Starting phenix.real_space_refine on Wed Feb 21 12:05:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8x_22734/02_2024/7k8x_22734.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8x_22734/02_2024/7k8x_22734.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8x_22734/02_2024/7k8x_22734.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8x_22734/02_2024/7k8x_22734.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8x_22734/02_2024/7k8x_22734.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k8x_22734/02_2024/7k8x_22734.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3238 atoms to isotropic. 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 127 5.16 5 C 17436 2.51 5 N 4520 2.21 5 O 5316 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 194": "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 GLU 309": "OE1" <-> "OE2" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 346": "NH1" <-> "NH2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A ARG 403": "NH1" <-> "NH2" Residue "A ASP 405": "OD1" <-> "OD2" Residue "A TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 457": "NH1" <-> "NH2" Residue "A GLU 471": "OE1" <-> "OE2" Residue "A TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 663": "OD1" <-> "OD2" Residue "A PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1041": "OD1" <-> "OD2" Residue "A TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 198": "OD1" <-> "OD2" Residue "B PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "B ARG 346": "NH1" <-> "NH2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 403": "NH1" <-> "NH2" Residue "B ASP 405": "OD1" <-> "OD2" Residue "B TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 457": "NH1" <-> "NH2" Residue "B ASP 467": "OD1" <-> "OD2" Residue "B TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 614": "OD1" <-> "OD2" Residue "B TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 663": "OD1" <-> "OD2" Residue "B TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 906": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 950": "OD1" <-> "OD2" Residue "B PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1017": "OE1" <-> "OE2" Residue "B PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 346": "NH1" <-> "NH2" Residue "C TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "C ASP 364": "OD1" <-> "OD2" Residue "C TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 403": "NH1" <-> "NH2" Residue "C TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 457": "NH1" <-> "NH2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 773": "OE1" <-> "OE2" Residue "C PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 918": "OE1" <-> "OE2" Residue "C PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 979": "OD1" <-> "OD2" Residue "C GLU 988": "OE1" <-> "OE2" Residue "C TYR 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 38": "NH1" <-> "NH2" Residue "D GLU 46": "OE1" <-> "OE2" Residue "D ARG 67": "NH1" <-> "NH2" Residue "D ARG 72": "NH1" <-> "NH2" Residue "D TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 98": "NH1" <-> "NH2" Residue "D TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 38": "NH1" <-> "NH2" Residue "E GLU 46": "OE1" <-> "OE2" Residue "E ARG 67": "NH1" <-> "NH2" Residue "E ARG 72": "NH1" <-> "NH2" Residue "E TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 98": "NH1" <-> "NH2" Residue "E TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 54": "NH1" <-> "NH2" Residue "F ARG 61": "NH1" <-> "NH2" Residue "F ASP 85": "OD1" <-> "OD2" Residue "G ARG 54": "NH1" <-> "NH2" Residue "G ARG 61": "NH1" <-> "NH2" Residue "G ASP 85": "OD1" <-> "OD2" Residue "G PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 27399 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 7823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7823 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 49, 'TRANS': 952} Chain breaks: 7 Chain: "B" Number of atoms: 7823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7823 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 49, 'TRANS': 952} Chain breaks: 7 Chain: "C" Number of atoms: 7823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7823 Classifications: {'peptide': 1002} Link IDs: {'CIS': 1, 'PTRANS': 49, 'TRANS': 951} Chain breaks: 7 Chain: "D" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 991 Classifications: {'peptide': 128} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 121} Chain: "E" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 991 Classifications: {'peptide': 128} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 121} Chain: "F" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 778 Classifications: {'peptide': 108} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 101} Chain: "G" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 778 Classifications: {'peptide': 108} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 101} Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 14.02, per 1000 atoms: 0.51 Number of scatterers: 27399 At special positions: 0 Unit cell: (131.252, 149.644, 201.476, 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 127 16.00 O 5316 8.00 N 4520 7.00 C 17436 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=43, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.04 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 709 " " NAG A1308 " - " ASN A 717 " " NAG A1309 " - " ASN A 801 " " NAG A1310 " - " ASN A1074 " " NAG B1301 " - " ASN B 234 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 616 " " NAG B1304 " - " ASN B 709 " " NAG B1305 " - " ASN B 717 " " NAG B1306 " - " ASN B 801 " " NAG B1307 " - " ASN B1134 " " NAG B1308 " - " ASN B 331 " " NAG C1301 " - " ASN C 122 " " NAG C1302 " - " ASN C 234 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 165 " " NAG C1305 " - " ASN C 331 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C 717 " " NAG C1309 " - " ASN C 801 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.00 Conformation dependent library (CDL) restraints added in 4.8 seconds 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6462 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 59 sheets defined 22.2% alpha, 30.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.64 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.805A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.344A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.632A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 4.019A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (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 886 through 891 removed outlier: 3.599A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.278A 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 removed outlier: 4.336A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.596A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.141A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.616A 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 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 737 through 744 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: 4.050A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.571A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.930A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.669A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 982 removed outlier: 3.554A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.324A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.052A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER B1147 " --> pdb=" O PRO B1143 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 405 through 410 removed outlier: 