Starting phenix.real_space_refine on Tue Mar 19 02:02:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a4n_11639/03_2024/7a4n_11639_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a4n_11639/03_2024/7a4n_11639.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a4n_11639/03_2024/7a4n_11639.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a4n_11639/03_2024/7a4n_11639.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a4n_11639/03_2024/7a4n_11639_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7a4n_11639/03_2024/7a4n_11639_neut.pdb" } resolution = 2.75 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 14576 2.51 5 N 3741 2.21 5 O 4396 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 427": "OD1" <-> "OD2" Residue "A TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 509": "NH1" <-> "NH2" Residue "A TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 646": "NH1" <-> "NH2" Residue "A ASP 663": "OD1" <-> "OD2" Residue "A TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 780": "OE1" <-> "OE2" Residue "A GLU 1031": "OE1" <-> "OE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1139": "OD1" <-> "OD2" Residue "B PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 427": "OD1" <-> "OD2" Residue "B TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 509": "NH1" <-> "NH2" Residue "B TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 646": "NH1" <-> "NH2" Residue "B ASP 663": "OD1" <-> "OD2" Residue "B TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 780": "OE1" <-> "OE2" Residue "B GLU 1031": "OE1" <-> "OE2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1139": "OD1" <-> "OD2" Residue "C TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 427": "OD1" <-> "OD2" Residue "C ARG 509": "NH1" <-> "NH2" Residue "C TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 646": "NH1" <-> "NH2" Residue "C TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 780": "OE1" <-> "OE2" Residue "C GLU 1031": "OE1" <-> "OE2" Residue "C TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1139": "OD1" <-> "OD2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 22809 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 7511 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 963, 7493 Classifications: {'peptide': 963} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 49, 'TRANS': 913} Chain breaks: 10 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 22 Conformer: "B" Number of residues, atoms: 963, 7493 Classifications: {'peptide': 963} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 49, 'TRANS': 913} Chain breaks: 10 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 22 bond proxies already assigned to first conformer: 7638 Chain: "B" Number of atoms: 7502 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 963, 7479 Classifications: {'peptide': 963} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 49, 'TRANS': 913} Chain breaks: 10 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'TYR:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 35 Conformer: "B" Number of residues, atoms: 963, 7479 Classifications: {'peptide': 963} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 49, 'TRANS': 913} Chain breaks: 10 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'TYR:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 35 bond proxies already assigned to first conformer: 7616 Chain: "C" Number of atoms: 7502 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 963, 7478 Classifications: {'peptide': 963} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 49, 'TRANS': 913} Chain breaks: 10 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'TYR:plan': 2, 'ARG:plan': 3, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 35 Conformer: "B" Number of residues, atoms: 963, 7478 Classifications: {'peptide': 963} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 49, 'TRANS': 913} Chain breaks: 10 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'TYR:plan': 2, 'ARG:plan': 3, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 35 bond proxies already assigned to first conformer: 7614 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: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 21.07, per 1000 atoms: 0.92 Number of scatterers: 22809 At special positions: 0 Unit cell: (165.528, 129.58, 126.236, 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 96 16.00 O 4396 8.00 N 3741 7.00 C 14576 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 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=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=1.88 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=1.89 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=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=1.87 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 A1301 " - " ASN A 709 " " NAG A1302 " - " ASN A 801 " " NAG A1303 " - " ASN A1074 " " NAG A1304 " - " ASN A1098 " " NAG A1305 " - " ASN A1134 " " NAG B1301 " - " ASN B 709 " " NAG B1302 " - " ASN B 801 " " NAG B1303 " - " ASN B1074 " " NAG B1304 " - " ASN B1098 " " NAG B1305 " - " ASN B1134 " " NAG C1301 " - " ASN C 709 " " NAG C1302 " - " ASN C 801 " " NAG C1303 " - " ASN C1074 " " NAG C1304 " - " ASN C1098 " " NAG C1305 " - " ASN C1134 " " NAG D 1 " - " ASN A 717 " " NAG E 1 " - " ASN B 717 " " NAG F 1 " - " ASN C 717 " Time building additional restraints: 8.11 Conformation dependent library (CDL) restraints added in 7.5 seconds 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5440 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 54 sheets defined 25.8% alpha, 26.