REVERT: B 1110 GLN cc_start: 0.8298 (OUTLIER) cc_final: 0.7940 (mm-40) REVERT: A 207 HIS cc_start: 0.7564 (t-90) cc_final: 0.7300 (m90) REVERT: A 244 LEU cc_start: 0.6363 (OUTLIER) cc_final: 0.6122 (pp) REVERT: A 613 GLN cc_start: 0.8616 (OUTLIER) cc_final: 0.7574 (mt0) REVERT: A 947 ASP cc_start: 0.7350 (m-30) cc_final: 0.6878 (m-30) REVERT: A 1104 ARG cc_start: 0.8066 (mtt90) cc_final: 0.7838 (mtt180) REVERT: A 1110 GLN cc_start: 0.8371 (OUTLIER) cc_final: 0.7996 (mm110) outliers start: 74 outliers final: 54 residues processed: 297 average time/residue: 1.1653 time to fit residues: 407.2254 Evaluate side-chains 296 residues out of total 2691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 230 time to evaluate : 2.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 637 SER Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1110 GLN Chi-restraints excluded: chain C residue 1123 CYS Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 965 SER Chi-restraints excluded: chain B residue 1007 GLN Chi-restraints excluded: chain B residue 1025 LYS Chi-restraints excluded: chain B residue 1034 SER Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1110 GLN Chi-restraints excluded: chain B residue 1123 CYS Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 737 MET Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1110 GLN Chi-restraints excluded: chain A residue 1123 CYS Chi-restraints excluded: chain A residue 1125 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 182 optimal weight: 5.9990 chunk 293 optimal weight: 0.9990 chunk 179 optimal weight: 0.9980 chunk 139 optimal weight: 10.0000 chunk 204 optimal weight: 7.9990 chunk 307 optimal weight: 9.9990 chunk 283 optimal weight: 6.9990 chunk 245 optimal weight: 0.9980 chunk 25 optimal weight: 30.0000 chunk 189 optimal weight: 8.9990 chunk 150 optimal weight: 1.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 951 GLN B 603 ASN B1098 HIS A 607 GLN A 951 GLN A1002 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25030 Z= 0.210 Angle : 0.561 9.429 34016 Z= 0.302 Chirality : 0.046 0.322 3934 Planarity : 0.005 0.065 4358 Dihedral : 7.723 113.146 3893 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 1.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.86 % Allowed : 21.27 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.14), residues: 3024 helix: 1.05 (0.20), residues: 696 sheet: 0.33 (0.19), residues: 705 loop : -2.18 (0.13), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 436 HIS 0.014 0.001 HIS B1098 PHE 0.016 0.001 PHE C 830 TYR 0.026 0.002 TYR A 901 ARG 0.008 0.000 ARG C1104 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 238 time to evaluate : 2.651 Fit side-chains revert: symmetry clash REVERT: C 207 HIS cc_start: 0.7673 (t-90) cc_final: 0.7277 (m90) REVERT: C 326 ILE cc_start: 0.8111 (OUTLIER) cc_final: 0.7659 (mp) REVERT: C 357 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.7313 (ttm170) REVERT: C 465 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7481 (mt-10) REVERT: C 613 GLN cc_start: 0.8517 (OUTLIER) cc_final: 0.7433 (mt0) REVERT: C 801 GLN cc_start: 0.7992 (mt0) cc_final: 0.7636 (mm110) REVERT: C 1110 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.7839 (mm110) REVERT: B 207 HIS cc_start: 0.7494 (t-90) cc_final: 0.7283 (m90) REVERT: B 239 GLN cc_start: 0.8624 (tt0) cc_final: 0.8330 (tt0) REVERT: B 244 LEU cc_start: 0.6221 (OUTLIER) cc_final: 0.5805 (pp) REVERT: B 321 GLN cc_start: 0.8332 (mm-40) cc_final: 0.8034 (mm110) REVERT: B 357 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.7168 (ttm170) REVERT: B 465 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7398 (mt-10) REVERT: B 801 GLN cc_start: 0.8025 (mt0) cc_final: 0.7759 (mm110) REVERT: B 947 ASP cc_start: 0.7323 (m-30) cc_final: 0.6905 (m-30) REVERT: B 1007 GLN cc_start: 0.8074 (OUTLIER) cc_final: 0.7763 (mt0) REVERT: B 1047 MET cc_start: 0.8720 (ptm) cc_final: 0.8445 (ptm) REVERT: B 1110 GLN cc_start: 0.8313 (OUTLIER) cc_final: 0.7948 (mm-40) REVERT: A 113 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7509 (mttt) REVERT: A 207 HIS cc_start: 0.7580 (t-90) cc_final: 0.7320 (m90) REVERT: A 244 LEU cc_start: 0.6431 (OUTLIER) cc_final: 0.6126 (pp) REVERT: A 613 GLN cc_start: 0.8624 (OUTLIER) cc_final: 0.7596 (mt0) REVERT: A 947 ASP cc_start: 0.7335 (m-30) cc_final: 0.6857 (m-30) REVERT: A 1104 ARG cc_start: 0.8050 (mtt90) cc_final: 0.7839 (mtt180) REVERT: A 1110 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.8001 (mm110) outliers start: 76 outliers final: 58 residues processed: 297 average time/residue: 1.1269 time to fit residues: 396.1449 Evaluate side-chains 307 residues out of total 2691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 235 time to evaluate : 2.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 187 LYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 465 GLU Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 637 SER Chi-restraints excluded: chain C residue 1074 THR Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1110 GLN Chi-restraints excluded: chain C residue 1123 CYS Chi-restraints excluded: chain C residue 1125 VAL Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 187 LYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 470 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 904 ASN Chi-restraints excluded: chain B residue 965 SER Chi-restraints excluded: chain B residue 1007 GLN Chi-restraints excluded: chain B residue 1025 LYS Chi-restraints excluded: chain B residue 1034 SER Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1110 GLN Chi-restraints excluded: chain B residue 1123 CYS Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 613 GLN Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1110 GLN Chi-restraints excluded: chain A residue 1123 CYS Chi-restraints excluded: chain A residue 1125 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.7757 > 50: distance: 129 - 133: 35.112 distance: 134 - 135: 60.309 distance: 134 - 137: 38.785 distance: 135 - 136: 57.944 distance: 135 - 141: 46.773 distance: 137 - 138: 49.754 distance: 138 - 139: 31.212 distance: 138 - 140: 36.045 distance: 141 - 142: 43.323 distance: 142 - 143: 39.810 distance: 142 - 145: 61.679 distance: 143 - 144: 9.007 distance: 143 - 149: 39.354 distance: 145 - 146: 53.837 distance: 146 - 147: 16.314 distance: 146 - 148: 6.406 distance: 149 - 150: 40.324 distance: 150 - 151: 39.244 distance: 150 - 153: 57.776 distance: 151 - 152: 39.596 distance: 151 - 158: 40.248 distance: 153 - 154: 45.831 distance: 154 - 155: 31.028 distance: 155 - 156: 41.328 distance: 156 - 157: 39.973 distance: 158 - 159: 57.654 distance: 158 - 164: 68.311 distance: 159 - 160: 39.620 distance: 159 - 162: 41.999 distance: 160 - 161: 3.068 distance: 160 - 165: 8.345 distance: 162 - 163: 10.365 distance: 165 - 166: 22.418 distance: 166 - 167: 23.799 distance: 166 - 169: 42.346 distance: 167 - 168: 38.956 distance: 167 - 176: 7.211 distance: 169 - 170: 21.857 distance: 170 - 171: 31.497 distance: 170 - 172: 42.990 distance: 171 - 173: 34.055 distance: 172 - 174: 3.037 distance: 173 - 175: 26.573 distance: 174 - 175: 13.120 distance: 176 - 177: 7.842 distance: 177 - 178: 40.044 distance: 178 - 185: 55.720 distance: 180 - 181: 41.489 distance: 181 - 182: 18.066 distance: 182 - 183: 41.148 distance: 182 - 184: 40.923 distance: 185 - 186: 13.541 distance: 186 - 187: 24.484 distance: 186 - 189: 40.142 distance: 187 - 188: 16.267 distance: 187 - 196: 33.366 distance: 189 - 190: 29.425 distance: 190 - 191: 32.781 distance: 191 - 192: 19.515 distance: 192 - 193: 27.024 distance: 193 - 195: 49.547 distance: 196 - 197: 18.587 distance: 197 - 198: 41.531 distance: 197 - 200: 36.709 distance: 198 - 199: 55.211 distance: 198 - 204: 24.847 distance: 200 - 201: 44.011 distance: 201 - 202: 29.283 distance: 201 - 203: 44.272 distance: 204 - 205: 7.095 distance: 205 - 206: 21.665 distance: 205 - 208: 33.167 distance: 206 - 207: 39.432 distance: 206 - 212: 30.264 distance: 208 - 209: 37.913 distance: 208 - 210: 43.006 distance: 209 - 211: 29.946 distance: 212 - 213: 5.588 distance: 213 - 214: 3.140 distance: 214 - 218: 34.973