6.106A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 3.697A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN C 919 " --> pdb=" O VAL C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.486A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.428A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 3.994A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'F' and resid 79 through 83 Processing helix chain 'G' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.908A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.585A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.355A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.091A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.963A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.246A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.242A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 314 through 319 removed outlier: 6.370A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.191A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.003A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ASN A 437 " --> pdb=" O PHE A 374 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N PHE A 374 " --> pdb=" O ASN A 437 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.137A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.542A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.069A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE A 666 " --> pdb=" O ILE A 670 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.878A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 712 through 715 Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.105A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.505A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 790 removed outlier: 5.834A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.157A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.921A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 36 through 37 removed outlier: 6.858A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.982A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.245A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.188A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.825A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.746A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.815A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.186A 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 448 through 454 removed outlier: 5.718A pdb=" N TYR B 449 " --> pdb=" O PHE B 497 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N PHE B 497 " --> pdb=" O TYR B 449 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N TYR B 451 " --> pdb=" O TYR B 495 " (cutoff:3.500A) 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 654 through 655 removed outlier: 6.437A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.182A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.536A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.536A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.530A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.131A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.266A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.144A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 5.822A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.632A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 325 through 328 removed outlier: 5.892A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE6, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.420A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE8, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.838A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.977A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 712 through 728 removed outlier: 3.606A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 712 through 728 removed outlier: 3.606A pdb=" N ILE C 714 " --> pdb=" O LYS C1073 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF4, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF5, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AF6, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.510A pdb=" N MET D 34 " --> pdb=" O TRP D 50 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N TRP D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N TRP D 36 " --> pdb=" O MET D 48 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.689A pdb=" N ASP D 118 " --> pdb=" O ARG D 98 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AF9, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.510A pdb=" N MET E 34 " --> pdb=" O TRP E 50 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N TRP E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N TRP E 36 " --> pdb=" O MET E 48 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.689A pdb=" N ASP E 118 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 9 through 13 removed outlier: 3.650A pdb=" N THR F 105 " --> pdb=" O VAL F 11 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N TRP F 35 " --> pdb=" O MET F 47 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 19 through 24 Processing sheet with id=AG4, first strand: chain 'G' and resid 9 through 13 removed outlier: 3.651A pdb=" N THR G 105 " --> pdb=" O VAL G 11 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N TRP G 35 " --> pdb=" O MET G 47 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'G' and resid 19 through 24 1140 hydrogen bonds defined for protein. 3075 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: 13.91 Time building geometry restraints manager: 11.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 8766 1.34 - 1.46: 6937 1.46 - 1.58: 12145 1.58 - 1.70: 0 1.70 - 1.82: 163 Bond restraints: 28011 Sorted by residual: bond pdb=" CA THR G 95A" pdb=" C THR G 95A" ideal model delta sigma weight residual 1.525 1.570 -0.045 2.10e-02 2.27e+03 4.63e+00 bond pdb=" N SER G 95 " pdb=" CA SER G 95 " ideal model delta sigma weight residual 1.456 1.483 -0.027 1.28e-02 6.10e+03 4.31e+00 bond pdb=" C1 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.60e+00 bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.93e+00 bond pdb=" C1 NAG B1304 " pdb=" O5 NAG B1304 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.63e+00 ... (remaining 28006 not shown) Histogram of bond angle deviations from ideal: 93.37 - 101.51: 34 101.51 - 109.66: 3156 109.66 - 117.80: 17716 117.80 - 125.94: 16871 125.94 - 134.09: 328 Bond angle restraints: 38105 Sorted by residual: angle pdb=" N LEU E 107 " pdb=" CA LEU E 107 " pdb=" C LEU E 107 " ideal model delta sigma weight residual 113.55 104.67 8.88 1.26e+00 6.30e-01 4.96e+01 angle pdb=" N PHE G 98 " pdb=" CA PHE G 98 " pdb=" C PHE G 98 " ideal model delta sigma weight residual 108.07 117.57 -9.50 1.38e+00 5.25e-01 4.74e+01 angle pdb=" O SER G 94 " pdb=" C SER G 94 " pdb=" N SER G 95 " ideal model delta sigma weight residual 122.72 116.59 6.13 1.15e+00 7.56e-01 2.84e+01 angle pdb=" CA SER G 94 " pdb=" C SER G 94 " pdb=" N SER G 95 " ideal model delta sigma weight residual 116.18 122.29 -6.11 1.29e+00 6.01e-01 2.24e+01 angle pdb=" CA SER G 95 " pdb=" C SER G 95 " pdb=" N THR G 95A" ideal model delta sigma weight residual 116.06 121.19 -5.13 1.29e+00 6.01e-01 1.58e+01 ... (remaining 38100 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 15597 17.82 - 35.65: 1057 35.65 - 53.47: 242 53.47 - 71.30: 91 71.30 - 89.12: 22 Dihedral angle restraints: 17009 sinusoidal: 6934 harmonic: 10075 Sorted by residual: dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual -86.00 -173.22 87.22 1 1.00e+01 1.00e-02 9.13e+01 dihedral pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " pdb=" SG CYS C 760 " pdb=" CB CYS C 760 " ideal model