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.43 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 344 removed outlier: 4.030A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.624A pdb=" N GLU A 619 " --> pdb=" O ASN A 616 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 616 through 620' Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.614A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.083A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 3.740A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.604A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.662A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 383 through 390 removed outlier: 4.624A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.554A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.225A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 3.762A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 344 removed outlier: 3.827A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.726A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 383 through 390 removed outlier: 4.293A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 removed outlier: 3.860A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.700A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.551A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 3.816A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 3.597A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 50 through 55 removed outlier: 3.994A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 89 through 92 removed outlier: 3.772A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 106 through 107 removed outlier: 4.314A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 118 through 121 Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.028A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.566A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 538 through 539 Processing sheet with id=AB4, first strand: chain 'A' and resid 542 through 543 Processing sheet with id=AB5, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.374A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.755A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.523A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.523A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.418A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 787 through 789 Processing sheet with id=AC2, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC3, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.626A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 50 through 55 removed outlier: 4.111A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 89 through 92 removed outlier: 3.796A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 118 through 121 Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.060A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC9, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.573A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD3, first strand: chain 'B' and resid 538 through 539 Processing sheet with id=AD4, first strand: chain 'B' and resid 542 through 543 Processing sheet with id=AD5, first strand: chain 'B' and resid 565 through 566 removed outlier: 6.663A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.380A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 701 through 703 removed outlier: 6.768A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.595A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.595A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.455A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE3, first strand: chain 'C' and resid 29 through 31 removed outlier: 3.613A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 50 through 55 removed outlier: 4.108A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 89 through 92 removed outlier: 3.668A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 118 through 121 Processing sheet with id=AE7, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.005A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE9, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.493A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF2, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF3, first strand: chain 'C' and resid 538 through 539 Processing sheet with id=AF4, first strand: chain 'C' and resid 542 through 543 Processing sheet with id=AF5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.279A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.512A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.512A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.403A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 1120 through 1122 957 hydrogen bonds defined for protein. 2595 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: 9.66 Time building geometry restraints manager: 8.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7280 1.34 - 1.46: 5803 1.46 - 1.58: 10123 1.58 - 1.70: 0 1.70 - 1.83: 120 Bond restraints: 23326 Sorted by residual: bond pdb=" N HIS C1101 " pdb=" CA HIS C1101 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.15e-02 7.56e+03 7.82e+00 bond pdb=" N THR C1100 " pdb=" CA THR C1100 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.06e-02 8.90e+03 6.31e+00 bond pdb=" N TRP C1102 " pdb=" CA TRP C1102 " ideal model delta sigma weight residual 1.455 1.485 -0.030 1.22e-02 6.72e+03 6.03e+00 bond pdb=" N PHE C1103 " pdb=" CA PHE C1103 " ideal model delta sigma weight residual 1.454 1.484 -0.030 1.29e-02 6.01e+03 5.55e+00 bond pdb=" N ASN C1098 " pdb=" CA ASN C1098 " ideal model delta sigma weight residual 1.457 1.485 -0.029 1.32e-02 5.74e+03 4.67e+00 ... (remaining 23321 not shown) Histogram of bond angle deviations from ideal: 86.87 - 97.59: 1 97.59 - 108.30: 1191 108.30 - 119.01: 17780 119.01 - 129.72: 12720 129.72 - 140.43: 82 Bond angle restraints: 31774 Sorted by residual: angle pdb=" CD LYS A 776 " pdb=" CE LYS A 776 " pdb=" NZ LYS A 776 " ideal model delta sigma weight residual 111.90 140.43 -28.53 3.20e+00 9.77e-02 7.95e+01 angle pdb=" CD LYS B 206 " pdb=" CE LYS B 206 " pdb=" NZ LYS B 206 " ideal model delta sigma weight residual 111.90 140.35 -28.45 3.20e+00 9.77e-02 7.90e+01 angle pdb=" CD LYS C 424 " pdb=" CE LYS C 424 " pdb=" NZ LYS C 424 " ideal model delta sigma weight residual 111.90 139.97 -28.07 3.20e+00 9.77e-02 7.69e+01 angle pdb=" CD LYS B 378 " pdb=" CE LYS B 378 " pdb=" NZ LYS B 378 " ideal model delta sigma weight residual 111.90 86.87 25.03 3.20e+00 9.77e-02 6.12e+01 angle pdb=" CG ARG A 357 " pdb=" CD ARG A 357 " pdb=" NE ARG A 357 " ideal model delta sigma weight residual 112.00 124.99 -12.99 2.20e+00 2.07e-01 3.49e+01 ... (remaining 31769 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 13126 17.78 - 35.56: 843 35.56 - 53.34: 172 53.34 - 71.11: 37 71.11 - 88.89: 23 Dihedral angle restraints: 14201 sinusoidal: 5746 harmonic: 8455 Sorted by residual: dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -11.72 -74.28 1 1.00e+01 1.00e-02 7.00e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -12.51 -73.49 1 1.00e+01 1.00e-02 6.87e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -14.47 -71.53 1 1.00e+01 1.00e-02 6.56e+01 ... (remaining 14198 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.358: 3700 0.358 - 0.716: 2 0.716 - 1.075: 0 1.075 - 1.433: 4 1.433 - 1.791: 7 Chirality restraints: 3713 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-02 2.50e+03 3.41e+02 chirality pdb=" CG LEU C1141 " pdb=" CB LEU C1141 " pdb=" CD1 LEU C1141 " pdb=" CD2 LEU C1141 " both_signs ideal model delta sigma weight residual False -2.59 -0.80 -1.79 2.00e-01 2.50e+01 8.02e+01 chirality pdb=" CG LEU A 189 " pdb=" CB LEU A 189 " pdb=" CD1 LEU A 189 " pdb=" CD2 LEU A 189 " both_signs ideal model delta sigma weight residual False -2.59 -0.80 -1.79 2.00e-01 2.50e+01 8.00e+01 ... (remaining 3710 not shown) Planarity restraints: 4096 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 189 " 0.010 2.00e-02 2.50e+03 1.97e-02 3.90e+00 pdb=" C LEU A 189 " -0.034 2.00e-02 2.50e+03 pdb=" O LEU A 189 " 0.013 2.00e-02 2.50e+03 pdb=" N ARG A 190 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 189 " 0.009 2.00e-02 2.50e+03 1.88e-02 3.54e+00 pdb=" C LEU B 189 " -0.033 2.00e-02 2.50e+03 pdb=" O LEU B 189 " 0.012 2.00e-02 2.50e+03 pdb=" N ARG B 190 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 189 " -0.009 2.00e-02 2.50e+03 1.81e-02 3.28e+00 pdb=" C LEU C 189 " 0.031 2.00e-02 2.50e+03 pdb=" O LEU C 189 " -0.012 2.00e-02 2.50e+03 pdb=" N ARG C 190 " -0.010 2.00e-02 2.50e+03 ... (remaining 4093 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 227 2.58 - 3.16: 19427 3.16 - 3.74: 33034 3.74 - 4.32: 50745 4.32 - 4.90: 84265 Nonbonded interactions: 187698 Sorted by model distance: nonbonded pdb=" OH TYR B 37 " pdb=" OD2 ASP B 53 " model vdw 2.003 2.440 nonbonded pdb=" OH TYR A 37 " pdb=" OD2 ASP A 53 " model vdw 2.098 2.440 nonbonded pdb=" OG1 THR A 618 " pdb=" OE1 GLU A 619 " model vdw 2.099 2.440 nonbonded pdb=" O LYS C 386 " pdb=" OD1 ASP C 389 " model vdw 2.111 3.040 nonbonded pdb=" OD1 ASP C 568 " pdb=" N ILE C 569 " model vdw 2.116 2.520 ... (remaining 187693 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 124 or (resid 125 and (name N or name CA or nam \ e C or name O or name CB )) or resid 126 through 318 or (resid 319 and (name N o \ r name CA or name C or name O or name CB )) or resid 320 through 339 or resid 34 \ 1 through 344 or resid 346 through 381 or resid 383 through 402 or (resid 403 an \ d (name N or name CA or name C or name O or name CB )) or resid 404 through 429 \ or resid 431 through 442 or resid 444 through 468 or resid 470 through 494 or (r \ esid 495 and (name N or name CA or name C or name O or name CB )) or resid 496 t \ hrough 504 or (resid 505 through 506 and (name N or name CA or name C or name O \ or name CB )) or resid 507 through 1147 or resid 1301 through 1305)) selection = (chain 'B' and (resid 27 through 318 or (resid 319 and (name N or name CA or nam \ e C or name O or name CB )) or resid 320 through 339 or resid 341 through 344 or \ resid 346 through 381 or resid 383 through 402 or (resid 403 and (name N or nam \ e CA or name C or name O or name CB )) or resid 404 through 429 or resid 431 thr \ ough 442 or resid 444 through 468 or resid 470 through 1141 or (resid 1142 and ( \ name N or name CA or name C or name O or name CB )) or resid 1143 through 1147 o \ r resid 1301 through 1305)) selection = (chain 'C' and (resid 