delta sinusoidal sigma weight residual -86.00 0.39 -86.39 1 1.00e+01 1.00e-02 9.00e+01 dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 -169.68 83.68 1 1.00e+01 1.00e-02 8.54e+01 ... (remaining 17006 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.277: 4392 0.277 - 0.555: 7 0.555 - 0.832: 0 0.832 - 1.109: 2 1.109 - 1.386: 1 Chirality restraints: 4402 Sorted by residual: chirality pdb=" C1 NAG A1307 " pdb=" ND2 ASN A 709 " pdb=" C2 NAG A1307 " pdb=" O5 NAG A1307 " both_signs ideal model delta sigma weight residual False -2.40 -1.01 -1.39 2.00e-01 2.50e+01 4.81e+01 chirality pdb=" C1 NAG A1306 " pdb=" ND2 ASN A 616 " pdb=" C2 NAG A1306 " pdb=" O5 NAG A1306 " both_signs ideal model delta sigma weight residual False -2.40 -1.38 -1.02 2.00e-01 2.50e+01 2.58e+01 chirality pdb=" C1 NAG A1310 " pdb=" ND2 ASN A1074 " pdb=" C2 NAG A1310 " pdb=" O5 NAG A1310 " both_signs ideal model delta sigma weight residual False -2.40 -3.34 0.94 2.00e-01 2.50e+01 2.19e+01 ... (remaining 4399 not shown) Planarity restraints: 4915 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " 0.063 2.00e-02 2.50e+03 6.29e-02 4.95e+01 pdb=" CG ASN A 331 " -0.023 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " -0.030 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " -0.089 2.00e-02 2.50e+03 pdb=" C1 NAG A1304 " 0.080 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A1074 " 0.063 2.00e-02 2.50e+03 5.89e-02 4.33e+01 pdb=" CG ASN A1074 " -0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN A1074 " -0.029 2.00e-02 2.50e+03 pdb=" ND2 ASN A1074 " -0.083 2.00e-02 2.50e+03 pdb=" C1 NAG A1310 " 0.072 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 343 " 0.046 2.00e-02 2.50e+03 4.83e-02 2.92e+01 pdb=" CG ASN A 343 " -0.018 2.00e-02 2.50e+03 pdb=" OD1 ASN A 343 " -0.019 2.00e-02 2.50e+03 pdb=" ND2 ASN A 343 " -0.071 2.00e-02 2.50e+03 pdb=" C1 NAG A1305 " 0.062 2.00e-02 2.50e+03 ... (remaining 4912 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 161 2.47 - 3.07: 18392 3.07 - 3.68: 42161 3.68 - 4.29: 61494 4.29 - 4.90: 99780 Nonbonded interactions: 221988 Sorted by model distance: nonbonded pdb=" CB TYR F 87 " pdb=" CD1 PHE F 98 " model vdw 1.857 3.740 nonbonded pdb=" O ALA D 109 " pdb=" OH TYR D 114 " model vdw 1.865 2.440 nonbonded pdb=" CD2 TRP E 47 " pdb=" CG2 THR G 95A" model vdw 1.938 3.680 nonbonded pdb=" O ALA E 109 " pdb=" N ASP E 111 " model vdw 1.984 2.520 nonbonded pdb=" ND2 ASN A1134 " pdb=" C1 NAG A1311 " model vdw 2.034 3.550 ... (remaining 221983 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 1147 or resid 1301 through 1308)) selection = chain 'B' selection = (chain 'C' and (resid 27 through 1147 or resid 1301 through 1308)) } ncs_group { reference = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 6.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.180 Construct map_model_manager: 0.020 Extract box with map and model: 20.360 Check model and map are aligned: 0.400 Set scattering table: 0.250 Process input model: 75.940 Find NCS groups from input model: 2.120 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 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 : 0.003 0.045 28011 Z= 0.190 Angle : 0.619 10.619 38105 Z= 0.353 Chirality : 0.056 1.386 4402 Planarity : 0.004 0.075 4888 Dihedral : 13.251 89.124 10418 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.33 % Favored : 96.41 % Rotamer: Outliers : 2.49 % Allowed : 3.36 % Favored : 94.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.12), residues: 3422 helix: -0.98 (0.17), residues: 678 sheet: -0.89 (0.15), residues: 891 loop : -1.74 (0.12), residues: 1853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 36 HIS 0.004 0.000 HIS B 519 PHE 0.021 0.001 PHE C 759 TYR 0.031 0.001 TYR E 115 ARG 0.026 0.000 ARG C 567 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 431 time to evaluate : 3.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.7585 (p0) cc_final: 0.6772 (m-40) REVERT: A 110 LEU cc_start: 0.7899 (pp) cc_final: 0.7650 (mm) REVERT: A 189 LEU cc_start: 0.9573 (tp) cc_final: 0.9327 (tt) REVERT: A 360 ASN cc_start: 0.9052 (m-40) cc_final: 0.8379 (p0) REVERT: A 388 ASN cc_start: 0.7436 (m-40) cc_final: 0.5935 (p0) REVERT: A 402 ILE cc_start: 0.8318 (tp) cc_final: 0.8066 (tt) REVERT: A 614 ASP cc_start: 0.8468 (t0) cc_final: 0.8164 (t0) REVERT: A 646 ARG cc_start: 0.8557 (mtt180) cc_final: 0.8347 (tpm170) REVERT: A 716 THR cc_start: 0.8879 (p) cc_final: 0.8671 (t) REVERT: A 740 MET cc_start: 0.9081 (ttt) cc_final: 0.8839 (ttp) REVERT: A 855 PHE cc_start: 0.7501 (m-80) cc_final: 0.7173 (m-80) REVERT: A 984 LEU cc_start: 0.7899 (tp) cc_final: 0.7641 (tp) REVERT: A 1114 ILE cc_start: 0.8268 (mm) cc_final: 0.8045 (pt) REVERT: B 223 LEU cc_start: 0.9066 (tp) cc_final: 0.8791 (tp) REVERT: B 773 GLU cc_start: 0.8418 (tp30) cc_final: 0.8187 (tp30) REVERT: B 869 MET cc_start: 0.9071 (mtt) cc_final: 0.8625 (mpp) REVERT: B 1119 ASN cc_start: 0.8412 (m-40) cc_final: 0.8123 (m-40) REVERT: B 1120 THR cc_start: 0.9043 (p) cc_final: 0.8788 (t) REVERT: B 1129 VAL cc_start: 0.6965 (t) cc_final: 0.6658 (m) REVERT: C 229 LEU cc_start: 0.8480 (tp) cc_final: 0.8203 (tp) REVERT: C 592 PHE cc_start: 0.7467 (p90) cc_final: 0.7229 (p90) REVERT: C 740 MET cc_start: 0.9072 (ttt) cc_final: 0.8845 (ttm) REVERT: C 773 GLU cc_start: 0.8491 (tp30) cc_final: 0.7758 (tm-30) REVERT: C 1129 VAL cc_start: 0.8215 (t) cc_final: 0.7936 (p) REVERT: D 47 TRP cc_start: 0.4118 (t60) cc_final: 0.3584 (t60) REVERT: D 73 ASP cc_start: 0.8769 (t0) cc_final: 0.8523 (t70) REVERT: D 93 VAL cc_start: 0.5692 (OUTLIER) cc_final: 0.5194 (t) REVERT: E 63 LYS cc_start: 0.8744 (mmtt) cc_final: 0.8054 (tptp) REVERT: E 80 TYR cc_start: 0.7997 (m-80) cc_final: 0.7495 (m-80) REVERT: E 86 LEU cc_start: 0.6202 (mt) cc_final: 0.5732 (mt) REVERT: F 32 LEU cc_start: 0.8355 (mp) cc_final: 0.8128 (tt) REVERT: F 34 SER cc_start: -0.0381 (OUTLIER) cc_final: -0.1380 (p) REVERT: F 49 TYR cc_start: 0.7710 (p90) cc_final: 0.7440 (p90) REVERT: F 59 SER cc_start: 0.4609 (OUTLIER) cc_final: 0.4405 (p) REVERT: F 63 SER cc_start: 0.5587 (OUTLIER) cc_final: 0.5135 (p) REVERT: F 67 SER cc_start: -0.0083 (OUTLIER) cc_final: -0.0378 (p) REVERT: G 34 SER cc_start: -0.1868 (OUTLIER) cc_final: -0.2126 (p) REVERT: G 42 LYS cc_start: 0.6771 (OUTLIER) cc_final: 0.5972 (ttpt) REVERT: G 48 ILE cc_start: 0.5672 (OUTLIER) cc_final: 0.4870 (mt) REVERT: G 54 ARG cc_start: 0.8291 (mtm-85) cc_final: 0.8041 (ttm110) REVERT: G 59 SER cc_start: 0.2454 (OUTLIER) cc_final: 0.1335 (p) REVERT: G 73 LEU cc_start: 0.7721 (tt) cc_final: 0.7273 (tt) REVERT: G 104 LEU cc_start: 0.7719 (tp) cc_final: 0.7292 (tt) REVERT: G 106 VAL cc_start: 0.6820 (OUTLIER) cc_final: 0.6408 (p) outliers start: 75 outliers final: 23 residues processed: 493 average time/residue: 0.4020 time to fit residues: 307.7582 Evaluate side-chains 215 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 182 time to evaluate : 3.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 59 SER Chi-restraints excluded: chain F residue 63 SER Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain G residue 27 SER Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 34 SER Chi-restraints excluded: chain G residue 42 LYS Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 89 CYS Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain G residue 98 PHE Chi-restraints excluded: chain G residue 106 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 290 optimal weight: 4.9990 chunk 260 optimal weight: 1.9990 chunk 144 optimal weight: 0.6980 chunk 89 optimal weight: 6.9990 chunk 175 optimal weight: 8.9990 chunk 139 optimal weight: 0.0170 chunk 269 optimal weight: 9.9990 chunk 104 optimal weight: 8.9990 chunk 163 optimal weight: 2.9990 chunk 200 optimal weight: 10.0000 chunk 312 optimal weight: 20.0000 overall best weight: 2.1424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 125 ASN A 165 ASN ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN B 49 HIS B 115 GLN B 207 HIS B 218 GLN B 394 ASN B 675 GLN B 762 GLN B 764 ASN B1023 ASN B1142 GLN C 52 GLN ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 414 GLN ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 644 GLN C 690 GLN C 751 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN C 953 ASN C 957 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1023 ASN C1074 ASN C1119 ASN D 6 GLN D 39 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 GLN F 17 GLN F 37 GLN F 38 GLN G 17 GLN G 37 GLN G 60 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 28011 Z= 0.235 Angle : 0.631 15.999 38105 Z= 0.318 Chirality : 0.046 0.336 4402 Planarity : 0.005 0.128 4888 Dihedral : 7.182 59.832 4357 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.68 % Favored : 96.26 % Rotamer: Outliers : 2.83 % Allowed : 11.04 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.13), residues: 3422 helix: 0.85 (0.20), residues: 679 sheet: -0.32 (0.16), residues: 878 loop : -1.16 (0.13), residues: 1865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP E 47 HIS 0.004 0.001 HIS A1083 PHE 0.029 0.001 PHE D 102 TYR 0.027 0.002 TYR E 33 ARG 0.015 0.001 ARG C1107 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 206 time to evaluate : 3.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.7279 (p0) cc_final: 0.6910 (m-40) REVERT: A 110 LEU cc_start: 0.7769 (pp) cc_final: 0.7430 (mm) REVERT: A 117 LEU cc_start: 0.9222 (mt) cc_final: 0.8884 (tp) REVERT: A 275 PHE cc_start: 0.7947 (m-10) cc_final: 0.7302 (m-10) REVERT: A 360 ASN cc_start: 0.9045 (m-40) cc_final: 0.8351 (p0) REVERT: A 402 ILE cc_start: 0.8330 (tp) cc_final: 0.8084 (tt) REVERT: A 471 GLU cc_start: 0.7714 (tp30) cc_final: 0.6575 (pp20) REVERT: A 512 VAL cc_start: 0.9552 (OUTLIER) cc_final: 0.9318 (m) REVERT: A 562 PHE cc_start: 0.7516 (p90) cc_final: 0.6835 (p90) REVERT: A 577 ARG cc_start: 0.6572 (OUTLIER) cc_final: 0.6054 (mtm-85) REVERT: A 614 ASP cc_start: 0.8616 (t0) cc_final: 0.8302 (t0) REVERT: A 740 MET cc_start: 0.9119 (ttt) cc_final: 0.8847 (ttp) REVERT: A 984 LEU cc_start: 0.8023 (tp) cc_final: 0.7710 (tp) REVERT: A 1034 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8810 (mm) REVERT: A 1081 ILE cc_start: 0.8773 (mt) cc_final: 0.8518 (tp) REVERT: B 565 PHE cc_start: 0.7047 (m-10) cc_final: 0.6847 (m-10) REVERT: B 613 GLN cc_start: 0.9022 (OUTLIER) cc_final: 0.8534 (mp10) REVERT: B 740 MET cc_start: 0.9414 (ttt) cc_final: 0.9165 (ttt) REVERT: B 773 GLU cc_start: 0.8783 (tp30) cc_final: 0.8444 (tp30) REVERT: B 869 MET cc_start: 0.9171 (mtt) cc_final: 0.8672 (mpp) REVERT: B 1119 ASN cc_start: 0.8568 (m-40) cc_final: 0.8311 (m-40) REVERT: B 1120 THR cc_start: 0.9153 (p) cc_final: 0.8942 (t) REVERT: B 1129 VAL cc_start: 0.7279 (t) cc_final: 0.7079 (m) REVERT: C 229 LEU cc_start: 0.8485 (tp) cc_final: 0.8107 (tp) REVERT: C 488 CYS cc_start: 0.3374 (OUTLIER) cc_final: 0.2936 (t) REVERT: C 592 PHE cc_start: 0.7620 (p90) cc_final: 0.7331 (p90) REVERT: C 697 MET cc_start: 0.8457 (OUTLIER) cc_final: 0.8075 (mtm) REVERT: C 740 MET cc_start: 0.9150 (ttt) cc_final: 0.8702 (ttm) REVERT: C 773 GLU cc_start: 0.8371 (tp30) cc_final: 0.8093 (tm-30) REVERT: C 868 GLU cc_start: 0.8570 (mp0) cc_final: 0.8348 (mm-30) REVERT: C 1129 VAL cc_start: 0.8384 (t) cc_final: 0.7980 (p) REVERT: D 47 TRP cc_start: 0.5042 (t60) cc_final: 0.4648 (t60) REVERT: D 48 MET cc_start: 0.3558 (ttm) cc_final: 0.3272 (ttm) REVERT: D 65 GLN cc_start: 0.6983 (mm-40) cc_final: 0.6721 (mm-40) REVERT: D 73 ASP cc_start: 0.8800 (t0) cc_final: 0.8530 (t70) REVERT: E 10 GLU cc_start: 0.7707 (tt0) cc_final: 0.7441 (tm-30) REVERT: E 29 PHE cc_start: 0.9068 (t80) cc_final: 0.8866 (t80) REVERT: E 48 MET cc_start: 0.7716 (mtt) cc_final: 0.7125 (mpp) REVERT: E 80 TYR cc_start: 0.7924 (m-80) cc_final: 0.7441 (m-80) REVERT: E 95 TYR cc_start: 0.6371 (m-80) cc_final: 0.6077 (m-10) REVERT: E 127 THR cc_start: 0.7704 (OUTLIER) cc_final: 0.7426 (t) REVERT: F 85 ASP cc_start: 0.5623 (p0) cc_final: 0.5061 (m-30) REVERT: G 33 VAL cc_start: 0.5711 (OUTLIER) cc_final: 0.5416 (p) REVERT: G 42 LYS cc_start: 0.7006 (mmtp) cc_final: 0.6299 (ttpt) REVERT: G 104 LEU cc_start: 0.8081 (tp) cc_final: 0.7830 (tt) outliers start: 85 outliers final: 46 residues processed: 275 average time/residue: 0.3828 time to fit residues: 169.3751 Evaluate side-chains 214 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 160 time to evaluate : 3.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 490 PHE Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 39 GLN Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 113 TYR Chi-restraints excluded: chain D residue 114 TYR Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 70 MET Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 114 TYR Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 89 CYS Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 27 SER Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 95 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 173 optimal weight: 5.9990 chunk 96 optimal weight: 0.7980 chunk 259 optimal weight: 0.5980 chunk 212 optimal weight: 10.0000 chunk 86 optimal weight: 0.5980 chunk 312 optimal weight: 20.0000 chunk 338 optimal weight: 0.9990 chunk 278 optimal weight: 5.9990 chunk 310 optimal weight: 0.0030 chunk 106 optimal weight: 6.9990 chunk 251 optimal weight: 0.5980 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 644 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 17 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 28011 Z= 0.144 Angle : 0.562 12.992 38105 Z= 0.277 Chirality : 0.045 0.333 4402 Planarity : 0.004 0.089 4888 Dihedral : 6.503 58.940 4329 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.45 % Favored : 96.52 % Rotamer: Outliers : 2.23 % Allowed : 13.46 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.14), residues: 3422 helix: 1.48 (0.21), residues: 677 sheet: -0.03 (0.16), residues: 879 loop : -0.96 (0.13), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 47 HIS 0.002 0.000 HIS A 49 PHE 0.023 0.001 PHE C 347 TYR 0.030 0.001 TYR D 95 ARG 0.007 0.000 ARG D 85 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 176 time to evaluate : 3.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.7133 (p0) cc_final: 0.6843 (m-40) REVERT: A 110 LEU cc_start: 0.7690 (pp) cc_final: 0.7412 (mm) REVERT: A 275 PHE cc_start: 0.7993 (m-10) cc_final: 0.7197 (m-10) REVERT: A 360 ASN cc_start: 0.8990 (m-40) cc_final: 0.8313 (p0) REVERT: A 512 VAL cc_start: 0.9551 (t) cc_final: 0.9320 (m) REVERT: A 562 PHE cc_start: 0.7496 (p90) cc_final: 0.6853 (p90) REVERT: A 577 ARG cc_start: 0.6470 (OUTLIER) cc_final: 0.6002 (mtm-85) REVERT: A 614 ASP cc_start: 0.8601 (t0) cc_final: 0.8237 (t0) REVERT: A 740 MET cc_start: 0.9101 (ttt) cc_final: 0.8801 (ttp) REVERT: A 855 PHE cc_start: 0.7602 (m-80) cc_final: 0.7377 (m-80) REVERT: A 869 MET cc_start: 0.9292 (mtm) cc_final: 0.8992 (mtm) REVERT: A 984 LEU cc_start: 0.8075 (tp) cc_final: 0.7787 (tp) REVERT: A 1034 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8821 (mm) REVERT: A 1081 ILE cc_start: 0.8862 (mt) cc_final: 0.8605 (tp) REVERT: A 1114 ILE cc_start: 0.8344 (mm) cc_final: 0.8134 (pt) REVERT: B 613 GLN cc_start: 0.8937 (OUTLIER) cc_final: 0.8580 (mp10) REVERT: B 740 MET cc_start: 0.9429 (ttt) cc_final: 0.9203 (ttt) REVERT: B 773 GLU cc_start: 0.8789 (tp30) cc_final: 0.8428 (tp30) REVERT: B 856 ASN cc_start: 0.8313 (OUTLIER) cc_final: 0.7925 (p0) REVERT: B 869 MET cc_start: 0.9177 (mtt) cc_final: 0.8803 (mtp) REVERT: B 957 GLN cc_start: 0.8754 (tp40) cc_final: 0.8417 (tm-30) REVERT: B 1119 ASN cc_start: 0.8605 (m-40) cc_final: 0.8347 (m-40) REVERT: B 1120 THR cc_start: 0.9107 (p) cc_final: 0.8891 (t) REVERT: B 1129 VAL cc_start: 0.7250 (t) cc_final: 0.7019 (m) REVERT: C 229 LEU cc_start: 0.8491 (tp) cc_final: 0.8097 (tp) REVERT: C 488 CYS cc_start: 0.3488 (OUTLIER) cc_final: 0.3109 (t) REVERT: C 592 PHE cc_start: 0.7449 (p90) cc_final: 0.7208 (p90) REVERT: C 740 MET cc_start: 0.9147 (ttt) cc_final: 0.8681 (ttm) REVERT: C 773 GLU cc_start: 0.8327 (tp30) cc_final: 0.8023 (tm-30) REVERT: C 912 THR cc_start: 0.6906 (OUTLIER) cc_final: 0.6608 (p) REVERT: D 47 TRP cc_start: 0.5035 (t60) cc_final: 0.4613 (t60) REVERT: D 65 GLN cc_start: 0.7021 (mm-40) cc_final: 0.6791 (mm-40) REVERT: D 73 ASP cc_start: 0.8823 (t0) cc_final: 0.8541 (t70) REVERT: E 10 GLU cc_start: 0.7846 (tt0) cc_final: 0.7559 (tm-30) REVERT: E 48 MET cc_start: 0.7699 (mtt) cc_final: 0.7086 (mpp) REVERT: E 80 TYR cc_start: 0.7892 (m-80) cc_final: 0.7390 (m-80) REVERT: E 95 TYR cc_start: 0.6318 (m-80) cc_final: 0.6025 (m-10) REVERT: F 47 MET cc_start: 0.7593 (mtm) cc_final: 0.7349 (mpp) REVERT: F 85 ASP cc_start: 0.5574 (p0) cc_final: 0.5032 (m-30) REVERT: G 33 VAL cc_start: 0.5929 (OUTLIER) cc_final: 0.5669 (p) REVERT: G 42 LYS cc_start: 0.7025 (mmtp) cc_final: 0.6300 (ttpt) REVERT: G 47 MET cc_start: 0.7551 (mmm) cc_final: 0.6198 (ttp) REVERT: G 86 TYR cc_start: 0.7112 (m-10) cc_final: 0.6761 (m-10) REVERT: G 104 LEU cc_start: 0.7975 (tp) cc_final: 0.7716 (tp) outliers start: 67 outliers final: 41 residues processed: 232 average time/residue: 0.3535 time to fit residues: 138.8612 Evaluate side-chains 198 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 150 time to evaluate : 3.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 169 GLU Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 113 TYR Chi-restraints excluded: chain D residue 114 TYR Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 70 MET Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 89 CYS Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 89 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 309 optimal weight: 20.0000 chunk 235 optimal weight: 20.0000 chunk 162 optimal weight: 2.9990 chunk 34 optimal weight: 9.9990 chunk 149 optimal weight: 0.9980 chunk 210 optimal weight: 5.9990 chunk 314 optimal weight: 20.0000 chunk 332 optimal weight: 0.9980 chunk 164 optimal weight: 0.1980 chunk 297 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 644 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1088 HIS ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28011 Z= 0.188 Angle : 0.558 9.766 38105 Z= 0.280 Chirality : 0.044 0.319 4402 Planarity : 0.004 0.064 4888 Dihedral : 6.173 57.531 4321 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.71 % Favored : 96.26 % Rotamer: Outliers : 2.59 % Allowed : 14.63 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.14), residues: 3422 helix: 1.69 (0.21), residues: 668 sheet: 0.05 (0.16), residues: 884 loop : -0.75 (0.14), residues: 1870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 47 HIS 0.003 0.001 HIS C1064 PHE 0.024 0.001 PHE D 102 TYR 0.017 0.001 TYR E 33 ARG 0.005 0.000 ARG C 466 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 155 time to evaluate : 3.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASN cc_start: 0.7154 (p0) cc_final: 0.6950 (m-40) REVERT: A 110 LEU cc_start: 0.7686 (pp) cc_final: 0.7390 (mm) REVERT: A 275 PHE cc_start: 0.8314 (m-10) cc_final: 0.8060 (m-10) REVERT: A 360 ASN cc_start: 0.9000 (m-40) cc_final: 0.8380 (p0) REVERT: A 562 PHE cc_start: 0.7598 (p90) cc_final: 0.7022 (p90) REVERT: A 577 ARG cc_start: 0.6735 (OUTLIER) cc_final: 0.6405 (mtm-85) REVERT: A 614 ASP cc_start: 0.8746 (t0) cc_final: 0.8414 (t0) REVERT: A 740 MET cc_start: 0.9094 (ttt) cc_final: 0.8781 (ttp) REVERT: A 869 MET cc_start: 0.9433 (mtm) cc_final: 0.9142 (mtm) REVERT: A 984 LEU cc_start: 0.8226 (tp) cc_final: 0.7912 (tp) REVERT: B 856 ASN cc_start: 0.8369 (OUTLIER) cc_final: 0.8037 (p0) REVERT: B 869 MET cc_start: 0.9188 (mtt) cc_final: 0.8798 (mtp) REVERT: B 1002 GLN cc_start: 0.9088 (OUTLIER) cc_final: 0.8774 (tm-30) REVERT: B 1029 MET cc_start: 0.8792 (tpp) cc_final: 0.8546 (tpp) REVERT: B 1119 ASN cc_start: 0.8707 (m-40) cc_final: 0.8472 (m-40) REVERT: B 1120 THR cc_start: 0.9220 (p) cc_final: 0.9011 (t) REVERT: C 229 LEU cc_start: 0.8498 (tp) cc_final: 0.8224 (tp) REVERT: C 488 CYS cc_start: 0.3741 (OUTLIER) cc_final: 0.3288 (t) REVERT: C 567 ARG cc_start: 0.7191 (OUTLIER) cc_final: 0.5297 (mmm-85) REVERT: C 592 PHE cc_start: 0.7412 (p90) cc_final: 0.7127 (p90) REVERT: C 740 MET cc_start: 0.9158 (ttt) cc_final: 0.8937 (ttm) REVERT: C 773 GLU cc_start: 0.8370 (tp30) cc_final: 0.8032 (tm-30) REVERT: C 912 THR cc_start: 0.7044 (OUTLIER) cc_final: 0.6765 (p) REVERT: D 47 TRP cc_start: 0.4928 (t60) cc_final: 0.4483 (t60) REVERT: D 70 MET cc_start: 0.6248 (tpp) cc_final: 0.5821 (tpp) REVERT: D 73 ASP cc_start: 0.8823 (t0) cc_final: 0.8437 (p0) REVERT: E 3 GLN cc_start: 0.7235 (mp10) cc_final: 0.7021 (mp10) REVERT: E 10 GLU cc_start: 0.7791 (tt0) cc_final: 0.7534 (tm-30) REVERT: E 48 MET cc_start: 0.7670 (mtt) cc_final: 0.7104 (mpp) REVERT: E 80 TYR cc_start: 0.7843 (m-80) cc_final: 0.7388 (m-80) REVERT: E 95 TYR cc_start: 0.6354 (m-80) cc_final: 0.5997 (m-10) REVERT: F 47 MET cc_start: 0.7677 (mtm) cc_final: 0.7360 (mpp) REVERT: F 85 ASP cc_start: 0.5514 (p0) cc_final: 0.5118 (m-30) REVERT: G 33 VAL cc_start: 0.6314 (OUTLIER) cc_final: 0.6006 (p) REVERT: G 42 LYS cc_start: 0.7040 (mmtp) cc_final: 0.6520 (ttpt) REVERT: G 47 MET cc_start: 0.7877 (mmm) cc_final: 0.6456 (ptt) REVERT: G 86 TYR cc_start: 0.7190 (m-10) cc_final: 0.6891 (m-10) REVERT: G 104 LEU cc_start: 0.7946 (tp) cc_final: 0.7723 (tp) outliers start: 78 outliers final: 46 residues processed: 222 average time/residue: 0.3897 time to fit residues: 146.9538 Evaluate side-chains 191 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 138 time to evaluate : 3.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 113 TYR Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 70 MET Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 60 ASN Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 89 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 276 optimal weight: 2.9990 chunk 188 optimal weight: 6.9990 chunk 4 optimal weight: 20.0000 chunk 247 optimal weight: 8.9990 chunk 137 optimal weight: 4.9990 chunk 283 optimal weight: 1.9990 chunk 229 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 169 optimal weight: 6.9990 chunk 298 optimal weight: 0.8980 chunk 83 optimal weight: 0.0370 overall best weight: 1.7864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 965 GLN B 762 GLN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN E 1 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.3657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28011 Z= 0.184 Angle : 0.546 9.854 38105 Z= 0.275 Chirality : 0.044 0.315 4402 Planarity : 0.004 0.066 4888 Dihedral : 5.976 57.394 4316 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.62 % Favored : 96.35 % Rotamer: Outliers : 2.56 % Allowed : 15.39 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.14), residues: 3422 helix: 1.81 (0.21), residues: 667 sheet: 0.13 (0.16), residues: 882 loop : -0.65 (0.14), residues: 1873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 47 HIS 0.003 0.001 HIS B1048 PHE 0.015 0.001 PHE A 562 TYR 0.012 0.001 TYR D 114 ARG 0.004 0.000 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 150 time to evaluate : 3.