27 through 124 or (resid 125 and (name N or name CA or nam \ e C or name O or name CB )) or resid 126 through 339 or resid 341 through 344 or \ resid 346 through 381 or resid 383 through 421 or (resid 422 and (name N or nam \ e CA or name C or name O or name CB )) or resid 423 through 429 or resid 431 thr \ ough 442 or resid 444 through 468 or resid 470 through 505 or (resid 506 and (na \ me N or name CA or name C or name O or name CB )) or resid 507 through 1141 or ( \ resid 1142 and (name N or name CA or name C or name O or name CB )) or resid 114 \ 3 through 1147 or resid 1301 through 1305)) } 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=0.50 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: 4.500 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: 19.090 Check model and map are aligned: 0.360 Set scattering table: 0.210 Process input model: 74.180 Find NCS groups from input model: 1.560 Set up NCS constraints: 0.190 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: 0.000 Load rotamer database and sin/cos tables:13.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 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 : 0.007 0.074 23326 Z= 0.485 Angle : 0.805 28.531 31774 Z= 0.403 Chirality : 0.098 1.791 3713 Planarity : 0.004 0.045 4078 Dihedral : 12.788 88.893 8653 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.20 % Allowed : 5.16 % Favored : 94.64 % Cbeta Deviations : 0.04 % 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: -2.00 (0.14), residues: 2840 helix: 0.25 (0.19), residues: 653 sheet: -1.47 (0.19), residues: 534 loop : -2.01 (0.13), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.006 0.001 HIS A1064 PHE 0.015 0.002 PHE C 65 TYR 0.022 0.002 TYR C1067 ARG 0.008 0.001 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 299 time to evaluate : 2.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 ASN cc_start: 0.4778 (m-40) cc_final: 0.4098 (p0) REVERT: A 127 VAL cc_start: 0.6693 (t) cc_final: 0.6468 (p) REVERT: A 192 PHE cc_start: 0.6298 (m-80) cc_final: 0.6006 (m-80) REVERT: A 979 ASP cc_start: 0.6732 (m-30) cc_final: 0.6529 (m-30) REVERT: B 368 LEU cc_start: 0.7377 (mm) cc_final: 0.7077 (mt) REVERT: B 421 TYR cc_start: 0.5292 (m-10) cc_final: 0.4870 (m-80) REVERT: C 28 TYR cc_start: 0.6564 (m-80) cc_final: 0.6307 (m-80) REVERT: C 196 ASN cc_start: 0.5012 (m-40) cc_final: 0.4494 (t0) REVERT: C 353 TRP cc_start: 0.7325 (p-90) cc_final: 0.6920 (p-90) REVERT: C 354 ASN cc_start: 0.6552 (p0) cc_final: 0.6154 (t0) REVERT: C 392 PHE cc_start: 0.7219 (m-80) cc_final: 0.6950 (m-80) outliers start: 4 outliers final: 1 residues processed: 303 average time/residue: 1.1681 time to fit residues: 412.5507 Evaluate side-chains 173 residues out of total 2506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 172 time to evaluate : 2.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1127 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 243 optimal weight: 1.9990 chunk 218 optimal weight: 1.9990 chunk 121 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 chunk 225 optimal weight: 0.8980 chunk 87 optimal weight: 0.7980 chunk 137 optimal weight: 0.9980 chunk 168 optimal weight: 2.9990 chunk 261 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN A 764 ASN A1083 HIS A1088 HIS A1101 HIS A1119 ASN B 239 GLN B 314 GLN B 321 GLN B 613 GLN B1002 GLN B1071 GLN ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 564 GLN C 603 ASN C1005 GLN C1088 HIS C1119 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 23326 Z= 0.232 Angle : 0.582 15.206 31774 Z= 0.299 Chirality : 0.046 0.169 3713 Planarity : 0.004 0.045 4078 Dihedral : 5.561 108.064 3546 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.07 % Allowed : 9.73 % Favored : 89.19 % 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: -1.10 (0.15), residues: 2840 helix: 1.24 (0.20), residues: 671 sheet: -1.05 (0.19), residues: 597 loop : -1.51 (0.14), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 436 HIS 0.004 0.001 HIS A 207 PHE 0.028 0.002 PHE B 168 TYR 0.024 0.002 TYR B 380 ARG 0.005 0.000 ARG B 646 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 170 time to evaluate : 2.671 Fit side-chains REVERT: A 61 ASN cc_start: 0.4777 (m-40) cc_final: 0.4169 (p0) REVERT: A 127 VAL cc_start: 0.6839 (t) cc_final: 0.6616 (p) REVERT: A 192 PHE cc_start: 0.6377 (m-80) cc_final: 0.6154 (m-80) REVERT: A 396 TYR cc_start: 0.7063 (m-80) cc_final: 0.6626 (m-10) REVERT: B 269 TYR cc_start: 0.5600 (m-10) cc_final: 0.5279 (m-80) REVERT: B 368 LEU cc_start: 0.7322 (mm) cc_final: 0.7039 (mt) REVERT: B 607 GLN cc_start: 0.7817 (pt0) cc_final: 0.7526 (pt0) REVERT: B 935 GLN cc_start: 0.6698 (tm130) cc_final: 0.6402 (tm-30) REVERT: B 1029 MET cc_start: 0.9159 (tpp) cc_final: 0.8745 (tpp) REVERT: C 28 TYR cc_start: 0.6620 (m-80) cc_final: 0.6288 (m-80) REVERT: C 196 ASN cc_start: 0.4969 (m-40) cc_final: 0.4581 (t0) REVERT: C 353 TRP cc_start: 0.7368 (p-90) cc_final: 0.7007 (p-90) outliers start: 26 outliers final: 12 residues processed: 189 average time/residue: 1.0812 time to fit residues: 241.8816 Evaluate side-chains 157 residues out of total 2506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 145 time to evaluate : 2.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 827 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 145 optimal weight: 0.4980 chunk 81 optimal weight: 2.9990 chunk 217 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 262 optimal weight: 0.9980 chunk 283 optimal weight: 0.7980 chunk 233 optimal weight: 1.9990 chunk 259 optimal weight: 0.2980 chunk 89 optimal weight: 0.5980 chunk 210 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 ASN A1002 GLN A1113 GLN A1119 ASN B 314 GLN B 354 ASN B1005 GLN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN C 603 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23326 Z= 0.173 Angle : 0.519 9.497 31774 Z= 0.268 Chirality : 0.044 0.148 3713 Planarity : 0.004 0.046 4078 Dihedral : 4.639 48.964 3544 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.31 % Allowed : 10.89 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.15), residues: 2840 helix: 1.69 (0.20), residues: 653 sheet: -0.62 (0.20), residues: 609 loop : -1.29 (0.14), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 436 HIS 0.002 0.001 HIS A1064 PHE 0.031 0.001 PHE B 168 TYR 0.034 0.001 TYR B 369 ARG 0.007 0.000 ARG B 995 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 164 time to evaluate : 2.664 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 ASN cc_start: 0.4742 (m-40) cc_final: 0.4173 (p0) REVERT: A 127 VAL cc_start: 0.6915 (t) cc_final: 0.6664 (p) REVERT: A 192 PHE cc_start: 0.6381 (m-80) cc_final: 0.6145 (m-80) REVERT: A 396 TYR cc_start: 0.7048 (m-80) cc_final: 0.6830 (m-10) REVERT: A 654 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.6951 (tp30) REVERT: A 748 GLU cc_start: 0.6937 (mp0) cc_final: 0.6687 (mp0) REVERT: B 269 TYR cc_start: 0.5704 (m-10) cc_final: 0.5436 (m-80) REVERT: B 368 LEU cc_start: 0.7283 (mm) cc_final: 0.6960 (mt) REVERT: B 567 ARG cc_start: 0.7409 (OUTLIER) cc_final: 0.6853 (tpt-90) REVERT: B 607 GLN cc_start: 0.7783 (pt0) cc_final: 0.7501 (pt0) REVERT: B 935 GLN cc_start: 0.6595 (tm130) cc_final: 0.6363 (tm-30) REVERT: C 28 TYR cc_start: 0.6596 (m-80) cc_final: 0.6357 (m-80) REVERT: C 196 ASN cc_start: 0.5009 (m-40) cc_final: 0.4683 (t0) REVERT: C 353 TRP cc_start: 0.7337 (p-90) cc_final: 0.7037 (p-90) outliers start: 32 outliers final: 18 residues processed: 187 average time/residue: 1.0543 time to fit residues: 234.7052 Evaluate side-chains 166 residues out of total 2506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 146 time to evaluate : 2.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 388 ASN Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 258 optimal weight: 1.9990 chunk 196 optimal weight: 0.0870 chunk 135 optimal weight: 0.4980 chunk 29 optimal weight: 10.0000 chunk 125 optimal weight: 0.9990 chunk 175 optimal weight: 0.0060 chunk 262 optimal weight: 1.9990 chunk 278 optimal weight: 1.9990 chunk 137 optimal weight: 0.6980 chunk 249 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 603 ASN A1002 GLN A1119 ASN B 121 ASN B 314 GLN B1005 GLN B1101 HIS C 564 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 23326 Z= 0.152 Angle : 0.495 8.042 31774 Z= 0.256 Chirality : 0.043 0.146 3713 Planarity : 0.003 0.044 4078 Dihedral : 4.227 36.259 3544 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.27 % Allowed : 11.68 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.15), residues: 2840 helix: 1.94 (0.20), residues: 656 sheet: -0.56 (0.19), residues: 639 loop : -1.12 (0.15), residues: 1545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 436 HIS 0.002 0.001 HIS B1064 PHE 0.027 0.001 PHE C 168 TYR 0.021 0.001 TYR C 369 ARG 0.004 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 160 time to evaluate : 3.559 Fit side-chains revert: symmetry clash REVERT: A 61 ASN cc_start: 0.4681 (m-40) cc_final: 0.4208 (p0) REVERT: A 127 VAL cc_start: 0.6881 (t) cc_final: 0.6614 (p) REVERT: A 192 PHE cc_start: 0.6371 (m-80) cc_final: 0.6138 (m-80) REVERT: A 378 LYS cc_start: 0.7266 (OUTLIER) cc_final: 0.7001 (pttp) REVERT: A 748 GLU cc_start: 0.7004 (mp0) cc_final: 0.6718 (mp0) REVERT: B 269 TYR cc_start: 0.5544 (m-10) cc_final: 0.5283 (m-10) REVERT: B 368 LEU cc_start: 0.7299 (mm) cc_final: 0.6965 (mt) REVERT: B 567 ARG cc_start: 0.7434 (OUTLIER) cc_final: 0.6863 (tpt-90) REVERT: B 571 ASP cc_start: 0.6207 (m-30) cc_final: 0.5972 (t0) REVERT: B 1010 GLN cc_start: 0.8047 (OUTLIER) cc_final: 0.6966 (mp10) REVERT: C 196 ASN cc_start: 0.5019 (m-40) cc_final: 0.4673 (t0) REVERT: C 207 HIS cc_start: 0.5451 (m-70) cc_final: 0.4415 (t70) REVERT: C 353 TRP cc_start: 0.7367 (p-90) cc_final: 0.7083 (p-90) REVERT: C 385 THR cc_start: 0.7452 (p) cc_final: 0.7214 (m) outliers start: 31 outliers final: 17 residues processed: 186 average time/residue: 1.0321 time to fit residues: 230.9722 Evaluate side-chains 163 residues out of total 2506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 143 time to evaluate : 2.