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 LEU cc_start: 0.7772 (pp) cc_final: 0.7431 (mm) REVERT: A 360 ASN cc_start: 0.9027 (m-40) cc_final: 0.8433 (p0) REVERT: A 562 PHE cc_start: 0.7726 (p90) cc_final: 0.7239 (p90) REVERT: A 614 ASP cc_start: 0.8763 (t0) cc_final: 0.8421 (t0) REVERT: A 731 MET cc_start: 0.9635 (ptm) cc_final: 0.9356 (ptm) REVERT: A 740 MET cc_start: 0.9079 (ttt) cc_final: 0.8864 (ttt) REVERT: A 869 MET cc_start: 0.9457 (mtm) cc_final: 0.9151 (mtm) REVERT: A 984 LEU cc_start: 0.8349 (tp) cc_final: 0.7997 (tp) REVERT: B 166 CYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7407 (m) REVERT: B 740 MET cc_start: 0.9474 (ttt) cc_final: 0.9264 (ttp) REVERT: B 869 MET cc_start: 0.9193 (mtt) cc_final: 0.8716 (mtp) REVERT: B 1002 GLN cc_start: 0.9071 (OUTLIER) cc_final: 0.8746 (tm-30) REVERT: B 1029 MET cc_start: 0.8863 (tpp) cc_final: 0.8624 (tpp) REVERT: B 1119 ASN cc_start: 0.8747 (m-40) cc_final: 0.8511 (m-40) REVERT: C 488 CYS cc_start: 0.3684 (OUTLIER) cc_final: 0.3239 (t) REVERT: C 567 ARG cc_start: 0.6996 (OUTLIER) cc_final: 0.5320 (mmm-85) REVERT: C 592 PHE cc_start: 0.7474 (p90) cc_final: 0.7250 (p90) REVERT: C 740 MET cc_start: 0.9182 (ttt) cc_final: 0.8936 (ttm) REVERT: C 773 GLU cc_start: 0.8360 (tp30) cc_final: 0.8012 (tm-30) REVERT: C 912 THR cc_start: 0.7062 (OUTLIER) cc_final: 0.6858 (p) REVERT: D 47 TRP cc_start: 0.4918 (t60) cc_final: 0.4511 (t60) REVERT: D 48 MET cc_start: 0.2917 (ttm) cc_final: 0.2124 (ttm) REVERT: D 65 GLN cc_start: 0.7008 (mm-40) cc_final: 0.6726 (mm-40) REVERT: D 70 MET cc_start: 0.5828 (tpp) cc_final: 0.5580 (tpp) REVERT: D 73 ASP cc_start: 0.8834 (t0) cc_final: 0.8568 (t70) REVERT: E 3 GLN cc_start: 0.7233 (mp10) cc_final: 0.6999 (mp10) REVERT: E 10 GLU cc_start: 0.7862 (tt0) cc_final: 0.7569 (tm-30) REVERT: E 48 MET cc_start: 0.7670 (mtt) cc_final: 0.7066 (mpp) REVERT: E 80 TYR cc_start: 0.7868 (m-80) cc_final: 0.7438 (m-80) REVERT: E 95 TYR cc_start: 0.6182 (m-80) cc_final: 0.5883 (m-10) REVERT: F 47 MET cc_start: 0.7720 (mtm) cc_final: 0.7416 (mpp) REVERT: F 85 ASP cc_start: 0.5493 (p0) cc_final: 0.5109 (m-30) REVERT: G 42 LYS cc_start: 0.7250 (mmtp) cc_final: 0.6633 (ttpt) REVERT: G 47 MET cc_start: 0.7946 (mmm) cc_final: 0.6448 (ptt) REVERT: G 86 TYR cc_start: 0.7163 (m-10) cc_final: 0.6949 (m-10) REVERT: G 104 LEU cc_start: 0.7849 (tp) cc_final: 0.7627 (tp) outliers start: 77 outliers final: 56 residues processed: 222 average time/residue: 0.3658 time to fit residues: 136.3435 Evaluate side-chains 196 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 135 time to evaluate : 3.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 113 TYR Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 89 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 111 optimal weight: 9.9990 chunk 299 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 195 optimal weight: 4.9990 chunk 82 optimal weight: 7.9990 chunk 332 optimal weight: 0.4980 chunk 276 optimal weight: 0.5980 chunk 154 optimal weight: 0.5980 chunk 27 optimal weight: 9.9990 chunk 110 optimal weight: 6.9990 chunk 174 optimal weight: 4.9990 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1134 ASN B 764 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.4202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 28011 Z= 0.227 Angle : 0.561 9.571 38105 Z= 0.284 Chirality : 0.044 0.303 4402 Planarity : 0.004 0.063 4888 Dihedral : 6.013 57.665 4315 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.92 % Favored : 96.05 % Rotamer: Outliers : 2.93 % Allowed : 15.56 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.14), residues: 3422 helix: 1.79 (0.21), residues: 669 sheet: 0.14 (0.17), residues: 864 loop : -0.57 (0.14), residues: 1889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 47 HIS 0.004 0.001 HIS E 35 PHE 0.016 0.001 PHE A 562 TYR 0.011 0.001 TYR D 94 ARG 0.009 0.000 ARG C 509 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 134 time to evaluate : 3.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7468 (mm) REVERT: A 360 ASN cc_start: 0.9009 (m-40) cc_final: 0.8437 (p0) REVERT: A 562 PHE cc_start: 0.7970 (p90) cc_final: 0.7579 (p90) REVERT: A 614 ASP cc_start: 0.8837 (t0) cc_final: 0.8504 (t0) REVERT: A 740 MET cc_start: 0.9061 (ttt) cc_final: 0.8849 (ttt) REVERT: A 869 MET cc_start: 0.9429 (mtm) cc_final: 0.9147 (mtm) REVERT: A 984 LEU cc_start: 0.8427 (tp) cc_final: 0.8058 (tp) REVERT: B 613 GLN cc_start: 0.8909 (OUTLIER) cc_final: 0.8651 (pm20) REVERT: B 740 MET cc_start: 0.9455 (ttt) cc_final: 0.9219 (ttt) REVERT: B 869 MET cc_start: 0.9090 (mtt) cc_final: 0.8648 (mtp) REVERT: B 1002 GLN cc_start: 0.9095 (OUTLIER) cc_final: 0.8771 (tm-30) REVERT: B 1029 MET cc_start: 0.8879 (tpp) cc_final: 0.8598 (tpp) REVERT: C 488 CYS cc_start: 0.3671 (OUTLIER) cc_final: 0.3198 (t) REVERT: C 567 ARG cc_start: 0.6975 (OUTLIER) cc_final: 0.5541 (mmm-85) REVERT: C 592 PHE cc_start: 0.7564 (p90) cc_final: 0.7319 (p90) REVERT: C 740 MET cc_start: 0.9211 (ttt) cc_final: 0.8954 (ttm) REVERT: C 773 GLU cc_start: 0.8394 (tp30) cc_final: 0.8029 (tm-30) REVERT: C 912 THR cc_start: 0.7104 (OUTLIER) cc_final: 0.6857 (p) REVERT: D 47 TRP cc_start: 0.4995 (t60) cc_final: 0.4424 (t60) REVERT: D 70 MET cc_start: 0.5547 (tpp) cc_final: 0.4624 (tpp) REVERT: D 73 ASP cc_start: 0.8889 (t0) cc_final: 0.8623 (t70) REVERT: D 102 PHE cc_start: 0.1059 (OUTLIER) cc_final: 0.0531 (p90) REVERT: D 112 TYR cc_start: 0.2678 (OUTLIER) cc_final: 0.0923 (m-10) REVERT: E 3 GLN cc_start: 0.7189 (mp10) cc_final: 0.6947 (mp10) REVERT: E 10 GLU cc_start: 0.7818 (tt0) cc_final: 0.7496 (tm-30) REVERT: E 48 MET cc_start: 0.7656 (mtt) cc_final: 0.7335 (mmm) REVERT: E 80 TYR cc_start: 0.7983 (m-80) cc_final: 0.7629 (m-80) REVERT: E 95 TYR cc_start: 0.6202 (m-80) cc_final: 0.5924 (m-10) REVERT: F 47 MET cc_start: 0.7781 (mtm) cc_final: 0.7455 (mpp) REVERT: F 85 ASP cc_start: 0.5608 (p0) cc_final: 0.5282 (m-30) REVERT: G 42 LYS cc_start: 0.7282 (mmtp) cc_final: 0.6640 (ttpt) outliers start: 88 outliers final: 63 residues processed: 213 average time/residue: 0.3428 time to fit residues: 123.5542 Evaluate side-chains 198 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 127 time to evaluate : 3.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 102 PHE Chi-restraints excluded: chain D residue 112 TYR Chi-restraints excluded: chain D residue 113 TYR Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 89 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 320 optimal weight: 20.0000 chunk 37 optimal weight: 0.9980 chunk 189 optimal weight: 6.9990 chunk 243 optimal weight: 0.7980 chunk 188 optimal weight: 5.9990 chunk 280 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 chunk 331 optimal weight: 30.0000 chunk 207 optimal weight: 8.9990 chunk 202 optimal weight: 6.9990 chunk 153 optimal weight: 9.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1005 GLN B 498 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.4887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 28011 Z= 0.252 Angle : 0.588 11.589 38105 Z= 0.297 Chirality : 0.045 0.295 4402 Planarity : 0.004 0.062 4888 Dihedral : 6.168 57.609 4315 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.44 % Favored : 95.53 % Rotamer: Outliers : 3.26 % Allowed : 15.99 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.14), residues: 3422 helix: 1.69 (0.21), residues: 671 sheet: 0.17 (0.17), residues: 863 loop : -0.65 (0.14), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 436 HIS 0.005 0.001 HIS C1048 PHE 0.017 0.001 PHE A 562 TYR 0.019 0.001 TYR E 32 ARG 0.011 0.001 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 126 time to evaluate : 3.