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 231 optimal weight: 5.9990 chunk 158 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 207 optimal weight: 5.9990 chunk 114 optimal weight: 0.0570 chunk 237 optimal weight: 0.9980 chunk 192 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 142 optimal weight: 6.9990 chunk 249 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 overall best weight: 1.5502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1002 GLN A1119 ASN B 121 ASN B 314 GLN B 334 ASN ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN C 564 GLN C1005 GLN C1106 GLN C1119 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 23326 Z= 0.326 Angle : 0.603 11.996 31774 Z= 0.310 Chirality : 0.047 0.262 3713 Planarity : 0.004 0.047 4078 Dihedral : 4.779 30.239 3544 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.95 % Allowed : 11.56 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.15), residues: 2840 helix: 1.71 (0.20), residues: 656 sheet: -0.69 (0.19), residues: 618 loop : -1.12 (0.15), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 436 HIS 0.005 0.001 HIS B1101 PHE 0.026 0.002 PHE C 168 TYR 0.025 0.002 TYR B 369 ARG 0.004 0.001 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 145 time to evaluate : 2.676 Fit side-chains revert: symmetry clash REVERT: A 28 TYR cc_start: 0.6823 (m-80) cc_final: 0.6446 (m-80) REVERT: A 127 VAL cc_start: 0.6925 (t) cc_final: 0.6662 (p) REVERT: A 192 PHE cc_start: 0.6417 (m-80) cc_final: 0.6130 (m-80) REVERT: A 378 LYS cc_start: 0.7309 (OUTLIER) cc_final: 0.7036 (pttp) REVERT: A 654 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6904 (tp30) REVERT: A 740 MET cc_start: 0.8106 (OUTLIER) cc_final: 0.7665 (tpt) REVERT: A 748 GLU cc_start: 0.7077 (mp0) cc_final: 0.6844 (mp0) REVERT: B 368 LEU cc_start: 0.7427 (mm) cc_final: 0.7058 (mt) REVERT: B 460 ASN cc_start: 0.4589 (m-40) cc_final: 0.4298 (t0) REVERT: B 567 ARG cc_start: 0.7419 (OUTLIER) cc_final: 0.6851 (tpt-90) REVERT: B 571 ASP cc_start: 0.6242 (m-30) cc_final: 0.6004 (t0) REVERT: B 1010 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.7000 (mp10) REVERT: C 378 LYS cc_start: 0.7123 (OUTLIER) cc_final: 0.6813 (ttmt) outliers start: 48 outliers final: 24 residues processed: 187 average time/residue: 1.0575 time to fit residues: 235.8171 Evaluate side-chains 171 residues out of total 2506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 141 time to evaluate : 2.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 827 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 93 optimal weight: 0.7980 chunk 250 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 chunk 163 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 278 optimal weight: 0.9980 chunk 231 optimal weight: 5.9990 chunk 129 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 146 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 613 GLN A1002 GLN B 314 GLN ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN B1005 GLN C 564 GLN C1005 GLN C1119 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 23326 Z= 0.206 Angle : 0.532 14.917 31774 Z= 0.275 Chirality : 0.044 0.299 3713 Planarity : 0.004 0.045 4078 Dihedral : 4.458 30.474 3544 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.47 % Allowed : 12.63 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.15), residues: 2840 helix: 2.05 (0.20), residues: 635 sheet: -0.54 (0.19), residues: 654 loop : -1.13 (0.15), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 436 HIS 0.003 0.001 HIS B1101 PHE 0.027 0.001 PHE C 168 TYR 0.020 0.001 TYR C1067 ARG 0.003 0.000 ARG B 995 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 150 time to evaluate : 2.708 Fit side-chains revert: symmetry clash REVERT: A 101 ILE cc_start: 0.3001 (OUTLIER) cc_final: 0.2462 (mt) REVERT: A 127 VAL cc_start: 0.6905 (t) cc_final: 0.6635 (p) REVERT: A 190 ARG cc_start: 0.5250 (mtp180) cc_final: 0.4874 (mmm-85) REVERT: A 192 PHE cc_start: 0.6398 (m-80) cc_final: 0.6165 (m-80) REVERT: A 378 LYS cc_start: 0.7337 (OUTLIER) cc_final: 0.7003 (pttp) REVERT: A 654 GLU cc_start: 0.7237 (OUTLIER) cc_final: 0.6879 (tp30) REVERT: A 748 GLU cc_start: 0.7008 (mp0) cc_final: 0.6691 (mp0) REVERT: B 33 THR cc_start: 0.6905 (p) cc_final: 0.6624 (p) REVERT: B 368 LEU cc_start: 0.7370 (mm) cc_final: 0.6985 (mt) REVERT: B 567 ARG cc_start: 0.7457 (OUTLIER) cc_final: 0.6919 (tpt-90) REVERT: B 571 ASP cc_start: 0.6164 (OUTLIER) cc_final: 0.5933 (t0) REVERT: B 916 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8411 (tp) REVERT: B 1010 GLN cc_start: 0.8040 (OUTLIER) cc_final: 0.6965 (mp10) REVERT: C 378 LYS cc_start: 0.7040 (OUTLIER) cc_final: 0.6784 (ttmt) REVERT: C 1101 HIS cc_start: 0.7575 (m90) cc_final: 0.7251 (m90) outliers start: 36 outliers final: 23 residues processed: 180 average time/residue: 1.0705 time to fit residues: 229.4237 Evaluate side-chains 170 residues out of total 2506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 139 time to evaluate : 2.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 786 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 268 optimal weight: 0.6980 chunk 31 optimal weight: 6.9990 chunk 158 optimal weight: 2.9990 chunk 203 optimal weight: 7.9990 chunk 157 optimal weight: 0.6980 chunk 234 optimal weight: 6.9990 chunk 155 optimal weight: 0.7980 chunk 277 optimal weight: 1.9990 chunk 173 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 128 optimal weight: 8.