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7533 (mm) REVERT: A 360 ASN cc_start: 0.9052 (m-40) cc_final: 0.8568 (p0) REVERT: A 562 PHE cc_start: 0.8160 (p90) cc_final: 0.7890 (p90) REVERT: A 614 ASP cc_start: 0.8884 (t0) cc_final: 0.8587 (t0) REVERT: A 759 PHE cc_start: 0.8624 (OUTLIER) cc_final: 0.7878 (t80) REVERT: A 869 MET cc_start: 0.9462 (mtm) cc_final: 0.9130 (mtm) REVERT: B 740 MET cc_start: 0.9442 (ttt) cc_final: 0.9206 (ttt) REVERT: B 869 MET cc_start: 0.9082 (mtt) cc_final: 0.8676 (mtp) REVERT: B 900 MET cc_start: 0.9057 (mmm) cc_final: 0.8850 (mmt) REVERT: B 1002 GLN cc_start: 0.9128 (OUTLIER) cc_final: 0.8766 (tm-30) REVERT: B 1029 MET cc_start: 0.8884 (tpp) cc_final: 0.8542 (tpp) REVERT: C 488 CYS cc_start: 0.3501 (OUTLIER) cc_final: 0.3040 (t) REVERT: C 740 MET cc_start: 0.9209 (ttt) cc_final: 0.8983 (ttm) REVERT: C 773 GLU cc_start: 0.8407 (tp30) cc_final: 0.8002 (tm-30) REVERT: C 912 THR cc_start: 0.7335 (OUTLIER) cc_final: 0.7086 (p) REVERT: C 1101 HIS cc_start: 0.3057 (OUTLIER) cc_final: 0.2774 (m90) REVERT: D 47 TRP cc_start: 0.4920 (t60) cc_final: 0.4380 (t60) REVERT: D 65 GLN cc_start: 0.6947 (mm-40) cc_final: 0.6654 (mm-40) REVERT: D 73 ASP cc_start: 0.8884 (t0) cc_final: 0.8644 (t70) REVERT: D 81 MET cc_start: 0.8178 (tmm) cc_final: 0.7188 (ttm) REVERT: D 82 GLU cc_start: 0.8711 (tp30) cc_final: 0.8035 (tp30) REVERT: D 112 TYR cc_start: 0.2424 (OUTLIER) cc_final: 0.1077 (m-10) REVERT: E 10 GLU cc_start: 0.7800 (tt0) cc_final: 0.7464 (tm-30) REVERT: E 48 MET cc_start: 0.7624 (mtt) cc_final: 0.7290 (mmm) REVERT: E 95 TYR cc_start: 0.6272 (m-80) cc_final: 0.5914 (m-10) REVERT: F 47 MET cc_start: 0.7826 (mtm) cc_final: 0.7485 (mpp) REVERT: F 85 ASP cc_start: 0.5521 (p0) cc_final: 0.5299 (m-30) REVERT: G 42 LYS cc_start: 0.7322 (mmtp) cc_final: 0.6648 (ttpt) REVERT: G 47 MET cc_start: 0.7595 (mmm) cc_final: 0.6334 (ptp) outliers start: 98 outliers final: 77 residues processed: 216 average time/residue: 0.3624 time to fit residues: 131.6933 Evaluate side-chains 200 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 116 time to evaluate : 2.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 112 TYR Chi-restraints excluded: chain D residue 113 TYR Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 114 TYR Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 65 SER Chi-restraints excluded: chain G residue 89 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 205 optimal weight: 9.9990 chunk 132 optimal weight: 10.0000 chunk 198 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 210 optimal weight: 0.9990 chunk 225 optimal weight: 6.9990 chunk 163 optimal weight: 2.9990 chunk 30 optimal weight: 10.0000 chunk 260 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 388 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.5277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 28011 Z= 0.294 Angle : 0.606 10.695 38105 Z= 0.307 Chirality : 0.045 0.294 4402 Planarity : 0.004 0.059 4888 Dihedral : 6.296 57.862 4315 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.50 % Favored : 95.47 % Rotamer: Outliers : 3.19 % Allowed : 16.02 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.14), residues: 3422 helix: 1.69 (0.21), residues: 671 sheet: 0.13 (0.17), residues: 860 loop : -0.68 (0.14), residues: 1891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 436 HIS 0.004 0.001 HIS A1048 PHE 0.019 0.001 PHE B 377 TYR 0.027 0.001 TYR E 115 ARG 0.007 0.001 ARG C1091 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 121 time to evaluate : 2.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7518 (mm) REVERT: A 360 ASN cc_start: 0.9065 (m-40) cc_final: 0.8577 (p0) REVERT: A 562 PHE cc_start: 0.8246 (p90) cc_final: 0.8006 (p90) REVERT: A 614 ASP cc_start: 0.8938 (t0) cc_final: 0.8600 (t0) REVERT: A 740 MET cc_start: 0.9351 (ttt) cc_final: 0.9120 (ttp) REVERT: A 759 PHE cc_start: 0.8681 (OUTLIER) cc_final: 0.8141 (t80) REVERT: A 869 MET cc_start: 0.9449 (mtm) cc_final: 0.9112 (mtm) REVERT: B 740 MET cc_start: 0.9420 (ttt) cc_final: 0.9201 (ttt) REVERT: B 869 MET cc_start: 0.9089 (mtt) cc_final: 0.8700 (mtp) REVERT: B 1002 GLN cc_start: 0.9156 (OUTLIER) cc_final: 0.8817 (tm-30) REVERT: B 1029 MET cc_start: 0.8924 (tpp) cc_final: 0.8573 (tpp) REVERT: C 740 MET cc_start: 0.9205 (ttt) cc_final: 0.8944 (ttt) REVERT: C 773 GLU cc_start: 0.8429 (tp30) cc_final: 0.8049 (tm-30) REVERT: C 912 THR cc_start: 0.7312 (OUTLIER) cc_final: 0.7066 (p) REVERT: C 1092 GLU cc_start: 0.8886 (mp0) cc_final: 0.7936 (pm20) REVERT: C 1101 HIS cc_start: 0.3330 (OUTLIER) cc_final: 0.3023 (m90) REVERT: D 4 LEU cc_start: 0.5410 (OUTLIER) cc_final: 0.4535 (pp) REVERT: D 47 TRP cc_start: 0.5051 (t60) cc_final: 0.4506 (t60) REVERT: D 70 MET cc_start: 0.6484 (tpp) cc_final: 0.5554 (mmm) REVERT: D 71 THR cc_start: 0.7181 (t) cc_final: 0.6509 (t) REVERT: D 73 ASP cc_start: 0.8930 (t0) cc_final: 0.8707 (t70) REVERT: D 102 PHE cc_start: 0.1080 (OUTLIER) cc_final: 0.0690 (p90) REVERT: D 112 TYR cc_start: 0.2308 (OUTLIER) cc_final: 0.1041 (m-10) REVERT: E 3 GLN cc_start: 0.7369 (mp10) cc_final: 0.6823 (mp10) REVERT: E 10 GLU cc_start: 0.7837 (tt0) cc_final: 0.7500 (tm-30) REVERT: E 48 MET cc_start: 0.7566 (mtt) cc_final: 0.7214 (mmm) REVERT: E 86 LEU cc_start: 0.6711 (mm) cc_final: 0.6032 (mt) REVERT: E 95 TYR cc_start: 0.6294 (m-80) cc_final: 0.5922 (m-10) REVERT: F 47 MET cc_start: 0.7919 (mtm) cc_final: 0.7514 (mpp) REVERT: F 85 ASP cc_start: 0.5490 (p0) cc_final: 0.5270 (m-30) REVERT: G 42 LYS cc_start: 0.7379 (mmtp) cc_final: 0.6626 (ttpt) REVERT: G 47 MET cc_start: 0.8005 (mmm) cc_final: 0.6741 (ptt) outliers start: 96 outliers final: 78 residues processed: 207 average time/residue: 0.3662 time to fit residues: 126.5234 Evaluate side-chains 199 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 113 time to evaluate : 3.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 722 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 102 PHE Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 112 TYR Chi-restraints excluded: chain D residue 113 TYR Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 114 TYR Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 89 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 301 optimal weight: 0.9980 chunk 317 optimal weight: 10.0000 chunk 289 optimal weight: 1.9990 chunk 308 optimal weight: 10.0000 chunk 185 optimal weight: 3.9990 chunk 134 optimal weight: 9.9990 chunk 242 optimal weight: 8.9990 chunk 94 optimal weight: 0.9980 chunk 279 optimal weight: 6.9990 chunk 292 optimal weight: 4.9990 chunk 307 optimal weight: 5.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 37 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.5477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 28011 Z= 0.237 Angle : 0.573 11.301 38105 Z= 0.289 Chirality : 0.045 0.291 4402 Planarity : 0.004 0.061 4888 Dihedral : 6.182 57.460 4315 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.65 % Favored : 95.32 % Rotamer: Outliers : 2.83 % Allowed : 16.46 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.14), residues: 3422 helix: 1.75 (0.21), residues: 675 sheet: 0.11 (0.17), residues: 869 loop : -0.65 (0.14), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 436 HIS 0.005 0.001 HIS F 39 PHE 0.017 0.001 PHE A 562 TYR 0.021 0.001 TYR E 115 ARG 0.006 0.000 ARG C 509 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 124 time to evaluate : 3.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 LEU cc_start: 0.8014 (OUTLIER) cc_final: 0.7505 (mm) REVERT: A 360 ASN cc_start: 0.9048 (m-40) cc_final: 0.8552 (p0) REVERT: A 562 PHE cc_start: 0.8316 (p90) cc_final: 0.8086 (p90) REVERT: A 614 ASP cc_start: 0.8942 (t0) cc_final: 0.8595 (t0) REVERT: A 740 MET cc_start: 0.9367 (ttt) cc_final: 0.9164 (ttp) REVERT: A 869 MET cc_start: 0.9422 (mtm) cc_final: 0.9114 (mtm) REVERT: B 740 MET cc_start: 0.9426 (ttt) cc_final: 0.9185 (ttt) REVERT: B 869 MET cc_start: 0.9083 (mtt) cc_final: 0.8705 (mtp) REVERT: B 1002 GLN cc_start: 0.9152 (OUTLIER) cc_final: 0.8805 (tm-30) REVERT: B 1029 MET cc_start: 0.8919 (tpp) cc_final: 0.8530 (tpp) REVERT: C 96 GLU cc_start: 0.7572 (tt0) cc_final: 0.7306 (pm20) REVERT: C 488 CYS cc_start: 0.3490 (OUTLIER) cc_final: 0.3011 (t) REVERT: C 740 MET cc_start: 0.9200 (ttt) cc_final: 0.8970 (ttm) REVERT: C 773 GLU cc_start: 0.8383 (tp30) cc_final: 0.7983 (tm-30) REVERT: C 869 MET cc_start: 0.9000 (mtm) cc_final: 0.8629 (pmm) REVERT: C 912 THR cc_start: 0.7190 (OUTLIER) cc_final: 0.6942 (p) REVERT: C 1101 HIS cc_start: 0.3357 (OUTLIER) cc_final: 0.3021 (m90) REVERT: D 4 LEU cc_start: 0.5488 (OUTLIER) cc_final: 0.4587 (pp) REVERT: D 47 TRP cc_start: 0.5009 (t60) cc_final: 0.4447 (t60) REVERT: D 48 MET cc_start: 0.2502 (ttm) cc_final: 0.1881 (ttp) REVERT: D 65 GLN cc_start: 0.6991 (mm-40) cc_final: 0.6726 (mm-40) REVERT: D 73 ASP cc_start: 0.8943 (t0) cc_final: 0.8703 (t70) REVERT: D 102 PHE cc_start: 0.1109 (OUTLIER) cc_final: 0.0743 (p90) REVERT: D 112 TYR cc_start: 0.2252 (OUTLIER) cc_final: 0.1304 (m-10) REVERT: E 3 GLN cc_start: 0.7344 (mp10) cc_final: 0.6802 (mp10) REVERT: E 10 GLU cc_start: 0.7767 (tt0) cc_final: 0.7461 (tm-30) REVERT: E 48 MET cc_start: 0.7457 (mtt) cc_final: 0.7143 (mmm) REVERT: E 86 LEU cc_start: 0.6989 (mm) cc_final: 0.6344 (mt) REVERT: E 122 GLN cc_start: 0.7586 (tm-30) cc_final: 0.6582 (tm-30) REVERT: F 47 MET cc_start: 0.7894 (mtm) cc_final: 0.7494 (mpp) REVERT: G 42 LYS cc_start: 0.7333 (mmtp) cc_final: 0.6562 (ttpt) REVERT: G 47 MET cc_start: 0.8002 (mmm) cc_final: 0.6696 (ptt) outliers start: 85 outliers final: 67 residues processed: 205 average time/residue: 0.3588 time to fit residues: 123.6862 Evaluate side-chains 189 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 114 time to evaluate : 3.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 1008 VAL Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1065 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 722 VAL Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1101 HIS Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 102 PHE Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 112 TYR Chi-restraints excluded: chain D residue 113 TYR Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 114 TYR Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 89 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 202 optimal weight: 0.9980 chunk 326 optimal weight: 30.0000 chunk 199 optimal weight: 0.0970 chunk 154 optimal weight: 9.9990 chunk 227 optimal weight: 0.4980 chunk 342 optimal weight: 8.9990 chunk 315 optimal weight: 20.0000 chunk 272 optimal weight: 2.9990 chunk 28 optimal weight: 0.3980 chunk 210 optimal weight: 7.9990 chunk 167 optimal weight: 0.2980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.5435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 28011 Z= 0.138 Angle : 0.547 9.901 38105 Z= 0.271 Chirality : 0.045 0.288 4402 Planarity : 0.004 0.063 4888 Dihedral : 5.910 57.704 4315 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.06 % Favored : 95.88 % Rotamer: Outliers : 1.93 % Allowed : 17.55 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.15), residues: 3422 helix: 1.85 (0.21), residues: 680 sheet: 0.23 (0.17), residues: 862 loop : -0.61 (0.15), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 47 HIS 0.013 0.001 HIS F 39 PHE 0.014 0.001 PHE A 562 TYR 0.034 0.001 TYR E 115 ARG 0.006 0.000 ARG C 509 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 126 time to evaluate : 3.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 LEU cc_start: 0.8003 (pp) cc_final: 0.7523 (mm) REVERT: A 360 ASN cc_start: 0.9032 (m-40) cc_final: 0.8530 (p0) REVERT: A 614 ASP cc_start: 0.8865 (t0) cc_final: 0.8506 (t0) REVERT: A 740 MET cc_start: 0.9305 (ttt) cc_final: 0.9081 (ttp) REVERT: A 869 MET cc_start: 0.9392 (mtm) cc_final: 0.9076 (mtm) REVERT: B 740 MET cc_start: 0.9434 (ttt) cc_final: 0.9174 (ttt) REVERT: B 869 MET cc_start: 0.9042 (mtt) cc_final: 0.8815 (mtp) REVERT: B 1002 GLN cc_start: 0.9124 (OUTLIER) cc_final: 0.8760 (tm-30) REVERT: B 1029 MET cc_start: 0.8880 (tpp) cc_final: 0.8471 (tpp) REVERT: C 488 CYS cc_start: 0.3613 (OUTLIER) cc_final: 0.3164 (t) REVERT: C 740 MET cc_start: 0.9216 (ttt) cc_final: 0.8830 (ttm) REVERT: C 773 GLU cc_start: 0.8260 (tp30) cc_final: 0.7885 (tm-30) REVERT: C 912 THR cc_start: 0.6816 (OUTLIER) cc_final: 0.6533 (p) REVERT: C 1092 GLU cc_start: 0.8810 (mp0) cc_final: 0.7934 (pm20) REVERT: D 4 LEU cc_start: 0.5361 (OUTLIER) cc_final: 0.4464 (pp) REVERT: D 47 TRP cc_start: 0.4918 (t60) cc_final: 0.4369 (t60) REVERT: D 73 ASP cc_start: 0.8959 (t0) cc_final: 0.8736 (t70) REVERT: D 81 MET cc_start: 0.7523 (tmm) cc_final: 0.7061 (tpp) REVERT: D 82 GLU cc_start: 0.8482 (tp30) cc_final: 0.7742 (tp30) REVERT: D 112 TYR cc_start: 0.1359 (OUTLIER) cc_final: 0.0612 (m-10) REVERT: E 10 GLU cc_start: 0.7805 (tt0) cc_final: 0.7518 (tm-30) REVERT: E 48 MET cc_start: 0.7299 (mtt) cc_final: 0.6730 (mpp) REVERT: E 86 LEU cc_start: 0.6985 (mm) cc_final: 0.6363 (mt) REVERT: E 122 GLN cc_start: 0.7588 (tm-30) cc_final: 0.7138 (tm-30) REVERT: F 47 MET cc_start: 0.7794 (mtm) cc_final: 0.7365 (mpp) REVERT: G 36 TYR cc_start: 0.7512 (m-80) cc_final: 0.7214 (m-80) REVERT: G 42 LYS cc_start: 0.7371 (mmtp) cc_final: 0.6626 (ttpt) REVERT: G 47 MET cc_start: 0.7828 (mmm) cc_final: 0.6597 (ptt) outliers start: 58 outliers final: 46 residues processed: 178 average time/residue: 0.3715 time to fit residues: 111.2616 Evaluate side-chains 165 residues out of total 3008 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 114 time to evaluate : 2.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 54 VAL Chi-restraints excluded: chain D residue 96 CYS Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 112 TYR Chi-restraints excluded: chain D residue 113 TYR Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 114 TYR Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 60 ASN Chi-restraints excluded: chain G residue 89 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 216 optimal weight: 6.9990 chunk 290 optimal weight: 5.9990 chunk 83 optimal weight: 8.9990 chunk 251 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 273 optimal weight: 0.8980 chunk 114 optimal weight: 6.9990 chunk 280 optimal weight: 0.1980 chunk 34 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 955 ASN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1011 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.068491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.046632 restraints weight = 148187.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.048042 restraints weight = 72806.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.048931 restraints weight = 44938.325| |-----------------------------------------------------------------------------| r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.5558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28011 Z= 0.188 Angle : 0.566 18.672 38105 Z= 0.279 Chirality : 0.045 0.284 4402 Planarity : 0.004 0.062 4888 Dihedral : 5.936 56.886 4315 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.32 % Favored : 95.62 % Rotamer: Outliers : 2.13 % Allowed : 17.62 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.15), residues: 3422 helix: 1.90 (0.21), residues: 673 sheet: 0.23 (0.17), residues: 864 loop : -0.57 (0.15), residues: 1885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 47 HIS 0.003 0.001 HIS B1048 PHE 0.026 0.001 PHE A 562 TYR 0.029 0.001 TYR E 115 ARG 0.005 0.000 ARG C 509 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5603.26 seconds wall clock time: 103 minutes 49.79 seconds (6229.79 seconds total)