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN A1002 GLN A1119 ASN B 314 GLN ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN B1005 GLN C1005 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 23326 Z= 0.278 Angle : 0.572 14.005 31774 Z= 0.294 Chirality : 0.046 0.279 3713 Planarity : 0.004 0.046 4078 Dihedral : 4.661 30.824 3544 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.15 % Allowed : 12.55 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.15), residues: 2840 helix: 1.97 (0.20), residues: 635 sheet: -0.61 (0.19), residues: 636 loop : -1.13 (0.15), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 436 HIS 0.004 0.001 HIS A1101 PHE 0.024 0.002 PHE C 168 TYR 0.027 0.002 TYR B 369 ARG 0.004 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 151 time to evaluate : 2.429 Fit side-chains revert: symmetry clash REVERT: A 101 ILE cc_start: 0.3282 (OUTLIER) cc_final: 0.2748 (mt) REVERT: A 127 VAL cc_start: 0.6903 (t) cc_final: 0.6646 (p) REVERT: A 190 ARG cc_start: 0.5396 (mtp180) cc_final: 0.4935 (mmm-85) REVERT: A 192 PHE cc_start: 0.6416 (m-80) cc_final: 0.6106 (m-80) REVERT: A 378 LYS cc_start: 0.7306 (OUTLIER) cc_final: 0.6932 (pttp) REVERT: A 654 GLU cc_start: 0.7254 (OUTLIER) cc_final: 0.6897 (tp30) REVERT: A 740 MET cc_start: 0.8118 (OUTLIER) cc_final: 0.7690 (tpt) REVERT: B 368 LEU cc_start: 0.7449 (mm) cc_final: 0.7060 (mt) REVERT: B 460 ASN cc_start: 0.4262 (t0) cc_final: 0.3988 (m-40) REVERT: B 567 ARG cc_start: 0.7475 (OUTLIER) cc_final: 0.6868 (tpt-90) REVERT: B 571 ASP cc_start: 0.6186 (m-30) cc_final: 0.5964 (t0) REVERT: B 916 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8470 (tp) REVERT: B 1010 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.6991 (mp10) REVERT: C 378 LYS cc_start: 0.7120 (OUTLIER) cc_final: 0.6809 (ttmt) outliers start: 53 outliers final: 34 residues processed: 195 average time/residue: 1.0061 time to fit residues: 235.9880 Evaluate side-chains 185 residues out of total 2506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 143 time to evaluate : 2.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 171 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 165 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 176 optimal weight: 1.9990 chunk 189 optimal weight: 0.4980 chunk 137 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 218 optimal weight: 0.9980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1002 GLN B 314 GLN B 954 GLN B1002 GLN B1005 GLN C 207 HIS C1005 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 23326 Z= 0.240 Angle : 0.546 13.476 31774 Z= 0.282 Chirality : 0.045 0.277 3713 Planarity : 0.004 0.045 4078 Dihedral : 4.536 31.273 3544 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.95 % Allowed : 12.95 % Favored : 85.10 % 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: -0.37 (0.15), residues: 2840 helix: 2.05 (0.20), residues: 635 sheet: -0.51 (0.19), residues: 651 loop : -1.13 (0.15), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 436 HIS 0.004 0.001 HIS C1101 PHE 0.025 0.002 PHE B 192 TYR 0.021 0.001 TYR A1067 ARG 0.006 0.000 ARG B 190 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 147 time to evaluate : 2.622 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 101 ILE cc_start: 0.3385 (OUTLIER) cc_final: 0.2337 (tp) REVERT: A 127 VAL cc_start: 0.6954 (t) cc_final: 0.6674 (p) REVERT: A 190 ARG cc_start: 0.5358 (mtp180) cc_final: 0.4874 (mmm-85) REVERT: A 192 PHE cc_start: 0.6419 (m-80) cc_final: 0.6126 (m-80) REVERT: A 654 GLU cc_start: 0.7230 (OUTLIER) cc_final: 0.6861 (tp30) REVERT: A 740 MET cc_start: 0.8119 (OUTLIER) cc_final: 0.7685 (tpt) REVERT: B 33 THR cc_start: 0.6977 (p) cc_final: 0.6686 (p) REVERT: B 368 LEU cc_start: 0.7440 (mm) cc_final: 0.7052 (mt) REVERT: B 564 GLN cc_start: 0.5898 (OUTLIER) cc_final: 0.5529 (mm-40) REVERT: B 567 ARG cc_start: 0.7469 (OUTLIER) cc_final: 0.6867 (tpt-90) REVERT: B 571 ASP cc_start: 0.6187 (OUTLIER) cc_final: 0.5959 (t0) REVERT: B 916 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8452 (tp) REVERT: B 1010 GLN cc_start: 0.8045 (OUTLIER) cc_final: 0.6974 (mp10) REVERT: C 55 PHE cc_start: 0.7105 (m-80) cc_final: 0.6737 (m-80) REVERT: C 207 HIS cc_start: 0.5373 (OUTLIER) cc_final: 0.4402 (t70) outliers start: 48 outliers final: 36 residues processed: 184 average time/residue: 1.0504 time to fit residues: 234.6956 Evaluate side-chains 187 residues out of total 2506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 142 time to evaluate : 2.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 252 optimal weight: 2.9990 chunk 265 optimal weight: 0.9990 chunk 242 optimal weight: 6.9990 chunk 258 optimal weight: 0.9990 chunk 155 optimal weight: 0.0970 chunk 112 optimal weight: 2.9990 chunk 203 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 233 optimal weight: 0.9990 chunk 244 optimal weight: 1.9990 chunk 257 optimal weight: 0.8980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1002 GLN B 314 GLN B1005 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 23326 Z= 0.209 Angle : 0.540 13.095 31774 Z= 0.279 Chirality : 0.044 0.269 3713 Planarity : 0.004 0.046 4078 Dihedral : 4.465 30.459 3544 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.67 % Allowed : 13.19 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.15), residues: 2840 helix: 2.12 (0.20), residues: 635 sheet: -0.54 (0.19), residues: 657 loop : -1.08 (0.15), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 436 HIS 0.007 0.001 HIS C 207 PHE 0.024 0.001 PHE C 168 TYR 0.027 0.001 TYR B 369 ARG 0.005 0.000 ARG B 190 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 154 time to evaluate : 2.528 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 101 ILE cc_start: 0.3356 (OUTLIER) cc_final: 0.2292 (tp) REVERT: A 127 VAL cc_start: 0.6938 (t) cc_final: 0.6658 (p) REVERT: A 190 ARG cc_start: 0.5515 (mtp180) cc_final: 0.4955 (mmm-85) REVERT: A 192 PHE cc_start: 0.6392 (m-80) cc_final: 0.6099 (m-80) REVERT: A 654 GLU cc_start: 0.7228 (OUTLIER) cc_final: 0.6859 (tp30) REVERT: A 740 MET cc_start: 0.8100 (OUTLIER) cc_final: 0.7635 (tpt) REVERT: A 748 GLU cc_start: 0.7043 (mp0) cc_final: 0.6735 (mp0) REVERT: B 33 THR cc_start: 0.6952 (p) cc_final: 0.6673 (p) REVERT: B 190 ARG cc_start: 0.6728 (mtt90) cc_final: 0.6419 (mtm-85) REVERT: B 368 LEU cc_start: 0.7421 (mm) cc_final: 0.7039 (mt) REVERT: B 460 ASN cc_start: 0.4131 (t0) cc_final: 0.3808 (m-40) REVERT: B 564 GLN cc_start: 0.5923 (OUTLIER) cc_final: 0.5561 (mm-40) REVERT: B 567 ARG cc_start: 0.7465 (OUTLIER) cc_final: 0.6880 (tpt-90) REVERT: B 571 ASP cc_start: 0.6182 (m-30) cc_final: 0.5956 (t0) REVERT: B 916 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8434 (tp) REVERT: B 1010 GLN cc_start: 0.8043 (OUTLIER) cc_final: 0.6964 (mp10) REVERT: C 55 PHE cc_start: 0.7095 (m-80) cc_final: 0.6724 (m-80) outliers start: 41 outliers final: 34 residues processed: 186 average time/residue: 1.0353 time to fit residues: 229.7749 Evaluate side-chains 192 residues out of total 2506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 151 time to evaluate : 2.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 169 optimal weight: 0.4980 chunk 273 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 190 optimal weight: 0.0770 chunk 286 optimal weight: 3.9990 chunk 264 optimal weight: 0.6980 chunk 228 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 176 optimal weight: 0.9990 chunk 140 optimal weight: 1.9990 overall best weight: 0.8542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN A1002 GLN B 314 GLN B1005 GLN C 207 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 23326 Z= 0.215 Angle : 0.539 12.951 31774 Z= 0.279 Chirality : 0.044 0.267 3713 Planarity : 0.004 0.045 4078 Dihedral : 4.448 29.730 3544 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.75 % Allowed : 13.39 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.15), residues: 2840 helix: 2.10 (0.20), residues: 638 sheet: -0.45 (0.19), residues: 651 loop : -1.08 (0.15), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 436 HIS 0.003 0.001 HIS A1101 PHE 0.025 0.001 PHE B 192 TYR 0.021 0.001 TYR C1067 ARG 0.004 0.000 ARG B 273 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 152 time to evaluate : 2.754 Fit side-chains revert: symmetry clash REVERT: A 101 ILE cc_start: 0.3241 (OUTLIER) cc_final: 0.2232 (tp) REVERT: A 127 VAL cc_start: 0.6957 (t) cc_final: 0.6664 (p) REVERT: A 190 ARG cc_start: 0.5493 (mtp180) cc_final: 0.4914 (mmm-85) REVERT: A 192 PHE cc_start: 0.6400 (m-80) cc_final: 0.6097 (m-80) REVERT: A 378 LYS cc_start: 0.7405 (OUTLIER) cc_final: 0.7063 (pttp) REVERT: A 654 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.6880 (tp30) REVERT: A 740 MET cc_start: 0.8111 (OUTLIER) cc_final: 0.7644 (tpt) REVERT: A 748 GLU cc_start: 0.7039 (mp0) cc_final: 0.6723 (mp0) REVERT: B 33 THR cc_start: 0.6891 (p) cc_final: 0.6609 (p) REVERT: B 190 ARG cc_start: 0.6725 (mtt90) cc_final: 0.6346 (mtm-85) REVERT: B 368 LEU cc_start: 0.7417 (mm) cc_final: 0.7020 (mt) REVERT: B 460 ASN cc_start: 0.4127 (t0) cc_final: 0.3792 (m-40) REVERT: B 567 ARG cc_start: 0.7456 (OUTLIER) cc_final: 0.6873 (tpt-90) REVERT: B 571 ASP cc_start: 0.6306 (m-30) cc_final: 0.6068 (t0) REVERT: B 916 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8438 (tp) REVERT: B 1010 GLN cc_start: 0.8042 (OUTLIER) cc_final: 0.6963 (mp10) REVERT: C 55 PHE cc_start: 0.7089 (m-80) cc_final: 0.6727 (m-80) outliers start: 43 outliers final: 32 residues processed: 186 average time/residue: 1.0755 time to fit residues: 239.6626 Evaluate side-chains 188 residues out of total 2506 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 149 time to evaluate : 2.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 378 LYS Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 604 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 1094 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 181 optimal weight: 0.0570 chunk 243 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 210 optimal weight: 2.9990 chunk 33 optimal weight: 0.0010 chunk 63 optimal weight: 0.0020 chunk 228 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 234 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 overall best weight: 1.0116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN A1002 GLN A1119 ASN B 314 GLN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.161793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.110437 restraints weight = 95782.909| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 4.18 r_work: 0.3030 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3020 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3020 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 23326 Z= 0.239 Angle : 0.548 12.967 31774 Z= 0.282 Chirality : 0.045 0.266 3713 Planarity : 0.004 0.045 4078 Dihedral : 4.511 30.535 3544 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.71 % Allowed : 13.63 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.15), residues: 2840 helix: 2.06 (0.20), residues: 638 sheet: -0.54 (0.19), residues: 636 loop : -1.06 (0.15), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 436 HIS 0.003 0.001 HIS A1101 PHE 0.024 0.002 PHE C 168 TYR 0.028 0.002 TYR B 369 ARG 0.004 0.000 ARG B 273 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6262.27 seconds wall clock time: 112 minutes 47.16 seconds (6767.16 seconds total)